From 4be59722d2d334d710da9a46624d5ef471507728 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 14 Jan 2025 17:07:43 +0100
Subject: [PATCH 01/63] WIP: Begin translation of GEOMAR-specifics to generic
treatment
---
.../sample-management-datamodel.yml | 4 +-
.../scripting/bin/register_new_containers.py | 23 +---------
.../bin/sample_helpers/container_name.py | 44 +++++++++++++++++++
.../bin/sample_helpers/default_constants.yml | 23 ++++++++++
.../scripting/bin/sample_helpers/utils.py | 18 ++++++++
5 files changed, 88 insertions(+), 24 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index f8deb9d..dd30639 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -65,8 +65,8 @@ Container:
obligatory_properties:
Responsible:
ContainerType:
- BIS Label:
- description: A standardized label for a container in BIS.
+ container_label:
+ description: A standardized label for a container
datatype: TEXT
suggested_properties:
Child container:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index f64e934..c1fc8d0 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -99,26 +99,6 @@ def set_label_counter(container_type_id, value):
ERROR_PREFIX, counter[0], ERROR_SUFFIX))
-def get_bis_label_prefix(responsible_entity):
- """
- @return The prefix for the BIS Label, i.e. the BIS lable without the container number.
- """
- try:
- if responsible_entity.get_parent("Person") is not None:
- research_unit = db.execute_query("FIND ResearchUnit WITH id = {}".format(
- responsible_entity.get_property("ResearchUnit").value))[0]
- return "{}_{}_{}".format(get_bis_label_prefix(research_unit), get_abbreviation(responsible_entity.id), get_current_year())
- elif responsible_entity.get_parent("ResearchUnit") is not None:
- research_division = db.execute_query("FIND ResearchDivision WITH id = {}".format(
- responsible_entity.get_property("ResearchDivision").value))[0]
- return "{}_{}".format(get_bis_label_prefix(research_division), get_abbreviation(responsible_entity.id))
- else:
- return "{}".format(get_abbreviation(responsible_entity.id))
- except:
- logger.error('{}The system could not auto-generate the BIS Label for {}.{}'.format(
- ERROR_PREFIX, responsible_entity, ERROR_SUFFIX))
-
-
def create_container_entities(responsible_id, container_type_id, container_size, number_of_containers, parent_container):
"""
Create the BIS Entities specified via the "Register Containers" Form in
@@ -132,8 +112,7 @@ def create_container_entities(responsible_id, container_type_id, container_size,
bis_label_prefix = get_bis_label_prefix(responsible_entity)
bis_label_counter = get_label_counter(container_type_id)
for i in range(number_of_containers):
- bis_label = "{}_{}_{}".format(
- bis_label_prefix, container_type_abbreviation, bis_label_counter + i)
+ bis_label =
container = db.Record(bis_label)
container.add_parent(name="Container")
container.add_property(name="Responsible", value=responsible_id)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
new file mode 100644
index 0000000..4bad0dd
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
@@ -0,0 +1,44 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+"""This module serves a function that generates a human-readable
+container name or label.
+
+"""
+
+import linkahead as db
+
+def get_container_name_prefix(responsible_id: int, container_type_id: int):
+ """Generate a container name prefix from the container type and
+ the responsible entity.
+
+ Parameters
+ ----------
+ responsible_id : int
+ LinkAhead id of the responsible entity (person, research
+ institution, ...)
+ container_type_id: int
+ LinkAhead id of the ContainerType Record corresponding to the
+ type of the given container.
+
+ Returns
+ -------
+ container_name_prefix : str
+ Name in the format `<responsible>_<container_type_name>`
+
+ """
+
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
new file mode 100644
index 0000000..db334d6
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -0,0 +1,23 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+entity_names:
+ container_rt: Container
+ containertype_rt: ContainerType
+ labelcounter_rt: LabelCounter
+ labelcounter_prop: Counter
+ container_label_prop: container_label
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
new file mode 100644
index 0000000..e6abcd4
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
@@ -0,0 +1,18 @@
+import os
+import yaml
+
+from pathlib import Path
+
+CONSTANTS = yaml.load(os.path.join(Path(__file__).parent, "default_constants.yml"))
+
+if os.path.isfile(os.path.join(Path(__file__).parent, "constants.yml")):
+ CONSTANTS.update(yaml.load(os.path.join(Path(__file__).parent, "constants.yml")))
+
+
+def get_entity_name(name: str):
+
+ if name in CONSTANTS["entity_names"]:
+
+ return CONSTANTS["entity_names"][name]
+
+ return name
--
GitLab
From c8ad59fecb6664e4a5fb071b0019e944b1a2f125 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 14 Jan 2025 17:18:54 +0100
Subject: [PATCH 02/63] ENH: Implement a generic container naming
---
.../scripting/bin/register_new_containers.py | 5 ++--
.../bin/sample_helpers/container_name.py | 23 ++++++++++++++++++-
.../bin/sample_helpers/default_constants.yml | 1 +
3 files changed, 26 insertions(+), 3 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index c1fc8d0..d3e87dc 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -35,6 +35,7 @@ from caosadvancedtools.serverside.logging import configure_server_side_logging
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
+from sample_helpers.container_name import get_container_name_prefix
ERROR_PREFIX = 'Something went wrong: '
@@ -109,10 +110,10 @@ def create_container_entities(responsible_id, container_type_id, container_size,
# Get BIS Label for responsible person
responsible_entity = db.execute_query("FIND {}".format(responsible_id))[0]
container_type_abbreviation = get_abbreviation(container_type_id)
- bis_label_prefix = get_bis_label_prefix(responsible_entity)
+ bis_label_prefix = get_container_name_prefix(responsible_id, container_type_id)
bis_label_counter = get_label_counter(container_type_id)
for i in range(number_of_containers):
- bis_label =
+ bis_label = f"{bis_label_prefix}_{bis_label_counter+i}"
container = db.Record(bis_label)
container.add_parent(name="Container")
container.add_property(name="Responsible", value=responsible_id)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
index 4bad0dd..cc64a42 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
@@ -22,7 +22,19 @@ container name or label.
import linkahead as db
-def get_container_name_prefix(responsible_id: int, container_type_id: int):
+from .utils import get_entity_name
+
+def get_record_string(rec: db.Record) -> str:
+
+ if rec.get_property(get_entity_name("abbreviation_prop")) is not None and rec.get_property(get_entity_name("abbreviation_prop")).value:
+ return rec.get_property(get_entity_name("abbreviation_prop")).value
+
+ if rec.name:
+ return rec.name
+
+ return ""
+
+def get_container_name_prefix(responsible_id: int, container_type_id: int) -> str:
"""Generate a container name prefix from the container type and
the responsible entity.
@@ -41,4 +53,13 @@ def get_container_name_prefix(responsible_id: int, container_type_id: int):
Name in the format `<responsible>_<container_type_name>`
"""
+ resp = db.cached_get_entity_by(eid=responsible_id)
+ ct = db.cached_get_entity_by(eid=container_type_id)
+ resp_str = get_record_string(resp)
+ ct_str = get_record_string(ct)
+
+ if resp_str:
+ return f"{resp_str}_{ct_str}"
+
+ return ct_str
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index db334d6..7c6d8ad 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -21,3 +21,4 @@ entity_names:
labelcounter_rt: LabelCounter
labelcounter_prop: Counter
container_label_prop: container_label
+ abbreviation_prop: Abbreviation
--
GitLab
From c0ca339c33b1818b53aba40f7cd7ed035e2f703b Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 14 Jan 2025 17:25:26 +0100
Subject: [PATCH 03/63] MAINT: Remove GEOMAR-specific container post processing
---
.../scripting/bin/register_new_containers.py | 32 +++++--------------
.../bin/sample_helpers/container_name.py | 4 ++-
.../bin/sample_helpers/default_constants.yml | 3 ++
3 files changed, 14 insertions(+), 25 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index d3e87dc..d855196 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -36,11 +36,11 @@ from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
from sample_helpers.container_name import get_container_name_prefix
+from sample_helpers.utils import CONSTANTS, get_entity_name
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
-BIS_URL = 'https://biosamples.geomar.de/Entity/'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
logger = logging.getLogger("caosadvancedtools")
@@ -58,16 +58,6 @@ def get_current_year():
return year
-def get_abbreviation(id):
- try:
- rd = db.execute_query("FIND {}".format(id))[0]
- return rd.get_property("Abbreviation").value
- except:
- entity_url = BIS_URL + str(id)
- logger.error('{}There was a problem while querying for the abbreviation of <a href="{}">this BIS Entity</a>.{}'.format(
- ERROR_PREFIX, entity_url, ERROR_SUFFIX))
-
-
def create_new_label_counter(container_type_id, value=1):
counter = db.Record()
counter.add_parent(name="LabelCounter")
@@ -109,25 +99,19 @@ def create_container_entities(responsible_id, container_type_id, container_size,
batch = db.Container()
# Get BIS Label for responsible person
responsible_entity = db.execute_query("FIND {}".format(responsible_id))[0]
- container_type_abbreviation = get_abbreviation(container_type_id)
bis_label_prefix = get_container_name_prefix(responsible_id, container_type_id)
bis_label_counter = get_label_counter(container_type_id)
for i in range(number_of_containers):
bis_label = f"{bis_label_prefix}_{bis_label_counter+i}"
container = db.Record(bis_label)
- container.add_parent(name="Container")
- container.add_property(name="Responsible", value=responsible_id)
- container.add_property(name="ContainerType", value=container_type_id)
- container.add_property(name="Container size", value=container_size)
- container.add_property(name="BIS label", value=bis_label)
- container.add_property(name="Child container", value=[])
+ container.add_parent(name=get_entity_name("Container"))
+ container.add_property(name=get_entity_name("Responsible"), value=responsible_id)
+ container.add_property(name=get_entity_name("ContainerType"), value=container_type_id)
+ container.add_property(name=get_entity_name("Container size"), value=container_size)
+ container.add_property(name=get_entity_name("Child container"), value=[])
batch += [container]
try:
batch.insert()
- for ent in batch:
- ent.retrieve_acl()
- ent.grant(role='Stock Manager', priority=False, permission="EDIT:ACL")
- ent.update_acl()
except:
logger.error("{}The registered containers could not be imported to the system.{}".format(
ERROR_PREFIX, ERROR_SUFFIX))
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
index cc64a42..0d45834 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
@@ -24,6 +24,7 @@ import linkahead as db
from .utils import get_entity_name
+
def get_record_string(rec: db.Record) -> str:
if rec.get_property(get_entity_name("abbreviation_prop")) is not None and rec.get_property(get_entity_name("abbreviation_prop")).value:
@@ -34,6 +35,7 @@ def get_record_string(rec: db.Record) -> str:
return ""
+
def get_container_name_prefix(responsible_id: int, container_type_id: int) -> str:
"""Generate a container name prefix from the container type and
the responsible entity.
@@ -55,7 +57,7 @@ def get_container_name_prefix(responsible_id: int, container_type_id: int) -> st
"""
resp = db.cached_get_entity_by(eid=responsible_id)
ct = db.cached_get_entity_by(eid=container_type_id)
-
+
resp_str = get_record_string(resp)
ct_str = get_record_string(ct)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 7c6d8ad..79d084d 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -22,3 +22,6 @@ entity_names:
labelcounter_prop: Counter
container_label_prop: container_label
abbreviation_prop: Abbreviation
+
+error_prefix: "Something went wrong:"
+error_suffix: "Please contact your administrator(s)."
--
GitLab
From d07e6313c957953ad6798b818ad2294586c5b56e Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 21 Jan 2025 14:58:20 +0100
Subject: [PATCH 04/63] ENH: Add post-processing to container registration
---
.../scripting/bin/register_new_containers.py | 6 +++
.../container_registration_post_processing.py | 53 +++++++++++++++++++
2 files changed, 59 insertions(+)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_post_processing.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index d855196..c7ae9a0 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -36,6 +36,8 @@ from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
from sample_helpers.container_name import get_container_name_prefix
+from sample_helpers.container_registration_post_processing import (
+ post_process_containers, post_process_parent_container)
from sample_helpers.utils import CONSTANTS, get_entity_name
@@ -110,6 +112,9 @@ def create_container_entities(responsible_id, container_type_id, container_size,
container.add_property(name=get_entity_name("Container size"), value=container_size)
container.add_property(name=get_entity_name("Child container"), value=[])
batch += [container]
+
+ # Post process child containers
+ batch = post_process_containers(batch)
try:
batch.insert()
except:
@@ -133,6 +138,7 @@ def create_container_entities(responsible_id, container_type_id, container_size,
parent_container.get_property("Child container").value = new_childs
else:
parent_container.get_property("Child container").value += new_childs
+ parent_container = post_process_parent_container(parent)
parent_container.update()
set_label_counter(container_type_id=container_type_id,
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_post_processing.py
new file mode 100644
index 0000000..8ab70ba
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_post_processing.py
@@ -0,0 +1,53 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+
+def post_process_containers(conts: db.Container):
+ """Dummy function to be overwritten by custom code if desired.
+
+ Parameters
+ ----------
+ conts : db.Container
+ Container of container entities to be post-processed.
+
+ Returns
+ -------
+ conts : db.Container
+ Container of post-processed container entities to be inserted.
+ """
+
+ return conts
+
+
+def post_process_parent_container(parent: db.Record):
+ """Dummy function to be overwritten by custom code if desired.
+
+ Parameters
+ ----------
+ parent : db.Record
+ parent container entitiy to be post-processed.
+
+ Returns
+ -------
+ parent : db.Record
+ Post-processed parent container entity to be
+ updated.
+ """
+
+ return parent
--
GitLab
From 3d58c8717387b997df5d3873420a7732178ebb98 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 11:05:26 +0100
Subject: [PATCH 05/63] ENH: Use lookup functions for entity names
---
.../scripting/bin/register_new_containers.py | 119 ++++++++++--------
.../container_registration_identifier.py | 43 +++++++
.../bin/sample_helpers/default_constants.yml | 12 +-
.../scripting/bin/sample_helpers/utils.py | 8 ++
4 files changed, 126 insertions(+), 56 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_identifier.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index c7ae9a0..c9626a6 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -36,6 +36,7 @@ from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
from sample_helpers.container_name import get_container_name_prefix
+from sample_helpers.container_registration_identifier import get_container_identifier
from sample_helpers.container_registration_post_processing import (
post_process_containers, post_process_parent_container)
from sample_helpers.utils import CONSTANTS, get_entity_name
@@ -62,30 +63,34 @@ def get_current_year():
def create_new_label_counter(container_type_id, value=1):
counter = db.Record()
- counter.add_parent(name="LabelCounter")
- counter.add_property(name="Counter", value=value)
- counter.add_property(name="ContainerType", value=container_type_id)
+ counter.add_parent(name=get_entity_name("labelcounter_rt"))
+ counter.add_property(name=get_entity_name("labelcounter_prop"), value=value)
+ counter.add_property(name=get_entity_name("containertype_rt"), value=container_type_id)
counter.insert()
def get_label_counter(container_type_id):
counter = db.execute_query(
- "FIND LabelCounter WITH ContainerType = {}".format(container_type_id))
+ f"FIND '{get_entity_name('labelcounter_rt')}' WITH "
+ f"'{get_entity_name('containertype_rt')}' = {container_type_id}"
+ )
if len(counter) == 0:
create_new_label_counter(container_type_id)
return 1
else:
- return counter[0].get_property("Counter").value
+ return counter[0].get_property(get_entity_name("labelcounter_prop")).value
def set_label_counter(container_type_id, value):
counter = db.execute_query(
- "FIND LabelCounter WITH ContainerType = {}".format(container_type_id))
+ f"FIND '{get_entity_name('labelcounter_rt')}' WITH "
+ f"'{get_entity_name('containertype_rt')}' = {container_type_id}"
+ )
if len(counter) == 0:
create_new_label_counter(container_type_id, value)
else:
try:
- counter[0].get_property("Counter").value = value
+ counter[0].get_property(get_entity_name("labelcounter_prop")).value = value
counter.update()
except:
logger.error('{}There was an error when updating the internal label counter {}.{}'.format(
@@ -93,10 +98,15 @@ def set_label_counter(container_type_id, value):
def create_container_entities(responsible_id, container_type_id, container_size, number_of_containers, parent_container):
+ """Create the container entities specified via the "Register
+ Containers" form in the web interface.
+
+ Returns
+ -------
+ conts : db.Container
+ A container of the newly registered container entities.
+
"""
- Create the BIS Entities specified via the "Register Containers" Form in
- ext_bis_stockmanagement.js.
- @return A list of the newly registered entities."""
# Create Batch for insert
batch = db.Container()
# Get BIS Label for responsible person
@@ -106,11 +116,11 @@ def create_container_entities(responsible_id, container_type_id, container_size,
for i in range(number_of_containers):
bis_label = f"{bis_label_prefix}_{bis_label_counter+i}"
container = db.Record(bis_label)
- container.add_parent(name=get_entity_name("Container"))
- container.add_property(name=get_entity_name("Responsible"), value=responsible_id)
- container.add_property(name=get_entity_name("ContainerType"), value=container_type_id)
- container.add_property(name=get_entity_name("Container size"), value=container_size)
- container.add_property(name=get_entity_name("Child container"), value=[])
+ container.add_parent(name=get_entity_name("container_rt"))
+ container.add_property(name=get_entity_name("responsible_rt"), value=responsible_id)
+ container.add_property(name=get_entity_name("containertype_rt"), value=container_type_id)
+ container.add_property(name=get_entity_name("container_size_prop"), value=container_size)
+ container.add_property(name=get_entity_name("child_container_prop"), value=[])
batch += [container]
# Post process child containers
@@ -125,20 +135,20 @@ def create_container_entities(responsible_id, container_type_id, container_size,
# Add to parent container
if parent_container is not None:
- new_childs = []
+ child_cont_prop = db.Property(name=get_entity_name("child_container_prop").retrieve()
+ new_childs=[]
for entity in batch:
new_childs += [entity.id]
# Check if property Child container exists:
- if parent_container.get_property("Child container") is None:
- child_cont_prop = db.Property(name="Child container").retrieve()
+ if parent_container.get_property(child_cont_prop.name) is None:
parent_container.add_property(id=child_cont_prop.id, value=new_childs)
else:
# Check if the container allready has childs
- if parent_container.get_property("Child container").value is None:
- parent_container.get_property("Child container").value = new_childs
+ if parent_container.get_property(child_cont_prop.name).value is None:
+ parent_container.get_property(child_cont_prop.name).value=new_childs
else:
- parent_container.get_property("Child container").value += new_childs
- parent_container = post_process_parent_container(parent)
+ parent_container.get_property(child_cont_prop.name).value += new_childs
+ parent_container=post_process_parent_container(parent)
parent_container.update()
set_label_counter(container_type_id=container_type_id,
@@ -147,23 +157,26 @@ def create_container_entities(responsible_id, container_type_id, container_size,
def get_template_name(container_entities, file_format_extension):
- first_id = container_entities[0].id
- last_id = container_entities[-1].id
+ first_id=container_entities[0].id
+ last_id=container_entities[-1].id
return "container_template_(IDs_{}_to_{}).{}".format(first_id, last_id, file_format_extension)
def get_parent_container(id):
try:
- parent = db.execute_query("FIND {}".format(id))[0]
+ parent=db.execute_query("FIND {}".format(id))[0]
return parent
except:
- logger.info("No parent container specified. The BIS ID or BIS label of the parent container has to be entered in the template before it is uploaded.")
+ logger.info(
+ "No parent container specified. The Contianer ID or label of the "
+ "parent container has to be entered in the template before it is uploaded."
+ )
return None
def get_container_type(id):
try:
- type = db.execute_query("FIND {}".format(id))[0]
+ type=db.execute_query("FIND {}".format(id))[0]
return type
except:
logger.error("{}The specified ContainerType could not be retrieved. {}".format(
@@ -172,29 +185,31 @@ def get_container_type(id):
def create_csv_template(template_internal_path, container_entities, container_type, container_size, parent_container):
if parent_container is None:
- parent_container_label = ""
+ parent_container_label=""
else:
- parent_container_label = parent_container.get_property("BIS label").value
+ parent_container_label=get_container_identifier(parent_container)
with open(template_internal_path, 'w') as template_csv:
- writer = csv.writer(template_csv)
+ writer=csv.writer(template_csv)
# Write header
- headers = [
- "BIS ID",
- "Container type",
- "Container size",
- "BIS label",
+ headers=[
+ "entity_id",
+ "container_type_rt",
+ "container_size_prop",
+ "container_label",
"PI",
"Collection",
"Parent container",
"Custom label",
"Container Contents",
- "PDFReport"]
+ "PDFReport"
+ ]
+ headers=[get_column_header_name(header) for header in headers]
writer.writerow(headers)
# Write description with leading '#'
- descriptions = get_description_row(headers)
+ descriptions=get_description_row(headers)
if descriptions:
writer.writerow(descriptions)
- options = get_options_row(headers)
+ options=get_options_row(headers)
if options:
writer.writerow(options)
# Write entity data to the lines
@@ -203,7 +218,7 @@ def create_csv_template(template_internal_path, container_entities, container_ty
entity.id,
container_type.name,
container_size,
- entity.get_property("BIS label").value,
+ get_container_identifier(entity),
"",
"",
parent_container_label,
@@ -212,34 +227,34 @@ def create_csv_template(template_internal_path, container_entities, container_ty
def main():
- parser = get_parser()
- args = parser.parse_args()
+ parser=get_parser()
+ args=parser.parse_args()
global logger
# Check whether executed locally or as an SSS depending on
# auth_token argument.
if hasattr(args, "auth_token") and args.auth_token:
db.configure_connection(auth_token=args.auth_token)
- debug_file = configure_server_side_logging()
+ debug_file=configure_server_side_logging()
# logger = logging.getLogger("caosadvancedtools")
else:
# logging config for local execution
# logger = logging.getLogger("caosadvancedtools")
logger.addHandler(logging.StreamHandler(sys.stdout))
logger.setLevel(logging.DEBUG)
- debug_file = None
+ debug_file=None
if hasattr(args, "filename") and args.filename:
# Read the input from the form (form.json)
with open(args.filename) as form_json:
- form_data = json.load(form_json)
+ form_data=json.load(form_json)
- parent_container = get_parent_container(form_data["parent_id"])
- container_type = get_container_type(form_data["container_type"])
- container_size = form_data["container_size"]
+ parent_container=get_parent_container(form_data["parent_id"])
+ container_type=get_container_type(form_data["container_type"])
+ container_size=form_data["container_size"]
# Create entities in BIS
- container_entities = create_container_entities(
+ container_entities=create_container_entities(
responsible_id=int(form_data["responsible_entity"]),
container_type_id=int(form_data["container_type"]),
container_size=container_size,
@@ -253,12 +268,10 @@ def main():
return 1
# Create template file on the server
- file_format_extension = form_data["file_format"]
- template_name = get_template_name(container_entities, file_format_extension)
- template_display_path, template_internal_path = helper.get_shared_filename(
+ file_format_extension=form_data["file_format"]
+ template_name=get_template_name(container_entities, file_format_extension)
+ template_display_path, template_internal_path=helper.get_shared_filename(
template_name)
- logger.info("Internal path: {}, Display path: {}".format(
- template_internal_path, template_display_path))
if (file_format_extension == "csv"):
create_csv_template(
template_internal_path=template_internal_path,
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_identifier.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_identifier.py
new file mode 100644
index 0000000..52943d7
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_identifier.py
@@ -0,0 +1,43 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from .utils import get_entity_name
+
+
+def get_container_identifier(cont: db.Record) -> str:
+ """Return an identifier string that uniquely identifies the given
+ container entity in a registration/upload/export table file.
+
+ Parameters
+ ----------
+ cont : db.Record
+ The container record to be identified.
+
+ Returns
+ -------
+ identifier : str
+ The identifying string that uniquly identifies the given
+ container.
+ """
+ if (cont.get_property(get_entity_name("container_label_prop")) is not None and
+ cont.get_property(get_entity_name("container_label_prop")).value):
+ return cont.get_property(get_entity_name("container_label_prop")).value
+ elif cont.name:
+ return cont.name
+ return cont.id
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 79d084d..729d795 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -15,13 +15,19 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
+csv_column_names:
+ entity_id: "LinkAhead ID"
+
entity_names:
+ abbreviation_prop: Abbreviation
+ child_container_prop: "Child container"
+ container_label_prop: container_label
container_rt: Container
+ container_size_prop: "Container size"
containertype_rt: ContainerType
- labelcounter_rt: LabelCounter
labelcounter_prop: Counter
- container_label_prop: container_label
- abbreviation_prop: Abbreviation
+ labelcounter_rt: LabelCounter
+ responsible_rt: Responsible
error_prefix: "Something went wrong:"
error_suffix: "Please contact your administrator(s)."
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
index e6abcd4..b80215b 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
@@ -16,3 +16,11 @@ def get_entity_name(name: str):
return CONSTANTS["entity_names"][name]
return name
+
+
+def get_column_header_name(name: str):
+
+ if name in CONSTANTS["csv_column_names"]:
+ return CONSTANTS["csv_column_names"]
+
+ return get_entity_name(name)
--
GitLab
From a6d08a74c139b6556a4f54e2f1c05b50af3c579b Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 11:08:07 +0100
Subject: [PATCH 06/63] FIX: Add missing import
---
.../caosdb-server/scripting/bin/register_new_containers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index c9626a6..f68c350 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -39,7 +39,7 @@ from sample_helpers.container_name import get_container_name_prefix
from sample_helpers.container_registration_identifier import get_container_identifier
from sample_helpers.container_registration_post_processing import (
post_process_containers, post_process_parent_container)
-from sample_helpers.utils import CONSTANTS, get_entity_name
+from sample_helpers.utils import CONSTANTS, get_column_header_name, get_entity_name
ERROR_PREFIX = CONSTANTS["error_prefix"]
--
GitLab
From 9e59dc9f8cf813ec7cc5f04a974f394c614a3b6a Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 11:15:00 +0100
Subject: [PATCH 07/63] FIX: Use correct sql dump name
---
test-profile/custom/other/restore/{caosdb.sql => caosdb.dump.sql} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename test-profile/custom/other/restore/{caosdb.sql => caosdb.dump.sql} (100%)
diff --git a/test-profile/custom/other/restore/caosdb.sql b/test-profile/custom/other/restore/caosdb.dump.sql
similarity index 100%
rename from test-profile/custom/other/restore/caosdb.sql
rename to test-profile/custom/other/restore/caosdb.dump.sql
--
GitLab
From 7ff39fa3e6384f6a023d2f2c8e164bf4fc44cb34 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 11:50:30 +0100
Subject: [PATCH 08/63] FIX: Fix typos and datamodel problems
---
.../sample-management-datamodel.yml | 2 +-
.../scripting/bin/register_new_containers.py | 12 +-
.../bin/sample_helpers/container_name.py | 4 +-
.../scripting/bin/sample_helpers/utils.py | 8 +-
.../custom/other/restore/caosdb.dump.sql | 403 ++++++++++++++----
5 files changed, 324 insertions(+), 105 deletions(-)
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index dd30639..78935e6 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -65,10 +65,10 @@ Container:
obligatory_properties:
Responsible:
ContainerType:
+ suggested_properties:
container_label:
description: A standardized label for a container
datatype: TEXT
- suggested_properties:
Child container:
datatype: LIST<Container>
Container size:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index f68c350..12d3224 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -28,7 +28,7 @@ import json
import logging
import sys
-import caosdb as db
+import linkahead as db
from caosadvancedtools.serverside import helper
from caosadvancedtools.serverside.logging import configure_server_side_logging
@@ -126,16 +126,18 @@ def create_container_entities(responsible_id, container_type_id, container_size,
# Post process child containers
batch = post_process_containers(batch)
try:
+ logger.info(batch)
batch.insert()
- except:
- logger.error("{}The registered containers could not be imported to the system.{}".format(
+ except Exception as e:
+ logger.error("{} The registered containers could not be imported to the system. {}".format(
ERROR_PREFIX, ERROR_SUFFIX))
+ logger.error(e)
return None
# TODO: Reset the internal_container_label_counter of person to its previous value if nothing has be inserted
# Add to parent container
if parent_container is not None:
- child_cont_prop = db.Property(name=get_entity_name("child_container_prop").retrieve()
+ child_cont_prop = db.Property(name=get_entity_name("child_container_prop")).retrieve()
new_childs=[]
for entity in batch:
new_childs += [entity.id]
@@ -148,7 +150,7 @@ def create_container_entities(responsible_id, container_type_id, container_size,
parent_container.get_property(child_cont_prop.name).value=new_childs
else:
parent_container.get_property(child_cont_prop.name).value += new_childs
- parent_container=post_process_parent_container(parent)
+ parent_container=post_process_parent_container(parent_container)
parent_container.update()
set_label_counter(container_type_id=container_type_id,
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
index 0d45834..efcab85 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
@@ -55,8 +55,8 @@ def get_container_name_prefix(responsible_id: int, container_type_id: int) -> st
Name in the format `<responsible>_<container_type_name>`
"""
- resp = db.cached_get_entity_by(eid=responsible_id)
- ct = db.cached_get_entity_by(eid=container_type_id)
+ resp = db.cached.cached_get_entity_by(eid=responsible_id)
+ ct = db.cached.cached_get_entity_by(eid=container_type_id)
resp_str = get_record_string(resp)
ct_str = get_record_string(ct)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
index b80215b..e345c22 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
@@ -3,10 +3,12 @@ import yaml
from pathlib import Path
-CONSTANTS = yaml.load(os.path.join(Path(__file__).parent, "default_constants.yml"))
+with open(os.path.join(Path(__file__).parent, "default_constants.yml")) as yaml_file:
+ CONSTANTS = yaml.safe_load(yaml_file)
if os.path.isfile(os.path.join(Path(__file__).parent, "constants.yml")):
- CONSTANTS.update(yaml.load(os.path.join(Path(__file__).parent, "constants.yml")))
+ with open(os.path.join(Path(__file__).parent, "constants.yml")) as custom_yaml_file:
+ CONSTANTS.update(yaml.safe_load(custom_yaml_file))
def get_entity_name(name: str):
@@ -21,6 +23,6 @@ def get_entity_name(name: str):
def get_column_header_name(name: str):
if name in CONSTANTS["csv_column_names"]:
- return CONSTANTS["csv_column_names"]
+ return CONSTANTS["csv_column_names"][name]
return get_entity_name(name)
diff --git a/test-profile/custom/other/restore/caosdb.dump.sql b/test-profile/custom/other/restore/caosdb.dump.sql
index 1182c12..1c57494 100644
--- a/test-profile/custom/other/restore/caosdb.dump.sql
+++ b/test-profile/custom/other/restore/caosdb.dump.sql
@@ -45,6 +45,8 @@ CREATE TABLE `archive_collection_type` (
LOCK TABLES `archive_collection_type` WRITE;
/*!40000 ALTER TABLE `archive_collection_type` DISABLE KEYS */;
+INSERT INTO `archive_collection_type` VALUES
+(0,153,177,'LIST',1);
/*!40000 ALTER TABLE `archive_collection_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -81,7 +83,24 @@ CREATE TABLE `archive_data_type` (
LOCK TABLES `archive_data_type` WRITE;
/*!40000 ALTER TABLE `archive_data_type` DISABLE KEYS */;
INSERT INTO `archive_data_type` VALUES
-(0,188,177,105,1);
+(0,0,144,13,1),
+(0,0,145,13,1),
+(0,0,146,13,1),
+(0,0,147,13,1),
+(0,111,177,101,1),
+(0,105,177,103,1),
+(0,106,177,105,1),
+(0,188,177,105,1),
+(0,111,178,110,1),
+(0,136,177,110,1),
+(0,118,178,111,1),
+(0,118,177,119,1),
+(0,118,179,120,1),
+(0,118,180,121,1),
+(0,119,178,138,1),
+(0,153,177,143,1),
+(0,150,177,148,1),
+(0,153,178,148,1);
/*!40000 ALTER TABLE `archive_data_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -249,15 +268,34 @@ CREATE TABLE `archive_entities` (
LOCK TABLES `archive_entities` WRITE;
/*!40000 ALTER TABLE `archive_entities` DISABLE KEYS */;
INSERT INTO `archive_entities` VALUES
+(103,NULL,'RECORDTYPE',2,1),
+(105,NULL,'RECORDTYPE',2,1),
+(106,NULL,'RECORDTYPE',2,1),
+(111,NULL,'RECORDTYPE',2,1),
+(118,NULL,'RECORDTYPE',2,1),
+(119,NULL,'RECORDTYPE',2,1),
+(136,NULL,'RECORDTYPE',2,1),
+(143,NULL,'RECORDTYPE',2,1),
+(144,'The depth of the water in meters as a positive value','PROPERTY',2,1),
+(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,1),
+(146,NULL,'PROPERTY',2,1),
+(147,NULL,'PROPERTY',2,1),
+(150,NULL,'RECORDTYPE',2,1),
+(153,NULL,'RECORDTYPE',2,1),
+(161,NULL,'RECORDTYPE',2,1),
+(162,NULL,'RECORDTYPE',2,1),
(188,NULL,'RECORD',2,1),
(192,NULL,'RECORD',2,1),
(193,NULL,'RECORD',2,1),
(193,NULL,'RECORD',3,2),
+(193,NULL,'RECORD',3,3),
(194,NULL,'RECORD',2,1),
(195,NULL,'RECORD',2,1),
(195,NULL,'RECORD',3,2),
+(195,NULL,'RECORD',3,3),
(196,NULL,'RECORD',2,1),
(197,NULL,'RECORD',2,1),
+(197,NULL,'RECORD',3,2),
(198,NULL,'RECORD',2,1);
/*!40000 ALTER TABLE `archive_entities` ENABLE KEYS */;
UNLOCK TABLES;
@@ -399,7 +437,19 @@ INSERT INTO `archive_isa` VALUES
(197,1,111,1),
(195,2,111,1),
(196,1,136,1),
-(198,1,118,1);
+(198,1,118,1),
+(103,1,100,0),
+(103,1,101,1),
+(105,1,100,0),
+(105,1,101,1),
+(106,1,100,0),
+(106,1,101,1),
+(153,1,150,1),
+(161,1,143,1),
+(162,1,143,1),
+(193,3,111,1),
+(195,3,111,1),
+(197,2,111,1);
/*!40000 ALTER TABLE `archive_isa` ENABLE KEYS */;
UNLOCK TABLES;
@@ -440,7 +490,26 @@ INSERT INTO `archive_name_data` VALUES
(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,1),
(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,2),
(0,197,20,'fad_mru_myn_2025_fri_1','FIX',0,1),
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UNLOCK TABLES;
@@ -477,9 +546,12 @@ LOCK TABLES `archive_name_overrides` WRITE;
INSERT INTO `archive_name_overrides` VALUES
(0,193,177,'BIS label',1),
(0,193,177,'BIS label',2),
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/*!40000 ALTER TABLE `archive_name_overrides` ENABLE KEYS */;
UNLOCK TABLES;
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/*!40000 ALTER TABLE `archive_null_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -588,28 +721,54 @@ INSERT INTO `archive_reference_data` VALUES
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/*!40000 ALTER TABLE `archive_reference_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -658,7 +817,25 @@ INSERT INTO `archive_text_data` VALUES
(0,197,113,'300 l','FIX',2,1),
(0,197,177,'fad_mru_myn_2025_fri_1','FIX',0,1),
(0,195,113,'30 m²','FIX',2,2),
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/*!40000 ALTER TABLE `archive_text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -752,7 +929,6 @@ INSERT INTO `data_type` VALUES
(0,0,113,14),
(0,0,114,14),
(0,0,115,14),
-(0,0,117,14),
(0,0,125,14),
(0,0,126,14),
(0,0,127,14),
@@ -772,6 +948,7 @@ INSERT INTO `data_type` VALUES
(0,0,158,14),
(0,0,164,14),
(0,0,166,14),
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(0,0,132,15),
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@@ -953,7 +1130,7 @@ CREATE TABLE `entities` (
PRIMARY KEY (`id`),
KEY `entity_entity_acl` (`acl`),
CONSTRAINT `entity_entity_acl` FOREIGN KEY (`acl`) REFERENCES `entity_acl` (`id`)
-) ENGINE=InnoDB AUTO_INCREMENT=212 DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB AUTO_INCREMENT=213 DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -998,7 +1175,6 @@ INSERT INTO `entities` VALUES
(114,'A custom label for a container that doesn\'t have to follow the BIS labeling guidelines.','PROPERTY',2),
(115,NULL,'PROPERTY',2),
(116,NULL,'PROPERTY',2),
-(117,'A standardized label for a container in BIS.','PROPERTY',2),
(118,NULL,'RECORDTYPE',2),
(119,NULL,'RECORDTYPE',2),
(120,NULL,'RECORDTYPE',2),
@@ -1092,7 +1268,8 @@ INSERT INTO `entities` VALUES
(208,NULL,'RECORD',2),
(209,NULL,'RECORD',2),
(210,NULL,'RECORD',2),
-(211,NULL,'RECORD',2);
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/*!40000 ALTER TABLE `entities` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1181,7 +1358,6 @@ INSERT INTO `entity_ids` VALUES
('116',114),
('117',115),
('118',116),
-('119',117),
('120',118),
('121',119),
('122',120),
@@ -1266,7 +1442,8 @@ INSERT INTO `entity_ids` VALUES
('201',208),
('202',209),
('203',210),
-('204',211);
+('204',211),
+('205',212);
/*!40000 ALTER TABLE `entity_ids` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1321,22 +1498,27 @@ INSERT INTO `entity_version` VALUES
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@@ -1354,6 +1536,7 @@ INSERT INTO `entity_version` VALUES
(134,NULL,'e9433547a60b486baaca979aec1608510a2f4541',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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(139,NULL,'54edec758a99a74f50577b74ba8a1ef187e08859',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1361,16 +1544,23 @@ INSERT INTO `entity_version` VALUES
(141,NULL,'56b4d616f183a665bd2b1e6de026cbe3a3555aff',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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@@ -1379,7 +1569,9 @@ INSERT INTO `entity_version` VALUES
(159,NULL,'728569f7e5de34afd82293e30bafcd11f106440e',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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@@ -1726,7 +1922,6 @@ INSERT INTO `name_data` VALUES
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@@ -1802,7 +1997,8 @@ INSERT INTO `name_data` VALUES
(0,206,20,'Fish','FIX',0),
(0,207,20,'Filet','FIX',0),
(0,208,20,'Water','FIX',0),
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LOCK TABLES `name_overrides` WRITE;
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UNLOCK TABLES;
@@ -2169,7 +2359,7 @@ CREATE TABLE `stats` (
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('TransactionBenchmark','¬í\0sr\00caosdb.server.database.misc.TransactionBenchmark„Cl=˜ÕãE\0J\0sinceL\0acct\0Ljava/util/HashMap;L\0countsq\0~\0xp\0\0lžèòWsr\0java.util.HashMapÚÁÃ`Ñ\0F\0\nloadFactorI\0 thresholdxp?@\0\0\0\0\0 w\0\0\0\0\0\0t\0 SyncStatssr\0java.lang.Long;‹äÌ#ß\0J\0valuexr\0java.lang.Number†¬• ”à‹\0\0xp\0\0\0\0\0\0\0t\0GetInfosq\0~\0\0\0\0\0\0\0 xsq\0~\0?@\0\0\0\0\0 w\0\0\0\0\0\0q\0~\0sr\0java.lang.Integerâ ¤÷‡8\0I\0valuexq\0~\0\0\0\0q\0~\0 sq\0~\0 \0\0\0x');
/*!40000 ALTER TABLE `stats` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2204,18 +2394,6 @@ CREATE TABLE `text_data` (
LOCK TABLES `text_data` WRITE;
/*!40000 ALTER TABLE `text_data` DISABLE KEYS */;
INSERT INTO `text_data` VALUES
-(143,146,21,'°','FIX',0),
-(143,147,21,'°','FIX',0),
-(143,144,21,'m','FIX',0),
-(143,145,21,'m','FIX',0),
-(0,144,21,'m','FIX',0),
-(0,145,21,'m','FIX',0),
-(0,146,21,'°','FIX',0),
-(0,147,21,'°','FIX',0),
-(161,146,21,'°','FIX',0),
-(161,147,21,'°','FIX',0),
-(162,146,21,'°','FIX',0),
-(162,147,21,'°','FIX',0),
(0,186,104,'Spannende Abteilung','FIX',0),
(0,186,102,'fad','FIX',1),
(0,187,102,'mru','FIX',0),
@@ -2227,12 +2405,6 @@ INSERT INTO `text_data` VALUES
(0,188,102,'myn','FIX',1),
(0,188,108,'Name','FIX',2),
(0,188,109,'my.name@example.com','FIX',3),
-(0,193,113,'20 rooms','FIX',2),
-(0,193,177,'fad_mru_myn_2025_bld_1','FIX',0),
-(0,197,113,'300 l','FIX',2),
-(0,197,177,'fad_mru_myn_2025_fri_1','FIX',0),
-(0,195,113,'30 m²','FIX',2),
-(0,195,177,'fad_mru_myn_2025_rom_1','FIX',0),
(0,200,149,'2m','FIX',0),
(0,202,142,'ABCD-1234','FIX',0),
(0,204,166,'Nails','FIX',0),
@@ -2240,7 +2412,22 @@ INSERT INTO `text_data` VALUES
(211,146,21,'°','FIX',0),
(211,147,21,'°','FIX',0),
(211,145,21,'m','FIX',0),
-(211,144,21,'m','FIX',0);
+(211,144,21,'m','FIX',0),
+(143,146,21,'°','FIX',0),
+(143,147,21,'°','FIX',0),
+(143,144,21,'m','FIX',0),
+(143,145,21,'m','FIX',0),
+(0,144,21,'m','FIX',0),
+(0,145,21,'m','FIX',0),
+(0,146,21,'°','FIX',0),
+(0,147,21,'°','FIX',0),
+(161,146,21,'°','FIX',0),
+(161,147,21,'°','FIX',0),
+(162,146,21,'°','FIX',0),
+(162,147,21,'°','FIX',0),
+(0,193,113,'20 rooms','FIX',2),
+(0,195,113,'30 m²','FIX',2),
+(0,197,113,'300 l','FIX',2);
/*!40000 ALTER TABLE `text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2381,7 +2568,28 @@ INSERT INTO `transaction_log` VALUES
('Insert','202','admin',1736265896,593000000,'PAM'),
('Insert','203','admin',1736265919,980000000,'PAM'),
('Insert','204','admin',1736265919,980000000,'PAM'),
-('Update','191','admin',1736265920,63000000,'PAM');
+('Update','191','admin',1736265920,63000000,'PAM'),
+('Insert','205','admin',1737542797,604000000,'PAM'),
+('Update','105','admin',1737542799,463000000,'PAM'),
+('Update','107','admin',1737542799,463000000,'PAM'),
+('Update','108','admin',1737542799,463000000,'PAM'),
+('Update','113','admin',1737542799,463000000,'PAM'),
+('Update','120','admin',1737542799,463000000,'PAM'),
+('Update','121','admin',1737542799,463000000,'PAM'),
+('Update','138','admin',1737542799,463000000,'PAM'),
+('Update','145','admin',1737542799,463000000,'PAM'),
+('Update','146','admin',1737542799,463000000,'PAM'),
+('Update','147','admin',1737542799,463000000,'PAM'),
+('Update','148','admin',1737542799,463000000,'PAM'),
+('Update','149','admin',1737542799,463000000,'PAM'),
+('Update','152','admin',1737542799,463000000,'PAM'),
+('Update','155','admin',1737542799,463000000,'PAM'),
+('Update','163','admin',1737542799,463000000,'PAM'),
+('Update','164','admin',1737542799,463000000,'PAM'),
+('Update','186','admin',1737542873,229000000,'PAM'),
+('Update','188','admin',1737542878,789000000,'PAM'),
+('Update','190','admin',1737542888,999000000,'PAM'),
+('Delete','119','admin',1737542900,973000000,'PAM');
/*!40000 ALTER TABLE `transaction_log` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2412,9 +2620,12 @@ INSERT INTO `transactions` VALUES
('032bc38a-28d3-4c59-9d31-1494b62a2ba4','admin','PAM',1736265920,63000000),
('06147cec-8ac2-4c72-9744-cab44e960e09','admin','PAM',1736265865,579000000),
('081a60fb-04b9-4d71-b025-d865b503fc7e','admin','PAM',1736265822,771000000),
+('090f0927-a7b8-46cf-a416-98d1185c3518','admin','PAM',1737542837,887000000),
('20f056fc-7deb-4c52-a54f-a80a92236315','admin','PAM',1736264636,79000000),
('22245d86-e095-4514-917a-7677616c544b','admin','PAM',1736265602,369000000),
+('26be7fc5-b8d5-47d9-bbd3-59e5a00be685','admin','PAM',1737542900,973000000),
('27f2534b-49b9-4e44-9232-53eadf8ba072','admin','PAM',1736264522,437000000),
+('29ff518f-b089-430e-85a9-3b42b08a9c0c','admin','PAM',1737542878,789000000),
('2d5a4ba7-517f-4b85-9727-b3d96988c485','admin','PAM',1736265392,478000000),
('2df660f0-e3a6-447e-837f-4778e5323f5d','admin','PAM',1736265392,576000000),
('34fade63-2811-4725-becf-0f2b1f84ad90','admin','PAM',1736265204,999000000),
@@ -2422,17 +2633,21 @@ INSERT INTO `transactions` VALUES
('488967a3-a042-43d4-b74d-485f4bf622a2','admin','PAM',1736265441,647000000),
('55dcaf7b-7372-4778-995a-a6a8bde1b471','admin','PAM',1736264805,952000000),
('7663f26d-982f-4710-aeab-073a44290f3a','admin','PAM',1736265841,217000000),
+('80009e0c-8c91-4add-9ada-6aed2ac526b7','admin','PAM',1737542797,604000000),
('8205d330-42ef-4519-9e5e-ade1e2465bed','admin','PAM',1736265392,368000000),
('84bd4faf-510c-4950-b827-4bab81546887','admin','PAM',1736264663,736000000),
('89a537e0-496a-4e50-b078-74f34cd21a07','admin','PAM',1736265441,688000000),
+('936c19b1-3e0c-47d2-a073-024623962a00','admin','PAM',1737542873,229000000),
('975ea8ec-ba79-452e-bc44-2d9432ce4993','admin','PAM',1736265742,101000000),
('9d2c4381-148f-4559-9d30-95a328169bbf','admin','PAM',1736265204,451000000),
('a41c5d15-6c9e-4e5c-a8fb-2fa7d38da140','admin','PAM',1736264752,282000000),
+('a61cf61b-8583-41ec-b204-bfa65e3a7807','admin','PAM',1737542799,463000000),
('aa019373-730c-4cec-8f83-3eb2f2ee9629','admin','PAM',1736265619,737000000),
('ada94a1f-e942-46e2-a5de-626a18cd2af9','admin','PAM',1736265702,487000000),
('b29fcae5-7964-4beb-b73a-2f7ce0a4809f','admin','PAM',1736265441,871000000),
('b51ffa82-bcf0-42a1-922c-9f4a845e6f42','admin','PAM',1736265919,980000000),
('c03fb8ed-a263-4997-a02b-37bf97af9563','admin','PAM',1736265441,780000000),
+('c1e6cb48-b70f-48df-bcbe-31351e3293ff','admin','PAM',1737542888,999000000),
('c6549725-13bb-4076-9d49-219c6b8192f3','admin','PAM',1736264700,733000000),
('ca9db47b-d2d5-4980-84da-7268869f9e3c','admin','PAM',1736264603,389000000),
('cad02c5b-f559-4400-9897-80e56c1035ba','admin','PAM',1736264740,329000000),
@@ -6916,4 +7131,4 @@ DELIMITER ;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
--- Dump completed on 2025-01-07 16:05:15
+-- Dump completed on 2025-01-22 10:48:39
--
GitLab
From b9c1ea004f2cbdb9997df18d54b96521c63abf17 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 11:51:37 +0100
Subject: [PATCH 09/63] MAINT: Remove debugging output
---
.../scripting/bin/register_new_containers.py | 53 +++++++++----------
1 file changed, 26 insertions(+), 27 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index 12d3224..76aa92e 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -126,7 +126,6 @@ def create_container_entities(responsible_id, container_type_id, container_size,
# Post process child containers
batch = post_process_containers(batch)
try:
- logger.info(batch)
batch.insert()
except Exception as e:
logger.error("{} The registered containers could not be imported to the system. {}".format(
@@ -138,7 +137,7 @@ def create_container_entities(responsible_id, container_type_id, container_size,
# Add to parent container
if parent_container is not None:
child_cont_prop = db.Property(name=get_entity_name("child_container_prop")).retrieve()
- new_childs=[]
+ new_childs = []
for entity in batch:
new_childs += [entity.id]
# Check if property Child container exists:
@@ -147,10 +146,10 @@ def create_container_entities(responsible_id, container_type_id, container_size,
else:
# Check if the container allready has childs
if parent_container.get_property(child_cont_prop.name).value is None:
- parent_container.get_property(child_cont_prop.name).value=new_childs
+ parent_container.get_property(child_cont_prop.name).value = new_childs
else:
parent_container.get_property(child_cont_prop.name).value += new_childs
- parent_container=post_process_parent_container(parent_container)
+ parent_container = post_process_parent_container(parent_container)
parent_container.update()
set_label_counter(container_type_id=container_type_id,
@@ -159,14 +158,14 @@ def create_container_entities(responsible_id, container_type_id, container_size,
def get_template_name(container_entities, file_format_extension):
- first_id=container_entities[0].id
- last_id=container_entities[-1].id
+ first_id = container_entities[0].id
+ last_id = container_entities[-1].id
return "container_template_(IDs_{}_to_{}).{}".format(first_id, last_id, file_format_extension)
def get_parent_container(id):
try:
- parent=db.execute_query("FIND {}".format(id))[0]
+ parent = db.execute_query("FIND {}".format(id))[0]
return parent
except:
logger.info(
@@ -178,7 +177,7 @@ def get_parent_container(id):
def get_container_type(id):
try:
- type=db.execute_query("FIND {}".format(id))[0]
+ type = db.execute_query("FIND {}".format(id))[0]
return type
except:
logger.error("{}The specified ContainerType could not be retrieved. {}".format(
@@ -187,13 +186,13 @@ def get_container_type(id):
def create_csv_template(template_internal_path, container_entities, container_type, container_size, parent_container):
if parent_container is None:
- parent_container_label=""
+ parent_container_label = ""
else:
- parent_container_label=get_container_identifier(parent_container)
+ parent_container_label = get_container_identifier(parent_container)
with open(template_internal_path, 'w') as template_csv:
- writer=csv.writer(template_csv)
+ writer = csv.writer(template_csv)
# Write header
- headers=[
+ headers = [
"entity_id",
"container_type_rt",
"container_size_prop",
@@ -205,13 +204,13 @@ def create_csv_template(template_internal_path, container_entities, container_ty
"Container Contents",
"PDFReport"
]
- headers=[get_column_header_name(header) for header in headers]
+ headers = [get_column_header_name(header) for header in headers]
writer.writerow(headers)
# Write description with leading '#'
- descriptions=get_description_row(headers)
+ descriptions = get_description_row(headers)
if descriptions:
writer.writerow(descriptions)
- options=get_options_row(headers)
+ options = get_options_row(headers)
if options:
writer.writerow(options)
# Write entity data to the lines
@@ -229,34 +228,34 @@ def create_csv_template(template_internal_path, container_entities, container_ty
def main():
- parser=get_parser()
- args=parser.parse_args()
+ parser = get_parser()
+ args = parser.parse_args()
global logger
# Check whether executed locally or as an SSS depending on
# auth_token argument.
if hasattr(args, "auth_token") and args.auth_token:
db.configure_connection(auth_token=args.auth_token)
- debug_file=configure_server_side_logging()
+ debug_file = configure_server_side_logging()
# logger = logging.getLogger("caosadvancedtools")
else:
# logging config for local execution
# logger = logging.getLogger("caosadvancedtools")
logger.addHandler(logging.StreamHandler(sys.stdout))
logger.setLevel(logging.DEBUG)
- debug_file=None
+ debug_file = None
if hasattr(args, "filename") and args.filename:
# Read the input from the form (form.json)
with open(args.filename) as form_json:
- form_data=json.load(form_json)
+ form_data = json.load(form_json)
- parent_container=get_parent_container(form_data["parent_id"])
- container_type=get_container_type(form_data["container_type"])
- container_size=form_data["container_size"]
+ parent_container = get_parent_container(form_data["parent_id"])
+ container_type = get_container_type(form_data["container_type"])
+ container_size = form_data["container_size"]
# Create entities in BIS
- container_entities=create_container_entities(
+ container_entities = create_container_entities(
responsible_id=int(form_data["responsible_entity"]),
container_type_id=int(form_data["container_type"]),
container_size=container_size,
@@ -270,9 +269,9 @@ def main():
return 1
# Create template file on the server
- file_format_extension=form_data["file_format"]
- template_name=get_template_name(container_entities, file_format_extension)
- template_display_path, template_internal_path=helper.get_shared_filename(
+ file_format_extension = form_data["file_format"]
+ template_name = get_template_name(container_entities, file_format_extension)
+ template_display_path, template_internal_path = helper.get_shared_filename(
template_name)
if (file_format_extension == "csv"):
create_csv_template(
--
GitLab
From 8c9ad657ffc2ec738ff4107ea2f15846b54a2f19 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 11:59:22 +0100
Subject: [PATCH 10/63] MAINT: Remove unused import
---
.../scripting/bin/register_new_containers.py | 8 --------
1 file changed, 8 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index 76aa92e..fb6bd65 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -23,7 +23,6 @@
#
import csv
-import datetime
import json
import logging
import sys
@@ -54,13 +53,6 @@ def get_parser():
return par
-def get_current_year():
- currentDateTime = datetime.datetime.now()
- date = currentDateTime.date()
- year = date.strftime("%Y")
- return year
-
-
def create_new_label_counter(container_type_id, value=1):
counter = db.Record()
counter.add_parent(name=get_entity_name("labelcounter_rt"))
--
GitLab
From 3d61f99fb192577ac6a6952de9da43b1db61c945 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 13:31:38 +0100
Subject: [PATCH 11/63] ENH: Adapt container export
---
.../scripting/bin/export_container_csv.py | 87 +++++++++++--------
.../bin/sample_helpers/default_constants.yml | 1 +
2 files changed, 50 insertions(+), 38 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
index a23c47a..2ddc7bd 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
@@ -37,17 +37,17 @@ from linkahead.exceptions import (EmptyUniqueQueryError,
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
send_mail_with_defaults)
+from sample_helpers.utils import (CONSTANTS, get_column_header_name,
+ get_entity_name)
# suppress warning of diff function
-apilogger = logging.getLogger("caosdb.apiutils")
+apilogger = logging.getLogger("linkahead.apiutils")
apilogger.setLevel(logging.ERROR)
logger = logging.getLogger("caosadvancedtools")
-CACHE = {}
-
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
def cached_query(query, unique=False):
@@ -66,18 +66,20 @@ def reverse_semicolon_separated_list(value):
def generate_label_text(entity):
- if entity.get_property("Custom label") is not None and entity.get_property("Custom label").value:
- label = entity.get_property("Custom label").value
+ custom_label_prop_name = get_entity_name("custom_label_prop")
+ if entity.get_property(custom_label_prop_name) is not None and entity.get_property(custom_label_prop_name).value:
+ label = entity.get_property(custom_label_prop_name).value
else:
- label = entity.get_property("BIS label").value if entity.get_property(
- "BIS label") is not None else None
+ container_label_prop_name = get_entity_name("container_label_prop")
+ label = entity.get_property(container_label_prop_name).value if entity.get_property(
+ container_label_prop_name) is not None else None
if not label:
if not entity.name:
return entity.id
return f"{entity.id} {entity.name}"
if f"{label}" == f"{entity.id}":
- # prevent special case of BisLabel = BisID resulting in a preview
+ # prevent special case of Label = ID resulting in a preview
# that looks like "id, id".
return entity.id
return f"{entity.id} {label}"
@@ -85,7 +87,9 @@ def generate_label_text(entity):
def extract_parent_container(record, key):
- possible_parents = cached_query(f"FIND Container WHICH REFERENCES {record.id}")
+ possible_parents = cached_query(
+ f"FIND {get_entity_name('container_rt')} WHICH REFERENCES {record.id}"
+ )
values = []
for par in possible_parents:
@@ -103,9 +107,11 @@ def extract_bis_id(record, key):
def extract_custom_label(record, key):
- if record.get_property("Custom label") is not None:
+ custom_label_prop_name = get_entity_name("custom_label_prop")
+
+ if record.get_property(custom_label_prop_name) is not None:
- return record.get_property("Custom label").value
+ return record.get_property(custom_label_prop_name).value
return None
@@ -117,8 +123,9 @@ def extract_pi(record, key):
pi_id = record.get_property("PI").value
pi_rec = cached_query(f"FIND RECORD Person WITH ID={pi_id}", unique=True)
- if pi_rec.get_property("Abbreviation") is not None and pi_rec.get_property("Abbreviation").value is not None:
- return pi_rec.get_property("Abbreviation").value
+ abbr_prop_name = get_entity_name("abbreviation_prop")
+ if pi_rec.get_property(abbr_prop_name) is not None and pi_rec.get_property(abbr_prop_name).value is not None:
+ return pi_rec.get_property(abbr_prop_name).value
return pi_id
return None
@@ -145,11 +152,14 @@ def extract_collection(record, key):
def extract_container_type(record, key):
- if record.get_property("ContainerType") is not None and record.get_property("ContainerType").value is not None:
- ct_id = record.get_property("ContainerType").value
- ctr = cached_query(f"FIND ContainerType WITH ID={ct_id}", unique=True)
- if ctr.get_property("Abbreviation") is not None and ctr.get_property("Abbreviation").value is not None:
- return ctr.get_property("Abbreviation").value
+ abbr_prop_name = get_entity_name("abbreviation_prop")
+ containertype_rt_name = get_entity_name("containertype_rt")
+
+ if record.get_property(containertype_rt_name) is not None and record.get_property(containertype_rt_name).value is not None:
+ ct_id = record.get_property(containertype_rt_name).value
+ ctr = cached_query(f"FIND {containertype_rt_name} WITH ID={ct_id}", unique=True)
+ if ctr.get_property(abbr_prop_name) is not None and ctr.get_property(abbr_prop_name).value is not None:
+ return ctr.get_property(abbr_prop_name).value
return ct_id
return None
@@ -159,7 +169,7 @@ def extract_storage_chain(record, key):
def find_referencing_containers(eid):
containing_containers = []
- candidates = cached_query(f"FIND CONTAINER WHICH REFERENCES {eid}")
+ candidates = cached_query(f"FIND {get_entity_name('container_rt')} WHICH REFERENCES {eid}")
if len(candidates) > 1:
logger.debug(f"Entity {eid} is referenced by more than one container.")
return []
@@ -183,25 +193,25 @@ def default_extractor(record, key):
EXTRACTORS = {
- "BIS ID": extract_bis_id,
- "BIS label": default_extractor,
- "Collection": extract_collection,
- "Container Contents": default_extractor,
- "Container size": default_extractor,
- "Container type": extract_container_type,
- "Custom label": extract_custom_label,
- "PDFReport": default_extractor,
- "PI": extract_pi,
- "Parent container": extract_parent_container,
- "Storage chain": extract_storage_chain,
+ get_column_header_name("entity_id"): extract_bis_id,
+ get_column_header_name("container_label_prop"): default_extractor,
+ get_column_header_name("Collection"): extract_collection,
+ get_column_header_name("container_size_prop"): default_extractor,
+ get_column_header_name("containertype_rt"): extract_container_type,
+ get_column_header_name("custom_label_prop"): extract_custom_label,
+ get_column_header_name("PDFReport"): default_extractor,
+ get_column_header_name("PI"): extract_pi,
+ get_column_header_name("Parent container"): extract_parent_container,
+ get_column_header_name("Storage chain"): extract_storage_chain,
}
# List of sample properties to be ignored because they are treated
# otherwise. Similar, but not identical to SPECIAL TREATMENT.
IGNORE_KEYS = [
- "Child container", # To be changed by updating the child, not the parent.
- "ContainerType", # handled separately above
- "Responsible", # Not to be changed via upload
+ # To be changed by updating the child, not the parent.
+ get_column_header_name("child_container_prop"),
+ get_column_header_name("containertype_rt"), # handled separately above
+ get_column_header_name("Responsible"), # Not to be changed via upload
]
@@ -230,7 +240,7 @@ def retrieve_containers(data):
try:
container.append(
cached_query(
- f"FIND RECORD Container WITH id = '{bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{bis_id}'",
unique=True))
except EmptyUniqueQueryError as e:
# we want to warn about these
@@ -241,7 +251,8 @@ def retrieve_containers(data):
try:
container.append(
cached_query(
- f"FIND RECORD Container WITH id = '{next_bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{
+ next_bis_id}'",
unique=True))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
@@ -355,7 +366,7 @@ def main():
f"{ke}\n\nPlease contact your admin."
)
else:
- msg = "{}export_sample_csv.py was called without the JSON file in args.{}".format(
+ msg = "{} export_container_csv.py was called without the JSON file in args. {}".format(
ERROR_PREFIX, ERROR_SUFFIX)
logger.error(msg)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 729d795..ff0dd5a 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -25,6 +25,7 @@ entity_names:
container_rt: Container
container_size_prop: "Container size"
containertype_rt: ContainerType
+ custom_label_prop: "Custom label"
labelcounter_prop: Counter
labelcounter_rt: LabelCounter
responsible_rt: Responsible
--
GitLab
From 5f2cb7fe596ce5c1b8ee2da6fa0c771dde4ef286 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 13:45:39 +0100
Subject: [PATCH 12/63] ENH: Make column descriptions configurable
---
.../caosdb-server/scripting/bin/bis_utils.py | 31 ++-----------------
.../scripting/bin/export_container_csv.py | 5 ++-
.../bin/sample_helpers/default_constants.yml | 27 ++++++++++++++++
3 files changed, 32 insertions(+), 31 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
index d705030..80165fc 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
@@ -32,6 +32,8 @@ from caosadvancedtools.serverside.helper import send_mail
from caoscrawler.config import get_config_setting
from linkahead import get_entity_by_name
+from sample_helpers.utils import CONSTANTS
+
SPECIAL_TREATMENT_SAMPLE = [
"BIS ID",
"Collection",
@@ -82,34 +84,7 @@ IGNORED_COLUMN_NAMES_SAMPLE = [
]
-# This can be used for hard-coded descriptions
-COLUMN_DESCRIPTIONS = {
- "BIS ID": "An ID generated by the BIS (either integer or URL to this entity). Do not change this column!",
- "BIS label": "The label automatically assigned by the BIS. Do not change this column.",
- "Collection": "Collection(s) to which this container or samples belongs (separated by ';')",
- "Container Contents": "Notes concerning the contents of this container",
- "Container size": "The size of the container (e.g 81 spaces)",
- "Container type": "The type of container. Do not change this column.",
- "Custom label": "Any additional custom label you put on the container",
- "Date collected start": "The start date in format YYYY-MM-DD",
- "Date collected stop": "The end date in format YYYY-MM-DD",
- "Gear configuration": "How gear is configured, meshsize of the net, filter pore size, what kind of trawl",
- "Latitude start": "Latitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for S",
- "Latitude stop": "Latitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for S",
- "Longitude start": "Longitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for W",
- "Longitude stop": "Longitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for W",
- "Notes / remarks": "Field for notes",
- "PDFReport": "A PDF containing additional information on the container or sampe contents",
- "PI": "The PI (by abbreviation) of the container or sample",
- "Parent container": "The BIS ID (integer or URL) or name or BIS label of the container where this container is stored.",
- "Sampling depth start": "The depth in meters where the sampling started as a positive value, not bottom depth",
- "Sampling depth stop": "The depth in meters where the sampling ended as a positive value,not bottom depth",
- "Storage ID": "BIS ID of the Container that holds this sample",
- "Subevent": "Subevent given by D-Ship in Stationlog. Expl. AL123_14-4",
- "Timezone": "Timezone: Either UTC, CET, .... or in the form +hh[:mm], -hh:[mm].",
- "Water depth start": "The bottom depth in meters where the sampling started as a positive value",
- "Water depth stop": "The bottom depth in meters where the sampling ended as a positive value",
-}
+COLUMN_DESCRIPTIONS = CONSTANTS["csv_column_descriptions"]
def get_do_not_insert_type_names(override_names: list[str] = []):
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
index 2ddc7bd..d30e91f 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
@@ -36,7 +36,7 @@ from linkahead.exceptions import (EmptyUniqueQueryError,
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
- send_mail_with_defaults)
+ get_options_row, send_mail_with_defaults)
from sample_helpers.utils import (CONSTANTS, get_column_header_name,
get_entity_name)
@@ -251,8 +251,7 @@ def retrieve_containers(data):
try:
container.append(
cached_query(
- f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{
- next_bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{next_bis_id}'",
unique=True))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index ff0dd5a..c773685 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -18,6 +18,33 @@
csv_column_names:
entity_id: "LinkAhead ID"
+csv_column_descriptions:
+ LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
+ container_label: "The label automatically assigned by LinkAhead sample management. Do not change this column."
+ Collection: "Collection(s) to which this container or samples belongs (separated by ';')"
+ Container Contents: "Notes concerning the contents of this container"
+ Container size: "The size of the container (e.g 81 spaces)"
+ Container type: "The type of container. Do not change this column."
+ Custom label: "Any additional custom label you put on the container"
+ Date collected start: "The start date in format YYYY-MM-DD"
+ Date collected stop: "The end date in format YYYY-MM-DD"
+ Gear configuration: "How gear is configured, meshsize of the net, filter pore size, what kind of trawl"
+ Latitude start: "Latitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for S"
+ Latitude stop: "Latitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for S"
+ Longitude start: "Longitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for W"
+ Longitude stop: "Longitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for W"
+ Notes / remarks: "Field for notes"
+ PDFReport: "A PDF containing additional information on the container or sampe contents"
+ PI: "The PI (by abbreviation) of the container or sample"
+ Parent container: "The LinkAhead ID (integer or URL) or name or BIS label of the container where this container is stored."
+ Sampling depth start: "The depth in meters where the sampling started as a positive value, not bottom depth"
+ Sampling depth stop: "The depth in meters where the sampling ended as a positive value,not bottom depth"
+ Storage ID: "LinkAhead ID of the Container that holds this sample"
+ Subevent: "Subevent given by D-Ship in Stationlog. Expl. AL123_14-4"
+ Timezone: "Timezone: Either UTC, CET, .... or in the form +hh[:mm], -hh:[mm]."
+ Water depth start: "The bottom depth in meters where the sampling started as a positive value"
+ Water depth stop: "The bottom depth in meters where the sampling ended as a positive value"
+
entity_names:
abbreviation_prop: Abbreviation
child_container_prop: "Child container"
--
GitLab
From d467dbd5c9cda08e83ade829faec1d4fe8ba8431 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 22 Jan 2025 14:08:25 +0100
Subject: [PATCH 13/63] ENH: Make parent container identification configurable
---
.../container_update_get_parent.py | 35 +++++++++++++++++++
.../scripting/bin/update_containers.py | 19 ++++------
2 files changed, 41 insertions(+), 13 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_get_parent.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_get_parent.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_get_parent.py
new file mode 100644
index 0000000..4d11a3b
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_get_parent.py
@@ -0,0 +1,35 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from .utils import get_entity_name
+
+
+def get_container_by_identifier(identifier: str) -> db.Record:
+ """Return a container identified by the given string identifier."""
+ # First try (integer) ID
+ try:
+ identifier = int(identifier)
+ query = f"FIND '{get_entity_name('container_rt')}' WITH ID={identifier}"
+ except ValueError:
+ # Then fall back to name or label
+ query = (f"FIND '{get_entity_name('container_rt')}' WITH "
+ f"name='{identifier}' OR WITH "
+ f"'{get_entity_name('container_label_prop')}'='{identifier}'")
+
+ return db.cached.cached_query(query)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 6334551..d484916 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -36,13 +36,15 @@ from linkahead.cached import cached_query, cached_get_entity_by
from bis_utils import (get_do_not_insert_type_names,
replace_entity_urls_by_ids, whitespace_cleanup_in_df)
+from sample_helpers.container_update_get_parent import get_container_by_identifier
+from sample_helpers.utils import CONSTANTS
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
apilogger.setLevel(logging.ERROR)
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
logger = logging.getLogger("caosadvancedtools")
@@ -55,15 +57,6 @@ def _value_in_row(key, row):
return True
-def _get_parent_by_identifier(parent_identifier):
- """Get parent specified either by BIS ID, name, or BIS label."""
- try:
- parent_identifier = int(parent_identifier)
- query = f"FIND Container WITH ID={parent_identifier}"
- except ValueError:
- query = (f"FIND Container WITH name='{parent_identifier}' "
- f"OR WITH 'BIS label'='{parent_identifier}'")
- return cached_query(query)
def get_parser():
@@ -111,7 +104,7 @@ def main():
if _value_in_row("Parent container", row):
parent_identifier = row["Parent container"]
- parent = _get_parent_by_identifier(parent_identifier)
+ parent = get_container_by_identifier(parent_identifier)
if len(parent) == 0:
logger.error(
f"Couldn't find parent with identifier '{parent_identifier}' in row {index+1}.")
@@ -143,7 +136,7 @@ def main():
if _value_in_row("Parent container", row):
parent_identifier = row["Parent container"]
# This has already been checked above for uniqueness
- candidate = _get_parent_by_identifier(parent_identifier)[0]
+ candidate = get_container_by_identifier(parent_identifier)[0]
# A bit redundant, but we need the exact Python object here that is in the parent_containers list.
parent = parent_containers.get_entity_by_id(candidate.id)
--
GitLab
From df38c60d1136e2528a28f402a4223fe1d692e503 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 11:02:26 +0100
Subject: [PATCH 14/63] ENH: Make sample and container id label in export
configurable
---
.../50.sample-management.conf | 4 +++-
.../src/ext/js/ext_bis_samplemanagemet.js | 15 ++++++++-------
.../src/ext/js/ext_bis_stockmanagement.js | 19 ++++++++++---------
3 files changed, 21 insertions(+), 17 deletions(-)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
index 185d75e..45d6d63 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
+++ b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
@@ -22,6 +22,8 @@ BUILD_MODULE_EXT_SSS_MARKDOWN=ENABLED
# Showing id in labels helps for the container/sample id columns
BUILD_MODULE_SHOW_ID_IN_LABEL=ENABLED
-# BIS specific variables
+# sample-management specific variables
BUILD_MODULE_EXT_BIS_SAMPLEMANAGEMENT=ENABLED
BUILD_MODULE_EXT_BIS_STOCKMANAGEMENT=ENABLED
+BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL="Sample ID"
+BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL="Container ID"
\ No newline at end of file
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
index 4228d64..09c64a8 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
@@ -29,6 +29,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
const upload_pdf_title = "Upload PDF file";
const export_csv_id = "export_sample_csv";
const export_csv_title = "Export Samples to CSV";
+ const sample_id_label = ("${BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL}" != "") ? "${BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL}" : "Sample ID";
const accepted_file_formats = [
".csv",
".CSV",
@@ -36,7 +37,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
"text/csv",
];
const required_column_names = [
- "BIS ID",
+ "LinkAhead ID",
"Date collected start",
"Main User",
"Gear",
@@ -56,11 +57,11 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
"Sample Context",
];
const requiredColumnNamesChildren = [
- "BIS ID",
+ "LinkAhead ID",
"Date sampled start",
"Fixation",
"Main User",
- "Parent BIS ID",
+ "Parent LinkAhead ID",
"Sample Context",
"Sample container",
"SampleType",
@@ -101,7 +102,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
"Date sampled stop",
"Time sampled start",
"Time sampled stop",
- "Parent BIS ID"
+ "Parent LinkAhead ID"
]
const allColumnNames = non_sample_rt_column_names.concat(requiredColumnNamesChildren).concat(required_column_names);
@@ -135,11 +136,11 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
fields: [{
type: "text",
name: "bis_ids",
- label: "BIS IDS",
+ label: sample_id_label,
required: false,
pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",
cached: false,
- help: "Comma-separated list of single BIS IDs or ranges, e.g. '124, 126-139, 242'",
+ help: `Comma-separated list of single ${sample_id_label}s or ranges, e.g. '124, 126-139, 242'`,
}, {
type: "text",
name: "query_string",
@@ -398,7 +399,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
});
};
-
+
const is_authorized = function() {
// return true //for testing
return isAuthenticated() //&& (userHasRole("stockmanager") || userHasRole("administration"))
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js
index b8630a4..c378703 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js
@@ -11,13 +11,14 @@
*
* @requires($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver)
*/
-const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_bis_stockmanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
const tool_box = "Storage Management" // The item that is shown in the top-navbar
///////////////// REGISTER NEW CONTAINERS START
const register_new_containers_title = "Register new Containers";
const register_new_containers_panel_id = "register_new_containers_form_panel";
+ const container_id_label = ("${BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL}" != "") ? "${BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL}" : "Container ID";
const register_new_containers_form_config = {
// the script can be found in profiles/default/custom/caosdb-server/scripting/bin/
// it is called like ./register_new_containers.py form.json where form.json
@@ -115,11 +116,11 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
fields: [{
type: "text",
name: "bis_ids",
- label: "BIS IDS",
+ label: container_id_label,
required: true,
pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",
cached: false,
- help: "Comma-separated list of single BIS IDs or ranges, e.g. '124, 126-139, 242'"
+ help: `Comma-separated list of single ${container_id_label}s or ranges, e.g. '124, 126-139, 242'`
}]
};
///////////////// EXPORT CONTAINER CSV END
@@ -130,7 +131,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
* dropdown for Container registration and for uploading filled-in container
* forms.
*/
- const init_show_stockmanagement_panel_buttons = function () {
+ const init_show_stockmanagement_panel_buttons = function() {
create_register_new_containers_button();
create_update_containers_button();
@@ -159,7 +160,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
});
};
- const create_register_new_containers_button = function () {
+ const create_register_new_containers_button = function() {
navbar.add_tool(register_new_containers_title, tool_box, {
callback: form_panel.create_show_form_callback(
register_new_containers_panel_id,
@@ -168,7 +169,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
});
};
- const create_update_containers_button = function () {
+ const create_update_containers_button = function() {
navbar.add_tool(update_containers_title, tool_box, {
callback: form_panel.create_show_form_callback(
update_containers_panel_id,
@@ -183,7 +184,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
* Check if the user is authenticated and has at least stockmanager or
* administrator role.
*/
- const is_authorized = function () {
+ const is_authorized = function() {
return isAuthenticated() && (userHasRole("Scientist") || userHasRole("Stock manager") || userHasRole("administration") || userHasRole("Curator"));
}
@@ -192,7 +193,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
* top-navbar is_authorized() returns true, i.e. the user is authenticated
* and has either stockmanager or administration role.
*/
- const init = function () {
+ const init = function() {
if (is_authorized()) {
init_show_stockmanagement_panel_buttons();
}
@@ -204,7 +205,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
};
}($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver); // this will be replaced by require.js in the future.
-$(document).ready(function () {
+$(document).ready(function() {
// use a variable starting with `BUILD_MODULE_` to this module
// the build variable has to be enabled in the `build.properties.d/` directory.
// Otherwise the module will not be activated.
--
GitLab
From da255a8b7fa9590c29fea1baec8dbaf66c28d9ab Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 11:07:15 +0100
Subject: [PATCH 15/63] MAINT: Rename stock management module
---
.../caosdb-webui/build.properties.d/50.sample-management.conf | 2 +-
.../js/{ext_bis_stockmanagement.js => ext_stockmanagement.js} | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
rename sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/{ext_bis_stockmanagement.js => ext_stockmanagement.js} (98%)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
index 45d6d63..9f114ce 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
+++ b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
@@ -24,6 +24,6 @@ BUILD_MODULE_SHOW_ID_IN_LABEL=ENABLED
# sample-management specific variables
BUILD_MODULE_EXT_BIS_SAMPLEMANAGEMENT=ENABLED
-BUILD_MODULE_EXT_BIS_STOCKMANAGEMENT=ENABLED
+BUILD_MODULE_EXT_STOCKMANAGEMENT=ENABLED
BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL="Sample ID"
BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL="Container ID"
\ No newline at end of file
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
similarity index 98%
rename from sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js
rename to sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
index c378703..8c79a10 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
@@ -209,8 +209,8 @@ $(document).ready(function() {
// use a variable starting with `BUILD_MODULE_` to this module
// the build variable has to be enabled in the `build.properties.d/` directory.
// Otherwise the module will not be activated.
- if ("${BUILD_MODULE_EXT_BIS_STOCKMANAGEMENT}" === "ENABLED") {
- caosdb_modules.register(ext_bis_stockmanagement);
+ if ("${BUILD_MODULE_EXT_STOCKMANAGEMENT}" === "ENABLED") {
+ caosdb_modules.register(ext_stockmanagement);
}
});
// const form = form_elements.make_form(config);
--
GitLab
From d8645b5845238f5487daf88fad15b301742d76cb Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 11:12:39 +0100
Subject: [PATCH 16/63] MAINT: Remove bis from container id variable in web
form
---
.../src/ext/js/ext_stockmanagement.js | 6 +-
.../scripting/bin/export_container_csv.py | 20 ++---
.../scripting/bin/update_containers.py | 82 +++++++++++--------
3 files changed, 62 insertions(+), 46 deletions(-)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
index 8c79a10..36e05ce 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
@@ -6,12 +6,12 @@
'use strict';
/**
- * @module ext_bis_stockmanagement
+ * @module ext_stockmanagement
* @version 0.2
*
* @requires($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver)
*/
-const ext_bis_stockmanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_stockmanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
const tool_box = "Storage Management" // The item that is shown in the top-navbar
@@ -115,7 +115,7 @@ const ext_bis_stockmanagement = function($, navbar, log, form_elements, form_pan
script: "export_container_csv.py",
fields: [{
type: "text",
- name: "bis_ids",
+ name: "container_ids",
label: container_id_label,
required: true,
pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
index d30e91f..13a2a1b 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
@@ -100,7 +100,7 @@ def extract_parent_container(record, key):
return reverse_semicolon_separated_list(values)
-def extract_bis_id(record, key):
+def extract_eid(record, key):
return record.id
@@ -193,7 +193,7 @@ def default_extractor(record, key):
EXTRACTORS = {
- get_column_header_name("entity_id"): extract_bis_id,
+ get_column_header_name("entity_id"): extract_eid,
get_column_header_name("container_label_prop"): default_extractor,
get_column_header_name("Collection"): extract_collection,
get_column_header_name("container_size_prop"): default_extractor,
@@ -235,29 +235,29 @@ def retrieve_containers(data):
container = []
not_found = []
- for bis_id in data:
- if isinstance(bis_id, int):
+ for eid in data:
+ if isinstance(eid, int):
try:
container.append(
cached_query(
- f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{eid}'",
unique=True))
except EmptyUniqueQueryError as e:
# we want to warn about these
- not_found.append(bis_id)
+ not_found.append(eid)
else:
found_at_least_one_in_range = False
- for next_bis_id in bis_id:
+ for next_eid in eid:
try:
container.append(
cached_query(
- f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{next_bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{next_eid}'",
unique=True))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
pass
if not found_at_least_one_in_range:
- not_found.append(f"{bis_id.start}-{bis_id.stop-1}")
+ not_found.append(f"{eid.start}-{eid.stop-1}")
return container, not_found
@@ -325,7 +325,7 @@ def main():
with open(args.filename) as form_json:
form_data = json.load(form_json)
- tmp = form_data["bis_ids"].split(",")
+ tmp = form_data["container_ids"].split(",")
data = []
for d in tmp:
if "-" in d:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index d484916..12ef9b6 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -37,7 +37,7 @@ from linkahead.cached import cached_query, cached_get_entity_by
from bis_utils import (get_do_not_insert_type_names,
replace_entity_urls_by_ids, whitespace_cleanup_in_df)
from sample_helpers.container_update_get_parent import get_container_by_identifier
-from sample_helpers.utils import CONSTANTS
+from sample_helpers.utils import (CONSTANTS, get_column_header_name, get_entity_name)
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -89,29 +89,35 @@ def main():
# Get referenced container entities
child_containers = db.Container()
parent_containers = db.Container()
+ id_column_name = get_column_header_name("entity_id")
+ parent_column_name = get_column_header_name("Parent container")
for index, row in data.iterrows():
- if not _value_in_row("BIS ID", row):
- logger.error(f"BIS ID is missing in row {index+1}. Nothing was updated.")
+ if not _value_in_row(id_column_name, row):
+ logger.error(f"{id_column_name} is missing in row {index+1}. Nothing was updated.")
return 1
try:
- child = db.Record(id=int(row["BIS ID"]))
+ child = db.Record(id=int(row[id_column_name]))
except ValueError:
logger.error(
- f"Invalid BIS ID {row['BIS ID']} in row {index + 1}. Nothing was updated.")
+ f"Invalid {id_column_name} {row[id_column_name]} in row {index + 1}. Nothing was updated.")
return 1
- child.add_parent("Container")
+ child.add_parent(get_entity_name("container_rt"))
child_containers.append(child)
-
- if _value_in_row("Parent container", row):
- parent_identifier = row["Parent container"]
+
+ if _value_in_row(parent_column_name, row):
+ parent_identifier = row[parent_column_name]
parent = get_container_by_identifier(parent_identifier)
if len(parent) == 0:
logger.error(
- f"Couldn't find parent with identifier '{parent_identifier}' in row {index+1}.")
+ f"Couldn't find parent with identifier '{parent_identifier}' "
+ f"in row {index+1}."
+ )
return 1
elif len(parent) > 1:
- logger.error(f"Parent with identifier '{parent_identifier}' in row {index+1} was not unique. "
- "Please specify with BIS ID instead.")
+ logger.error(
+ f"Parent with identifier '{parent_identifier}' in row "
+ f"{index+1} was not unique. Please specify with "
+ f"{id_column_name} instead.")
return 1
parent = parent[0]
try:
@@ -125,16 +131,22 @@ def main():
return 1
# Get IDs of proerperties
- child_container_prop = cached_get_entity_by(query="FIND Property WITH name = 'Child container'")
- custom_label_prop = cached_get_entity_by(query="FIND Property WITH name = 'Custom label'")
- pdf_rt = cached_get_entity_by(query="FIND RECORDTYPE WITH name=PDFReport")
+ child_container_prop = cached_get_entity_by(
+ query=f"FIND Property WITH name = '{get_entity_name('child_container_prop')}'"
+ )
+ custom_label_prop = cached_get_entity_by(
+ query=f"FIND Property WITH name = '{get_entity_name('custom_label_prop')}'"
+ )
+ pdf_rt = cached_get_entity_by(
+ query=f"FIND RECORDTYPE WITH name='{get_entity_name('PDFReport')}'"
+ )
# Update (/create) container entities
for index, row in data.iterrows():
# Add child to parent
parent = None
- if _value_in_row("Parent container", row):
- parent_identifier = row["Parent container"]
+ if _value_in_row(parent_column_name, row):
+ parent_identifier = row[parent_column_name]
# This has already been checked above for uniqueness
candidate = get_container_by_identifier(parent_identifier)[0]
# A bit redundant, but we need the exact Python object here that is in the parent_containers list.
@@ -142,17 +154,21 @@ def main():
if parent.get_property(child_container_prop.id) is None:
parent.add_property(id=child_container_prop.id,
- name=child_container_prop.name, value=[int(row["BIS ID"])])
+ name=child_container_prop.name, value=[int(row[id_column_name])])
else:
if parent.get_property(child_container_prop.id).value is None:
- parent.get_property(child_container_prop.id).value = [int(row["BIS ID"])]
+ parent.get_property(child_container_prop.id).value = [int(row[id_column_name])]
else:
- if int(row["BIS ID"]) not in parent.get_property(child_container_prop.id).value:
+ if int(row[id_column_name]) not in parent.get_property(child_container_prop.id).value:
parent.get_property(child_container_prop.id).value.append(
- int(row["BIS ID"]))
-
- # remove the current child from all other parents (don't do anything if the parent didn't change)
- old_parents = cached_query(f"FIND Container WHICH REFERENCES {int(row['BIS ID'])}")
+ int(row[id_column_name]))
+
+ # remove the current child from all other parents (don't
+ # do anything if the parent didn't change)
+ old_parents = cached_query(
+ f"FIND {get_entity_name('container_rt')} WHICH REFERENCES "
+ f"{int(row[id_column_name])}"
+ )
for old_parent in old_parents:
if parent is not None and old_parent.id == parent.id:
# old parent also is new parent
@@ -162,20 +178,20 @@ def main():
old_parent = parent_containers.get_entity_by_id(old_parent.id)
except KeyError:
parent_containers.append(old_parent)
- old_parent.remove_value_from_property("Child container", int(
- row["BIS ID"]), remove_if_empty_afterwards=False)
- if old_parent.get_property("Child container").value is None:
- old_parent.get_property("Child container").value = []
+ old_parent.remove_value_from_property(child_container_prop.name, int(
+ row[id_column_name]), remove_if_empty_afterwards=False)
+ if old_parent.get_property(child_container_prop.name).value is None:
+ old_parent.get_property(child_container_prop.name).value = []
# Add custom label o child
- child = child_containers.get_entity_by_id(id=int(row["BIS ID"]))
- if _value_in_row("Custom label", row):
- child.name = row["Custom label"]
+ child = child_containers.get_entity_by_id(id=int(row[id_column_name]))
+ if _value_in_row(get_column_header_name("custom_label_prop"), row):
+ child.name = row[get_column_header_name("custom_label_prop")]
if child.get_property(custom_label_prop.id) is None:
child.add_property(id=custom_label_prop.id,
- name=custom_label_prop.name, value=row["Custom label"])
+ name=custom_label_prop.name, value=row[get_column_header_name("custom_label_prop")])
else:
- child.get_property(custom_label_prop.id).value = row["Custom label"]
+ child.get_property(custom_label_prop.id).value = row[get_column_header_name("custom_label_prop")]
# Treat PI
if _value_in_row("PI", row):
--
GitLab
From b484c52ed64ad0f12ffb514c2b554f8f605ed196 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 11:30:18 +0100
Subject: [PATCH 17/63] MAINT: Remove unused responsible entities from data
model
---
.../sample-management-datamodel.yml | 23 +-
.../custom/other/restore/caosdb.dump.sql | 344 ++++++++++++------
2 files changed, 245 insertions(+), 122 deletions(-)
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index 78935e6..d2cb68d 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -1,7 +1,6 @@
#
-#
-# Copyright (C) 2024 IndiScale <info@indiscale.com>
-# Copyright (C) 2024 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+# Copyright (C) 2024-2025 IndiScale <info@indiscale.com>
+# Copyright (C) 2024-2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -28,21 +27,8 @@ Responsible:
- ControlledRecordType
obligatory_properties:
Abbreviation:
- description: An abbreviation for this entity that is used for creating BIS labels
- datatype: TEXT
-ResearchDivision:
- inherit_from_obligatory:
- - Responsible
- obligatory_properties:
- German name:
- description: A german name for an entitiy. This can be used in queries since it is an alias.
+ description: An abbreviation for this entity that is used for identification purposes
datatype: TEXT
-ResearchUnit:
- inherit_from_obligatory:
- - Responsible
- obligatory_properties:
- German name:
- ResearchDivision:
Person:
inherit_from_obligatory:
- Responsible
@@ -53,7 +39,6 @@ Person:
datatype: TEXT
Email:
datatype: TEXT
- ResearchUnit:
ContainerType:
inherit_from_obligatory:
@@ -75,7 +60,7 @@ Container:
description: The size of the container, e.g. number of spaces or dimension
datatype: TEXT
Custom label:
- description: A custom label for a container that doesn't have to follow the BIS labeling guidelines.
+ description: A custom label for a container that doesn't have to follow the automatic labeling guidelines.
datatype: TEXT
Container Contents:
datatype: TEXT
diff --git a/test-profile/custom/other/restore/caosdb.dump.sql b/test-profile/custom/other/restore/caosdb.dump.sql
index 1c57494..913434b 100644
--- a/test-profile/custom/other/restore/caosdb.dump.sql
+++ b/test-profile/custom/other/restore/caosdb.dump.sql
@@ -46,7 +46,8 @@ CREATE TABLE `archive_collection_type` (
LOCK TABLES `archive_collection_type` WRITE;
/*!40000 ALTER TABLE `archive_collection_type` DISABLE KEYS */;
INSERT INTO `archive_collection_type` VALUES
-(0,153,177,'LIST',1);
+(0,153,177,'LIST',1),
+(0,153,177,'LIST',2);
/*!40000 ALTER TABLE `archive_collection_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -84,23 +85,37 @@ LOCK TABLES `archive_data_type` WRITE;
/*!40000 ALTER TABLE `archive_data_type` DISABLE KEYS */;
INSERT INTO `archive_data_type` VALUES
(0,0,144,13,1),
+(0,0,144,13,2),
(0,0,145,13,1),
+(0,0,145,13,2),
(0,0,146,13,1),
+(0,0,146,13,2),
(0,0,147,13,1),
+(0,0,147,13,2),
+(0,0,102,14,1),
+(0,0,114,14,1),
(0,111,177,101,1),
-(0,105,177,103,1),
-(0,106,177,105,1),
-(0,188,177,105,1),
+(0,111,177,101,2),
(0,111,178,110,1),
+(0,111,178,110,2),
(0,136,177,110,1),
+(0,136,177,110,2),
(0,118,178,111,1),
+(0,118,178,111,2),
(0,118,177,119,1),
+(0,118,177,119,2),
(0,118,179,120,1),
+(0,118,179,120,2),
(0,118,180,121,1),
+(0,118,180,121,2),
(0,119,178,138,1),
+(0,119,178,138,2),
(0,153,177,143,1),
+(0,153,177,143,2),
(0,150,177,148,1),
-(0,153,178,148,1);
+(0,150,177,148,2),
+(0,153,178,148,1),
+(0,153,178,148,2);
/*!40000 ALTER TABLE `archive_data_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -268,23 +283,40 @@ CREATE TABLE `archive_entities` (
LOCK TABLES `archive_entities` WRITE;
/*!40000 ALTER TABLE `archive_entities` DISABLE KEYS */;
INSERT INTO `archive_entities` VALUES
-(103,NULL,'RECORDTYPE',2,1),
-(105,NULL,'RECORDTYPE',2,1),
+(101,NULL,'RECORDTYPE',2,1),
+(102,'An abbreviation for this entity that is used for creating BIS labels','PROPERTY',2,1),
(106,NULL,'RECORDTYPE',2,1),
+(106,NULL,'RECORDTYPE',2,2),
+(110,NULL,'RECORDTYPE',2,1),
(111,NULL,'RECORDTYPE',2,1),
+(111,NULL,'RECORDTYPE',2,2),
+(114,'A custom label for a container that doesn\'t have to follow the BIS labeling guidelines.','PROPERTY',2,1),
(118,NULL,'RECORDTYPE',2,1),
+(118,NULL,'RECORDTYPE',2,2),
(119,NULL,'RECORDTYPE',2,1),
+(119,NULL,'RECORDTYPE',2,2),
(136,NULL,'RECORDTYPE',2,1),
+(136,NULL,'RECORDTYPE',2,2),
(143,NULL,'RECORDTYPE',2,1),
+(143,NULL,'RECORDTYPE',2,2),
(144,'The depth of the water in meters as a positive value','PROPERTY',2,1),
+(144,'The depth of the water in meters as a positive value','PROPERTY',2,2),
(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,1),
+(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,2),
(146,NULL,'PROPERTY',2,1),
+(146,NULL,'PROPERTY',2,2),
(147,NULL,'PROPERTY',2,1),
+(147,NULL,'PROPERTY',2,2),
(150,NULL,'RECORDTYPE',2,1),
+(150,NULL,'RECORDTYPE',2,2),
(153,NULL,'RECORDTYPE',2,1),
+(153,NULL,'RECORDTYPE',2,2),
(161,NULL,'RECORDTYPE',2,1),
+(161,NULL,'RECORDTYPE',2,2),
(162,NULL,'RECORDTYPE',2,1),
+(162,NULL,'RECORDTYPE',2,2),
(188,NULL,'RECORD',2,1),
+(188,NULL,'RECORD',2,2),
(192,NULL,'RECORD',2,1),
(193,NULL,'RECORD',2,1),
(193,NULL,'RECORD',3,2),
@@ -438,10 +470,6 @@ INSERT INTO `archive_isa` VALUES
(195,2,111,1),
(196,1,136,1),
(198,1,118,1),
-(103,1,100,0),
-(103,1,101,1),
-(105,1,100,0),
-(105,1,101,1),
(106,1,100,0),
(106,1,101,1),
(153,1,150,1),
@@ -449,7 +477,17 @@ INSERT INTO `archive_isa` VALUES
(162,1,143,1),
(193,3,111,1),
(195,3,111,1),
-(197,2,111,1);
+(197,2,111,1),
+(101,1,100,1),
+(106,2,100,0),
+(106,2,101,1),
+(110,1,100,1),
+(153,2,150,1),
+(161,2,143,1),
+(162,2,143,1),
+(188,2,100,0),
+(188,2,101,0),
+(188,2,106,1);
/*!40000 ALTER TABLE `archive_isa` ENABLE KEYS */;
UNLOCK TABLES;
@@ -491,8 +529,6 @@ INSERT INTO `archive_name_data` VALUES
(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,2),
(0,197,20,'fad_mru_myn_2025_fri_1','FIX',0,1),
(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,2),
-(0,103,20,'ResearchDivision','FIX',0,1),
-(0,105,20,'ResearchUnit','FIX',0,1),
(0,106,20,'Person','FIX',0,1),
(0,111,20,'Container','FIX',0,1),
(0,118,20,'Sample','FIX',0,1),
@@ -509,7 +545,26 @@ INSERT INTO `archive_name_data` VALUES
(0,162,20,'StopPosition','FIX',0,1),
(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,3),
(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,3),
-(0,197,20,'fad_mru_myn_2025_fri_1','FIX',0,2);
+(0,197,20,'fad_mru_myn_2025_fri_1','FIX',0,2),
+(0,101,20,'Responsible','FIX',0,1),
+(0,102,20,'Abbreviation','FIX',0,1),
+(0,106,20,'Person','FIX',0,2),
+(0,110,20,'ContainerType','FIX',0,1),
+(0,111,20,'Container','FIX',0,2),
+(0,114,20,'Custom label','FIX',0,1),
+(0,118,20,'Sample','FIX',0,2),
+(0,119,20,'NagoyaCase','FIX',0,2),
+(0,136,20,'LabelCounter','FIX',0,2),
+(0,143,20,'Position','FIX',0,2),
+(0,144,20,'Water depth','FIX',0,2),
+(0,145,20,'Sampling depth','FIX',0,2),
+(0,146,20,'Latitude','FIX',0,2),
+(0,147,20,'Longitude','FIX',0,2),
+(0,150,20,'Event','FIX',0,2),
+(0,153,20,'SourceEvent','FIX',0,2),
+(0,161,20,'StartPosition','FIX',0,2),
+(0,162,20,'StopPosition','FIX',0,2),
+(0,188,20,'My Name','FIX',0,2);
/*!40000 ALTER TABLE `archive_name_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -593,11 +648,6 @@ INSERT INTO `archive_null_data` VALUES
(0,195,178,'FIX',0,2),
(0,198,111,'FIX',1,1),
(0,198,119,'FIX',2,1),
-(0,103,104,'OBLIGATORY',0,1),
-(0,103,102,'OBLIGATORY',0,1),
-(0,105,104,'OBLIGATORY',0,1),
-(0,105,177,'OBLIGATORY',0,1),
-(0,105,102,'OBLIGATORY',0,1),
(0,106,107,'OBLIGATORY',0,1),
(0,106,108,'OBLIGATORY',1,1),
(0,106,109,'OBLIGATORY',2,1),
@@ -653,7 +703,65 @@ INSERT INTO `archive_null_data` VALUES
(0,161,147,'OBLIGATORY',0,1),
(0,162,146,'OBLIGATORY',0,1),
(0,162,147,'OBLIGATORY',0,1),
-(0,197,178,'FIX',0,2);
+(0,197,178,'FIX',0,2),
+(0,101,102,'OBLIGATORY',0,1),
+(0,106,107,'OBLIGATORY',0,2),
+(0,106,108,'OBLIGATORY',1,2),
+(0,106,109,'OBLIGATORY',2,2),
+(0,106,177,'OBLIGATORY',0,2),
+(0,106,102,'OBLIGATORY',0,2),
+(0,110,102,'OBLIGATORY',0,1),
+(0,111,177,'OBLIGATORY',0,2),
+(0,111,178,'OBLIGATORY',0,2),
+(0,111,212,'SUGGESTED',2,2),
+(0,111,179,'SUGGESTED',0,2),
+(0,111,113,'SUGGESTED',4,2),
+(0,111,114,'SUGGESTED',5,2),
+(0,111,115,'SUGGESTED',6,2),
+(0,111,116,'SUGGESTED',7,2),
+(0,118,177,'RECOMMENDED',0,2),
+(0,118,178,'RECOMMENDED',0,2),
+(0,118,179,'RECOMMENDED',0,2),
+(0,118,180,'RECOMMENDED',0,2),
+(0,118,122,'RECOMMENDED',4,2),
+(0,118,123,'RECOMMENDED',5,2),
+(0,118,124,'RECOMMENDED',6,2),
+(0,118,181,'SUGGESTED',0,2),
+(0,118,182,'SUGGESTED',0,2),
+(0,118,183,'SUGGESTED',0,2),
+(0,118,184,'SUGGESTED',0,2),
+(0,118,185,'SUGGESTED',0,2),
+(0,118,130,'SUGGESTED',12,2),
+(0,118,131,'SUGGESTED',13,2),
+(0,118,132,'SUGGESTED',14,2),
+(0,118,133,'SUGGESTED',15,2),
+(0,118,134,'SUGGESTED',16,2),
+(0,119,142,'OBLIGATORY',0,2),
+(0,119,140,'RECOMMENDED',1,2),
+(0,119,177,'SUGGESTED',0,2),
+(0,119,178,'SUGGESTED',0,2),
+(0,136,137,'OBLIGATORY',0,2),
+(0,136,177,'OBLIGATORY',0,2),
+(0,143,146,'OBLIGATORY',0,2),
+(0,143,147,'OBLIGATORY',1,2),
+(0,143,144,'RECOMMENDED',2,2),
+(0,143,145,'RECOMMENDED',3,2),
+(0,150,177,'OBLIGATORY',0,2),
+(0,150,151,'RECOMMENDED',1,2),
+(0,150,152,'SUGGESTED',2,2),
+(0,153,177,'OBLIGATORY',0,2),
+(0,153,178,'OBLIGATORY',0,2),
+(0,153,154,'RECOMMENDED',2,2),
+(0,153,155,'RECOMMENDED',3,2),
+(0,153,156,'RECOMMENDED',4,2),
+(0,153,157,'RECOMMENDED',5,2),
+(0,153,158,'SUGGESTED',6,2),
+(0,153,151,'RECOMMENDED',0,2),
+(0,153,152,'SUGGESTED',0,2),
+(0,161,146,'OBLIGATORY',0,2),
+(0,161,147,'OBLIGATORY',0,2),
+(0,162,146,'OBLIGATORY',0,2),
+(0,162,147,'OBLIGATORY',0,2);
/*!40000 ALTER TABLE `archive_null_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -717,8 +825,6 @@ CREATE TABLE `archive_reference_data` (
LOCK TABLES `archive_reference_data` WRITE;
/*!40000 ALTER TABLE `archive_reference_data` DISABLE KEYS */;
INSERT INTO `archive_reference_data` VALUES
-(0,188,177,187,NULL,'FIX',0,1),
-(0,188,105,177,NULL,'REPLACEMENT',4,1),
(0,193,101,188,NULL,'FIX',0,1),
(0,193,110,189,NULL,'FIX',1,1),
(0,193,112,178,NULL,'REPLACEMENT',4,1),
@@ -738,8 +844,6 @@ INSERT INTO `archive_reference_data` VALUES
(0,195,112,178,NULL,'REPLACEMENT',4,2),
(0,196,110,191,NULL,'FIX',1,1),
(0,198,124,188,NULL,'FIX',0,1),
-(0,105,103,177,NULL,'REPLACEMENT',1,1),
-(0,106,105,177,NULL,'REPLACEMENT',3,1),
(0,111,101,177,NULL,'REPLACEMENT',0,1),
(0,111,110,178,NULL,'REPLACEMENT',1,1),
(0,111,112,179,NULL,'REPLACEMENT',3,1),
@@ -768,7 +872,25 @@ INSERT INTO `archive_reference_data` VALUES
(0,195,112,178,NULL,'REPLACEMENT',4,3),
(0,197,101,188,NULL,'FIX',0,2),
(0,197,110,191,NULL,'FIX',1,2),
-(0,197,112,178,NULL,'REPLACEMENT',4,2);
+(0,197,112,178,NULL,'REPLACEMENT',4,2),
+(0,111,101,177,NULL,'REPLACEMENT',0,2),
+(0,111,110,178,NULL,'REPLACEMENT',1,2),
+(0,111,112,179,NULL,'REPLACEMENT',3,2),
+(0,118,119,177,NULL,'REPLACEMENT',0,2),
+(0,118,111,178,NULL,'REPLACEMENT',1,2),
+(0,118,120,179,NULL,'REPLACEMENT',2,2),
+(0,118,121,180,NULL,'REPLACEMENT',3,2),
+(0,118,125,181,NULL,'REPLACEMENT',7,2),
+(0,118,126,182,NULL,'REPLACEMENT',8,2),
+(0,118,127,183,NULL,'REPLACEMENT',9,2),
+(0,118,128,184,NULL,'REPLACEMENT',10,2),
+(0,118,129,185,NULL,'REPLACEMENT',11,2),
+(0,119,141,177,NULL,'REPLACEMENT',2,2),
+(0,119,138,178,NULL,'REPLACEMENT',3,2),
+(0,136,110,177,NULL,'REPLACEMENT',1,2),
+(0,150,148,177,NULL,'REPLACEMENT',0,2),
+(0,153,143,177,NULL,'REPLACEMENT',0,2),
+(0,153,148,178,NULL,'REPLACEMENT',1,2);
/*!40000 ALTER TABLE `archive_reference_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -835,7 +957,23 @@ INSERT INTO `archive_text_data` VALUES
(0,195,113,'30 m²','FIX',2,3),
(0,195,177,'fad_mru_myn_2025_rom_1','FIX',0,3),
(0,197,113,'300 l','FIX',2,2),
-(0,197,177,'fad_mru_myn_2025_fri_1','FIX',0,2);
+(0,197,177,'fad_mru_myn_2025_fri_1','FIX',0,2),
+(143,146,21,'°','FIX',0,2),
+(143,147,21,'°','FIX',0,2),
+(143,144,21,'m','FIX',0,2),
+(143,145,21,'m','FIX',0,2),
+(0,144,21,'m','FIX',0,2),
+(0,145,21,'m','FIX',0,2),
+(0,146,21,'°','FIX',0,2),
+(0,147,21,'°','FIX',0,2),
+(161,146,21,'°','FIX',0,2),
+(161,147,21,'°','FIX',0,2),
+(162,146,21,'°','FIX',0,2),
+(162,147,21,'°','FIX',0,2),
+(0,188,107,'My','FIX',0,2),
+(0,188,102,'myn','FIX',1,2),
+(0,188,108,'Name','FIX',2,2),
+(0,188,109,'my.name@example.com','FIX',3,2);
/*!40000 ALTER TABLE `archive_text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -954,10 +1092,6 @@ INSERT INTO `data_type` VALUES
(0,0,151,15),
(0,0,152,15),
(0,111,177,101),
-(0,105,177,103),
-(0,187,177,103),
-(0,106,177,105),
-(0,188,177,105),
(0,0,116,106),
(0,0,123,106),
(0,0,124,106),
@@ -1160,10 +1294,8 @@ INSERT INTO `entities` VALUES
(24,'Description of an entity.','PROPERTY',0),
(100,'Abstract type to denote that a RecordType is controlled, i.e.,\nthat no new Records of this type may be created during\nsample/container upload. Add this type as a parent to any\nRecordType you want to be controlled.\n','RECORDTYPE',2),
(101,NULL,'RECORDTYPE',2),
-(102,'An abbreviation for this entity that is used for creating BIS labels','PROPERTY',2),
-(103,NULL,'RECORDTYPE',2),
+(102,'An abbreviation for this entity that is used for identification purposes','PROPERTY',2),
(104,'A german name for an entitiy. This can be used in queries since it is an alias.','PROPERTY',2),
-(105,NULL,'RECORDTYPE',2),
(106,NULL,'RECORDTYPE',2),
(107,NULL,'PROPERTY',2),
(108,NULL,'PROPERTY',2),
@@ -1172,7 +1304,7 @@ INSERT INTO `entities` VALUES
(111,NULL,'RECORDTYPE',2),
(112,NULL,'PROPERTY',2),
(113,'The size of the container, e.g. number of spaces or dimension','PROPERTY',2),
-(114,'A custom label for a container that doesn\'t have to follow the BIS labeling guidelines.','PROPERTY',2),
+(114,'A custom label for a container that doesn\'t have to follow the automatic labeling guidelines.','PROPERTY',2),
(115,NULL,'PROPERTY',2),
(116,NULL,'PROPERTY',2),
(118,NULL,'RECORDTYPE',2),
@@ -1243,8 +1375,6 @@ INSERT INTO `entities` VALUES
(183,NULL,'_REPLACEMENT',0),
(184,NULL,'_REPLACEMENT',0),
(185,NULL,'_REPLACEMENT',0),
-(186,NULL,'RECORD',2),
-(187,NULL,'RECORD',2),
(188,NULL,'RECORD',2),
(189,NULL,'RECORD',2),
(190,NULL,'RECORD',2),
@@ -1344,9 +1474,7 @@ INSERT INTO `entity_ids` VALUES
('102',100),
('103',101),
('104',102),
-('105',103),
('106',104),
-('107',105),
('108',106),
('109',107),
('110',108),
@@ -1417,8 +1545,6 @@ INSERT INTO `entity_ids` VALUES
('176',174),
('177',175),
('178',176),
-('179',186),
-('180',187),
('181',188),
('182',189),
('183',190),
@@ -1496,29 +1622,33 @@ INSERT INTO `entity_version` VALUES
(24,NULL,'d78e2b50954d74d6946d2c113cb7393b3b6146f3',1,NULL,'cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e'),
(100,NULL,'49a9b9af29eee9abeae35df062b9c427583e1f82',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(101,NULL,'d761933f0fb660cb3c456896d7a5cfb9da7b3ec6',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
+(101,NULL,'31093347d3ba357def98cef3ffa6f0c1ccf0c76b',2,1,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
(102,NULL,'3a411f4a8633301cd3775e9eca91c456839ae455',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
-(103,NULL,'e9435f7be29bab1d255485c653b42323ab472061',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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(119,NULL,'9bfc33ae0c6be37cb027a62afd792d1c311d006a',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(119,NULL,'61ee09a05b915dba2c6d158244966d3688ccef1a',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
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(120,NULL,'46a17aea4446446e72aeaffc3a01ee2f2d5d9957',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(121,NULL,'cecee2780f2756778d57180bb6579333c6743420',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(122,NULL,'1ae73a81970c7cffda61f4354d3747495252da95',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1537,6 +1667,7 @@ INSERT INTO `entity_version` VALUES
(135,NULL,'0f0c45a83c79dbdf7211691715154849d6f4b4f3',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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(136,NULL,'a65d632df3b40a0d9cdd748c0c578f9bfd538c27',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
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(137,NULL,'acd17699d752e90015eb8010e2f17ab5566a4241',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(138,NULL,'3c63009effd95704bc52400dc38ed7c8ccc63495',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(139,NULL,'54edec758a99a74f50577b74ba8a1ef187e08859',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1545,22 +1676,29 @@ INSERT INTO `entity_version` VALUES
(142,NULL,'dc06b53bfef5dc59ccd33b646cb62cb66a37873e',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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(145,NULL,'535909011d32dc82dc3368b463c01f471c72b5f6',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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(148,NULL,'3dc270e8ab4ffded2b7f3412e97469022a389a62',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
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(150,NULL,'ac659db37f8e5c0874677706da69a6d060a93f0f',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
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(151,NULL,'c5eb1e4ec70baa761c151d708676e4c436f28587',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(152,NULL,'8abed6579e778a2bf94e6e12b38791c7a7308b61',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(153,NULL,'a5e4f99ff9324eae679f20131b8b8da68846b1ad',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(153,NULL,'80a3d9eebdd6664a84a8b445c1716dba3cd747ba',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
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(154,NULL,'3f8eb5ecfd51c5a745a4862013547d518b7b2955',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(155,NULL,'afbd70a177d0724af03b005dfa54d7a67825082a',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(156,NULL,'34e04866309d1f335fc6767aa9993ef6ee88dbd3',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1570,8 +1708,10 @@ INSERT INTO `entity_version` VALUES
(160,NULL,'2c4ec676f3a5a7e6f7f322d047cef0ccd7e794f7',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(161,NULL,'2e5f4fab2cdd47e184fced9b5ea6dd54ba45cdb3',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(161,NULL,'bae9c9da4e3784233fa93ea8562bdf8109570eb9',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
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(162,NULL,'49fd42751089f19e7d6bb5da57df79ba6cc546d2',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(162,NULL,'5d512dd3f177da0402db804e1f2f7d811302bddd',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
+(162,NULL,'97e7860660e9f9bfdc54aff4eb8f1494ae975ca4',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
(163,NULL,'ac2b6777efb772874d95a88bc0062c520e4851c9',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(164,NULL,'767121db8cfc7592f4c50814393559b72614384d',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(165,NULL,'162195b8d54378680140bcc63a78109e83756525',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1586,10 +1726,9 @@ INSERT INTO `entity_version` VALUES
(174,NULL,'f5ab8459832337b7f5e21367039ccee6939334f0',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(175,NULL,'bf5412505c9414f6c376eb92fd327eb12c1af328',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(176,NULL,'f5ae5b2f08624ee694e4a9b05eb59cd0d17501c9',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
-(186,NULL,'4f341d574b7e8dede90e20f885bb16de0ef96be2',1,NULL,'ca9db47b-d2d5-4980-84da-7268869f9e3c'),
-(187,NULL,'8a275960e8f28e8683d0fde450c1d6670b353199',1,NULL,'84bd4faf-510c-4950-b827-4bab81546887'),
(188,NULL,'d5051e0414a4d4ceddc945eb0fffea1d4ee58a1a',1,NULL,'c6549725-13bb-4076-9d49-219c6b8192f3'),
(188,NULL,'2358d20bb098701deefca886d99a9782ddc5918c',2,1,'55dcaf7b-7372-4778-995a-a6a8bde1b471'),
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(189,NULL,'ed034b9364773357f149ad6027b35ba79488c8b6',1,NULL,'ce298544-326b-4b86-96fd-03de11548c9b'),
(190,NULL,'ac6b26b6839869e664429dca95f29f8fbd44d50d',1,NULL,'cad02c5b-f559-4400-9897-80e56c1035ba'),
(191,NULL,'ddb59c87045f1ef36a80194e9859b59a132d3f2c',1,NULL,'a41c5d15-6c9e-4e5c-a8fb-2fa7d38da140'),
@@ -1776,10 +1915,6 @@ LOCK TABLES `isa_cache` WRITE;
/*!40000 ALTER TABLE `isa_cache` DISABLE KEYS */;
INSERT INTO `isa_cache` VALUES
(101,100,'101'),
-(103,100,'101'),
-(103,101,'103'),
-(105,100,'101'),
-(105,101,'105'),
(106,100,'101'),
(106,101,'106'),
(110,100,'110'),
@@ -1804,12 +1939,6 @@ INSERT INTO `isa_cache` VALUES
(174,100,'174'),
(175,100,'175'),
(176,100,'176'),
-(186,100,'103>101'),
-(186,101,'103'),
-(186,103,'186'),
-(187,100,'105>101'),
-(187,101,'105'),
-(187,105,'187'),
(188,100,'106>101'),
(188,101,'106'),
(188,106,'188'),
@@ -1908,9 +2037,7 @@ INSERT INTO `name_data` VALUES
(0,100,20,'ControlledRecordType','FIX',0),
(0,101,20,'Responsible','FIX',0),
(0,102,20,'Abbreviation','FIX',0),
-(0,103,20,'ResearchDivision','FIX',0),
(0,104,20,'German name','FIX',0),
-(0,105,20,'ResearchUnit','FIX',0),
(0,106,20,'Person','FIX',0),
(0,107,20,'First name','FIX',0),
(0,108,20,'Last name','FIX',0),
@@ -1981,8 +2108,6 @@ INSERT INTO `name_data` VALUES
(0,174,20,'commonEnglishName','FIX',0),
(0,175,20,'Taxonomic group/Species','FIX',0),
(0,176,20,'Sample container','FIX',0),
-(0,186,20,'Fancy Division','FIX',0),
-(0,187,20,'MyResearchUnit','FIX',0),
(0,188,20,'My Name','FIX',0),
(0,189,20,'Building','FIX',0),
(0,190,20,'Room','FIX',0),
@@ -2064,8 +2189,6 @@ CREATE TABLE `null_data` (
LOCK TABLES `null_data` WRITE;
/*!40000 ALTER TABLE `null_data` DISABLE KEYS */;
INSERT INTO `null_data` VALUES
-(0,101,102,'OBLIGATORY',0),
-(0,110,102,'OBLIGATORY',0),
(0,138,139,'OBLIGATORY',0),
(0,148,149,'RECOMMENDED',0),
(0,163,177,'RECOMMENDED',0),
@@ -2075,16 +2198,13 @@ INSERT INTO `null_data` VALUES
(0,199,149,'RECOMMENDED',0),
(0,211,145,'FIX',2),
(0,211,144,'FIX',3),
-(0,103,104,'OBLIGATORY',0),
-(0,103,102,'OBLIGATORY',0),
-(0,105,104,'OBLIGATORY',0),
-(0,105,177,'OBLIGATORY',0),
-(0,105,102,'OBLIGATORY',0),
+(0,197,177,'FIX',0),
+(0,101,102,'OBLIGATORY',0),
(0,106,107,'OBLIGATORY',0),
(0,106,108,'OBLIGATORY',1),
(0,106,109,'OBLIGATORY',2),
-(0,106,177,'OBLIGATORY',0),
(0,106,102,'OBLIGATORY',0),
+(0,110,102,'OBLIGATORY',0),
(0,111,177,'OBLIGATORY',0),
(0,111,178,'OBLIGATORY',0),
(0,111,212,'SUGGESTED',2),
@@ -2135,8 +2255,7 @@ INSERT INTO `null_data` VALUES
(0,161,146,'OBLIGATORY',0),
(0,161,147,'OBLIGATORY',0),
(0,162,146,'OBLIGATORY',0),
-(0,162,147,'OBLIGATORY',0),
-(0,197,177,'FIX',0);
+(0,162,147,'OBLIGATORY',0);
/*!40000 ALTER TABLE `null_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2252,10 +2371,6 @@ LOCK TABLES `reference_data` WRITE;
/*!40000 ALTER TABLE `reference_data` DISABLE KEYS */;
INSERT INTO `reference_data` VALUES
(0,163,164,177,'REPLACEMENT',0,NULL),
-(0,187,177,186,'FIX',0,NULL),
-(0,187,103,177,'REPLACEMENT',1,NULL),
-(0,188,177,187,'FIX',0,NULL),
-(0,188,105,177,'REPLACEMENT',4,NULL),
(0,192,110,189,'FIX',1,NULL),
(0,194,110,190,'FIX',1,NULL),
(0,196,110,191,'FIX',1,NULL),
@@ -2278,8 +2393,17 @@ INSERT INTO `reference_data` VALUES
(0,198,160,207,'FIX',9,NULL),
(0,198,180,209,'FIX',0,NULL),
(0,198,171,180,'REPLACEMENT',10,NULL),
-(0,105,103,177,'REPLACEMENT',1,NULL),
-(0,106,105,177,'REPLACEMENT',3,NULL),
+(0,193,101,188,'FIX',0,NULL),
+(0,193,110,189,'FIX',1,NULL),
+(0,193,177,195,'FIX',0,NULL),
+(0,193,112,177,'REPLACEMENT',3,NULL),
+(0,195,101,188,'FIX',0,NULL),
+(0,195,110,190,'FIX',1,NULL),
+(0,195,177,197,'FIX',0,NULL),
+(0,195,112,177,'REPLACEMENT',3,NULL),
+(0,197,101,188,'FIX',0,NULL),
+(0,197,110,191,'FIX',1,NULL),
+(0,197,112,177,'REPLACEMENT',3,NULL),
(0,111,101,177,'REPLACEMENT',0,NULL),
(0,111,110,178,'REPLACEMENT',1,NULL),
(0,111,112,179,'REPLACEMENT',3,NULL),
@@ -2297,18 +2421,7 @@ INSERT INTO `reference_data` VALUES
(0,136,110,177,'REPLACEMENT',1,NULL),
(0,150,148,177,'REPLACEMENT',0,NULL),
(0,153,143,177,'REPLACEMENT',0,NULL),
-(0,153,148,178,'REPLACEMENT',1,NULL),
-(0,193,101,188,'FIX',0,NULL),
-(0,193,110,189,'FIX',1,NULL),
-(0,193,177,195,'FIX',0,NULL),
-(0,193,112,177,'REPLACEMENT',3,NULL),
-(0,195,101,188,'FIX',0,NULL),
-(0,195,110,190,'FIX',1,NULL),
-(0,195,177,197,'FIX',0,NULL),
-(0,195,112,177,'REPLACEMENT',3,NULL),
-(0,197,101,188,'FIX',0,NULL),
-(0,197,110,191,'FIX',1,NULL),
-(0,197,112,177,'REPLACEMENT',3,NULL);
+(0,153,148,178,'REPLACEMENT',1,NULL);
/*!40000 ALTER TABLE `reference_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2359,7 +2472,7 @@ CREATE TABLE `stats` (
LOCK TABLES `stats` WRITE;
/*!40000 ALTER TABLE `stats` DISABLE KEYS */;
INSERT INTO `stats` VALUES
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('TransactionBenchmark','¬í\0sr\00caosdb.server.database.misc.TransactionBenchmark„Cl=˜ÕãE\0J\0sinceL\0acct\0Ljava/util/HashMap;L\0countsq\0~\0xp\0\0lžèòWsr\0java.util.HashMapÚÁÃ`Ñ\0F\0\nloadFactorI\0 thresholdxp?@\0\0\0\0\0 w\0\0\0\0\0\0t\0 SyncStatssr\0java.lang.Long;‹äÌ#ß\0J\0valuexr\0java.lang.Number†¬• ”à‹\0\0xp\0\0\0\0\0\0\0t\0GetInfosq\0~\0\0\0\0\0\0\0 xsq\0~\0?@\0\0\0\0\0 w\0\0\0\0\0\0q\0~\0sr\0java.lang.Integerâ ¤÷‡8\0I\0valuexq\0~\0\0\0\0q\0~\0 sq\0~\0 \0\0\0x');
/*!40000 ALTER TABLE `stats` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2394,17 +2507,9 @@ CREATE TABLE `text_data` (
LOCK TABLES `text_data` WRITE;
/*!40000 ALTER TABLE `text_data` DISABLE KEYS */;
INSERT INTO `text_data` VALUES
-(0,186,104,'Spannende Abteilung','FIX',0),
-(0,186,102,'fad','FIX',1),
-(0,187,102,'mru','FIX',0),
-(0,187,104,'Meine Forschungsgruppe','FIX',2),
(0,189,102,'bld','FIX',0),
(0,190,102,'rom','FIX',0),
(0,191,102,'fri','FIX',0),
-(0,188,107,'My','FIX',0),
-(0,188,102,'myn','FIX',1),
-(0,188,108,'Name','FIX',2),
-(0,188,109,'my.name@example.com','FIX',3),
(0,200,149,'2m','FIX',0),
(0,202,142,'ABCD-1234','FIX',0),
(0,204,166,'Nails','FIX',0),
@@ -2413,6 +2518,9 @@ INSERT INTO `text_data` VALUES
(211,147,21,'°','FIX',0),
(211,145,21,'m','FIX',0),
(211,144,21,'m','FIX',0),
+(0,193,113,'20 rooms','FIX',2),
+(0,195,113,'30 m²','FIX',2),
+(0,197,113,'300 l','FIX',2),
(143,146,21,'°','FIX',0),
(143,147,21,'°','FIX',0),
(143,144,21,'m','FIX',0),
@@ -2425,9 +2533,10 @@ INSERT INTO `text_data` VALUES
(161,147,21,'°','FIX',0),
(162,146,21,'°','FIX',0),
(162,147,21,'°','FIX',0),
-(0,193,113,'20 rooms','FIX',2),
-(0,195,113,'30 m²','FIX',2),
-(0,197,113,'300 l','FIX',2);
+(0,188,107,'My','FIX',0),
+(0,188,102,'myn','FIX',1),
+(0,188,108,'Name','FIX',2),
+(0,188,109,'my.name@example.com','FIX',3);
/*!40000 ALTER TABLE `text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2589,7 +2698,30 @@ INSERT INTO `transaction_log` VALUES
('Update','186','admin',1737542873,229000000,'PAM'),
('Update','188','admin',1737542878,789000000,'PAM'),
('Update','190','admin',1737542888,999000000,'PAM'),
-('Delete','119','admin',1737542900,973000000,'PAM');
+('Delete','119','admin',1737542900,973000000,'PAM'),
+('Update','103','admin',1737714440,921000000,'PAM'),
+('Update','104','admin',1737714440,921000000,'PAM'),
+('Update','108','admin',1737714440,921000000,'PAM'),
+('Update','112','admin',1737714440,921000000,'PAM'),
+('Update','113','admin',1737714440,921000000,'PAM'),
+('Update','116','admin',1737714440,921000000,'PAM'),
+('Update','120','admin',1737714440,921000000,'PAM'),
+('Update','121','admin',1737714440,921000000,'PAM'),
+('Update','138','admin',1737714440,921000000,'PAM'),
+('Update','145','admin',1737714440,921000000,'PAM'),
+('Update','146','admin',1737714440,921000000,'PAM'),
+('Update','147','admin',1737714440,921000000,'PAM'),
+('Update','148','admin',1737714440,921000000,'PAM'),
+('Update','149','admin',1737714440,921000000,'PAM'),
+('Update','152','admin',1737714440,921000000,'PAM'),
+('Update','155','admin',1737714440,921000000,'PAM'),
+('Update','163','admin',1737714440,921000000,'PAM'),
+('Update','164','admin',1737714440,921000000,'PAM'),
+('Update','181','admin',1737714467,357000000,'PAM'),
+('Delete','180','admin',1737714483,466000000,'PAM'),
+('Delete','179','admin',1737714485,611000000,'PAM'),
+('Delete','107','admin',1737714497,308000000,'PAM'),
+('Delete','105','admin',1737714500,565000000,'PAM');
/*!40000 ALTER TABLE `transaction_log` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2621,6 +2753,9 @@ INSERT INTO `transactions` VALUES
('06147cec-8ac2-4c72-9744-cab44e960e09','admin','PAM',1736265865,579000000),
('081a60fb-04b9-4d71-b025-d865b503fc7e','admin','PAM',1736265822,771000000),
('090f0927-a7b8-46cf-a416-98d1185c3518','admin','PAM',1737542837,887000000),
+('188f6885-b663-496d-a87a-8b85326b0aa6','admin','PAM',1737714500,565000000),
+('1df25a73-1003-4d10-9684-2945d2bd8b3f','admin','PAM',1737714485,611000000),
+('1e0cf9db-9fbc-448a-a2eb-e6e5dd48f301','admin','PAM',1737714497,308000000),
('20f056fc-7deb-4c52-a54f-a80a92236315','admin','PAM',1736264636,79000000),
('22245d86-e095-4514-917a-7677616c544b','admin','PAM',1736265602,369000000),
('26be7fc5-b8d5-47d9-bbd3-59e5a00be685','admin','PAM',1737542900,973000000),
@@ -2629,6 +2764,7 @@ INSERT INTO `transactions` VALUES
('2d5a4ba7-517f-4b85-9727-b3d96988c485','admin','PAM',1736265392,478000000),
('2df660f0-e3a6-447e-837f-4778e5323f5d','admin','PAM',1736265392,576000000),
('34fade63-2811-4725-becf-0f2b1f84ad90','admin','PAM',1736265204,999000000),
+('372c0d25-a1ab-45d2-bf7e-76e583bf5192','admin','PAM',1737714467,357000000),
('3c931e13-7e9f-4835-99df-d325020b887d','admin','PAM',1736265488,391000000),
('488967a3-a042-43d4-b74d-485f4bf622a2','admin','PAM',1736265441,647000000),
('55dcaf7b-7372-4778-995a-a6a8bde1b471','admin','PAM',1736264805,952000000),
@@ -2654,12 +2790,14 @@ INSERT INTO `transactions` VALUES
('cbb111a6-b62c-4705-b1c4-36f055b3c815','admin','PAM',1736265656,336000000),
('cd4b5be6-82c4-4444-bb3e-143ea3c1fcfe','admin','PAM',1736265896,593000000),
('ce298544-326b-4b86-96fd-03de11548c9b','admin','PAM',1736264727,998000000),
+('cf5b2beb-6960-4eaf-8d7b-5e747f29f7be','admin','PAM',1737714440,921000000),
('cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e','administration','CaosDB',0,0),
('d0af8a57-7550-42b2-aba9-4b254897976b','admin','PAM',1736265392,704000000),
('da56170f-ae54-4ecf-9aa4-342d7512384f','admin','PAM',1736265798,309000000),
('daa492ef-1495-4123-9966-9951328211b3','admin','PAM',1736265204,580000000),
('dbf1dd0f-405c-4952-b8b6-62e169c79397','admin','PAM',1736265204,802000000),
('df3a0e97-6feb-42aa-8800-074ee5520428','admin','PAM',1736265392,321000000),
+('e27923fa-df80-4883-9f70-03ed7dbe8fcc','admin','PAM',1737714483,466000000),
('f284f0d8-aba2-44e9-bfc7-ae68fab970b9','admin','PAM',1736265770,375000000),
('fe535f2d-6865-41b7-bab1-781f412454f6','admin','PAM',1736265441,988000000);
/*!40000 ALTER TABLE `transactions` ENABLE KEYS */;
@@ -7131,4 +7269,4 @@ DELIMITER ;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
--- Dump completed on 2025-01-22 10:48:39
+-- Dump completed on 2025-01-24 10:29:19
--
GitLab
From 67b31746431d9ef7afa5c4090a52b5fc66e2140d Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 11:32:22 +0100
Subject: [PATCH 18/63] ENH: Make PI column name configurable
---
.../caosdb-server/scripting/bin/update_containers.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 12ef9b6..985a5d1 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -194,13 +194,13 @@ def main():
child.get_property(custom_label_prop.id).value = row[get_column_header_name("custom_label_prop")]
# Treat PI
- if _value_in_row("PI", row):
- pi = row["PI"]
- pi_prop = cached_get_entity_by(query="FIND PROPERTY Pi")
+ if _value_in_row(get_column_header_name("PI"), row):
+ pi = row[get_column_header_name("PI")]
+ pi_prop = cached_get_entity_by(query=f"FIND PROPERTY {get_entity_name{'PI'}")
try:
query = f"FIND RECORD Person WITH ID={int(pi)}"
except ValueError:
- query = f"FIND RECORD Person WITH AN Abbreviation='{pi}'"
+ query = f"FIND RECORD Person WITH AN '{get_entity_name('abbreviation_prop')}'='{pi}'"
try:
pi_rec = cached_get_entity_by(query=query)
if child.get_property(pi_prop.name) is not None:
@@ -208,7 +208,7 @@ def main():
else:
child.add_property(id=pi_prop.id, name=pi_prop.name, value=pi_rec.id)
except db.EmptyUniqueQueryError:
- logger.warning(f"There is no PI with BIS ID or abbreviation {pi}. Skipping.")
+ logger.warning(f"There is no PI with ID or {get_entity_name('abbreviation_prop')} {pi}. Skipping.")
# Collection(s)
if _value_in_row("Collection", row):
--
GitLab
From 2127218c8296ec144965b109a1e63dcf9748e8c1 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 14:59:41 +0100
Subject: [PATCH 19/63] ENH: Make more rt and property names configurable
---
.../scripting/bin/update_containers.py | 58 +++++++++----------
1 file changed, 27 insertions(+), 31 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 985a5d1..4739d5c 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -211,64 +211,60 @@ def main():
logger.warning(f"There is no PI with ID or {get_entity_name('abbreviation_prop')} {pi}. Skipping.")
# Collection(s)
- if _value_in_row("Collection", row):
- collection_rt = cached_get_entity_by(query="FIND RECORDTYPE Collection")
- if not ";" in str(row["Collection"]):
- collections = [row["Collection"]]
+ if _value_in_row(get_column_header_name("Collection"), row):
+ collection_rt = cached_get_entity_by(query=f"FIND RECORDTYPE '{get_entity_name('Collection')}'")
+ if not ";" in str(row[get_column_header_name("Collection")]):
+ collections = [row[get_column_header_name("Collection")]]
else:
- collections = [coll.strip() for coll in str(row["Collection"]).split(';')]
+ collections = [coll.strip() for coll in str(row[get_column_header_name("Collection")]).split(';')]
prop_val = []
for coll in collections:
try:
- query = f"FIND RECORD Collection WITH ID={int(coll)}"
+ query = f"FIND '{collection_rt.name}' WITH ID={int(coll)}"
except ValueError:
- query = f"FIND RECORD Collection WITH name='{coll}'"
+ query = f"FIND RECORD '{collection_rt.name}' WITH name='{coll}'"
try:
coll_rec = cached_get_entity_by(query=query)
prop_val.append(coll_rec.id)
except db.EmptyUniqueQueryError:
- logger.warning(f"There is no collection with name or BIS ID {coll}. Skipping.")
+ logger.warning(f"There is no {collection_rt.name} with name or ID {coll}. Skipping.")
continue
if prop_val:
- if child.get_property("Collection") is not None:
- child.get_property("Collection").datatype = db.LIST("Collection")
- child.get_property("Collection").value = prop_val
+ if child.get_property(collection_rt.name) is not None:
+ child.get_property(collection_rt.name).datatype = db.LIST(collection_rt.name)
+ child.get_property(collection_rt.name).value = prop_val
else:
child.add_property(id=collection_rt.id, name=collection_rt.name, datatype=db.LIST(
- "Collection"), value=prop_val)
+ collection_rt.name), value=prop_val)
# Treat Container Contents
- if _value_in_row("Container Contents", row):
- if not (_value_in_row("PI", row) and _value_in_row("Collection", row)):
- logger.error(
- f"Container Contents are given for container {child.id} but it "
- "is missing PI and/or Collection info. No updates have been performed."
- )
- return 1
- contents_prop = cached_get_entity_by(query="FIND PROPERTY 'Container Contents'")
+ if _value_in_row(get_column_header_name("Container Contents"), row):
+ contents_prop = cached_get_entity_by(
+ query=f"FIND PROPERTY '{get_entity_name('Container Contents')}'"
+ )
if child.get_property(contents_prop.name) is not None:
- child.get_property(contents_prop.name).value = row["Container Contents"]
+ child.get_property(contents_prop.name).value = row[get_column_header_name("Container Contents")]
else:
child.add_property(id=contents_prop.id, name=contents_prop.name,
- value=row["Container Contents"])
+ value=row[get_column_header_name("Container Contents")])
# Treat PDF Report
- if _value_in_row("PDFReport", row):
- pdf_id = row["PDFReport"]
+ if _value_in_row(get_column_header_name("PDFReport"), row):
+ pdf_id = row[get_column_header_name("PDFReport")]
try:
pdf_id = int(pdf_id)
- pdf_rec = cached_query(f"FIND FILE PDFReport WITH ID={pdf_id}")
+ pdf_rec = cached_query(f"FIND FILE {get_entity_name('PDFReport')} WITH ID={pdf_id}")
if not pdf_rec:
logger.warning(
- f"There is no PDFReport with Bis ID {pdf_id}, so no PDF is attached to container {child.id}.")
+ f"There is no PDFReport with ID {pdf_id}, so no PDF is attached to container {child.id}.")
else:
- if child.get_property("PDFReport") is not None:
- child.get_property("PDFReport").value = pdf_id
+ if child.get_property(get_entity_name("PDFReport")) is not None:
+ child.get_property(get_property("PDFReport")).value = pdf_id
else:
child.add_property(id=pdf_rt.id, name=pdf_rt.name, value=pdf_id)
except ValueError:
logger.warning(
- f"There is no valid Bis ID provided for container {child.id}."
+ f"There is no valid ID provided for container {child.id}."
f"Provided was {pdf_id}. Skipping")
# This is a workaround for weird merging errors in the
@@ -276,13 +272,13 @@ def main():
# following release.
merged = []
for par in parent_containers:
- if (data['BIS ID'] == par.id).any():
+ if (data[id_column_name] == par.id).any():
# A container to be updated is used as another containers parent:
child = child_containers.get_entity_by_id(par.id)
# All parents have a child sample property with a value (which may
# be empty). No child sample has this property, so the following is
# okay without checks:
- prop = par.get_property("Child container")
+ prop = par.get_property(child_container_prop.name)
child.add_property(name=prop.name, id=prop.id, value=prop.value)
merged.append(par)
for par in merged:
--
GitLab
From 4c7073e351b8082d198b35c8af862d753fbb6de7 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 15:06:02 +0100
Subject: [PATCH 20/63] ENH: Add container-upload post processing
---
.../container_update_post_processing.py | 33 +++++++++++++++++++
.../scripting/bin/update_containers.py | 9 ++---
2 files changed, 38 insertions(+), 4 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_post_processing.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_post_processing.py
new file mode 100644
index 0000000..e8f696b
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_post_processing.py
@@ -0,0 +1,33 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+
+def post_process_containers_before_sync(child_containers):
+
+ return child_containers
+
+
+def post_process_parent_containers_before_sync(parent_containers):
+
+ return parent_containers
+
+
+def post_process_inserts_and_updates(inserts, updates):
+
+ return inserts, updates
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 4739d5c..44c6c73 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -37,6 +37,7 @@ from linkahead.cached import cached_query, cached_get_entity_by
from bis_utils import (get_do_not_insert_type_names,
replace_entity_urls_by_ids, whitespace_cleanup_in_df)
from sample_helpers.container_update_get_parent import get_container_by_identifier
+from sample_helpers.container_update_post_processing import (post_process_containers_before_sync, post_process_parent_containers_before_sync, post_process_inserts_and_updates)
from sample_helpers.utils import (CONSTANTS, get_column_header_name, get_entity_name)
# suppress warning of diff function
@@ -287,6 +288,8 @@ def main():
parent_containers.remove(par)
# TODO Add notes as CommentAnnotation
crawler = Crawler(securityMode=SecurityMode.UPDATE)
+ child_containers = post_process_containers_before_sync(child_containers)
+ parent_containers = post_process_parent_containers_before_sync(parent_containers)
to_be_synchronized = child_containers + parent_containers
inserts, updates = crawler.synchronize(
@@ -296,10 +299,8 @@ def main():
if "SHARED_DIR" in os.environ:
_notify_about_inserts_and_updates(len(inserts), len(updates), htmluserlog_public,
crawler.run_id)
- for ent in inserts + updates:
- ent.retrieve_acl()
- ent.grant(role='Stock Manager', priority=False, permission="EDIT:ACL")
- ent.update_acl()
+ inserts, updates = post_process_inserts_and_updates(isnerts, updates)
+
logger.info(f"Successfully processed {len(child_containers)} containers and "
f"{len(parent_containers)} parent containers.")
--
GitLab
From 9a3017ae6680988f568e954825309138172deab8 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 15:06:28 +0100
Subject: [PATCH 21/63] STY: autopep8'd
---
.../caosdb-server/scripting/bin/update_containers.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 44c6c73..8cf819d 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -37,7 +37,8 @@ from linkahead.cached import cached_query, cached_get_entity_by
from bis_utils import (get_do_not_insert_type_names,
replace_entity_urls_by_ids, whitespace_cleanup_in_df)
from sample_helpers.container_update_get_parent import get_container_by_identifier
-from sample_helpers.container_update_post_processing import (post_process_containers_before_sync, post_process_parent_containers_before_sync, post_process_inserts_and_updates)
+from sample_helpers.container_update_post_processing import (
+ post_process_containers_before_sync, post_process_parent_containers_before_sync, post_process_inserts_and_updates)
from sample_helpers.utils import (CONSTANTS, get_column_header_name, get_entity_name)
# suppress warning of diff function
@@ -58,8 +59,6 @@ def _value_in_row(key, row):
return True
-
-
def get_parser():
par = helper.get_argument_parser()
return par
@@ -104,7 +103,7 @@ def main():
return 1
child.add_parent(get_entity_name("container_rt"))
child_containers.append(child)
-
+
if _value_in_row(parent_column_name, row):
parent_identifier = row[parent_column_name]
parent = get_container_by_identifier(parent_identifier)
@@ -192,7 +191,8 @@ def main():
child.add_property(id=custom_label_prop.id,
name=custom_label_prop.name, value=row[get_column_header_name("custom_label_prop")])
else:
- child.get_property(custom_label_prop.id).value = row[get_column_header_name("custom_label_prop")]
+ child.get_property(
+ custom_label_prop.id).value = row[get_column_header_name("custom_label_prop")]
# Treat PI
if _value_in_row(get_column_header_name("PI"), row):
--
GitLab
From 7d6ad35918592fc4ee57a03531f8d0079e166292 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 15:14:11 +0100
Subject: [PATCH 22/63] FIX: Typo
---
.../caosdb-server/scripting/bin/update_containers.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 8cf819d..4a03f1d 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -197,7 +197,7 @@ def main():
# Treat PI
if _value_in_row(get_column_header_name("PI"), row):
pi = row[get_column_header_name("PI")]
- pi_prop = cached_get_entity_by(query=f"FIND PROPERTY {get_entity_name{'PI'}")
+ pi_prop = cached_get_entity_by(query=f"FIND PROPERTY {get_entity_name('PI')}")
try:
query = f"FIND RECORD Person WITH ID={int(pi)}"
except ValueError:
@@ -299,7 +299,7 @@ def main():
if "SHARED_DIR" in os.environ:
_notify_about_inserts_and_updates(len(inserts), len(updates), htmluserlog_public,
crawler.run_id)
- inserts, updates = post_process_inserts_and_updates(isnerts, updates)
+ inserts, updates = post_process_inserts_and_updates(inserts, updates)
logger.info(f"Successfully processed {len(child_containers)} containers and "
f"{len(parent_containers)} parent containers.")
--
GitLab
From 1c8aef7183bbca12ace16ac43b4887ea2e9cb4d4 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 27 Jan 2025 13:15:28 +0100
Subject: [PATCH 23/63] ENH: Add sample post-processing dummy
---
.../scripting/bin/register_new_samples.py | 9 ++++---
.../sample_registration_post_processing.py | 26 +++++++++++++++++++
2 files changed, 32 insertions(+), 3 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_post_processing.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
index 7724b57..5ce3110 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
@@ -11,10 +11,12 @@ from caosadvancedtools.serverside.logging import configure_server_side_logging
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
+from sample_helpers.sample_registration_post_processing import post_process_samples
+from sample_helpers.utils import CONSTANTS, get_column_header_name, get_entity_name
+
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
-BIS_URL = 'https://localhost:10443/Entity/'
logger = logging.getLogger("caosadvancedtools")
@@ -75,6 +77,7 @@ def create_sample_entities(data):
if add_state:
sample.state = db.State(name="Registered", model="Sample life-cycle")
batch += [sample]
+ batch = post_process_samples(batch)
batch.insert()
return batch
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_post_processing.py
new file mode 100644
index 0000000..6d8fe9d
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_post_processing.py
@@ -0,0 +1,26 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+
+def post_process_samples(samples: db.Container) -> db.Container:
+ """Post process the container of samples to be registerd before
+ they are inserted. Dummy function to be overwritten.
+
+ """
+ return samples
--
GitLab
From f8ff9bafe177a1087e405c2464dfe30d4b9d00d9 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 27 Jan 2025 13:41:09 +0100
Subject: [PATCH 24/63] MAINT: Remove BIS from some variable and module names
---
.../build.properties.d/50.sample-management.conf | 2 +-
.../src/ext/js/ext_bis_samplemanagemet.js | 12 ++++++------
.../scripting/bin/register_new_samples.py | 4 ----
3 files changed, 7 insertions(+), 11 deletions(-)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
index 9f114ce..6727bd1 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
+++ b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
@@ -23,7 +23,7 @@ BUILD_MODULE_EXT_SSS_MARKDOWN=ENABLED
BUILD_MODULE_SHOW_ID_IN_LABEL=ENABLED
# sample-management specific variables
-BUILD_MODULE_EXT_BIS_SAMPLEMANAGEMENT=ENABLED
+BUILD_MODULE_EXT_SAMPLEMANAGEMENT=ENABLED
BUILD_MODULE_EXT_STOCKMANAGEMENT=ENABLED
BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL="Sample ID"
BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL="Container ID"
\ No newline at end of file
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
index 09c64a8..27a9494 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
@@ -6,9 +6,9 @@
'use strict';
/**
- * This module adds to forms to BIS that relate to sample management.
- * One form allows to register samples.
- * The other allows to update registered samples.
+ * This module adds to forms to LinkAhead that relate to sample
+ * management; there are forms for sample registration, upload, and
+ * export.
*
* @module ext_flight_preview
* @version 0.1
@@ -16,7 +16,7 @@
* @requires nothing yet
* (pass the dependencies as arguments)
*/
-const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_samplemanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
const logger = log.getLogger("samplemanagement_form");
const tool_box = "Sample Management"
const upload_sample_template_title = "Upload sample template"; // title of the form and text in the toolbox
@@ -424,7 +424,7 @@ $(document).ready(function() {
// use a variable starting with `BUILD_MODULE_` to enable your module
// the build variable has to be enabled in the `build.properties.d/` directory.
// Otherwise the module will not be activated.
- if ("${BUILD_MODULE_EXT_BIS_SAMPLEMANAGEMENT}" === "ENABLED") {
- caosdb_modules.register(ext_bis_samplemanagement);
+ if ("${BUILD_MODULE_EXT_SAMPLEMANAGEMENT}" === "ENABLED") {
+ caosdb_modules.register(ext_samplemanagement);
}
});
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
index 5ce3110..a93d78e 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
@@ -65,7 +65,6 @@ def get_column_names(data):
def create_sample_entities(data):
responsible_person_id = get_responsible_person_id(data)
number_of_samples = get_number_of_samples(data)
- add_state = len(db.execute_query("FIND 'Sample life-cycle'"))
batch = db.Container()
for index in range(number_of_samples):
@@ -73,9 +72,6 @@ def create_sample_entities(data):
sample.add_parent(name="Sample")
sample.add_property(name="Main User", value=responsible_person_id)
sample.add_property("Container")
- sample.add_property("NagoyaCase")
- if add_state:
- sample.state = db.State(name="Registered", model="Sample life-cycle")
batch += [sample]
batch = post_process_samples(batch)
batch.insert()
--
GitLab
From 74ce91808f3fdc400564740087a71060d36eebf7 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 27 Jan 2025 15:38:28 +0100
Subject: [PATCH 25/63] ENH: Make sample registration compatible
---
.../sample-management-datamodel.yml | 4 +-
.../ext/js/bis_custom_reference_resolver.js | 4 +-
.../src/ext/js/ext_stockmanagement.js | 2 +-
.../scripting/bin/register_new_samples.py | 48 ++++---------------
.../bin/sample_helpers/default_constants.yml | 2 +
...mple_registration_get_person_identifier.py | 44 +++++++++++++++++
6 files changed, 60 insertions(+), 44 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index d2cb68d..74828ea 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -33,9 +33,9 @@ Person:
inherit_from_obligatory:
- Responsible
obligatory_properties:
- First name:
+ first_name:
datatype: TEXT
- Last name:
+ last_name:
datatype: TEXT
Email:
datatype: TEXT
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js
index 780a0c2..7059cb5 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js
@@ -1,7 +1,7 @@
var bis_custom_reference_resolver = new function (getEntityID, getEntityName, getParents, getProperty, query) {
- const lastname_prop_name = "Last name";
- const firstname_prop_name = "First name";
+ const lastname_prop_name = "last_name";
+ const firstname_prop_name = "first_name";
const person_rt_name = "Person";
const bis_label_prop_name = "BIS label";
const custom_label_prop_name = "Custom label"
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
index 36e05ce..8afbebb 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
@@ -35,7 +35,7 @@ const ext_stockmanagement = function($, navbar, log, form_elements, form_panel,
name: "responsible_entity",
label: "Responsible entity",
query: "FIND RECORD Responsible",
- make_desc: getEntityName,
+ make_desc: bis_custom_reference_resolver.resolve_person_reference,
required: true
},
{
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
index a93d78e..1b912ee 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
@@ -11,6 +11,7 @@ from caosadvancedtools.serverside.logging import configure_server_side_logging
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
+from sample_helpers.sample_registration_get_person_identifier import get_person_identifier
from sample_helpers.sample_registration_post_processing import post_process_samples
from sample_helpers.utils import CONSTANTS, get_column_header_name, get_entity_name
@@ -25,53 +26,26 @@ def get_parser():
return par
-def get_responsible_person_id(data):
- return int(data["responsible_person"])
-
-
-def get_responsible_person_abbreviation(data):
- person = db.execute_query("FIND {}".format(get_responsible_person_id(data)))[0]
- return person.get_property("Abbreviation").value
-
-
-def get_number_of_samples(data):
- return int(data["number_of_samples"])
-# def is_samples_from_cruise(data):
-# return ("samples_from_cruise" in data and data["samples_from_cruise"] == "on")
-# def has_start_and_end_time(data):
-# return ("start_and_end_time" in data and data["start_and_end_time"] == "on")
-# def get_number_of_locations(data):
-# number_of_locations = int(data["number_of_locations"])
-# if number_of_locations < 1:
-# number_of_locations = 1 # At least one location is OBLIGATORY
-# return number_of_locations
-
-
-def get_reference_properties(data):
- return data["reference_properties"]
-
-
def get_column_names(data):
# Make sure each header starts with BIS ID and Main User
- starting_names = ["BIS ID", "Main User"]
+ starting_names = ["entity_id", "Main User"]
# required_column_names is just a string of column names separated by
# commas.
other_names = data["required_column_names"].split(',') + data["column_names"]
starting_names.extend([name.strip()
for name in other_names if name.strip() not in starting_names])
- return starting_names
+ return [get_column_header_name(name) for name in starting_names]
def create_sample_entities(data):
- responsible_person_id = get_responsible_person_id(data)
- number_of_samples = get_number_of_samples(data)
+ responsible_person_id = int(data["responsible_person"])
+ number_of_samples = int(data["number_of_samples"])
batch = db.Container()
for index in range(number_of_samples):
sample = db.Record()
- sample.add_parent(name="Sample")
- sample.add_property(name="Main User", value=responsible_person_id)
- sample.add_property("Container")
+ sample.add_parent(name=get_entity_name("Sample"))
+ sample.add_property(name=get_entity_name("Main User"), value=responsible_person_id)
batch += [sample]
batch = post_process_samples(batch)
batch.insert()
@@ -118,12 +92,8 @@ def read_input(args, log=False):
def create_csv_template(template_name, samples, form_input):
template_display_path, template_internal_path = helper.get_shared_filename(template_name)
# Read form_input
- responsible_person_abbreviation = get_responsible_person_abbreviation(form_input)
- number_of_samples = get_number_of_samples(form_input)
- # samples_from_cruise = is_samples_from_cruise(form_input)
- # start_and_end_time = has_start_and_end_time(form_input)
- # number_of_locations = get_number_of_locations(form_input)
- # reference_properties = get_reference_properties(form_input)
+ responsible_person_abbreviation = get_person_identifier(form_input)
+ number_of_samples = int(form_input["number_of_samples"])
header = get_column_names(form_input)
with open(template_internal_path, 'w') as csv_template:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index c773685..2db07b9 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -56,6 +56,8 @@ entity_names:
labelcounter_prop: Counter
labelcounter_rt: LabelCounter
responsible_rt: Responsible
+ first_name_prop: first_name
+ last_name_prop: last_name
error_prefix: "Something went wrong:"
error_suffix: "Please contact your administrator(s)."
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
new file mode 100644
index 0000000..329dc3d
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
@@ -0,0 +1,44 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from .utils import get_entity_name
+
+
+def get_person_identifier(form_data: dict) -> str:
+ """Retrieve a person record from the given id, and replace by
+ abbreviation if present, else "last name, first name".
+
+ """
+ person_rec = db.cached.cached_get_entity_by(eid=form_data["responsible_person"])
+ # Use abbreviation if present
+ if (person_rec.get_property(get_entity_name("abbreviation_prop")) is not None and
+ person_rec.get_property(get_entity_name("abbreviation_prop")).value):
+ return person_rec.get_property(get_entity_name("abbreviation_prop")).value
+ first_name = person_rec.get_property(get_entity_name("first_name_prop")).value if person_rec.get_property(
+ get_entity_name("first_name_prop")) is not None else ""
+ last_name = person_rec.get_property(get_entity_name("last_name_prop")).value if person_rec.get_property(
+ get_entity_name("last_name_prop")) is not None else ""
+ # Else use first and last name ...
+ if first_name and last_name:
+ return f"{last_name}, {first_name}"
+ # ... or just last name if no first name
+ if last_name:
+ return last_name
+ # Last fallback id
+ return person_rec.id
--
GitLab
From 21679db68b0c45348f44613a104894555cb42c42 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 27 Jan 2025 16:09:07 +0100
Subject: [PATCH 26/63] MAINT: Adapt data model and test dump
---
.../sample-management-datamodel.yml | 5 +-
.../bin/sample_helpers/default_constants.yml | 4 +-
.../custom/other/restore/caosdb.dump.sql | 215 ++++++++++++++++--
3 files changed, 200 insertions(+), 24 deletions(-)
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index 74828ea..8067eac 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -25,18 +25,19 @@ ControlledRecordType:
Responsible:
inherit_from_obligatory:
- ControlledRecordType
- obligatory_properties:
+ recommended_properties:
Abbreviation:
description: An abbreviation for this entity that is used for identification purposes
datatype: TEXT
Person:
- inherit_from_obligatory:
+ inherit_from_recommended:
- Responsible
obligatory_properties:
first_name:
datatype: TEXT
last_name:
datatype: TEXT
+ recommended_properties:
Email:
datatype: TEXT
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 2db07b9..687b32c 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -46,14 +46,14 @@ csv_column_descriptions:
Water depth stop: "The bottom depth in meters where the sampling ended as a positive value"
entity_names:
- abbreviation_prop: Abbreviation
+ abbreviation_prop: abbreviation
child_container_prop: "Child container"
container_label_prop: container_label
container_rt: Container
container_size_prop: "Container size"
containertype_rt: ContainerType
custom_label_prop: "Custom label"
- labelcounter_prop: Counter
+ labelcounter_prop: counter
labelcounter_rt: LabelCounter
responsible_rt: Responsible
first_name_prop: first_name
diff --git a/test-profile/custom/other/restore/caosdb.dump.sql b/test-profile/custom/other/restore/caosdb.dump.sql
index 913434b..3dac867 100644
--- a/test-profile/custom/other/restore/caosdb.dump.sql
+++ b/test-profile/custom/other/restore/caosdb.dump.sql
@@ -47,7 +47,8 @@ LOCK TABLES `archive_collection_type` WRITE;
/*!40000 ALTER TABLE `archive_collection_type` DISABLE KEYS */;
INSERT INTO `archive_collection_type` VALUES
(0,153,177,'LIST',1),
-(0,153,177,'LIST',2);
+(0,153,177,'LIST',2),
+(0,153,177,'LIST',3);
/*!40000 ALTER TABLE `archive_collection_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -86,36 +87,53 @@ LOCK TABLES `archive_data_type` WRITE;
INSERT INTO `archive_data_type` VALUES
(0,0,144,13,1),
(0,0,144,13,2),
+(0,0,144,13,3),
(0,0,145,13,1),
(0,0,145,13,2),
+(0,0,145,13,3),
(0,0,146,13,1),
(0,0,146,13,2),
+(0,0,146,13,3),
(0,0,147,13,1),
(0,0,147,13,2),
+(0,0,147,13,3),
(0,0,102,14,1),
+(0,0,107,14,1),
+(0,0,108,14,1),
(0,0,114,14,1),
(0,111,177,101,1),
(0,111,177,101,2),
+(0,111,177,101,3),
(0,111,178,110,1),
(0,111,178,110,2),
+(0,111,178,110,3),
(0,136,177,110,1),
(0,136,177,110,2),
+(0,136,177,110,3),
(0,118,178,111,1),
(0,118,178,111,2),
+(0,118,178,111,3),
(0,118,177,119,1),
(0,118,177,119,2),
+(0,118,177,119,3),
(0,118,179,120,1),
(0,118,179,120,2),
+(0,118,179,120,3),
(0,118,180,121,1),
(0,118,180,121,2),
+(0,118,180,121,3),
(0,119,178,138,1),
(0,119,178,138,2),
+(0,119,178,138,3),
(0,153,177,143,1),
(0,153,177,143,2),
+(0,153,177,143,3),
(0,150,177,148,1),
(0,150,177,148,2),
+(0,150,177,148,3),
(0,153,178,148,1),
-(0,153,178,148,2);
+(0,153,178,148,2),
+(0,153,178,148,3);
/*!40000 ALTER TABLE `archive_data_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -287,34 +305,50 @@ INSERT INTO `archive_entities` VALUES
(102,'An abbreviation for this entity that is used for creating BIS labels','PROPERTY',2,1),
(106,NULL,'RECORDTYPE',2,1),
(106,NULL,'RECORDTYPE',2,2),
+(106,NULL,'RECORDTYPE',2,3),
+(107,NULL,'PROPERTY',2,1),
+(108,NULL,'PROPERTY',2,1),
(110,NULL,'RECORDTYPE',2,1),
(111,NULL,'RECORDTYPE',2,1),
(111,NULL,'RECORDTYPE',2,2),
+(111,NULL,'RECORDTYPE',2,3),
(114,'A custom label for a container that doesn\'t have to follow the BIS labeling guidelines.','PROPERTY',2,1),
(118,NULL,'RECORDTYPE',2,1),
(118,NULL,'RECORDTYPE',2,2),
+(118,NULL,'RECORDTYPE',2,3),
(119,NULL,'RECORDTYPE',2,1),
(119,NULL,'RECORDTYPE',2,2),
+(119,NULL,'RECORDTYPE',2,3),
(136,NULL,'RECORDTYPE',2,1),
(136,NULL,'RECORDTYPE',2,2),
+(136,NULL,'RECORDTYPE',2,3),
(143,NULL,'RECORDTYPE',2,1),
(143,NULL,'RECORDTYPE',2,2),
+(143,NULL,'RECORDTYPE',2,3),
(144,'The depth of the water in meters as a positive value','PROPERTY',2,1),
(144,'The depth of the water in meters as a positive value','PROPERTY',2,2),
+(144,'The depth of the water in meters as a positive value','PROPERTY',2,3),
(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,1),
(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,2),
+(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,3),
(146,NULL,'PROPERTY',2,1),
(146,NULL,'PROPERTY',2,2),
+(146,NULL,'PROPERTY',2,3),
(147,NULL,'PROPERTY',2,1),
(147,NULL,'PROPERTY',2,2),
+(147,NULL,'PROPERTY',2,3),
(150,NULL,'RECORDTYPE',2,1),
(150,NULL,'RECORDTYPE',2,2),
+(150,NULL,'RECORDTYPE',2,3),
(153,NULL,'RECORDTYPE',2,1),
(153,NULL,'RECORDTYPE',2,2),
+(153,NULL,'RECORDTYPE',2,3),
(161,NULL,'RECORDTYPE',2,1),
(161,NULL,'RECORDTYPE',2,2),
+(161,NULL,'RECORDTYPE',2,3),
(162,NULL,'RECORDTYPE',2,1),
(162,NULL,'RECORDTYPE',2,2),
+(162,NULL,'RECORDTYPE',2,3),
(188,NULL,'RECORD',2,1),
(188,NULL,'RECORD',2,2),
(192,NULL,'RECORD',2,1),
@@ -487,7 +521,12 @@ INSERT INTO `archive_isa` VALUES
(162,2,143,1),
(188,2,100,0),
(188,2,101,0),
-(188,2,106,1);
+(188,2,106,1),
+(106,3,100,0),
+(106,3,101,1),
+(153,3,150,1),
+(161,3,143,1),
+(162,3,143,1);
/*!40000 ALTER TABLE `archive_isa` ENABLE KEYS */;
UNLOCK TABLES;
@@ -564,7 +603,23 @@ INSERT INTO `archive_name_data` VALUES
(0,153,20,'SourceEvent','FIX',0,2),
(0,161,20,'StartPosition','FIX',0,2),
(0,162,20,'StopPosition','FIX',0,2),
-(0,188,20,'My Name','FIX',0,2);
+(0,188,20,'My Name','FIX',0,2),
+(0,107,20,'First name','FIX',0,1),
+(0,108,20,'Last name','FIX',0,1),
+(0,106,20,'Person','FIX',0,3),
+(0,111,20,'Container','FIX',0,3),
+(0,118,20,'Sample','FIX',0,3),
+(0,119,20,'NagoyaCase','FIX',0,3),
+(0,136,20,'LabelCounter','FIX',0,3),
+(0,143,20,'Position','FIX',0,3),
+(0,144,20,'Water depth','FIX',0,3),
+(0,145,20,'Sampling depth','FIX',0,3),
+(0,146,20,'Latitude','FIX',0,3),
+(0,147,20,'Longitude','FIX',0,3),
+(0,150,20,'Event','FIX',0,3),
+(0,153,20,'SourceEvent','FIX',0,3),
+(0,161,20,'StartPosition','FIX',0,3),
+(0,162,20,'StopPosition','FIX',0,3);
/*!40000 ALTER TABLE `archive_name_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -761,7 +816,62 @@ INSERT INTO `archive_null_data` VALUES
(0,161,146,'OBLIGATORY',0,2),
(0,161,147,'OBLIGATORY',0,2),
(0,162,146,'OBLIGATORY',0,2),
-(0,162,147,'OBLIGATORY',0,2);
+(0,162,147,'OBLIGATORY',0,2),
+(0,106,107,'OBLIGATORY',0,3),
+(0,106,108,'OBLIGATORY',1,3),
+(0,106,109,'OBLIGATORY',2,3),
+(0,106,102,'OBLIGATORY',0,3),
+(0,111,177,'OBLIGATORY',0,3),
+(0,111,178,'OBLIGATORY',0,3),
+(0,111,212,'SUGGESTED',2,3),
+(0,111,179,'SUGGESTED',0,3),
+(0,111,113,'SUGGESTED',4,3),
+(0,111,114,'SUGGESTED',5,3),
+(0,111,115,'SUGGESTED',6,3),
+(0,111,116,'SUGGESTED',7,3),
+(0,118,177,'RECOMMENDED',0,3),
+(0,118,178,'RECOMMENDED',0,3),
+(0,118,179,'RECOMMENDED',0,3),
+(0,118,180,'RECOMMENDED',0,3),
+(0,118,122,'RECOMMENDED',4,3),
+(0,118,123,'RECOMMENDED',5,3),
+(0,118,124,'RECOMMENDED',6,3),
+(0,118,181,'SUGGESTED',0,3),
+(0,118,182,'SUGGESTED',0,3),
+(0,118,183,'SUGGESTED',0,3),
+(0,118,184,'SUGGESTED',0,3),
+(0,118,185,'SUGGESTED',0,3),
+(0,118,130,'SUGGESTED',12,3),
+(0,118,131,'SUGGESTED',13,3),
+(0,118,132,'SUGGESTED',14,3),
+(0,118,133,'SUGGESTED',15,3),
+(0,118,134,'SUGGESTED',16,3),
+(0,119,142,'OBLIGATORY',0,3),
+(0,119,140,'RECOMMENDED',1,3),
+(0,119,177,'SUGGESTED',0,3),
+(0,119,178,'SUGGESTED',0,3),
+(0,136,137,'OBLIGATORY',0,3),
+(0,136,177,'OBLIGATORY',0,3),
+(0,143,146,'OBLIGATORY',0,3),
+(0,143,147,'OBLIGATORY',1,3),
+(0,143,144,'RECOMMENDED',2,3),
+(0,143,145,'RECOMMENDED',3,3),
+(0,150,177,'OBLIGATORY',0,3),
+(0,150,151,'RECOMMENDED',1,3),
+(0,150,152,'SUGGESTED',2,3),
+(0,153,177,'OBLIGATORY',0,3),
+(0,153,178,'OBLIGATORY',0,3),
+(0,153,154,'RECOMMENDED',2,3),
+(0,153,155,'RECOMMENDED',3,3),
+(0,153,156,'RECOMMENDED',4,3),
+(0,153,157,'RECOMMENDED',5,3),
+(0,153,158,'SUGGESTED',6,3),
+(0,153,151,'RECOMMENDED',0,3),
+(0,153,152,'SUGGESTED',0,3),
+(0,161,146,'OBLIGATORY',0,3),
+(0,161,147,'OBLIGATORY',0,3),
+(0,162,146,'OBLIGATORY',0,3),
+(0,162,147,'OBLIGATORY',0,3);
/*!40000 ALTER TABLE `archive_null_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -890,7 +1000,25 @@ INSERT INTO `archive_reference_data` VALUES
(0,136,110,177,NULL,'REPLACEMENT',1,2),
(0,150,148,177,NULL,'REPLACEMENT',0,2),
(0,153,143,177,NULL,'REPLACEMENT',0,2),
-(0,153,148,178,NULL,'REPLACEMENT',1,2);
+(0,153,148,178,NULL,'REPLACEMENT',1,2),
+(0,111,101,177,NULL,'REPLACEMENT',0,3),
+(0,111,110,178,NULL,'REPLACEMENT',1,3),
+(0,111,112,179,NULL,'REPLACEMENT',3,3),
+(0,118,119,177,NULL,'REPLACEMENT',0,3),
+(0,118,111,178,NULL,'REPLACEMENT',1,3),
+(0,118,120,179,NULL,'REPLACEMENT',2,3),
+(0,118,121,180,NULL,'REPLACEMENT',3,3),
+(0,118,125,181,NULL,'REPLACEMENT',7,3),
+(0,118,126,182,NULL,'REPLACEMENT',8,3),
+(0,118,127,183,NULL,'REPLACEMENT',9,3),
+(0,118,128,184,NULL,'REPLACEMENT',10,3),
+(0,118,129,185,NULL,'REPLACEMENT',11,3),
+(0,119,141,177,NULL,'REPLACEMENT',2,3),
+(0,119,138,178,NULL,'REPLACEMENT',3,3),
+(0,136,110,177,NULL,'REPLACEMENT',1,3),
+(0,150,148,177,NULL,'REPLACEMENT',0,3),
+(0,153,143,177,NULL,'REPLACEMENT',0,3),
+(0,153,148,178,NULL,'REPLACEMENT',1,3);
/*!40000 ALTER TABLE `archive_reference_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -973,7 +1101,19 @@ INSERT INTO `archive_text_data` VALUES
(0,188,107,'My','FIX',0,2),
(0,188,102,'myn','FIX',1,2),
(0,188,108,'Name','FIX',2,2),
-(0,188,109,'my.name@example.com','FIX',3,2);
+(0,188,109,'my.name@example.com','FIX',3,2),
+(143,146,21,'°','FIX',0,3),
+(143,147,21,'°','FIX',0,3),
+(143,144,21,'m','FIX',0,3),
+(143,145,21,'m','FIX',0,3),
+(0,144,21,'m','FIX',0,3),
+(0,145,21,'m','FIX',0,3),
+(0,146,21,'°','FIX',0,3),
+(0,147,21,'°','FIX',0,3),
+(161,146,21,'°','FIX',0,3),
+(161,147,21,'°','FIX',0,3),
+(162,146,21,'°','FIX',0,3),
+(162,147,21,'°','FIX',0,3);
/*!40000 ALTER TABLE `archive_text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1629,14 +1769,18 @@ INSERT INTO `entity_version` VALUES
(106,NULL,'48edf0033a82b59a298788a8fd1134aaf5f0cb69',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(106,NULL,'32f2857be024df66d734a79c908061ae8d9fcedc',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(106,NULL,'00d1bb93d150633c1944bdb05c2361f2feeb485f',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(106,NULL,'6e0b9fdfa9030ad27b3ca0ca4cf81f297f218e62',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(107,NULL,'c07e48a5242cec75dd484535af46788b845fc0c0',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
+(107,NULL,'2b8b4d4c142e82b618fe6350afb9a08bf58e3817',2,1,'ddaf373d-6625-4b97-ab3d-7f91f13e7c27'),
(108,NULL,'ee1eae1aa831261b54a3b302f2a8fe3832caa821',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
+(108,NULL,'3658ab2ab072727a6caa6d87ae9edbab37cc3058',2,1,'37b23e09-803b-4ea2-8caf-00f0242d9c66'),
(109,NULL,'8faa2c5a80f734b894d60dd7f41a69f9686b323f',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(110,NULL,'969e58211cc801b7f29f7d9cf2d386843af3418e',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(110,NULL,'bcac18af5682f2b21c7675fc4eb6de3be39ae49a',2,1,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
(111,NULL,'36c265d80cb5abb79d5671a1b431dd62e971e9b5',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(111,NULL,'83299d432a84245a01410042af78b1e332315114',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(111,NULL,'d14f134f53a5225fdf9f0377b8af341ae783b294',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(111,NULL,'04c60831fa49d7597f55e2c85c94e731f3c4d987',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(112,NULL,'fb580fe4757eee3dba822814fa51c18a18b761ca',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(113,NULL,'271372b1dfdd98d82b290ad3f40335fbf51d23b1',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(114,NULL,'cf3ab7cfb60c2492e90ddf765784084060508a7d',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1646,9 +1790,11 @@ INSERT INTO `entity_version` VALUES
(118,NULL,'68c8f4408696307d47f93015ecf286b079bd50ba',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(118,NULL,'f8a7baed3750fddb91d5109c5ed4fd6865500883',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(118,NULL,'a02a1cdfe936c3c73e957e5c097e978f50e50c73',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(118,NULL,'b7faa7d99b719cf37ad085fa3331ddb8c89557b5',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(119,NULL,'9bfc33ae0c6be37cb027a62afd792d1c311d006a',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(119,NULL,'61ee09a05b915dba2c6d158244966d3688ccef1a',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(119,NULL,'74f9449229abf6deadb11c428fd38c437f937f40',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(119,NULL,'8b84a456a3e07f22f76ca80cae004e7c3b278990',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(120,NULL,'46a17aea4446446e72aeaffc3a01ee2f2d5d9957',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(121,NULL,'cecee2780f2756778d57180bb6579333c6743420',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(122,NULL,'1ae73a81970c7cffda61f4354d3747495252da95',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1668,6 +1814,7 @@ INSERT INTO `entity_version` VALUES
(136,NULL,'6902c75485499ba6513b1faefb733322d9cb0239',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(136,NULL,'a65d632df3b40a0d9cdd748c0c578f9bfd538c27',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(136,NULL,'b46bbccd0a67d55e67d8df85a31132a8d77e3c93',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(136,NULL,'103283c5c47772933bbd3d7eb66447c49dbcf7b0',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(137,NULL,'acd17699d752e90015eb8010e2f17ab5566a4241',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(138,NULL,'3c63009effd95704bc52400dc38ed7c8ccc63495',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(139,NULL,'54edec758a99a74f50577b74ba8a1ef187e08859',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1677,28 +1824,35 @@ INSERT INTO `entity_version` VALUES
(143,NULL,'2a1014ad624089133ffbe85a7a39e82beeab2007',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(143,NULL,'96f98bad0aa7f4cf14e5e59a8608ede0cc2e4507',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(143,NULL,'4b5c04e5674df7eaae698b73caed073a6345e90a',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(143,NULL,'b0772c4e25b6d6121491024d7ed6ac541e9e2381',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(144,NULL,'a1d4da47f82593afbb269cbf6fc2311b059812d7',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(144,NULL,'a80b7c60c82df12adde5a14916dd39832bfc6c02',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(144,NULL,'9acc339307deafd15e156c9510ff5ae67fdec6fb',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(144,NULL,'53bd67181fbafaaff7020e358e62b60310b92397',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(145,NULL,'535909011d32dc82dc3368b463c01f471c72b5f6',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(145,NULL,'b881b96d70e6900c63fb9dd2709a3682e65028e9',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(145,NULL,'2c0bf525e0375c3d1ab95d1954202f929924aebf',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(145,NULL,'7b39b67649b72ffa178ce6b74efd9b4d5cf6efe6',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(146,NULL,'8ab9de04122cf31364610d3372f0d922b4e110a5',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(146,NULL,'26cf3920bc49690f1e071d1362d90ad3dde4051f',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(146,NULL,'2cf5987178082192f54fe85144721e28fb29cb20',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(146,NULL,'65f6807c333e902177b44aa3affba219903e6317',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(147,NULL,'affd3537da482fb6655fc65cd223befedc845cb1',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(147,NULL,'f2f3f1bafbee48263ab7c5184a17b036f528bf8a',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(147,NULL,'3b26886ba59708accac6f63a5bb54cc94c4f7ece',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(147,NULL,'760b388bc1624c0cb8e2f61f2513f144ce882bb0',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(148,NULL,'3dc270e8ab4ffded2b7f3412e97469022a389a62',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(149,NULL,'949f9468c06c34881820eeeea6bb999e510c3fac',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(150,NULL,'5a0c0116c267a8165eec4bdb0f6bc9393af4ebac',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(150,NULL,'ac659db37f8e5c0874677706da69a6d060a93f0f',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(150,NULL,'f6fd4f82e33dd54b6299106de95283f573f34973',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(150,NULL,'cb341cff740100314ada1c62dbaac7d3ddb98632',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(151,NULL,'c5eb1e4ec70baa761c151d708676e4c436f28587',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(152,NULL,'8abed6579e778a2bf94e6e12b38791c7a7308b61',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(153,NULL,'a5e4f99ff9324eae679f20131b8b8da68846b1ad',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(153,NULL,'80a3d9eebdd6664a84a8b445c1716dba3cd747ba',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(153,NULL,'bf5595aedf69bb49b3ecf17fa8db422740b39aee',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(153,NULL,'15113924b012e7e32a07e48a7ff1ee437bdc03e5',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(154,NULL,'3f8eb5ecfd51c5a745a4862013547d518b7b2955',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(155,NULL,'afbd70a177d0724af03b005dfa54d7a67825082a',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(156,NULL,'34e04866309d1f335fc6767aa9993ef6ee88dbd3',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -1709,9 +1863,11 @@ INSERT INTO `entity_version` VALUES
(161,NULL,'2e5f4fab2cdd47e184fced9b5ea6dd54ba45cdb3',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(161,NULL,'bae9c9da4e3784233fa93ea8562bdf8109570eb9',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(161,NULL,'906ccfbc2adfdaaa0894f188becc08a2aedbf2e1',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(161,NULL,'30577d8ee9a80c7861d1a92d6c91c7cf0cf595b9',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(162,NULL,'49fd42751089f19e7d6bb5da57df79ba6cc546d2',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(162,NULL,'5d512dd3f177da0402db804e1f2f7d811302bddd',2,1,'a61cf61b-8583-41ec-b204-bfa65e3a7807'),
(162,NULL,'97e7860660e9f9bfdc54aff4eb8f1494ae975ca4',3,2,'cf5b2beb-6960-4eaf-8d7b-5e747f29f7be'),
+(162,NULL,'df6816d130ef6abccb6e0dd8c3fc700bbbc68461',4,3,'7ef74091-1b29-40bf-b690-0f94a3b1c9b7'),
(163,NULL,'ac2b6777efb772874d95a88bc0062c520e4851c9',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(164,NULL,'767121db8cfc7592f4c50814393559b72614384d',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
(165,NULL,'162195b8d54378680140bcc63a78109e83756525',1,NULL,'27f2534b-49b9-4e44-9232-53eadf8ba072'),
@@ -2039,8 +2195,8 @@ INSERT INTO `name_data` VALUES
(0,102,20,'Abbreviation','FIX',0),
(0,104,20,'German name','FIX',0),
(0,106,20,'Person','FIX',0),
-(0,107,20,'First name','FIX',0),
-(0,108,20,'Last name','FIX',0),
+(0,107,20,'first_name','FIX',0),
+(0,108,20,'last_name','FIX',0),
(0,109,20,'Email','FIX',0),
(0,110,20,'ContainerType','FIX',0),
(0,111,20,'Container','FIX',0),
@@ -2200,11 +2356,11 @@ INSERT INTO `null_data` VALUES
(0,211,144,'FIX',3),
(0,197,177,'FIX',0),
(0,101,102,'OBLIGATORY',0),
+(0,110,102,'OBLIGATORY',0),
(0,106,107,'OBLIGATORY',0),
(0,106,108,'OBLIGATORY',1),
-(0,106,109,'OBLIGATORY',2),
-(0,106,102,'OBLIGATORY',0),
-(0,110,102,'OBLIGATORY',0),
+(0,106,109,'RECOMMENDED',2),
+(0,106,102,'RECOMMENDED',0),
(0,111,177,'OBLIGATORY',0),
(0,111,178,'OBLIGATORY',0),
(0,111,212,'SUGGESTED',2),
@@ -2472,7 +2628,7 @@ CREATE TABLE `stats` (
LOCK TABLES `stats` WRITE;
/*!40000 ALTER TABLE `stats` DISABLE KEYS */;
INSERT INTO `stats` VALUES
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+('RootBenchmark','¬í\0sr\0-org.caosdb.server.database.misc.RootBenchmarkþ¼ƒQk]\0\0xr\04org.caosdb.server.database.misc.TransactionBenchmarkþ¼ƒQk]\0J\0sinceL\0 measurementst\0Ljava/util/Map;[\0stackTraceElementst\0 [Ljava/lang/StackTraceElement;L\0\rsubBenchmarksq\0~\0xp\0\0”¨4‰‡sr\0java.util.HashMapÚÁÃ`Ñ\0F\0\nloadFactorI\0 thresholdxp?@\0\0\0\0\0\0w\0\0\0\0\0\0\0xur\0 [Ljava.lang.StackTraceElement;F*<<ý\"9\0\0xp\0\0\0sr\0java.lang.StackTraceElementa Åš&6Ý…\0B\0formatI\0\nlineNumberL\0classLoaderNamet\0Ljava/lang/String;L\0declaringClassq\0~\0\nL\0fileNameq\0~\0\nL\0\nmethodNameq\0~\0\nL\0\nmoduleNameq\0~\0\nL\0\rmoduleVersionq\0~\0\nxp\0\0Spt\0java.lang.Threadt\0 Thread.javat\0\rgetStackTracet\0 java.baset\017.0.13sq\0~\0 \0\0!t\0appt\04org.caosdb.server.database.misc.TransactionBenchmarkt\0TransactionBenchmark.javat\0<init>ppsq\0~\0 \0\0\0ƒq\0~\0t\0-org.caosdb.server.database.misc.RootBenchmarkq\0~\0q\0~\0ppsq\0~\0 \0\0q\0~\0q\0~\0q\0~\0t\0<clinit>ppsq\0~\0 \0\0fq\0~\0t\0 org.caosdb.server.CaosDBServert\0CaosDBServer.javat\0 initBackendppsq\0~\0 \0\0\0 q\0~\0q\0~\0q\0~\0 t\0mainppsq\0~\0?@\0\0\0\0\0 w\0\0\0\0\0\0t\0Infosr\0,org.caosdb.server.database.misc.SubBenchmarkþ¼ƒQk]\0L\0nameq\0~\0\nxq\0~\0\0\0”¨4‰Šsq\0~\0?@\0\0\0\0\0\0w\0\0\0\0\0\0\0xuq\0~\0\0\0\0\nsq\0~\0 \0\0Spq\0~\0 q\0~\0\rq\0~\0q\0~\0q\0~\0sq\0~\0 \0\0!q\0~\0q\0~\0q\0~\0q\0~\0ppsq\0~\0 \0\0\0×q\0~\0t\0,org.caosdb.server.database.misc.SubBenchmarkq\0~\0q\0~\0ppsq\0~\0 \0\0šq\0~\0q\0~\0q\0~\0t\0 getBenchmarkppsq\0~\0 \0\0£q\0~\0q\0~\0q\0~\0q\0~\0+ppsq\0~\0 \0\0\0$q\0~\0t\02org.caosdb.server.transaction.TransactionInterfacet\0TransactionInterface.javat\0getTransactionBenchmarkppsq\0~\0 \0\0\00q\0~\0q\0~\0.q\0~\0/t\0executeppsq\0~\0 \0\0\0õq\0~\0t\0 org.caosdb.server.utils.Infot\0 Info.javat\0 syncDatabaseppsq\0~\0 \0\0\0–q\0~\0t\0/org.caosdb.server.database.misc.RootBenchmark$1q\0~\0t\0runppsq\0~\0 \0\0Hpq\0~\0 q\0~\0\rq\0~\09q\0~\0q\0~\0sq\0~\0?@\0\0\0\0\0 w\0\0\0\0\0\0t\0 SyncStatssq\0~\0\"\0\0”¨4‰Šsq\0~\0?@\0\0\0\0\0\0w\0\0\0\0\0\0\0xuq\0~\0\0\0\0 sq\0~\0 \0\0Spq\0~\0 q\0~\0\rq\0~\0q\0~\0q\0~\0sq\0~\0 \0\0!q\0~\0q\0~\0q\0~\0q\0~\0ppsq\0~\0 \0\0\0×q\0~\0q\0~\0)q\0~\0q\0~\0ppsq\0~\0 \0\0šq\0~\0q\0~\0q\0~\0q\0~\0+ppsq\0~\0 \0\0£q\0~\0q\0~\0q\0~\0q\0~\0+ppsq\0~\0 \0\0\00q\0~\0q\0~\0.q\0~\0/q\0~\02ppsq\0~\0 \0\0\0õq\0~\0q\0~\04q\0~\05q\0~\06ppsq\0~\0 \0\0\0–q\0~\0q\0~\08q\0~\0q\0~\09ppsq\0~\0 \0\0Hpq\0~\0 q\0~\0\rq\0~\09q\0~\0q\0~\0sq\0~\0?@\0\0\0\0\0 w\0\0\0\0\0\0t\0MySQLSyncStatssq\0~\0\"\0\0”¨4‰‹sq\0~\0?@\0\0\0\0\0\0w\0\0\0\0\0\0\0xuq\0~\0\0\0\0 sq\0~\0 \0\0Spq\0~\0 q\0~\0\rq\0~\0q\0~\0q\0~\0sq\0~\0 \0\0!q\0~\0q\0~\0q\0~\0q\0~\0ppsq\0~\0 \0\0\0×q\0~\0q\0~\0)q\0~\0q\0~\0ppsq\0~\0 \0\0šq\0~\0q\0~\0q\0~\0q\0~\0+ppsq\0~\0 \0\0£q\0~\0q\0~\0q\0~\0q\0~\0+ppsq\0~\0 \0\0 q\0~\0t\0-org.caosdb.server.database.BackendTransactiont\0BackendTransaction.javat\0getImplementationppsq\0~\0 \0\0\0+q\0~\0t\08org.caosdb.server.database.backend.transaction.SyncStatst\0SyncStats.javaq\0~\02ppsq\0~\0 \0\0\0žq\0~\0q\0~\0Tq\0~\0Ut\0executeTransactionppsq\0~\0 \0\0\01q\0~\0q\0~\0.q\0~\0/q\0~\02ppsq\0~\0 \0\0\0õq\0~\0q\0~\04q\0~\05q\0~\06ppsq\0~\0 \0\0\0–q\0~\0q\0~\08q\0~\0q\0~\09ppsq\0~\0 \0\0Hpq\0~\0 q\0~\0\rq\0~\09q\0~\0q\0~\0sq\0~\0?@\0\0\0\0\0\0w\0\0\0\0\0\0\0xq\0~\0Jxq\0~\0<xq\0~\0!x'),
('TransactionBenchmark','¬í\0sr\00caosdb.server.database.misc.TransactionBenchmark„Cl=˜ÕãE\0J\0sinceL\0acct\0Ljava/util/HashMap;L\0countsq\0~\0xp\0\0lžèòWsr\0java.util.HashMapÚÁÃ`Ñ\0F\0\nloadFactorI\0 thresholdxp?@\0\0\0\0\0 w\0\0\0\0\0\0t\0 SyncStatssr\0java.lang.Long;‹äÌ#ß\0J\0valuexr\0java.lang.Number†¬• ”à‹\0\0xp\0\0\0\0\0\0\0t\0GetInfosq\0~\0\0\0\0\0\0\0 xsq\0~\0?@\0\0\0\0\0 w\0\0\0\0\0\0q\0~\0sr\0java.lang.Integerâ ¤÷‡8\0I\0valuexq\0~\0\0\0\0q\0~\0 sq\0~\0 \0\0\0x');
/*!40000 ALTER TABLE `stats` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2521,6 +2677,10 @@ INSERT INTO `text_data` VALUES
(0,193,113,'20 rooms','FIX',2),
(0,195,113,'30 m²','FIX',2),
(0,197,113,'300 l','FIX',2),
+(0,188,107,'My','FIX',0),
+(0,188,102,'myn','FIX',1),
+(0,188,108,'Name','FIX',2),
+(0,188,109,'my.name@example.com','FIX',3),
(143,146,21,'°','FIX',0),
(143,147,21,'°','FIX',0),
(143,144,21,'m','FIX',0),
@@ -2532,11 +2692,7 @@ INSERT INTO `text_data` VALUES
(161,146,21,'°','FIX',0),
(161,147,21,'°','FIX',0),
(162,146,21,'°','FIX',0),
-(162,147,21,'°','FIX',0),
-(0,188,107,'My','FIX',0),
-(0,188,102,'myn','FIX',1),
-(0,188,108,'Name','FIX',2),
-(0,188,109,'my.name@example.com','FIX',3);
+(162,147,21,'°','FIX',0);
/*!40000 ALTER TABLE `text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2721,7 +2877,23 @@ INSERT INTO `transaction_log` VALUES
('Delete','180','admin',1737714483,466000000,'PAM'),
('Delete','179','admin',1737714485,611000000,'PAM'),
('Delete','107','admin',1737714497,308000000,'PAM'),
-('Delete','105','admin',1737714500,565000000,'PAM');
+('Delete','105','admin',1737714500,565000000,'PAM'),
+('Update','109','admin',1737990337,853000000,'PAM'),
+('Update','110','admin',1737990350,365000000,'PAM'),
+('Update','108','admin',1737990395,730000000,'PAM'),
+('Update','113','admin',1737990395,730000000,'PAM'),
+('Update','120','admin',1737990395,730000000,'PAM'),
+('Update','121','admin',1737990395,730000000,'PAM'),
+('Update','138','admin',1737990395,730000000,'PAM'),
+('Update','145','admin',1737990395,730000000,'PAM'),
+('Update','146','admin',1737990395,730000000,'PAM'),
+('Update','147','admin',1737990395,730000000,'PAM'),
+('Update','148','admin',1737990395,730000000,'PAM'),
+('Update','149','admin',1737990395,730000000,'PAM'),
+('Update','152','admin',1737990395,730000000,'PAM'),
+('Update','155','admin',1737990395,730000000,'PAM'),
+('Update','163','admin',1737990395,730000000,'PAM'),
+('Update','164','admin',1737990395,730000000,'PAM');
/*!40000 ALTER TABLE `transaction_log` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2765,10 +2937,12 @@ INSERT INTO `transactions` VALUES
('2df660f0-e3a6-447e-837f-4778e5323f5d','admin','PAM',1736265392,576000000),
('34fade63-2811-4725-becf-0f2b1f84ad90','admin','PAM',1736265204,999000000),
('372c0d25-a1ab-45d2-bf7e-76e583bf5192','admin','PAM',1737714467,357000000),
+('37b23e09-803b-4ea2-8caf-00f0242d9c66','admin','PAM',1737990350,365000000),
('3c931e13-7e9f-4835-99df-d325020b887d','admin','PAM',1736265488,391000000),
('488967a3-a042-43d4-b74d-485f4bf622a2','admin','PAM',1736265441,647000000),
('55dcaf7b-7372-4778-995a-a6a8bde1b471','admin','PAM',1736264805,952000000),
('7663f26d-982f-4710-aeab-073a44290f3a','admin','PAM',1736265841,217000000),
+('7ef74091-1b29-40bf-b690-0f94a3b1c9b7','admin','PAM',1737990395,730000000),
('80009e0c-8c91-4add-9ada-6aed2ac526b7','admin','PAM',1737542797,604000000),
('8205d330-42ef-4519-9e5e-ade1e2465bed','admin','PAM',1736265392,368000000),
('84bd4faf-510c-4950-b827-4bab81546887','admin','PAM',1736264663,736000000),
@@ -2796,6 +2970,7 @@ INSERT INTO `transactions` VALUES
('da56170f-ae54-4ecf-9aa4-342d7512384f','admin','PAM',1736265798,309000000),
('daa492ef-1495-4123-9966-9951328211b3','admin','PAM',1736265204,580000000),
('dbf1dd0f-405c-4952-b8b6-62e169c79397','admin','PAM',1736265204,802000000),
+('ddaf373d-6625-4b97-ab3d-7f91f13e7c27','admin','PAM',1737990337,853000000),
('df3a0e97-6feb-42aa-8800-074ee5520428','admin','PAM',1736265392,321000000),
('e27923fa-df80-4883-9f70-03ed7dbe8fcc','admin','PAM',1737714483,466000000),
('f284f0d8-aba2-44e9-bfc7-ae68fab970b9','admin','PAM',1736265770,375000000),
@@ -7269,4 +7444,4 @@ DELIMITER ;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
--- Dump completed on 2025-01-24 10:29:19
+-- Dump completed on 2025-01-27 15:08:09
--
GitLab
From 0528293da4fe6956654cac1c528511b2e18bdcd9 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 27 Jan 2025 16:14:20 +0100
Subject: [PATCH 27/63] MAINT: Remove bis from names of js modules
---
..._bis_samplemanagemet.js => ext_samplemanagement.js} | 8 ++++----
.../caosdb-webui/src/ext/js/ext_stockmanagement.js | 10 +++++-----
...lver.js => sample_management_reference_resolver.js} | 2 +-
3 files changed, 10 insertions(+), 10 deletions(-)
rename sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/{ext_bis_samplemanagemet.js => ext_samplemanagement.js} (98%)
rename sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/{bis_custom_reference_resolver.js => sample_management_reference_resolver.js} (96%)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
similarity index 98%
rename from sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
rename to sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index 27a9494..afa88df 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -16,7 +16,7 @@
* @requires nothing yet
* (pass the dependencies as arguments)
*/
-const ext_samplemanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_samplemanagement = function($, navbar, log, form_elements, form_panel, sample_management_reference_resolver) {
const logger = log.getLogger("samplemanagement_form");
const tool_box = "Sample Management"
const upload_sample_template_title = "Upload sample template"; // title of the form and text in the toolbox
@@ -182,7 +182,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
name: "responsible_person",
label: "Main user",
query: "FIND RECORD Person",
- make_desc: bis_custom_reference_resolver.resolve_person_reference,
+ make_desc: sample_management_reference_resolver.resolve_person_reference,
required: true
},
{
@@ -263,7 +263,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
name: "main_user",
label: "Main user",
query: "FIND RECORD Person",
- make_desc: bis_custom_reference_resolver.resolve_person_reference,
+ make_desc: sample_management_reference_resolver.resolve_person_reference,
required: true
}, {
type: "select",
@@ -417,7 +417,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
return {
init: init,
};
-}($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver);
+}($, navbar, log, form_elements, form_panel, sample_management_reference_resolver);
// this will be replaced by require.js in the future.
$(document).ready(function() {
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
index 8afbebb..4775b9d 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
@@ -9,9 +9,9 @@
* @module ext_stockmanagement
* @version 0.2
*
- * @requires($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver)
+ * @requires($, navbar, log, form_elements, form_panel, sample_management_reference_resolver)
*/
-const ext_stockmanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_stockmanagement = function($, navbar, log, form_elements, form_panel, sample_management_reference_resolver) {
const tool_box = "Storage Management" // The item that is shown in the top-navbar
@@ -35,7 +35,7 @@ const ext_stockmanagement = function($, navbar, log, form_elements, form_panel,
name: "responsible_entity",
label: "Responsible entity",
query: "FIND RECORD Responsible",
- make_desc: bis_custom_reference_resolver.resolve_person_reference,
+ make_desc: sample_management_reference_resolver.resolve_person_reference,
required: true
},
{
@@ -77,7 +77,7 @@ const ext_stockmanagement = function($, navbar, log, form_elements, form_panel,
name: "parent_id",
label: "Parent container",
query: "FIND RECORD Container",
- make_desc: bis_custom_reference_resolver.resolve_default,
+ make_desc: sample_management_reference_resolver.resolve_default,
required: false
},
],
@@ -203,7 +203,7 @@ const ext_stockmanagement = function($, navbar, log, form_elements, form_panel,
return {
init: init,
};
-}($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver); // this will be replaced by require.js in the future.
+}($, navbar, log, form_elements, form_panel, sample_management_reference_resolver); // this will be replaced by require.js in the future.
$(document).ready(function() {
// use a variable starting with `BUILD_MODULE_` to this module
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/sample_management_reference_resolver.js
similarity index 96%
rename from sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js
rename to sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/sample_management_reference_resolver.js
index 7059cb5..ec82f14 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/sample_management_reference_resolver.js
@@ -1,4 +1,4 @@
-var bis_custom_reference_resolver = new function (getEntityID, getEntityName, getParents, getProperty, query) {
+var sample_management_reference_resolver = new function (getEntityID, getEntityName, getParents, getProperty, query) {
const lastname_prop_name = "last_name";
const firstname_prop_name = "first_name";
--
GitLab
From e145e16c9c349b44e3117b3a7e3a0ad2676957b1 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 27 Jan 2025 16:20:56 +0100
Subject: [PATCH 28/63] FIX: Rename to respect order of js copying
---
...ent_reference_resolver.js => ext_sample_reference_resolver.js} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/{sample_management_reference_resolver.js => ext_sample_reference_resolver.js} (100%)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/sample_management_reference_resolver.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
similarity index 100%
rename from sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/sample_management_reference_resolver.js
rename to sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
--
GitLab
From 600603bad7d9cf64e286591c6ce0c868a828315c Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 29 Jan 2025 10:25:05 +0100
Subject: [PATCH 29/63] ENH: Automatically replace all column keys by custom
definitions
---
.../caosdb-server/scripting/bin/bis_utils.py | 51 +-------
.../scripting/bin/upload_sample_template.py | 119 +-----------------
2 files changed, 5 insertions(+), 165 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
index 80165fc..1bcc322 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
@@ -32,57 +32,10 @@ from caosadvancedtools.serverside.helper import send_mail
from caoscrawler.config import get_config_setting
from linkahead import get_entity_by_name
+from sample_helpers.sample_upload_column_definitions import (
+ IGNORED_COLUMN_NAMES_SAMPLE, SPECIAL_TREATMENT_SAMPLE)
from sample_helpers.utils import CONSTANTS
-SPECIAL_TREATMENT_SAMPLE = [
- "BIS ID",
- "Collection",
- "Date collected start",
- "Date collected stop",
- "Date sampled start",
- "Date sampled stop",
- "Gear configuration",
- "Gear",
- "Hol",
- "Latitude start",
- "Latitude stop",
- "Longitude start",
- "Longitude stop",
- "Main User",
- "Nagoya case number",
- "PDFReport",
- "PI",
- "Parent BIS ID",
- "Person",
- "Sampling Person",
- "Sampling depth start",
- "Sampling depth stop",
- "Sphere",
- "Station ID",
- "Station number",
- "Storage Container Label",
- "Storage ID",
- "Subevent",
- "Time collected start",
- "Time collected stop",
- "Time sampled start",
- "Time sampled stop",
- "Timezone",
- "Water depth start",
- "Water depth stop",
-]
-
-IGNORED_COLUMN_NAMES_SAMPLE = [
- "BIS URL",
- "Date",
- "IGSN URL",
- "IGSN", # TODO This will be relevant for external IGSNs in the future.
- "Parent Sample",
- "Sampling depth",
- "Storage chain",
- "Water depth",
-]
-
COLUMN_DESCRIPTIONS = CONSTANTS["csv_column_descriptions"]
diff --git a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
index f66744a..7d71282 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
@@ -27,12 +27,9 @@ import json
import logging
import os
import pandas as pd
-import re
import subprocess
import sys
-from datetime import date, datetime
-from dateutil.relativedelta import relativedelta
from pathlib import Path
from tempfile import NamedTemporaryFile
@@ -45,128 +42,18 @@ from caoscrawler.logging import configure_server_side_logging
from bis_utils import (replace_entity_urls_by_ids,
SPECIAL_TREATMENT_SAMPLE, whitespace_cleanup_in_df)
+from sample_helpers.utils import CONSTANTS
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
apilogger.setLevel(logging.ERROR)
-def semicolon_separated_list(text):
- return [el.strip() for el in text.split(";") if el != ""]
-
-
-def _embargo_converter(text: str):
-
- datepattern = r"^(?P<year>\d{4,4})-(?P<month>\d{2,2})-(?P<day>\d{2,2})"
- matches = re.match(datepattern, str(text))
- if matches:
- return date(int(matches.groupdict()["year"]), int(matches.groupdict()["month"]), int(matches.groupdict()["day"]))
- if f"{text}".lower() in ["true", "yes"]:
- # yes means embargo until today in one year
- return date.today() + relativedelta(years=1)
- if f"{text}".lower() in ["false", "no"]:
- return ""
- raise ValueError(
- f"The embargo should be either a date in YYYY-MM-DD format, or 'true'/'yes' or 'false'/'no', but is {text}.")
-
-
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
# Column datatypes
-DATATYPE_DEFINITIONS = {
- "AphiaID": int,
- "BIS ID": str,
- "Campaign": str,
- "Date collected start": str,
- "Date collected stop": str,
- "Date sampled start": str,
- "Date sampled stop": str,
- "Fixation": str,
- "Gear configuration": str,
- "Gear": str,
- "Hol": int,
- "Latitude start": float,
- "Latitude stop": float,
- "Longitude start": float,
- "Longitude stop": float,
- "Main User": str,
- "Nagoya case number": str,
- "PI": str,
- "Parent BIS ID": str,
- "Platform": str,
- "Sample Context": str,
- "Sample container": str,
- "SampleType": str,
- "SampleTypeSpecific": str,
- "Sampling Person": str,
- "Sampling depth start": float,
- "Sampling depth stop": float,
- "Sampling method": str,
- "Station ID": str,
- "Station number": str,
- "Storage Container Label": str,
- "Storage ID": str,
- "StorageTemperature": str,
- "Subevent": str,
- "Time collected start": str,
- "Time collected stop": str,
- "Time sampled start": str,
- "Time sampled stop": str,
- "Timezone": str,
- "Water depth start": float,
- "Water depth stop": float,
-}
-
-# Obligatory columns: Must exist and must not be empty
-# Must exist
-OBLIGATORY_COLUMNS = [
- "BIS ID",
- "Collection",
- "Date collected start",
- "Fixation",
- "Gear",
- "Latitude start",
- "Longitude start",
- "Main User",
- "Nagoya case number",
- "PI",
- "Sample Context",
- "Sample container",
- "SampleType",
- "SampleTypeSpecific",
- "Sphere",
- "Storage ID",
- "StorageTemperature",
-]
-
-OBLIGATORY_COLUMNS_CHILD = [
- "BIS ID",
- "Date sampled start",
- "Fixation",
- "Main User",
- "Parent BIS ID",
- "Sample Context",
- "Sample container",
- "SampleType",
- "SampleTypeSpecific",
- "Sphere",
- "Storage ID",
- "StorageTemperature",
-]
-
-COLUMN_CONVERTER = {
- "Collection": semicolon_separated_list,
- "Ecotaxa URL": semicolon_separated_list,
- "NCBI Accession": semicolon_separated_list,
- "NCBI BioProject": semicolon_separated_list,
- "NCBI BioSample": semicolon_separated_list,
- "OSIS URL": semicolon_separated_list,
- "Embargo": _embargo_converter,
- "Publications": semicolon_separated_list,
- "Sphere": semicolon_separated_list,
-}
logger = logging.getLogger("caosadvancedtools")
--
GitLab
From dc1aebc50160698295b53ef9d7b4e280e7a2194e Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 29 Jan 2025 15:15:31 +0100
Subject: [PATCH 30/63] ENH: Addapt upload sample script to configurable column
names
---
.../caosdb-server/scripting/bin/upload_sample_template.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
index 7d71282..484e651 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
@@ -42,7 +42,7 @@ from caoscrawler.logging import configure_server_side_logging
from bis_utils import (replace_entity_urls_by_ids,
SPECIAL_TREATMENT_SAMPLE, whitespace_cleanup_in_df)
-from sample_helpers.utils import CONSTANTS
+from sample_helpers.utils import CONSTANTS, get_column_header_name
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -66,7 +66,7 @@ def get_parser():
def _is_child_sample_table(filename):
tmp_data = pd.read_csv(filename, sep=',')
if 'Parent BIS ID' in tmp_data.columns:
- return not tmp_data["Parent BIS ID"].isnull().all()
+ return not tmp_data[get_column_header_name("Parent LinkAhead ID")].isnull().all()
return False
@@ -171,7 +171,8 @@ def main():
OBLIGATORY_COLUMNS.append(property_name)
try:
data = read_data_from_file(path)
- data = replace_entity_urls_by_ids(data, ["BIS ID", "Storage ID", "Parent BIS ID"])
+ data = replace_entity_urls_by_ids(data, [get_column_header_name(name) for name in [
+ "entity_id", "Storage ID", "Parent LinkAhead ID"]])
pickle_out = NamedTemporaryFile(delete=False, suffix=".pkl")
data.to_pickle(pickle_out.name)
except DataInconsistencyError as err:
--
GitLab
From c0d0740d6ff02f214401b40b8d0847958591247a Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 29 Jan 2025 17:05:41 +0100
Subject: [PATCH 31/63] ENH: Add sample postprocessing
---
.../scripting/bin/crawl_sample_data_async.py | 26 ++-
.../sample_upload_column_definitions.py | 192 ++++++++++++++++++
.../sample_upload_post_processing.py | 23 +++
3 files changed, 231 insertions(+), 10 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index 1c578f9..1e17a33 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -47,6 +47,8 @@ from bis_utils import (get_do_not_insert_type_names,
return_value_if_not_none,
send_mail_with_defaults,
SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.sample_upload_post_processing import post_process_samples
+from sample_helpers.utils import get_column_header_name
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -139,19 +141,20 @@ def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_pref
except dateparser.ParserError as perr:
logger.error(
f"There is a problem in '{colname_date_start}': {date_start}"
- f" of sample {data['BIS ID']}: {perr}"
+ f" of sample {data[get_column_header_name('entity_id')]}: {perr}"
)
raise DataInconsistencyError
if colname_time_start in data and return_value_if_not_none(data[colname_time_start]) is not None:
- if not "Timezone" in data or return_value_if_not_none(data["Timezone"]) is None:
+ if not get_column_header_name("Timezone") in data or return_value_if_not_none(data[get_column_header_name("Timezone")]) is None:
logger.error(f"{colname_time_start} but no timezone given for sample "
- f"{data['BIS ID']}.")
+ f"{data[get_column_header_name('entity_id')]}.")
raise DataInconsistencyError
time_start = return_value_if_not_none(data[colname_time_start])
- timezone = return_value_if_not_none(data["Timezone"])
+ timezone = return_value_if_not_none(data[get_column_header_name("Timezone")])
if date_start is None:
logger.error(
- f"{colname_time_start} is given but {colname_date_start} is missing for sample {data['BIS ID']}.")
+ f"{colname_time_start} is given but {colname_date_start} is missing for "
+ f"sample {data[get_column_header_name('entity_id')]}.")
raise DataInconsistencyError
try:
_val = str(dateparser.parse(f"{date_start}T{time_start}{timezone}"))
@@ -159,7 +162,7 @@ def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_pref
except dateparser.ParserError as perr:
logger.error(
f"Couldn't parse {colname_time_start}: {time_start} with timezone {timezone} "
- f"of sample {data['BIS ID']}: {perr}"
+ f"of sample {data[get_column_header_name('entity_id')]}: {perr}"
)
raise DataInconsistencyError
elif date_start is not None:
@@ -170,7 +173,8 @@ def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_pref
date_stop = return_value_if_not_none(data[colname_date_stop])
if date_stop is not None and date_start is None:
logger.error(
- f"{colname_date_stop} is given but {colname_date_start} is missing for sample {data['BIS ID']}.")
+ f"{colname_date_stop} is given but {colname_date_start} is missing for "
+ f"sample {data[get_column_header_name('entity_id')]}.")
raise DataInconsistencyError
if date_stop is None:
_date_stop = date_start
@@ -180,7 +184,7 @@ def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_pref
except dateparser.ParserError as perr:
logger.error(
f"There is a problem in '{colname_date_stop}': {date_stop}"
- f" of sample {data['BIS ID']}: {perr}"
+ f" of sample {data[get_column_header_name('entity_id')]}: {perr}"
)
raise DataInconsistencyError
@@ -188,7 +192,8 @@ def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_pref
time_stop = return_value_if_not_none(data[colname_time_stop])
if time_start is None:
logger.error(
- f"{colname_time_stop} is given but {colname_time_start} is missing for sample {data['BIS ID']}.")
+ f"{colname_time_stop} is given but {colname_time_start} is missing for "
+ f"sample {data[get_column_header_name('entity_id')]}.")
raise DataInconsistencyError
# timezone is set by time start; if it hadn't been there, we would already have an error.
try:
@@ -196,7 +201,7 @@ def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_pref
except dateparser.ParserError as perr:
logger.error(
f"Couldn't parse {colname_time_stop}: {time_stop} with timezone {timezone} "
- f"of sample {data['BIS ID']}: {perr}"
+ f"of sample {data[get_column_header_name('entity_id')]}: {perr}"
)
raise DataInconsistencyError
ent = _update_property(ent, prop_stop.id, property_name=prop_stop.name, value=_val)
@@ -587,6 +592,7 @@ def update_sample_records(data, htmluserlog_public):
samples.append(sample)
+ samples = post_process_samples(samples, data)
synchroize(samples, additional_property_ents, htmluserlog_public)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
new file mode 100644
index 0000000..c1155d7
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -0,0 +1,192 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import re
+
+from datetime import date, datetime
+from dateutil.relativedelta import relativedelta
+from typing import Union
+
+from .utils import get_column_header_name
+
+
+def semicolon_separated_list(text):
+ return [el.strip() for el in text.split(";") if el != ""]
+
+
+def _embargo_converter(text: str):
+
+ datepattern = r"^(?P<year>\d{4,4})-(?P<month>\d{2,2})-(?P<day>\d{2,2})"
+ matches = re.match(datepattern, str(text))
+ if matches:
+ return date(int(matches.groupdict()["year"]), int(matches.groupdict()["month"]), int(matches.groupdict()["day"]))
+ if f"{text}".lower() in ["true", "yes"]:
+ # yes means embargo until today in one year
+ return date.today() + relativedelta(years=1)
+ if f"{text}".lower() in ["false", "no"]:
+ return ""
+ raise ValueError(
+ f"The embargo should be either a date in YYYY-MM-DD format, or 'true'/'yes' or 'false'/'no', but is {text}.")
+
+
+def _use_custom_names(definition: Union[list, dict]):
+ """Replace names in list or dict keys by custom names with
+ `utils.get_column_header_name`.
+
+ """
+ if isinstance(definition, list):
+ return [get_column_header_name(name) for name in definition]
+ elif isinstance(definition, dict):
+ return {get_column_header_name(key): value for key, value in definition.items()}
+
+ raise ValueError(f"Expected dict or list, but got {type(definition)}.")
+
+
+DATATYPE_DEFINITIONS = _use_custom_names({
+ "AphiaID": int,
+ "entity_id": str,
+ "Campaign": str,
+ "Date collected start": str,
+ "Date collected stop": str,
+ "Date sampled start": str,
+ "Date sampled stop": str,
+ "Fixation": str,
+ "Gear configuration": str,
+ "Gear": str,
+ "Hol": int,
+ "Latitude start": float,
+ "Latitude stop": float,
+ "Longitude start": float,
+ "Longitude stop": float,
+ "Main User": str,
+ "Nagoya case number": str,
+ "PI": str,
+ "Parent LinkAhead ID": str,
+ "Platform": str,
+ "Sample Context": str,
+ "Sample container": str,
+ "SampleType": str,
+ "SampleTypeSpecific": str,
+ "Sampling Person": str,
+ "Sampling depth start": float,
+ "Sampling depth stop": float,
+ "Sampling method": str,
+ "Station ID": str,
+ "Station number": str,
+ "Storage Container Label": str,
+ "Storage ID": str,
+ "StorageTemperature": str,
+ "Subevent": str,
+ "Time collected start": str,
+ "Time collected stop": str,
+ "Time sampled start": str,
+ "Time sampled stop": str,
+ "Timezone": str,
+ "Water depth start": float,
+ "Water depth stop": float,
+})
+
+# Obligatory columns: Must exist and must not be empty
+# Must exist
+OBLIGATORY_COLUMNS = _use_custom_names([
+ "entity_id",
+ "Date collected start",
+ "Device",
+ "Latitude start",
+ "Longitude start",
+ "Main User",
+ "PI",
+ "Sample container",
+ "SampleType",
+ "Sphere",
+ "Storage ID",
+ "StorageTemperature",
+])
+
+OBLIGATORY_COLUMNS_CHILD = _use_custom_names([
+ "entity_id",
+ "Date sampled start",
+ "Main User",
+ "Parent LinkAhead ID",
+ "Sample container",
+ "SampleType",
+ "SampleTypeSpecific",
+ "Sphere",
+ "Storage ID",
+ "StorageTemperature",
+])
+
+COLUMN_CONVERTER = _use_custom_names({
+ "Collection": semicolon_separated_list,
+ "Ecotaxa URL": semicolon_separated_list,
+ "NCBI Accession": semicolon_separated_list,
+ "NCBI BioProject": semicolon_separated_list,
+ "NCBI BioSample": semicolon_separated_list,
+ "OSIS URL": semicolon_separated_list,
+ "Embargo": _embargo_converter,
+ "Publications": semicolon_separated_list,
+ "Sphere": semicolon_separated_list,
+})
+
+SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
+ "entity_id",
+ "Collection",
+ "Date collected start",
+ "Date collected stop",
+ "Date sampled start",
+ "Date sampled stop",
+ "Gear configuration",
+ "Gear",
+ "Hol",
+ "Latitude start",
+ "Latitude stop",
+ "Longitude start",
+ "Longitude stop",
+ "Main User",
+ "Nagoya case number",
+ "PDFReport",
+ "PI",
+ "Parent Linkahead ID",
+ "Person",
+ "Sampling Person",
+ "Sampling depth start",
+ "Sampling depth stop",
+ "Sphere",
+ "Station ID",
+ "Station number",
+ "Storage Container Label",
+ "Storage ID",
+ "Subevent",
+ "Time collected start",
+ "Time collected stop",
+ "Time sampled start",
+ "Time sampled stop",
+ "Timezone",
+ "Water depth start",
+ "Water depth stop",
+])
+
+IGNORED_COLUMN_NAMES_SAMPLE = _use_custom_names([
+ "LinkAhead URL",
+ "Date",
+ "IGSN URL",
+ "IGSN", # TODO This will be relevant for external IGSNs in the future.
+ "Parent Sample",
+ "Sampling depth",
+ "Storage chain",
+ "Water depth",
+])
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
new file mode 100644
index 0000000..54a0347
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
@@ -0,0 +1,23 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+import pandas as pd
+
+def post_process_samples(samples: db.Container, data: pd.DataFrame) -> db.Container:
+
+ return samples
--
GitLab
From fe4d2ca453d659841940054f721bf6f4e0a43322 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 29 Jan 2025 18:20:16 +0100
Subject: [PATCH 32/63] DOC: Add a brief description of customizations to the
README
---
README.md | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/README.md b/README.md
index a91b7e5..ff11a58 100644
--- a/README.md
+++ b/README.md
@@ -29,6 +29,31 @@ instance's data model (e.g., by [synchronizing with the LinkAhead
advanced user
tools](https://docs.indiscale.com//caosdb-advanced-user-tools/yaml_interface.html)).
+## Customization
+
+The sample management module can be customized by overwriting
+indivdual code and config files by using files of the same name and
+with the same relative path in your LinkAhead profile's custom
+directory. E.g., if you want to overwrite how sample entities are post-processed in the sample upload, you overwrite
+
+```
+sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
+```
+
+from this repository by a
+
+```
+profile/custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
+```
+
+in your server profile. When doing so, it is important that in your
+custom file, you use the exact same function names, signatures, and
+return types as in the original file. In our example, the custom
+`sample_upload_post_processing.py` needs to contain a
+`post_process_samples` that takes the samples and the csv data as
+arguments and returns the list of post processed samples.
+
+
## Testing
There is a pre-configured `test-profile` that you can use for testing
--
GitLab
From 9f0ecc0e440d0f18b02d027aab590ff1f75ae641 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 30 Jan 2025 16:30:24 +0100
Subject: [PATCH 33/63] MAINT: Remove geomar specific time properties
---
models_and_helper_scripts/sample-management-datamodel.yml | 8 ++------
.../scripting/bin/crawl_sample_data_async.py | 6 ------
.../scripting/bin/sample_helpers/default_constants.yml | 2 ++
3 files changed, 4 insertions(+), 12 deletions(-)
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index 8067eac..d769e01 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -97,10 +97,6 @@ Sample:
datatype: TEXT
Notes:
datatype: TEXT
- Time sampled start:
- datatype: DATETIME
- Time sampled stop:
- datatype: DATETIME
AphiaID:
description: An ID for this taxon that allows to uniquely identify it on http://www.marinespecies.org.
datatype: INTEGER
@@ -171,11 +167,11 @@ Event:
obligatory_properties:
Gear:
recommended_properties:
- Time start:
+ start_date:
description: The date and time the event started.
datatype: DATETIME
suggested_properties:
- Time stop:
+ end_date:
description: The date and time the event ended.
datatype: DATETIME
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index 1e17a33..7d99c3a 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -557,15 +557,9 @@ def update_sample_records(data, htmluserlog_public):
.add_parent(name="Sphere")
for el in row["Sphere"]])
- if "Date collected start" in row and return_value_if_not_none(row["Date collected start"]) is not None:
- sample = _update_property(entity=sample, property_id=event_property_id, property_name='SourceEvent', value=get_event(
- row, get_gear(row)))
if "PDFReport" in data.columns:
sample = _update_property(
entity=sample, property_id=pdfreport_property_id, property_name="PDFReport", value=row["PDFReport"])
- if "Date sampled start" in data.columns:
- sample = _append_times_to_entity(ent=sample, data=row, propname_prefix="Time sampled",
- colname_time_prefix="Time sampled", colname_date_prefix="Date sampled")
# Add additional properties
for property_name in additional_property_ids.keys():
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 687b32c..de676e0 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -58,6 +58,8 @@ entity_names:
responsible_rt: Responsible
first_name_prop: first_name
last_name_prop: last_name
+ start_date_prop: start_date
+ end_date_prop: end_date
error_prefix: "Something went wrong:"
error_suffix: "Please contact your administrator(s)."
--
GitLab
From 6615797ac35de3feac9419fa3872ca4f8c63fb56 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 31 Jan 2025 12:00:34 +0100
Subject: [PATCH 34/63] ENH: Make get_person customizable in sample upload
---
.../scripting/bin/crawl_sample_data_async.py | 45 +-----------
.../sample_upload_get_person.py | 70 +++++++++++++++++++
2 files changed, 72 insertions(+), 43 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index 7d99c3a..3c3c093 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -47,8 +47,9 @@ from bis_utils import (get_do_not_insert_type_names,
return_value_if_not_none,
send_mail_with_defaults,
SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.sample_upload_get_person import get_person
from sample_helpers.sample_upload_post_processing import post_process_samples
-from sample_helpers.utils import get_column_header_name
+from sample_helpers.utils import get_column_header_name, get_entity_name
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -396,48 +397,6 @@ def get_nagoya_case(data):
return nagoya_case
-def get_person(text) -> db.Record:
- """
- Return the BIS ID of the person that is specifed as 'Main User' or 'Sampling Person' in data.
-
- If the Person is not present in the database, an Exception is raised. Creating new Person Reconrds can only be done by a priviledged user.
- """
- # Check in which format the person is identified:
- person_identifier = text.split(", ")
- if len(person_identifier) == 1:
- person = _get_person_by_abbreviation(person_identifier[0])
- else:
- person = _get_person_by_fullname(person_identifier[1], person_identifier[0])
-
- return person
-
-
-def _get_person_by_fullname(first_name, last_name):
- # seach for person in db
- res = db.execute_query(
- "FIND RECORD Person WITH 'First name' = '{}' AND 'Last name' = '{}'".format(first_name, last_name))
- # if person doesn't exist in database...
- if len(res) == 0:
- # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
- error_msg = "There is no person Record with 'First name' = '{}' AND 'Last name' = '{}' in the database. ".format(
- first_name, last_name)
- raise DataInconsistencyError(error_msg)
- else:
- return res[0]
-
-
-def _get_person_by_abbreviation(abbreviation):
- # seach for person in db
- res = db.execute_query("FIND RECORD Person WITH 'Abbreviation' = '{}'".format(abbreviation))
- # if person doesn't exist in database...
- if len(res) == 0:
- # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
- error_msg = "There is no Person Record with Abbreviation = '{}'".format(abbreviation)
- raise DataInconsistencyError(error_msg)
- else:
- return res[0]
-
-
def synchroize(records, additional_property_ents, htmluserlog_public):
crawler = Crawler(securityMode=SecurityMode.UPDATE)
identifiables_definition_file = os.path.expanduser("~/identifiables.yml")
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
new file mode 100644
index 0000000..49c34f6
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
@@ -0,0 +1,70 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_entity_name
+
+
+def get_person(text: str) -> db.Record:
+ """Return the Person Record that is specifed as 'Main User' or
+ 'Sampling Person' in data.
+
+ If the Person is not present in the database, an Exception is
+ raised. Creating new Person Reconrds can only be done by a
+ priviledged user.
+
+ """
+ # Check in which format the person is identified:
+ person_identifier = text.split(", ")
+ if len(person_identifier) == 1:
+ person = _get_person_by_id(person_identifier[0])
+ else:
+ person = _get_person_by_fullname(person_identifier[1], person_identifier[0])
+
+ return person
+
+
+def _get_person_by_fullname(first_name: str, last_name: str) -> db.Record:
+ # seach for person in db
+ res = db.execute_query(
+ f"FIND '{get_entity_name('Person')}' WITH '{
+ get_entity_name('first_name_prop')}'='{first_name}' "
+ f"AND '{get_entity_name('last_name_prop')}'='{last_name}'"
+ )
+ # if person doesn't exist in database...
+ if len(res) == 0:
+ # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
+ error_msg = (
+ f"There is no person Record with '{get_entity_name('first_name_prop')}' = '{
+ first_name}' "
+ f"AND '{get_entity_name('last_name_prop')}' = '{last_name}' in the database. ")
+ raise DataInconsistencyError(error_msg)
+ else:
+ return res[0]
+
+
+def _get_person_by_id(eid: str) -> db.Record:
+
+ try:
+ return db.get_entity_by_id(eid, role=get_entity_name("Person"))
+ except db.EmptyUniqueQueryError:
+ raise DataInconsistencyError(
+ f"Could not find a {get_entity_name('Person')} with ID {eid}."
+ )
--
GitLab
From 0cadc8dfa4f34bb016ea8a9f05781a7c56de0cee Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 4 Feb 2025 16:02:19 +0100
Subject: [PATCH 35/63] ENH: Remove GEOMAR-specific date treatment
---
.../scripting/bin/crawl_sample_data_async.py | 108 ------------------
.../sample_upload_column_definitions.py | 11 --
2 files changed, 119 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index 3c3c093..e538e64 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -105,114 +105,6 @@ def _update_property(entity: db.Record, property_id: int, value, property_name="
return entity
-def _treat_date(date_val: str):
-
- date_pattern = r"^[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2}$"
- # Check general pattern since dateutil.parse is unreliable with incomplete
- # dates (e.g., 2024-01) or wrong formats (e.g., 01.12.2024 is parsed as
- # 2024-01-12).
- if re.match(date_pattern, date_val) is None:
- # ParserError for simplified error handling down the line.
- raise dateparser.ParserError(f"{date_val} is not of the format YYYY-MM-DD.")
- # Use dateutils.parser despite having checked the pattern to exclude
- # nonsense dates like 2024-13-54.
- return str(dateparser.parse(date_val).date())
-
-
-def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_prefix="Time collected", colname_date_prefix="Date collected"):
- propname_start = f"{propname_prefix} start"
- propname_stop = f"{propname_prefix} stop"
- prop_start = cached_get_entity_by(name=propname_start)
- prop_stop = cached_get_entity_by(name=propname_stop)
- colname_time_start = f"{colname_time_prefix} start"
- colname_time_stop = f"{colname_time_prefix} stop"
- colname_date_start = f"{colname_date_prefix} start"
- colname_date_stop = f"{colname_date_prefix} stop"
-
- date_start = None
- date_stop = None
- time_start = None
- time_stop = None
- timezone = None
- # Time start
- if colname_date_start in data and return_value_if_not_none(data[colname_date_start]) is not None:
- date_start = return_value_if_not_none(data[colname_date_start])
- try:
- date_start = _treat_date(date_start)
- except dateparser.ParserError as perr:
- logger.error(
- f"There is a problem in '{colname_date_start}': {date_start}"
- f" of sample {data[get_column_header_name('entity_id')]}: {perr}"
- )
- raise DataInconsistencyError
- if colname_time_start in data and return_value_if_not_none(data[colname_time_start]) is not None:
- if not get_column_header_name("Timezone") in data or return_value_if_not_none(data[get_column_header_name("Timezone")]) is None:
- logger.error(f"{colname_time_start} but no timezone given for sample "
- f"{data[get_column_header_name('entity_id')]}.")
- raise DataInconsistencyError
- time_start = return_value_if_not_none(data[colname_time_start])
- timezone = return_value_if_not_none(data[get_column_header_name("Timezone")])
- if date_start is None:
- logger.error(
- f"{colname_time_start} is given but {colname_date_start} is missing for "
- f"sample {data[get_column_header_name('entity_id')]}.")
- raise DataInconsistencyError
- try:
- _val = str(dateparser.parse(f"{date_start}T{time_start}{timezone}"))
- ent = _update_property(ent, prop_start.id, property_name=prop_start.name, value=_val)
- except dateparser.ParserError as perr:
- logger.error(
- f"Couldn't parse {colname_time_start}: {time_start} with timezone {timezone} "
- f"of sample {data[get_column_header_name('entity_id')]}: {perr}"
- )
- raise DataInconsistencyError
- elif date_start is not None:
- ent = _update_property(ent, prop_start.id, value=date_start, property_name=prop_start.name)
-
- # Time stop; raise error in case of stop without start
- if colname_date_stop in data and return_value_if_not_none(data[colname_date_stop]) is not None:
- date_stop = return_value_if_not_none(data[colname_date_stop])
- if date_stop is not None and date_start is None:
- logger.error(
- f"{colname_date_stop} is given but {colname_date_start} is missing for "
- f"sample {data[get_column_header_name('entity_id')]}.")
- raise DataInconsistencyError
- if date_stop is None:
- _date_stop = date_start
- else:
- try:
- _date_stop = _treat_date(date_stop)
- except dateparser.ParserError as perr:
- logger.error(
- f"There is a problem in '{colname_date_stop}': {date_stop}"
- f" of sample {data[get_column_header_name('entity_id')]}: {perr}"
- )
- raise DataInconsistencyError
-
- if colname_time_stop in data and return_value_if_not_none(data[colname_time_stop]) is not None:
- time_stop = return_value_if_not_none(data[colname_time_stop])
- if time_start is None:
- logger.error(
- f"{colname_time_stop} is given but {colname_time_start} is missing for "
- f"sample {data[get_column_header_name('entity_id')]}.")
- raise DataInconsistencyError
- # timezone is set by time start; if it hadn't been there, we would already have an error.
- try:
- _val = str(dateparser.parse(f"{_date_stop}T{time_stop}{timezone}"))
- except dateparser.ParserError as perr:
- logger.error(
- f"Couldn't parse {colname_time_stop}: {time_stop} with timezone {timezone} "
- f"of sample {data[get_column_header_name('entity_id')]}: {perr}"
- )
- raise DataInconsistencyError
- ent = _update_property(ent, prop_stop.id, property_name=prop_stop.name, value=_val)
- elif date_stop is not None:
- # We check date_stop but we used the cleaned-up _date_stop as value
- ent = _update_property(ent, prop_stop.id, property_name=prop_stop.name, value=_date_stop)
-
- return ent
-
-
def get_container(data):
"""
Retrun the BIS ID of the Container Record that is identified by 'Storage contianer' in data.
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index c1155d7..2f74f2e 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -60,10 +60,6 @@ DATATYPE_DEFINITIONS = _use_custom_names({
"AphiaID": int,
"entity_id": str,
"Campaign": str,
- "Date collected start": str,
- "Date collected stop": str,
- "Date sampled start": str,
- "Date sampled stop": str,
"Fixation": str,
"Gear configuration": str,
"Gear": str,
@@ -104,7 +100,6 @@ DATATYPE_DEFINITIONS = _use_custom_names({
# Must exist
OBLIGATORY_COLUMNS = _use_custom_names([
"entity_id",
- "Date collected start",
"Device",
"Latitude start",
"Longitude start",
@@ -119,7 +114,6 @@ OBLIGATORY_COLUMNS = _use_custom_names([
OBLIGATORY_COLUMNS_CHILD = _use_custom_names([
"entity_id",
- "Date sampled start",
"Main User",
"Parent LinkAhead ID",
"Sample container",
@@ -145,10 +139,6 @@ COLUMN_CONVERTER = _use_custom_names({
SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"entity_id",
"Collection",
- "Date collected start",
- "Date collected stop",
- "Date sampled start",
- "Date sampled stop",
"Gear configuration",
"Gear",
"Hol",
@@ -182,7 +172,6 @@ SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
IGNORED_COLUMN_NAMES_SAMPLE = _use_custom_names([
"LinkAhead URL",
- "Date",
"IGSN URL",
"IGSN", # TODO This will be relevant for external IGSNs in the future.
"Parent Sample",
--
GitLab
From 57ef07b19879499342f97d8ca4e68c29fc680656 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 4 Feb 2025 16:08:31 +0100
Subject: [PATCH 36/63] MAINT: Also remove timezones from special treatment
---
.../sample_upload_column_definitions.py | 12 +-----------
1 file changed, 1 insertion(+), 11 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 2f74f2e..10557cb 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -17,7 +17,7 @@
#
import re
-from datetime import date, datetime
+from datetime import date
from dateutil.relativedelta import relativedelta
from typing import Union
@@ -87,11 +87,6 @@ DATATYPE_DEFINITIONS = _use_custom_names({
"Storage ID": str,
"StorageTemperature": str,
"Subevent": str,
- "Time collected start": str,
- "Time collected stop": str,
- "Time sampled start": str,
- "Time sampled stop": str,
- "Timezone": str,
"Water depth start": float,
"Water depth stop": float,
})
@@ -161,11 +156,6 @@ SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"Storage Container Label",
"Storage ID",
"Subevent",
- "Time collected start",
- "Time collected stop",
- "Time sampled start",
- "Time sampled stop",
- "Timezone",
"Water depth start",
"Water depth stop",
])
--
GitLab
From 421f0ee2c4e2c3efca1a71a7e2f628de0ab64fa0 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 4 Feb 2025 18:09:26 +0100
Subject: [PATCH 37/63] WIP: Add treatment for events
---
.../src/ext/js/ext_samplemanagement.js | 3 -
.../sample_helpers/sample_upload_get_event.py | 94 +++++++++++++++++++
2 files changed, 94 insertions(+), 3 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index afa88df..a0fc26c 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -38,10 +38,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
];
const required_column_names = [
"LinkAhead ID",
- "Date collected start",
"Main User",
- "Gear",
- "Gear configuration",
"Latitude start",
"Longitude start",
"Collection",
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
new file mode 100644
index 0000000..a149876
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -0,0 +1,94 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+import pandas as pd
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_column_header_name, get_entity_name
+from ..bis_utils import return_value_if_not_none
+
+
+def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
+ """Take a given sample and attach an event Record from the
+ data. Then, return the sample.
+
+ """
+
+ _perform_sanity_checks(sample, data)
+
+
+ return sample
+
+
+def _create_position(mode: str, lat: float, lng: float, ele: float):
+ pos = db.Record()
+ if mode.lower() == "start":
+ pos.add_parent(get_entity_name("StartPosition"))
+ elif mode.lower() == "stop":
+ pos.add_parent(get_entity_name("StopPosition"))
+ else:
+ pos.add_parent(get_entity_name("Position"))
+
+ pos.add_property(name=get_entity_name("latitude"), value=lat)
+ pos.add_property(name=get_entity_name("longitude"), value=lng)
+ pos.add_property(name=get_entity_name("elevation"), value=ele)
+
+ return pos
+
+
+def _perform_sanity_checks(sample, data):
+
+ if (get_column_header_name("end_date") in data and
+ return_value_if_not_none(data[get_column_header_name("end_date")]) is not None):
+ if (get_column_header_name("start_date") not in data or
+ return_value_if_not_none(data[get_column_header_name("start_date")]) is None):
+ raise DataInconsistencyError(
+ f"Sample with {get_entity_name('entity_id')} {sample.id} has a "
+ f"{get_column_header_name('end_date')} but no valid "
+ f"{get_column_header_name('start_date')}."
+ )
+
+ for name in ["start", "stop"]:
+ bool_list = [get_column_header_name(f"{val}_{name}") in data for val in [
+ "latitude", "longitude", "elevation"]]
+ raise_error = False
+ if bool_list.any():
+ if not bool_list.all():
+ raise_error = True
+ elif [return_value_if_not_none(data[get_column_header_name(f"{val}_{name}")]) is None for val in ["latitude", "longitude", "elevation"]].any():
+ raise_error = True
+
+ if raise_error:
+ raise DataInconsistencyError(
+ f"Sample with {get_entity_name('entity_id')} {sample.id} has an "
+ f"invalid {name} position. Please make sure that latitude, longitude, "
+ "and elevation are provided."
+ )
+
+ # only need to check lat since we already checked that if lat is
+ # present, lng and ele are present, too
+ if (get_column_header_name("latitude_stop") in data and
+ return_value_if_not_none(data[get_column_header_name("latitude_stop")]) is not None):
+ if (get_column_header_name("latitude_start") not in data or
+ return_value_if_not_none(data[get_column_header_name("latitude_start")]) is not None):
+ raise DataInconsistencyError(
+ f"Sample with {get_entity_name('entity_id')} {sample.id} has a "
+ f"{get_entity_name('StopPosition')} but no valid "
+ f"{get_entity_name('StartPosition')}."
+ )
--
GitLab
From 7e29c2d62e123517aa49b95410fa60c28f0d2435 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 5 Feb 2025 16:40:34 +0100
Subject: [PATCH 38/63] WIP: Remove unused properties and recordtypes
---
.../sample-management-datamodel.yml | 12 +++++++++++-
.../caosdb-webui/src/ext/js/ext_samplemanagement.js | 13 ++-----------
2 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index d769e01..cc55407 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -47,6 +47,15 @@ ContainerType:
obligatory_properties:
Abbreviation:
+ConditionType:
+ inherit_from_recommended:
+ - ControlledRecordtype
+StorageCondition:
+ recommended_properties:
+ ConditionType:
+ condition_value:
+ datatype: TEXT
+
Container:
obligatory_properties:
Responsible:
@@ -60,13 +69,14 @@ Container:
Container size:
description: The size of the container, e.g. number of spaces or dimension
datatype: TEXT
- Custom label:
+ custom_label:
description: A custom label for a container that doesn't have to follow the automatic labeling guidelines.
datatype: TEXT
Container Contents:
datatype: TEXT
PI:
datatype: Person
+ StorageCondition:
Sample:
recommended_properties:
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index a0fc26c..e55c823 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -41,6 +41,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"Main User",
"Latitude start",
"Longitude start",
+ "Elevation start",
"Collection",
"PI",
"Storage ID",
@@ -73,10 +74,6 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"Station ID",
"Station number",
"Subevent",
- "Time collected start",
- "Date collected stop",
- "Time collected stop",
- "Timezone",
"Hol",
"Sampling depth start",
"Sampling depth stop",
@@ -84,6 +81,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"Water depth stop",
"Latitude stop",
"Longitude stop",
+ "Elevation stop",
"Taxonomic group/Species",
"AphiaID",
"On-board sampleID",
@@ -95,10 +93,6 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"OSIS URL",
"Ecotaxa URL",
"PDFReport",
- "Date sampled start",
- "Date sampled stop",
- "Time sampled start",
- "Time sampled stop",
"Parent LinkAhead ID"
]
const allColumnNames = non_sample_rt_column_names.concat(requiredColumnNamesChildren).concat(required_column_names);
@@ -110,9 +104,6 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
'NagoyaCase',
"Parent Sample",
"Person",
- "SampleType",
- "Time start",
- "Time stop"
]
const upload_sample_template_form_config = {
--
GitLab
From c20672a61a809331f69e1803132fc7ef8f4b1973 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 5 Feb 2025 16:40:51 +0100
Subject: [PATCH 39/63] FIX: Use correct label names
---
.../scripting/bin/sample_helpers/default_constants.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index de676e0..27fa797 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -47,12 +47,12 @@ csv_column_descriptions:
entity_names:
abbreviation_prop: abbreviation
- child_container_prop: "Child container"
+ child_container_prop: "Child_Container"
container_label_prop: container_label
container_rt: Container
container_size_prop: "Container size"
containertype_rt: ContainerType
- custom_label_prop: "Custom label"
+ custom_label_prop: custom_label
labelcounter_prop: counter
labelcounter_rt: LabelCounter
responsible_rt: Responsible
--
GitLab
From 9e577d312462b83c2ea1beb034be4285d96dd68c Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 5 Feb 2025 16:42:09 +0100
Subject: [PATCH 40/63] FIX: Add missing custom label header name
---
.../scripting/bin/sample_helpers/default_constants.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 27fa797..303c414 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -17,6 +17,7 @@
#
csv_column_names:
entity_id: "LinkAhead ID"
+ custom_label_prop: "Custom Label"
csv_column_descriptions:
LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
--
GitLab
From 6cde3c3117108be3af05b6c289479610f847bfbe Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 6 Feb 2025 18:09:04 +0100
Subject: [PATCH 41/63] ENH: Use separate event-adding module
---
.../scripting/bin/crawl_sample_data_async.py | 22 ++-----------------
.../sample_helpers/sample_upload_get_event.py | 2 +-
2 files changed, 3 insertions(+), 21 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index e538e64..063b153 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -47,6 +47,7 @@ from bis_utils import (get_do_not_insert_type_names,
return_value_if_not_none,
send_mail_with_defaults,
SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.sample_upload_get_event import add_event_to_sample
from sample_helpers.sample_upload_get_person import get_person
from sample_helpers.sample_upload_post_processing import post_process_samples
from sample_helpers.utils import get_column_header_name, get_entity_name
@@ -383,30 +384,10 @@ def update_sample_records(data, htmluserlog_public):
sample = _update_property(entity=sample, property_id=db.get_entity_by_name("PI").id,
property_name="PI",
value=get_person(row["PI"]))
- if "Nagoya case number" in row and return_value_if_not_none(row["Nagoya case number"]) is not None:
- sample = _update_property(entity=sample, property_id=nagoya_case_property_id,
- property_name="NagoyaCase",
- value=get_nagoya_case(row))
if "Storage ID" in row and return_value_if_not_none(row["Storage ID"]) is not None:
sample = _update_property(entity=sample, property_id=container_property_id,
property_name="Container",
value=get_container(row))
- if "Collection" in row and return_value_if_not_none(row["Collection"]) is not None:
- sample = _update_property(entity=sample,
- property_id=db.get_entity_by_name("Collection").id,
- property_name="Collection",
- datatype=db.LIST("Collection"),
- value=[db.Record(name=el)
- .add_parent(name="Collection")
- for el in row["Collection"]])
- if "Sphere" in row and return_value_if_not_none(row["Sphere"]) is not None:
- sample = _update_property(entity=sample,
- property_id=db.get_entity_by_name("Sphere").id,
- property_name="Sphere",
- datatype=db.LIST("Sphere"),
- value=[db.Record(name=el)
- .add_parent(name="Sphere")
- for el in row["Sphere"]])
if "PDFReport" in data.columns:
sample = _update_property(
@@ -435,6 +416,7 @@ def update_sample_records(data, htmluserlog_public):
entity=sample, property_id=additional_property_ids[property_name],
value=value, property_name=property_name)
+ sample = add_event_to_sample(sample, row)
samples.append(sample)
samples = post_process_samples(samples, data)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index a149876..aa62498 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -31,7 +31,7 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
"""
_perform_sanity_checks(sample, data)
-
+ # TODO Add event-specific columns
return sample
--
GitLab
From c1a64649362eaf1184250ca0b899246a2360ab8d Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 11:19:39 +0100
Subject: [PATCH 42/63] ENH: Use correct datamodel in sample registration
---
.../src/ext/js/ext_samplemanagement.js | 59 +++++--------------
.../bin/sample_helpers/default_constants.yml | 8 ++-
2 files changed, 21 insertions(+), 46 deletions(-)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index e55c823..92a854e 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -41,69 +41,40 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"Main User",
"Latitude start",
"Longitude start",
- "Elevation start",
- "Collection",
- "PI",
+ "Elevation start",
"Storage ID",
- "Nagoya case number",
- "Sample container",
- "Fixation",
- "StorageTemperature",
- "SampleType",
- "SampleTypeSpecific",
- "Sphere",
- "Sample Context",
+ "Device"
];
const requiredColumnNamesChildren = [
"LinkAhead ID",
- "Date sampled start",
- "Fixation",
"Main User",
"Parent LinkAhead ID",
- "Sample Context",
- "Sample container",
"SampleType",
- "SampleTypeSpecific",
- "Sphere",
"Storage ID",
- "StorageTemperature",
];
const non_sample_rt_column_names = [
- "Platform",
+ "Biome",
"Campaign",
- "Station ID",
- "Station number",
- "Subevent",
- "Hol",
- "Sampling depth start",
- "Sampling depth stop",
- "Water depth start",
- "Water depth stop",
+ "Start date",
+ "End date",
+ "IGSN DOI",
+ "Level",
+ "Locality description",
+ "Locality name",
+ "Sphere",
+ "Event responsible",
"Latitude stop",
"Longitude stop",
- "Elevation stop",
- "Taxonomic group/Species",
- "AphiaID",
- "On-board sampleID",
- "Extraction ID",
- "Duplicate number",
- "Other fixations",
- "Notes / remarks",
- "Forlmaldehyde_box",
- "OSIS URL",
- "Ecotaxa URL",
+ "Elevation stop",
"PDFReport",
- "Parent LinkAhead ID"
- ]
+ "Parent LinkAhead ID",
+ ];
const allColumnNames = non_sample_rt_column_names.concat(requiredColumnNamesChildren).concat(required_column_names);
const unused_property_names = [
- 'Container',
- 'Event',
"Main User",
'NagoyaCase',
- "Parent Sample",
- "Person",
+ "Parent_Sample",
]
const upload_sample_template_form_config = {
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 303c414..033a05e 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -18,6 +18,9 @@
csv_column_names:
entity_id: "LinkAhead ID"
custom_label_prop: "Custom Label"
+ start_date_prop: "Date start"
+ end_date_prop: "Date stop"
+ igsn_doi_prop: "IGSN DOI"
csv_column_descriptions:
LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
@@ -27,8 +30,8 @@ csv_column_descriptions:
Container size: "The size of the container (e.g 81 spaces)"
Container type: "The type of container. Do not change this column."
Custom label: "Any additional custom label you put on the container"
- Date collected start: "The start date in format YYYY-MM-DD"
- Date collected stop: "The end date in format YYYY-MM-DD"
+ Date start: "The start date or datetime in ISO format"
+ Date stop: "The end date or datetime in ISO format"
Gear configuration: "How gear is configured, meshsize of the net, filter pore size, what kind of trawl"
Latitude start: "Latitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for S"
Latitude stop: "Latitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for S"
@@ -61,6 +64,7 @@ entity_names:
last_name_prop: last_name
start_date_prop: start_date
end_date_prop: end_date
+ igsn_doi_prop: igsn_doi
error_prefix: "Something went wrong:"
error_suffix: "Please contact your administrator(s)."
--
GitLab
From 16ab9c3d65a3e4339cb877e6337d08d4311167fd Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 11:31:21 +0100
Subject: [PATCH 43/63] MAINT: Remove more unused GEOMAR entities from
datamodel
---
.../sample-management-datamodel.yml | 148 ++++++------------
1 file changed, 44 insertions(+), 104 deletions(-)
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index cc55407..04b74cc 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -54,8 +54,8 @@ StorageCondition:
recommended_properties:
ConditionType:
condition_value:
- datatype: TEXT
-
+ datatype: TEXT
+
Container:
obligatory_properties:
Responsible:
@@ -80,36 +80,25 @@ Container:
Sample:
recommended_properties:
- NagoyaCase:
Container:
- FunctionalGroup:
SampleType:
Parent sample:
datatype: Sample
- Sampling Person:
- datatype: Person
Main User:
datatype: Person
- suggested_properties:
- Custom ID:
- datatype: LIST<TEXT>
- Publications:
- description: DOIs of publications related to this sample.
- datatype: LIST<TEXT>
- NCBI BioProject:
- datatype: LIST<TEXT>
- NCBI BioSample:
- datatype: LIST<TEXT>
- NCBI Accession:
- datatype: LIST<TEXT>
- Sampling method:
- description: A short description of the sampling methodology used for this sample.
- datatype: TEXT
- Notes:
+ Collector:
+ datatype: LIST(Person)
+ Curator:
+ datatype: LIST(Person)
+ Device:
+ material_left:
+ datatype: BOOLEAN
+ Event:
+ SampleMethod:
+ nagoya_link:
datatype: TEXT
- AphiaID:
- description: An ID for this taxon that allows to uniquely identify it on http://www.marinespecies.org.
- datatype: INTEGER
+ nagoya_relevance:
+ datatype: BOOLEAN
Collection:
@@ -146,65 +135,54 @@ NagoyaCase:
Position:
obligatory_properties:
- Latitude:
+ latitude:
datatype: DOUBLE
unit: °
- Longitude:
+ longitude:
datatype: DOUBLE
unit: °
- recommended_properties:
- Water depth:
- description: The depth of the water in meters as a positive value
+ elevation:
datatype: DOUBLE
- unit: m
- Sampling depth:
- description: The depth in meters where the sampling took place as a positive value
- datatype: DOUBLE
- unit: m
-FunctionalGroup:
+EventType:
inherit_from_obligatory:
- ControlledRecordType
-Gear:
- inherit_from_obligatory:
- - ControlledRecordType
- recommended_properties:
- Configuration:
- datatype: TEXT
+Biome:
+ inherit_from_recommended:
+ - ControlledRecordtype
+
+Device:
+ inherit_from_recommended:
+ - ControlledRecordtype
Event:
- obligatory_properties:
- Gear:
recommended_properties:
+ Parent_Event:
+ datatype: Event
+ Biome:
+ Campaign:
+ Device:
+ Position:
+ datatype: LIST(Position)
start_date:
description: The date and time the event started.
datatype: DATETIME
- suggested_properties:
end_date:
description: The date and time the event ended.
datatype: DATETIME
-
-SourceEvent:
- inherit_from_suggested:
- - Event
- obligatory_properties:
- Position:
- datatype: LIST<Position>
- Gear:
- recommended_properties:
- Hol:
+ EventType:
+ igsn_doi:
datatype: TEXT
- Station Number:
+ level:
datatype: TEXT
- IGSN:
+ locality_description:
datatype: TEXT
- DOI:
- datatype: TEXT
- suggested_properties:
- Station ID:
- description: The name/identifier of a station where regular sampling activity takes place.
+ locality_name:
datatype: TEXT
+ Sphere:
+ Responsible_Person:
+ datatype: LIST(Person)
Platform:
inherit_from_obligatory:
@@ -214,9 +192,10 @@ SampleType:
inherit_from_obligatory:
- ControlledRecordType
-SampleTypeSpecific:
- inherit_from_obligatory:
- - ControlledRecordType
+SampleMethod:
+ recommended_properties:
+ Parent_SampleMethod:
+ datatype: SampleMethod
StartPosition:
inherit_from_obligatory:
@@ -231,25 +210,6 @@ RegisterSampleTemplate:
column_names:
datatype: LIST<TEXT>
-MeshPoreSize:
- inherit_from_obligatory:
- - ControlledRecordType
- recommended_properties:
- enumValue:
- datatype: TEXT
-
-Fixation:
- inherit_from_obligatory:
- - ControlledRecordType
- recommended_properties:
- enumValue:
-
-StorageTemperature:
- inherit_from_obligatory:
- - ControlledRecordType
- recommended_properties:
- enumValue:
-
Campaign:
inherit_from_obligatory:
- ControlledRecordType
@@ -259,27 +219,7 @@ Sphere:
inherit_from_obligatory:
- ControlledRecordType
-Sample context:
- inherit_from_obligatory:
- - ControlledRecordType
-
PDFReport:
inherit_from_obligatory:
- ControlledRecordType
description: PDF files which contain reports and additional information about samples, collections, or containers
-
-commonGermanName:
- inherit_from_obligatory:
- - ControlledRecordType
-
-commonEnglishName:
- inherit_from_obligatory:
- - ControlledRecordType
-
-Taxonomic group/Species:
- inherit_from_obligatory:
- - ControlledRecordType
-
-Sample container:
- inherit_from_obligatory:
- - ControlledRecordType
--
GitLab
From 206daaef2b632a5a499e65d76f02c93ff4fae13c Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 11:48:48 +0100
Subject: [PATCH 44/63] ENH: Move adding of special sample properties to
separate module
---
.../scripting/bin/crawl_sample_data_async.py | 26 ++------------
.../sample_upload_add_special_properties.py | 35 +++++++++++++++++++
2 files changed, 38 insertions(+), 23 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index 063b153..804e8e4 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -47,6 +47,7 @@ from bis_utils import (get_do_not_insert_type_names,
return_value_if_not_none,
send_mail_with_defaults,
SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.sample_upload_add_special_properties import add_special_properties
from sample_helpers.sample_upload_get_event import add_event_to_sample
from sample_helpers.sample_upload_get_person import get_person
from sample_helpers.sample_upload_post_processing import post_process_samples
@@ -369,29 +370,8 @@ def update_sample_records(data, htmluserlog_public):
msg = "There is no Sample with ID = {} in the system.".format(row["BIS ID"])
raise DataInconsistencyError(msg)
- sample = _update_property(entity=sample, property_id=person_property_id,
- property_name="Main User",
- value=get_person(row["Main User"]))
- if "Parent BIS ID" in row and return_value_if_not_none(row["Parent BIS ID"]) is not None:
- sample = _update_property(entity=sample, property_id=parent_sample_property_id,
- value=row["Parent BIS ID"])
- if ("Sampling Person" in row
- and return_value_if_not_none(row["Sampling Person"]) is not None):
- sample = _update_property(entity=sample, property_id=sampling_person_property_id,
- property_name="Sampling Person",
- value=get_person(row["Sampling Person"]))
- if "PI" in row and return_value_if_not_none(row["PI"]) is not None:
- sample = _update_property(entity=sample, property_id=db.get_entity_by_name("PI").id,
- property_name="PI",
- value=get_person(row["PI"]))
- if "Storage ID" in row and return_value_if_not_none(row["Storage ID"]) is not None:
- sample = _update_property(entity=sample, property_id=container_property_id,
- property_name="Container",
- value=get_container(row))
-
- if "PDFReport" in data.columns:
- sample = _update_property(
- entity=sample, property_id=pdfreport_property_id, property_name="PDFReport", value=row["PDFReport"])
+ # All special properties are added here
+ sample = add_special_properties(sample, row)
# Add additional properties
for property_name in additional_property_ids.keys():
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
new file mode 100644
index 0000000..edda834
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -0,0 +1,35 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+import pandas as pd
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_column_header_name, get_entity_name
+from ..bis_utils import return_value_if_not_none
+
+
+def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
+ """This function adds all the properties that can not be added
+ trivially from the given data row to the sample.
+
+ """
+
+ # TODO Add special treatment properties to sample
+
+ return sample
--
GitLab
From 5fa73e89efec2cb9871a7857d3f7178f2ecc73fd Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 12:52:14 +0100
Subject: [PATCH 45/63] ENH: Use correct datamodel in special tretment lists
---
.../sample_upload_column_definitions.py | 87 +++++--------------
1 file changed, 20 insertions(+), 67 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 10557cb..c4c4c82 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -57,115 +57,68 @@ def _use_custom_names(definition: Union[list, dict]):
DATATYPE_DEFINITIONS = _use_custom_names({
- "AphiaID": int,
- "entity_id": str,
"Campaign": str,
- "Fixation": str,
- "Gear configuration": str,
- "Gear": str,
- "Hol": int,
+ "Elevation start": float,
+ "Elevation stop": float,
"Latitude start": float,
"Latitude stop": float,
"Longitude start": float,
"Longitude stop": float,
"Main User": str,
- "Nagoya case number": str,
"PI": str,
"Parent LinkAhead ID": str,
- "Platform": str,
- "Sample Context": str,
- "Sample container": str,
+ "SampleMethod": str,
"SampleType": str,
- "SampleTypeSpecific": str,
- "Sampling Person": str,
- "Sampling depth start": float,
- "Sampling depth stop": float,
- "Sampling method": str,
- "Station ID": str,
- "Station number": str,
- "Storage Container Label": str,
"Storage ID": str,
- "StorageTemperature": str,
- "Subevent": str,
- "Water depth start": float,
- "Water depth stop": float,
+ "entity_id": str,
})
# Obligatory columns: Must exist and must not be empty
# Must exist
OBLIGATORY_COLUMNS = _use_custom_names([
"entity_id",
- "Device",
- "Latitude start",
- "Longitude start",
- "Main User",
- "PI",
- "Sample container",
- "SampleType",
- "Sphere",
- "Storage ID",
- "StorageTemperature",
])
OBLIGATORY_COLUMNS_CHILD = _use_custom_names([
"entity_id",
- "Main User",
"Parent LinkAhead ID",
- "Sample container",
- "SampleType",
- "SampleTypeSpecific",
- "Sphere",
- "Storage ID",
- "StorageTemperature",
])
COLUMN_CONVERTER = _use_custom_names({
- "Collection": semicolon_separated_list,
- "Ecotaxa URL": semicolon_separated_list,
- "NCBI Accession": semicolon_separated_list,
- "NCBI BioProject": semicolon_separated_list,
- "NCBI BioSample": semicolon_separated_list,
- "OSIS URL": semicolon_separated_list,
+ "Collector": semicolon_separated_list,
+ "Curator": semicolon_separated_list,
"Embargo": _embargo_converter,
- "Publications": semicolon_separated_list,
+ "Event responsible": semicolon_separated_list,
"Sphere": semicolon_separated_list,
})
SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
- "entity_id",
- "Collection",
- "Gear configuration",
- "Gear",
- "Hol",
+ "Biome",
+ "Campaign",
+ "Elevation start",
+ "Elevation stop",
+ "End date",
+ "Event responsible",
+ "IGSN DOI",
"Latitude start",
"Latitude stop",
+ "Level",
+ "Locality description",
+ "Locality name",
"Longitude start",
"Longitude stop",
"Main User",
- "Nagoya case number",
"PDFReport",
- "PI",
"Parent Linkahead ID",
- "Person",
- "Sampling Person",
- "Sampling depth start",
- "Sampling depth stop",
"Sphere",
- "Station ID",
- "Station number",
- "Storage Container Label",
+ "Sphere",
+ "Start date",
"Storage ID",
- "Subevent",
- "Water depth start",
- "Water depth stop",
+ "entity_id",
])
IGNORED_COLUMN_NAMES_SAMPLE = _use_custom_names([
"LinkAhead URL",
- "IGSN URL",
- "IGSN", # TODO This will be relevant for external IGSNs in the future.
"Parent Sample",
- "Sampling depth",
"Storage chain",
- "Water depth",
])
--
GitLab
From 0fbb980a8aeedbdaf3f1d6dbffb8cfbd5659006c Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 13:05:15 +0100
Subject: [PATCH 46/63] MAINT: Remove unused GEOMAR specail property functions
---
.../scripting/bin/crawl_sample_data_async.py | 244 +-----------------
.../scripting/bin/sample_helpers/utils.py | 38 +++
2 files changed, 48 insertions(+), 234 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index 804e8e4..ace23ee 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -51,7 +51,7 @@ from sample_helpers.sample_upload_add_special_properties import add_special_prop
from sample_helpers.sample_upload_get_event import add_event_to_sample
from sample_helpers.sample_upload_get_person import get_person
from sample_helpers.sample_upload_post_processing import post_process_samples
-from sample_helpers.utils import get_column_header_name, get_entity_name
+from sample_helpers.utils import (get_column_header_name, get_entity_name, update_property)
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -71,226 +71,6 @@ def _is_ignored_column_name(name, parent_suffix="_parent"):
return name in IGNORED_COLUMN_NAMES_SAMPLE or name.endswith(parent_suffix)
-def _update_property(entity: db.Record, property_id: int, value, property_name="", datatype=None):
- """
- Set the property of an entity.
-
- If the entity already has the property, just the value is set.
- Else, the property is added to the entity
- """
- # TODO: Replace by assure_property_is etc.
-
- # If the value in the spreadsheet is empty (nan)
- if ((isinstance(value, list) and len(value) == 0)
- or (not isinstance(value, list) and pd.isna(value))):
- # Remove the property from te Entity if it has it
- try:
- entity.get_properties().get_by_name(property_name)
- entity.remove_property(property_name)
- except KeyError:
- pass
- return entity
- if entity.get_property(property_id) is None:
- if datatype:
- entity.add_property(id=property_id, value=value, name=property_name, datatype=datatype)
- else:
- entity.add_property(id=property_id, value=value, name=property_name)
- logger.debug("{}: Adding {} = {}".format(entity.id, property_id, value.id if
- isinstance(value, db.Entity) else value))
- else:
- if isinstance(value, list) and not entity.get_property(property_id).datatype.startswith("LIST"):
- entity.get_property(property_id).datatype = db.LIST(
- entity.get_property(property_id).datatype)
- entity.get_property(property_id).value = value
- logger.debug("{}: Setting {} = {}".format(entity.id, property_id, value.id if
- isinstance(value, db.Entity) else value))
- return entity
-
-
-def get_container(data):
- """
- Retrun the BIS ID of the Container Record that is identified by 'Storage contianer' in data.
- A Container can either be identified via a BIS ID or via a BIS Label.
-
- If no Container can be identified, an Error is raised, since creating/registering new
- Containers has to be done before registering samples.
- """
- identified_by_label = False
- container_identifier = data["Storage ID"]
- # If the ID is not spcified, try to get the label
- if "Storage Container Label" in data and pd.isnull(container_identifier):
- container_identifier = data["Storage Container Label"]
- identified_by_label = True
-
- if identified_by_label:
- container = _get_container_by_label(container_identifier)
- else:
- container = _get_container_by_id(container_identifier)
-
- if container is not None:
- return container
- else:
- msg = "Container: '{}' could not be identified.".format(container_identifier)
- raise DataInconsistencyError(msg)
-
-
-def _get_container_by_id(id):
- res = db.execute_query("FIND RECORD Container WITH id = '{}'".format(id))
- if len(res) > 0:
- return res[0]
- else:
- return None
-
-
-def _get_container_by_label(label):
- res = db.execute_query("FIND RECORD Container WITH 'BIS Label' = '{}'".format(label))
- if len(res) > 0:
- return res[0]
- else:
- return None
-
-
-def get_event(data, gear_id):
- # Events only have names if they have the subevent property.
- if "Subevent" in data and return_value_if_not_none(data["Subevent"]) is not None:
- event_name = f"{data['Subevent']}"
- return _create_new_source_event(event_name, data, gear_id)
-
- return _create_new_source_event(name=None, data=data, gear_id=gear_id)
-
-
-def _create_new_source_event(name, data, gear_id) -> db.Record:
- event = db.Record(name)
- event.add_parent("SourceEvent")
- event = _append_times_to_entity(event, data)
-
- event.add_property(name="Gear", value=gear_id)
- event.add_property(name="Position", value=_get_positions(
- data), datatype=db.common.datatype.LIST("Position")) # type: ignore
- if "Station ID" in data and return_value_if_not_none(data["Station ID"]) is not None:
- event.add_property(name="Station ID", value=str(data["Station ID"]))
- if "Station number" in data and return_value_if_not_none(data["Station number"]) is not None:
- event.add_property(name="Station number", value=str(data["Station number"]))
- if "Hol" in data and return_value_if_not_none(data["Hol"]) is not None:
- event.add_property(name="Hol", value=str(data["Hol"]))
- return event
-
-
-def _get_positions(data):
- # TODO: Refactor
- if "Latitude start" in data:
- latitude_start = return_value_if_not_none(data["Latitude start"])
- else:
- latitude_start = None
- if "Latitude stop" in data:
- latitude_stop = return_value_if_not_none(data["Latitude stop"])
- else:
- latitude_stop = None
- if "Longitude start" in data:
- longitude_start = return_value_if_not_none(data["Longitude start"])
- else:
- longitude_start = None
- if "Longitude stop" in data:
- longitude_stop = return_value_if_not_none(data["Longitude stop"])
- else:
- longitude_stop = None
- if "Sampling depth start" in data:
- sampling_depth_start = return_value_if_not_none(data["Sampling depth start"])
- else:
- sampling_depth_start = None
- if "Sampling depth stop" in data:
- sampling_depth_stop = return_value_if_not_none(data["Sampling depth stop"])
- else:
- sampling_depth_stop = None
- if "Water depth start" in data:
- water_depth_start = return_value_if_not_none(data["Water depth start"])
- else:
- water_depth_start = None
- if "Water depth stop" in data:
- water_depth_stop = return_value_if_not_none(data["Water depth stop"])
- else:
- water_depth_stop = None
- # insert start position
- position_start = db.Record()
- position_start.add_parent("StartPosition")
- position_start.add_property(name="Latitude", value=latitude_start)
- position_start.add_property(name="Longitude", value=longitude_start)
- if not pd.isna(sampling_depth_start):
- if sampling_depth_start < 0.0:
- sampling_depth_start *= -1.0
- # identifiable, so add even if it is None
- position_start.add_property(name="Sampling depth", value=sampling_depth_start)
- if not pd.isna(water_depth_start):
- if water_depth_start < 0:
- water_depth_start *= -1
- # identifiable, so add even if it is None
- position_start.add_property(name="Water depth", value=water_depth_start)
-
- # A stop position may be specified by depth stop alone:
- if not (pd.isna(sampling_depth_stop) and pd.isna(water_depth_stop)):
- # Copy all empty info from start position
- if pd.isna(latitude_stop) and pd.isna(longitude_stop):
- latitude_stop = latitude_start
- longitude_stop = longitude_start
- if pd.isna(sampling_depth_stop):
- sampling_depth_stop = sampling_depth_start
- if pd.isna(water_depth_stop):
- water_depth_stop = water_depth_start
- # If there is an endposition: insert endposition
- if not (pd.isna(latitude_stop) or pd.isna(longitude_stop)):
-
- position_end = db.Record()
- # position_end = db.Record("({}, {})".format(latitude_stop, longitude_stop))
- position_end.add_parent("StopPosition")
- position_end.add_property(name="Latitude", value=latitude_stop)
- position_end.add_property(name="Longitude", value=longitude_stop)
- if not pd.isna(sampling_depth_stop):
- if sampling_depth_stop < 0:
- sampling_depth_stop *= -1
- # position_end.name = position_end.name + " at -{}m".format(sampling_depth_stop)
- # identifiable, so add even if it is None
- position_end.add_property(name="Sampling depth", value=sampling_depth_stop)
- if not pd.isna(water_depth_stop):
- if water_depth_stop < 0:
- water_depth_stop *= -1
- # identifiable, so add even if it is None
- position_end.add_property(name="Water depth", value=water_depth_stop)
- # position_end.insert(unique=False)
- return [position_start, position_end]
- else:
- return [position_start]
-
-
-def get_gear(data):
- """
- Return the BIS ID of the Gear that is specified by 'Gear' and 'Gear configuration' in data.
-
- If no Such Gear Record exists, a new Gear Record is created.
- """
-
- qtext = f"FIND RECORD '{data['Gear']}'"
- if "Gear configuration" in data and pd.notnull(data["Gear configuration"]):
- qtext += f" WITH 'Configuration'='{data['Gear configuration']}'"
- try:
- res = db.execute_query(qtext, unique=True)
- except db.exceptions.EmptyUniqueQueryError:
- raise DataInconsistencyError(f"The query\n{qtext}\nreturned no results.")
- except db.exceptions.QueryNotUniqueError:
- raise DataInconsistencyError(f"The query\n{qtext}\nreturned more than one result.")
- return res
-
-
-def get_nagoya_case(data):
- """Create and retrun a NagoyaCase Record."""
- nagoya_case_number = return_value_if_not_none(data["Nagoya case number"])
-
- nagoya_case = db.Record(nagoya_case_number)
- nagoya_case.add_parent(name="NagoyaCase")
- nagoya_case.add_property(name="Nagoya Case Number", value=nagoya_case_number)
-
- return nagoya_case
-
-
def synchroize(records, additional_property_ents, htmluserlog_public):
crawler = Crawler(securityMode=SecurityMode.UPDATE)
identifiables_definition_file = os.path.expanduser("~/identifiables.yml")
@@ -326,15 +106,6 @@ def update_sample_records(data, htmluserlog_public):
# TODO Check data first and if there are Errors in the data: Provide the user with a download
# link to a template with Error descriptions.
- # Get property ids:
- person_property_id = db.get_entity_by_name("Main User").id
- sampling_person_property_id = db.get_entity_by_name("Sampling Person").id
- nagoya_case_property_id = get_id_of_datatype("NagoyaCase")
- container_property_id = get_id_of_datatype("Container")
- event_property_id = get_id_of_datatype("SourceEvent")
- pdfreport_property_id = get_id_of_datatype("PDFReport")
- parent_sample_property_id = db.get_entity_by_name("Parent Sample").id
-
additional_properties = data.keys().to_list()
additional_property_ids = {} # name-> id
additional_property_ents = {} # name-> Entity
@@ -360,14 +131,17 @@ def update_sample_records(data, htmluserlog_public):
for index, row in data.iterrows():
- sample_id_exists = not pd.isnull(row["BIS ID"])
+ sample_id_exists = not pd.isnull(row[get_column_header_name("entity_id")])
if not sample_id_exists:
raise DataInconsistencyError(f"Missing sample ID in row {index}")
try:
sample = db.execute_query(
- "FIND RECORD Sample WITH id = {}".format(row["BIS ID"]), unique=True)
+ "FIND RECORD Sample WITH id = {}".format(
+ row[get_column_header_name("entity_id")]),
+ unique=True)
except db.exceptions.EmptyUniqueQueryError:
- msg = "There is no Sample with ID = {} in the system.".format(row["BIS ID"])
+ msg = "There is no Sample with ID = {} in the system.".format(
+ row[get_column_header_name("entity_id")])
raise DataInconsistencyError(msg)
# All special properties are added here
@@ -392,13 +166,15 @@ def update_sample_records(data, htmluserlog_public):
name=ent.properties[0].name, value=return_value_if_not_none(row[property_name]))
else:
value = return_value_if_not_none(row[property_name])
- sample = _update_property(
+ sample = update_property(
entity=sample, property_id=additional_property_ids[property_name],
value=value, property_name=property_name)
+ # Now, treat events and event data
sample = add_event_to_sample(sample, row)
samples.append(sample)
+ # Samples might need additional post processing
samples = post_process_samples(samples, data)
synchroize(samples, additional_property_ents, htmluserlog_public)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
index e345c22..11d4683 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
@@ -3,6 +3,8 @@ import yaml
from pathlib import Path
+import linkahead as db
+
with open(os.path.join(Path(__file__).parent, "default_constants.yml")) as yaml_file:
CONSTANTS = yaml.safe_load(yaml_file)
@@ -26,3 +28,39 @@ def get_column_header_name(name: str):
return CONSTANTS["csv_column_names"][name]
return get_entity_name(name)
+
+
+def update_property(entity: db.Record, property_id: int, value, property_name="", datatype=None):
+ """
+ Set the property of an entity.
+
+ If the entity already has the property, just the value is set.
+ Else, the property is added to the entity
+ """
+ # TODO: Replace by assure_property_is etc.
+
+ # If the value in the spreadsheet is empty (nan)
+ if ((isinstance(value, list) and len(value) == 0)
+ or (not isinstance(value, list) and pd.isna(value))):
+ # Remove the property from te Entity if it has it
+ try:
+ entity.get_properties().get_by_name(property_name)
+ entity.remove_property(property_name)
+ except KeyError:
+ pass
+ return entity
+ if entity.get_property(property_id) is None:
+ if datatype:
+ entity.add_property(id=property_id, value=value, name=property_name, datatype=datatype)
+ else:
+ entity.add_property(id=property_id, value=value, name=property_name)
+ logger.debug("{}: Adding {} = {}".format(entity.id, property_id, value.id if
+ isinstance(value, db.Entity) else value))
+ else:
+ if isinstance(value, list) and not entity.get_property(property_id).datatype.startswith("LIST"):
+ entity.get_property(property_id).datatype = db.LIST(
+ entity.get_property(property_id).datatype)
+ entity.get_property(property_id).value = value
+ logger.debug("{}: Setting {} = {}".format(entity.id, property_id, value.id if
+ isinstance(value, db.Entity) else value))
+ return entity
--
GitLab
From 1a9e185706c34028c84cece88da9868e884ad528 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 13:37:45 +0100
Subject: [PATCH 47/63] ENH: Add separate module for container identification
---
.../sample_upload_add_special_properties.py | 18 +++++++-
.../sample_upload_column_definitions.py | 4 +-
.../sample_upload_get_container.py | 43 +++++++++++++++++++
3 files changed, 62 insertions(+), 3 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
index edda834..2242305 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -20,7 +20,9 @@ import pandas as pd
from caosadvancedtools.datainconsistency import DataInconsistencyError
-from .utils import get_column_header_name, get_entity_name
+from .sample_upload_get_container import get_container
+from .sample_upload_get_person import get_person
+from .utils import get_column_header_name, get_entity_name, update_property
from ..bis_utils import return_value_if_not_none
@@ -30,6 +32,18 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
"""
- # TODO Add special treatment properties to sample
+ main_user_prop = db.get_entity_by_name(get_entity_name("Main User"))
+ container_rt = db.get_entity_name(get_entity_name("container_rt"))
+
+ if (get_column_header_name("Main User") in data and
+ return_value_if_not_none(data[get_column_header_name("Main User")]) is not None):
+ main_user = get_person(return_value_if_not_none(data[get_column_header_name("Main User")]))
+ sample = update_property(sample, main_user_prop.id, main_user)
+
+ if (get_column_header_name("Storage ID") in data and
+ return_value_if_not_none(data[get_column_header_name("Storage ID")]) is not None):
+ container = get_container(return_value_if_not_none(
+ data[get_column_header_name("Storage ID")]))
+ sample = update_property(sample, container_rt.id, contianer)
return sample
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index c4c4c82..8384ed9 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -95,8 +95,11 @@ COLUMN_CONVERTER = _use_custom_names({
SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"Biome",
"Campaign",
+ "Collector",
+ "Curator",
"Elevation start",
"Elevation stop",
+ "Embargo",
"End date",
"Event responsible",
"IGSN DOI",
@@ -111,7 +114,6 @@ SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"PDFReport",
"Parent Linkahead ID",
"Sphere",
- "Sphere",
"Start date",
"Storage ID",
"entity_id",
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.py
new file mode 100644
index 0000000..40e2e73
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.py
@@ -0,0 +1,43 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_entity_name
+
+
+def get_container(identifier: str) -> db.Record:
+ """Return the container record for a given identifier string. By
+ default, that's simply the id but may be overwritten for
+ customization.
+
+ """
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('container_rt')}' WITH ID='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('container_rt')}' WITH name='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ raise DataInconsistencyError(
+ f"Couldn't find a {get_entity_name('container_rt')} with name or id {identifier}."
+ )
--
GitLab
From 7d04de0cd1728a61551f689acdfe9c5d82371984 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 13:43:27 +0100
Subject: [PATCH 48/63] ENH: Add special properties treatment for samples
---
.../sample_upload_add_special_properties.py | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
index 2242305..b4e1330 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -44,6 +44,15 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
return_value_if_not_none(data[get_column_header_name("Storage ID")]) is not None):
container = get_container(return_value_if_not_none(
data[get_column_header_name("Storage ID")]))
- sample = update_property(sample, container_rt.id, contianer)
+ sample = update_property(sample, container_rt.id, container)
+
+ for name in ["Curator", "Collector"]:
+ prop = db.get_entity_by_name(name)
+ if (get_column_header_name(name) in data and
+ return_value_if_not_none(data[get_column_header_name(name)]) is not None):
+ persons = [get_person(id_str) for id_str in return_value_if_not_none(
+ data[get_column_header_name(name)])]
+ sample = update_property(sample, prop.id, persons,
+ datatype=db.LIST(get_entity_name("Person")))
return sample
--
GitLab
From 29dc4b4295404d2be12e4282ecd07d9ae387fd9e Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 13:51:13 +0100
Subject: [PATCH 49/63] EN: Also support parent/child samples
---
.../scripting/bin/sample_helpers/default_constants.yml | 1 +
.../sample_upload_add_special_properties.py | 9 ++++++++-
2 files changed, 9 insertions(+), 1 deletion(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 033a05e..046cca5 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -65,6 +65,7 @@ entity_names:
start_date_prop: start_date
end_date_prop: end_date
igsn_doi_prop: igsn_doi
+ parent_sample_prop: Parent_Sample
error_prefix: "Something went wrong:"
error_suffix: "Please contact your administrator(s)."
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
index b4e1330..d32c3de 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -34,6 +34,7 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
main_user_prop = db.get_entity_by_name(get_entity_name("Main User"))
container_rt = db.get_entity_name(get_entity_name("container_rt"))
+ parent_sample_prop = db.get_entity_name(get_entity_name("parent_sample_prop"))
if (get_column_header_name("Main User") in data and
return_value_if_not_none(data[get_column_header_name("Main User")]) is not None):
@@ -46,8 +47,14 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
data[get_column_header_name("Storage ID")]))
sample = update_property(sample, container_rt.id, container)
+ if (get_column_header_name("Parent LinkAhead ID") in data and
+ return_value_if_not_none(data[get_column_header_name("Parent LinkAhead ID")]) is not None):
+ parent = return_value_if_not_none(
+ data[get_column_header_name("Parent LinkAhead ID")])
+ sample = update_property(sample, parent_sample_prop.id, parent)
+
for name in ["Curator", "Collector"]:
- prop = db.get_entity_by_name(name)
+ prop = db.get_entity_by_name(get_entity_name(name))
if (get_column_header_name(name) in data and
return_value_if_not_none(data[get_column_header_name(name)]) is not None):
persons = [get_person(id_str) for id_str in return_value_if_not_none(
--
GitLab
From dbb061c0347d6a4772d4a3227b6a261964687658 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 14:07:53 +0100
Subject: [PATCH 50/63] ENH: Add position treatment to events
---
.../bin/sample_helpers/default_constants.yml | 11 ++++----
.../sample_helpers/sample_upload_get_event.py | 28 +++++++++++++++++--
2 files changed, 32 insertions(+), 7 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 046cca5..12edef8 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -57,15 +57,16 @@ entity_names:
container_size_prop: "Container size"
containertype_rt: ContainerType
custom_label_prop: custom_label
+ end_date_prop: end_date
+ event_rt: Event
+ first_name_prop: first_name
+ igsn_doi_prop: igsn_doi
labelcounter_prop: counter
labelcounter_rt: LabelCounter
- responsible_rt: Responsible
- first_name_prop: first_name
last_name_prop: last_name
- start_date_prop: start_date
- end_date_prop: end_date
- igsn_doi_prop: igsn_doi
parent_sample_prop: Parent_Sample
+ responsible_rt: Responsible
+ start_date_prop: start_date
error_prefix: "Something went wrong:"
error_suffix: "Please contact your administrator(s)."
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index aa62498..d15eed6 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -20,7 +20,8 @@ import pandas as pd
from caosadvancedtools.datainconsistency import DataInconsistencyError
-from .utils import get_column_header_name, get_entity_name
+from .sample_upload_get_person import get_person
+from .utils import get_column_header_name, get_entity_name, update_property
from ..bis_utils import return_value_if_not_none
@@ -31,7 +32,30 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
"""
_perform_sanity_checks(sample, data)
- # TODO Add event-specific columns
+ event = db.Record().add_parent(get_entity_name("event_rt"))
+
+ # We performed the sanity checks so we can assume that if the
+ # Start/Stop Latitude exists, all start/stop data exist.
+ positions = []
+ position_prop = db.get_entity_name(get_entity_name("Position"))
+
+ # Take care of positions
+ for mode in ["start", "stop"]:
+ if (get_column_header_name(f"Latitude {mode}") in data and
+ return_value_if_not_none(data[get_column_header_name(f"Latitude {mode}")]) is not None):
+ position.append(
+ _create_position(
+ mode=mode,
+ lat=return_value_if_not_none(data[get_column_header_name(f"Latitude {mode}")]),
+ lng=return_value_if_not_none(data[get_column_header_name(f"Longitude {mode}")]),
+ ele=return_value_if_not_none(data[get_column_header_name(f"Elevation {mode}")]),
+ )
+ )
+ if positions:
+ update_property(event, position_prop.id, positions,
+ datatype=db.LIST(get_entity_name("Position")))
+
+ # TODO: Start/end date, remaining event props
return sample
--
GitLab
From 3d636dab3945d083fc53a132bfde8da560fc0fd6 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 14:12:52 +0100
Subject: [PATCH 51/63] ENH: Define identifiables
---
.../scripting/home/identifiables.yml | 45 ++++++-------------
1 file changed, 14 insertions(+), 31 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
index f37c5c3..01181ef 100644
--- a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
+++ b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
@@ -1,40 +1,23 @@
-NagoyaCase:
- - 'Nagoya case number'
-Device:
+ControlledRecordType:
- name
-SourceEvent:
- - Gear
- - Time start
+Event:
+ - Device
+ - start_date
- Position
-Gear:
- # TODO?
- - name
-Fixation:
- # TODO?
- - enumValue
-Platform:
- # TODO?
- - name
-FunctionalGroup:
- # TODO?
- - name
SampleType:
- # TODO?
- - name
-Collection:
- name
-SampleTypeSpecific:
- # TODO?
+SampleMethod:
- name
Sphere:
- name
StartPosition:
- - Latitude
- - Longitude
- - Water depth
- - Sampling depth
+ - latitude
+ - longitude
+ - elevation
StopPosition:
- - Latitude
- - Longitude
- - Water depth
- - Sampling depth
+ - latitude
+ - longitude
+ - elevation
+Person:
+ - first_name
+ - last_name
--
GitLab
From a447505b7797469204a52981c29225fadf69fde1 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 15:49:20 +0100
Subject: [PATCH 52/63] ENH: Add event to sample
---
.../scripting/bin/sample_helpers/sample_upload_get_event.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index d15eed6..9006643 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -32,7 +32,8 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
"""
_perform_sanity_checks(sample, data)
- event = db.Record().add_parent(get_entity_name("event_rt"))
+ event_rt = db.get_entity_by_name(get_entity_name("event_rt"), role="RECORDTYPE")
+ event = db.Record().add_parent(event_rt)
# We performed the sanity checks so we can assume that if the
# Start/Stop Latitude exists, all start/stop data exist.
@@ -57,6 +58,8 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
# TODO: Start/end date, remaining event props
+ sample = update_property(sample, event_rt.id, event)
+
return sample
--
GitLab
From e80097017192c733e1ffd820ee86c9b65b7719a8 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 15:54:08 +0100
Subject: [PATCH 53/63] WIP: Remove some entries from sample exporter
---
.../scripting/bin/export_sample_csv.py | 55 +------------------
1 file changed, 1 insertion(+), 54 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
index 4f47b48..4b79fdd 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
@@ -63,19 +63,6 @@ ERROR_PREFIX = 'Something went wrong: '
ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
-# Declare mapping of different time/date column names to property names
-TIME_NAME_MAPPINGS = {
- "date collected start": "time start",
- "time collected start": "time start",
- "date collected stop": "time stop",
- "time collected stop": "time stop",
- "date sampled start": "time sampled start",
- "time sampled start": "time sampled start",
- "date sampled stop": "time sampled stop",
- "time sampled stop": "time sampled stop",
-}
-
-
def cached_record(i):
return cached_get_entity_by(eid=i)
@@ -212,29 +199,6 @@ def extract_date_time(record, p):
return extract_value_as_list(record, p)
-def extract_date(record, key):
- if key.lower() in TIME_NAME_MAPPINGS.keys():
- time_key = TIME_NAME_MAPPINGS[key.lower()]
- else:
- time_key = key
- date_times = extract_date_time(record, time_key)
- return [isoparse(t).date().isoformat() for t in date_times]
-
-
-def extract_time(record, key):
- if key.lower() in TIME_NAME_MAPPINGS.keys():
- time_key = TIME_NAME_MAPPINGS[key.lower()]
- else:
- time_key = key
- date_times = extract_date_time(record, time_key)
- return [isoparse(t).time().isoformat() for t in date_times]
-
-
-def extract_time_zone(record, key):
- date_times = extract_date_time(record, "Time start")
- return [isoparse(t).tzname() for t in date_times]
-
-
def extract_station_number(record, key):
source_ev = retrieve_source_event(record)
return [e.get_property(key).value for e in source_ev if
@@ -377,7 +341,7 @@ def extract_event_url(record, key):
return None
-# must be same keys as SPECIAL_TREATMENT
+# must include all keys from SPECIAL_TREATMENT
EXTRACTORS = {
"BIS ID": lambda record, key: record.id,
"Parent BIS ID": extract_parent_sample,
@@ -399,11 +363,6 @@ EXTRACTORS = {
"Nagoya case number": extract_nagoya_case_number,
"PDFReport": extract_pdf_id,
"Subevent": extract_source_event_name,
- "Time collected start": extract_time,
- "Time collected stop": extract_time,
- "Time sampled start": extract_time,
- "Time sampled stop": extract_time,
- "Timezone": extract_time_zone,
"Station ID": extract_station_id,
"Station number": extract_station_number,
"Sampling depth start": extract_sampling_depth_start,
@@ -436,14 +395,9 @@ REVERSE_COLUMN_CONVERTER = {
# List of sample properties to be ignored because they are treated
# otherwise. Similar, but not identical to SPECIAL TREATMENT.
IGNORE_KEYS = [
- "NagoyaCase",
"Parent Sample",
"Container",
- "SourceEvent",
"Event",
- "Date",
- "Sampling depth",
- "Water depth"
]
# Additional list of keys to be ignored when extracting parent sample information
@@ -455,15 +409,8 @@ IGNORE_KEYS_PARENT = IGNORE_KEYS + [
# the import.
ADDITIONAL_EXPORTS = [
"BIS URL",
- "Date sampled start",
- "Date sampled stop",
- "IGSN URL",
- "IGSN",
"Parent BIS ID",
"Storage chain",
- "Time sampled start",
- "Time sampled stop",
- "URL SourceEvent"
]
--
GitLab
From 232ea81267f16ff56020279858ff3619f94138b2 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 17:08:53 +0100
Subject: [PATCH 54/63] ENH: Add start/end time treatment
---
.../scripting/bin/register_new_samples.py | 2 +-
.../sample_helpers/sample_upload_get_event.py | 17 ++++++++++++-----
2 files changed, 13 insertions(+), 6 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
index 1b912ee..15e22bd 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
@@ -28,7 +28,7 @@ def get_parser():
def get_column_names(data):
# Make sure each header starts with BIS ID and Main User
- starting_names = ["entity_id", "Main User"]
+ starting_names = [get_column_header_name(name) for name in ["entity_id", "Main User"]]
# required_column_names is just a string of column names separated by
# commas.
other_names = data["required_column_names"].split(',') + data["column_names"]
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index 9006643..cf02752 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -53,13 +53,20 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
)
)
if positions:
- update_property(event, position_prop.id, positions,
- datatype=db.LIST(get_entity_name("Position")))
+ event = update_property(event, position_prop.id, positions,
+ datatype=db.LIST(get_entity_name("Position")))
- # TODO: Start/end date, remaining event props
+ for time_p in ["start_date_prop", "end_date_prop"]:
+ prop = db.get_entity_by_name(get_entity_name(time_p))
+ if (get_column_header_name(time_p) in data and
+ return_value_if_not_none(data[get_column_header_name(time_p)]) is not None):
+ event = update_property(event, prop.id, return_value_if_not_none(
+ data[get_column_header_name(time_p)]))
+
+ # only add if there was any event data at all:
+ if len(event.properties) > 0:
+ sample = update_property(sample, event_rt.id, event)
- sample = update_property(sample, event_rt.id, event)
-
return sample
--
GitLab
From 77930b323719781319309fab271774692aba1ac5 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 17:28:34 +0100
Subject: [PATCH 55/63] FIX: Typos
---
.../caosdb-server/scripting/bin/bis_utils.py | 18 +-----------------
.../sample_upload_add_special_properties.py | 3 +--
.../sample_helpers/sample_upload_get_event.py | 3 +--
.../sample_helpers/sample_upload_get_person.py | 8 ++++----
.../scripting/bin/sample_helpers/utils.py | 17 +++++++++++++++++
.../scripting/bin/upload_sample_template.py | 3 +++
6 files changed, 27 insertions(+), 25 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
index 1bcc322..00699e5 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
@@ -34,7 +34,7 @@ from linkahead import get_entity_by_name
from sample_helpers.sample_upload_column_definitions import (
IGNORED_COLUMN_NAMES_SAMPLE, SPECIAL_TREATMENT_SAMPLE)
-from sample_helpers.utils import CONSTANTS
+from sample_helpers.utils import CONSTANTS, return_value_if_not_none
COLUMN_DESCRIPTIONS = CONSTANTS["csv_column_descriptions"]
@@ -131,22 +131,6 @@ def replace_entity_urls_by_ids(data: pd.DataFrame, eid_columns: list[str] = ["BI
return data
-def return_value_if_not_none(val):
- """Workaround for somewhat weird pandas behavior. Return value if actual
- value, otherwise, return None.
-
- """
- if isinstance(val, list):
- if len(val) == 0:
- return None
- if len(val) == 1:
- if pd.isnull(val[0]) or val[0] is None or f"{val[0]}".lower() == "nan" or f"{val[0]}" == "":
- return None
- elif pd.isnull(val) or val is None or f"{val}".lower() == "nan" or f"{val}" == "":
- return None
- return val
-
-
def whitespace_cleanup_in_df(df: pd.DataFrame):
"""Strip all leading and trailing whitespaces from all str values in df."""
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
index d32c3de..cb7ce01 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -22,8 +22,7 @@ from caosadvancedtools.datainconsistency import DataInconsistencyError
from .sample_upload_get_container import get_container
from .sample_upload_get_person import get_person
-from .utils import get_column_header_name, get_entity_name, update_property
-from ..bis_utils import return_value_if_not_none
+from .utils import get_column_header_name, get_entity_name, update_property, return_value_if_not_none
def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index cf02752..39ca204 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -21,8 +21,7 @@ import pandas as pd
from caosadvancedtools.datainconsistency import DataInconsistencyError
from .sample_upload_get_person import get_person
-from .utils import get_column_header_name, get_entity_name, update_property
-from ..bis_utils import return_value_if_not_none
+from .utils import get_column_header_name, get_entity_name, update_property, return_value_if_not_none
def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
index 49c34f6..1872f62 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
@@ -44,16 +44,16 @@ def get_person(text: str) -> db.Record:
def _get_person_by_fullname(first_name: str, last_name: str) -> db.Record:
# seach for person in db
res = db.execute_query(
- f"FIND '{get_entity_name('Person')}' WITH '{
- get_entity_name('first_name_prop')}'='{first_name}' "
+ f"FIND '{get_entity_name('Person')}' WITH "
+ f"'{get_entity_name('first_name_prop')}'='{first_name}' "
f"AND '{get_entity_name('last_name_prop')}'='{last_name}'"
)
# if person doesn't exist in database...
if len(res) == 0:
# There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
error_msg = (
- f"There is no person Record with '{get_entity_name('first_name_prop')}' = '{
- first_name}' "
+ f"There is no person Record with '{get_entity_name('first_name_prop')}' "
+ f"= '{first_name}' "
f"AND '{get_entity_name('last_name_prop')}' = '{last_name}' in the database. ")
raise DataInconsistencyError(error_msg)
else:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
index 11d4683..c482eee 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
@@ -4,6 +4,7 @@ import yaml
from pathlib import Path
import linkahead as db
+import pandas as pd
with open(os.path.join(Path(__file__).parent, "default_constants.yml")) as yaml_file:
CONSTANTS = yaml.safe_load(yaml_file)
@@ -64,3 +65,19 @@ def update_property(entity: db.Record, property_id: int, value, property_name=""
logger.debug("{}: Setting {} = {}".format(entity.id, property_id, value.id if
isinstance(value, db.Entity) else value))
return entity
+
+
+def return_value_if_not_none(val):
+ """Workaround for somewhat weird pandas behavior. Return value if actual
+ value, otherwise, return None.
+
+ """
+ if isinstance(val, list):
+ if len(val) == 0:
+ return None
+ if len(val) == 1:
+ if pd.isnull(val[0]) or val[0] is None or f"{val[0]}".lower() == "nan" or f"{val[0]}" == "":
+ return None
+ elif pd.isnull(val) or val is None or f"{val}".lower() == "nan" or f"{val}" == "":
+ return None
+ return val
diff --git a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
index 484e651..4551b35 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
@@ -42,6 +42,9 @@ from caoscrawler.logging import configure_server_side_logging
from bis_utils import (replace_entity_urls_by_ids,
SPECIAL_TREATMENT_SAMPLE, whitespace_cleanup_in_df)
+from sample_helpers.sample_upload_column_definitions import (
+ COLUMN_CONVERTER, DATATYPE_DEFINITIONS,
+ OBLIGATORY_COLUMNS, OBLIGATORY_COLUMNS_CHILD, SPECIAL_TREATMENT_SAMPLE)
from sample_helpers.utils import CONSTANTS, get_column_header_name
# suppress warning of diff function
--
GitLab
From 092be437b68302f80f7034e5a9ec45912798e285 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 7 Feb 2025 18:07:04 +0100
Subject: [PATCH 56/63] ENH: Add separate getter for devices, too
---
.../scripting/bin/crawl_sample_data_async.py | 1 +
.../bin/sample_helpers/default_constants.yml | 4 +-
.../sample_upload_add_special_properties.py | 20 ++++++---
.../sample_upload_column_definitions.py | 1 +
.../sample_upload_get_device.py | 42 +++++++++++++++++++
.../sample_helpers/sample_upload_get_event.py | 16 +++----
.../scripting/bin/sample_helpers/utils.py | 4 --
.../scripting/home/identifiables.yml | 1 -
8 files changed, 68 insertions(+), 21 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_device.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index ace23ee..f3fff6d 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -176,6 +176,7 @@ def update_sample_records(data, htmluserlog_public):
# Samples might need additional post processing
samples = post_process_samples(samples, data)
+ logger.info(samples)
synchroize(samples, additional_property_ents, htmluserlog_public)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 12edef8..119abc9 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -18,8 +18,8 @@
csv_column_names:
entity_id: "LinkAhead ID"
custom_label_prop: "Custom Label"
- start_date_prop: "Date start"
- end_date_prop: "Date stop"
+ start_date_prop: "Start date"
+ end_date_prop: "End date"
igsn_doi_prop: "IGSN DOI"
csv_column_descriptions:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
index cb7ce01..5c559d4 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -21,6 +21,7 @@ import pandas as pd
from caosadvancedtools.datainconsistency import DataInconsistencyError
from .sample_upload_get_container import get_container
+from .sample_upload_get_device import get_device
from .sample_upload_get_person import get_person
from .utils import get_column_header_name, get_entity_name, update_property, return_value_if_not_none
@@ -32,25 +33,32 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
"""
main_user_prop = db.get_entity_by_name(get_entity_name("Main User"))
- container_rt = db.get_entity_name(get_entity_name("container_rt"))
- parent_sample_prop = db.get_entity_name(get_entity_name("parent_sample_prop"))
+ container_rt = db.get_entity_by_name(get_entity_name("container_rt"))
+ device_rt = db.get_entity_by_name(get_entity_name("Device"))
+ parent_sample_prop = db.get_entity_by_name(get_entity_name("parent_sample_prop"))
if (get_column_header_name("Main User") in data and
return_value_if_not_none(data[get_column_header_name("Main User")]) is not None):
main_user = get_person(return_value_if_not_none(data[get_column_header_name("Main User")]))
- sample = update_property(sample, main_user_prop.id, main_user)
+ sample = update_property(sample, main_user_prop.id, main_user, property_name=main_user_prop.name)
if (get_column_header_name("Storage ID") in data and
return_value_if_not_none(data[get_column_header_name("Storage ID")]) is not None):
container = get_container(return_value_if_not_none(
data[get_column_header_name("Storage ID")]))
- sample = update_property(sample, container_rt.id, container)
+ sample = update_property(sample, container_rt.id, container, property_name=container_rt.name)
+
+ if (get_column_header_name("Device") in data and
+ return_value_if_not_none(data[get_column_header_name("Device")]) is not None):
+ device = get_device(return_value_if_not_none(
+ data[get_column_header_name("Device")]))
+ sample = update_property(sample, device_rt.id, device, property_name=device_rt.name)
if (get_column_header_name("Parent LinkAhead ID") in data and
return_value_if_not_none(data[get_column_header_name("Parent LinkAhead ID")]) is not None):
parent = return_value_if_not_none(
data[get_column_header_name("Parent LinkAhead ID")])
- sample = update_property(sample, parent_sample_prop.id, parent)
+ sample = update_property(sample, parent_sample_prop.id, parent, property_name=parent_sample_prop.name)
for name in ["Curator", "Collector"]:
prop = db.get_entity_by_name(get_entity_name(name))
@@ -59,6 +67,6 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
persons = [get_person(id_str) for id_str in return_value_if_not_none(
data[get_column_header_name(name)])]
sample = update_property(sample, prop.id, persons,
- datatype=db.LIST(get_entity_name("Person")))
+ datatype=db.LIST(get_entity_name("Person")), property_name=prop.name)
return sample
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 8384ed9..235d694 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -97,6 +97,7 @@ SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"Campaign",
"Collector",
"Curator",
+ "Device",
"Elevation start",
"Elevation stop",
"Embargo",
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_device.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_device.py
new file mode 100644
index 0000000..08cf3f0
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_device.py
@@ -0,0 +1,42 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_entity_name
+
+def get_device(identifier: str) -> db.Record:
+ """Return the container record for a given identifier string. By
+ default, that's simply the id but may be overwritten for
+ customization.
+
+ """
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('Device')}' WITH ID='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('Device')}' WITH name='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ raise DataInconsistencyError(
+ f"Couldn't find a {get_entity_name('Device')} with name or id {identifier}."
+ )
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index 39ca204..7c762df 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -37,13 +37,13 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
# We performed the sanity checks so we can assume that if the
# Start/Stop Latitude exists, all start/stop data exist.
positions = []
- position_prop = db.get_entity_name(get_entity_name("Position"))
+ position_prop = db.get_entity_by_name(get_entity_name("Position"))
# Take care of positions
for mode in ["start", "stop"]:
if (get_column_header_name(f"Latitude {mode}") in data and
return_value_if_not_none(data[get_column_header_name(f"Latitude {mode}")]) is not None):
- position.append(
+ positions.append(
_create_position(
mode=mode,
lat=return_value_if_not_none(data[get_column_header_name(f"Latitude {mode}")]),
@@ -53,18 +53,18 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
)
if positions:
event = update_property(event, position_prop.id, positions,
- datatype=db.LIST(get_entity_name("Position")))
+ datatype=db.LIST(get_entity_name("Position")), property_name=position_prop.name)
for time_p in ["start_date_prop", "end_date_prop"]:
prop = db.get_entity_by_name(get_entity_name(time_p))
if (get_column_header_name(time_p) in data and
return_value_if_not_none(data[get_column_header_name(time_p)]) is not None):
event = update_property(event, prop.id, return_value_if_not_none(
- data[get_column_header_name(time_p)]))
+ data[get_column_header_name(time_p)]), property_name=prop.name)
# only add if there was any event data at all:
if len(event.properties) > 0:
- sample = update_property(sample, event_rt.id, event)
+ sample = update_property(sample, event_rt.id, event, property_name=event_rt.name)
return sample
@@ -101,10 +101,10 @@ def _perform_sanity_checks(sample, data):
bool_list = [get_column_header_name(f"{val}_{name}") in data for val in [
"latitude", "longitude", "elevation"]]
raise_error = False
- if bool_list.any():
- if not bool_list.all():
+ if any(bool_list):
+ if not all(bool_list):
raise_error = True
- elif [return_value_if_not_none(data[get_column_header_name(f"{val}_{name}")]) is None for val in ["latitude", "longitude", "elevation"]].any():
+ elif any([return_value_if_not_none(data[get_column_header_name(f"{val}_{name}")]) is None for val in ["latitude", "longitude", "elevation"]]):
raise_error = True
if raise_error:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
index c482eee..d047e6b 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
@@ -55,15 +55,11 @@ def update_property(entity: db.Record, property_id: int, value, property_name=""
entity.add_property(id=property_id, value=value, name=property_name, datatype=datatype)
else:
entity.add_property(id=property_id, value=value, name=property_name)
- logger.debug("{}: Adding {} = {}".format(entity.id, property_id, value.id if
- isinstance(value, db.Entity) else value))
else:
if isinstance(value, list) and not entity.get_property(property_id).datatype.startswith("LIST"):
entity.get_property(property_id).datatype = db.LIST(
entity.get_property(property_id).datatype)
entity.get_property(property_id).value = value
- logger.debug("{}: Setting {} = {}".format(entity.id, property_id, value.id if
- isinstance(value, db.Entity) else value))
return entity
diff --git a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
index 01181ef..25a6e4a 100644
--- a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
+++ b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
@@ -1,7 +1,6 @@
ControlledRecordType:
- name
Event:
- - Device
- start_date
- Position
SampleType:
--
GitLab
From 84933ee09d2ce0af13a528cd871e08c1de66f34a Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 17 Feb 2025 14:37:15 +0100
Subject: [PATCH 57/63] ENH: Add missing event properties
---
.../bin/sample_helpers/default_constants.yml | 6 ++++++
.../sample_upload_column_definitions.py | 6 +++---
.../sample_helpers/sample_upload_get_event.py | 21 +++++++++++++++++++
.../scripting/home/identifiables.yml | 2 ++
4 files changed, 32 insertions(+), 3 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 119abc9..c7f1baa 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -21,6 +21,9 @@ csv_column_names:
start_date_prop: "Start date"
end_date_prop: "End date"
igsn_doi_prop: "IGSN DOI"
+ locality_description_prop: "Locality description"
+ locality_name_prop: "Locality name"
+ responsible_person_event: "Event responsible"
csv_column_descriptions:
LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
@@ -67,6 +70,9 @@ entity_names:
parent_sample_prop: Parent_Sample
responsible_rt: Responsible
start_date_prop: start_date
+ locality_description_prop: locality_description
+ locality_name_prop: locality_name
+ responsible_person_event: Responsible_Person
error_prefix: "Something went wrong:"
error_suffix: "Please contact your administrator(s)."
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 235d694..d6a62cb 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -103,12 +103,12 @@ SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"Embargo",
"End date",
"Event responsible",
- "IGSN DOI",
+ "igsn_doi_prop",
"Latitude start",
"Latitude stop",
"Level",
- "Locality description",
- "Locality name",
+ "locality_description_prop",
+ "locality_name_prop",
"Longitude start",
"Longitude stop",
"Main User",
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index 7c762df..c15df79 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -55,6 +55,27 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
event = update_property(event, position_prop.id, positions,
datatype=db.LIST(get_entity_name("Position")), property_name=position_prop.name)
+ # Further event properties
+ for event_p in ["Biome", "Campaign", "Device", "EventType",
+ "igsn_doi_prop", "level", "locality_description_prop",
+ "locality_name_prop", "Sphere"]:
+ prop = db.get_entity_by_name(get_entity_name(event_p))
+ if (get_column_header_name(event_p) in data and
+ return_value_if_not_none(data[get_column_header_name(event_p)]) is not None):
+ event = update_property(event, prop.id, return_value_if_not_none(
+ data[get_column_header_name(event_p)]), property_name=prop.name)
+
+ # Special treatment for (list of) persons
+ resp_prop = db.get_entity_by_name(get_entity_name("responsible_person_event"))
+ if (get_column_header_name("responsible_person_event") in data and
+ return_value_if_not_none(data[get_column_header_name("responsible_person_event")]) is not None):
+ resps = return_value_if_not_none(data[get_column_header_name("responsible_person_event")])
+ if not isinstance(resps, list):
+ resps = [resps]
+ recs = [get_person(resp) for resp in resps]
+ event = update_property(event, resp_prop.id, recs, datatype=db.LIST(
+ "Person"), property_name=resp_prop.name)
+
for time_p in ["start_date_prop", "end_date_prop"]:
prop = db.get_entity_by_name(get_entity_name(time_p))
if (get_column_header_name(time_p) in data and
diff --git a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
index 25a6e4a..c3df242 100644
--- a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
+++ b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
@@ -1,3 +1,5 @@
+Campaign:
+ - name
ControlledRecordType:
- name
Event:
--
GitLab
From 7a4660ddf8aeecb3c274538b0fb7d60bf6189486 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 17 Feb 2025 15:14:36 +0100
Subject: [PATCH 58/63] ENH: Use configurable server URL in sample export
---
.../src/ext/js/ext_samplemanagement.js | 2 +-
.../scripting/bin/export_sample_csv.py | 68 +++++++------------
2 files changed, 24 insertions(+), 46 deletions(-)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index 92a854e..ba4dcb4 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -94,7 +94,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
script: "export_sample_csv.py",
fields: [{
type: "text",
- name: "bis_ids",
+ name: "ids",
label: sample_id_label,
required: false,
pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
index 4b79fdd..41ca25f 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
@@ -25,33 +25,28 @@ import logging
import os
import sys
import urllib
-from datetime import date, datetime
-from typing import List
import linkahead as db
import pandas as pd
-from caosadvancedtools.datainconsistency import DataInconsistencyError
from caosadvancedtools.serverside import helper
from caosadvancedtools.table_export import BaseTableExporter
-from caosadvancedtools.table_importer import CSVImporter
-from caoscrawler import Crawler, SecurityMode
-from caoscrawler.crawl import ForbiddenTransaction
-from caoscrawler.identifiable_adapters import CaosDBIdentifiableAdapter
+from caoscrawler.config import get_config_setting
from caoscrawler.logging import configure_server_side_logging
from linkahead.cached import cached_get_entity_by, cached_query as cquery
from linkahead.common.datatype import get_id_of_datatype
from linkahead.exceptions import (EmptyUniqueQueryError, QueryNotUniqueError,
TransactionError)
-from dateutil import parser as dateparser
-from dateutil.parser import isoparse
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
- get_options_row, send_mail_with_defaults,
- SPECIAL_TREATMENT_SAMPLE as SPECIAL_TREATMENT)
+ get_options_row, send_mail_with_defaults)
from export_container_csv import (generate_label_text,
extract_storage_chain as container_storage_chain)
-from upload_sample_template import DATATYPE_DEFINITIONS
+from sample_helpers.sample_upload_column_definitions import (
+ DATATYPE_DEFINITIONS, SPECIAL_TREATMENT_SAMPLE as SPECIAL_TREATMENT)
+from sample_helpers.utils import (CONSTANTS, get_column_header_name,
+ get_entity_name)
+
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -59,8 +54,8 @@ apilogger.setLevel(logging.ERROR)
logger = logging.getLogger("caosadvancedtools")
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
def cached_record(i):
@@ -283,7 +278,7 @@ def extract_hol(record, key):
def extract_bis_url(record, key):
# base_uri = db.get_config().get("Connection", "url")
- base_uri = "https://biosamples.geomar.de/"
+ base_uri = get_config_setting("public_host_url")
return urllib.parse.urljoin(base_uri, f"Entity/{record.id}")
@@ -336,7 +331,7 @@ def extract_event_url(record, key):
if not events:
return None
if len(events) == 1:
- return urllib.parse.urljoin("https://biosamples.geomar.de", f"Entity/{events[0].id}")
+ return urllib.parse.urljoin(get_config_setting("public_host_url"), f"Entity/{events[0].id}")
logger.debug(f"Sample {record.id} has multiple events.")
return None
@@ -347,10 +342,6 @@ EXTRACTORS = {
"Parent BIS ID": extract_parent_sample,
"AphiaID": default_find,
"Collection": extract_reference_name,
- "Date collected start": extract_date,
- "Date collected stop": extract_date,
- "Date sampled start": extract_date,
- "Date sampled stop": extract_date,
"Main User": extract_person,
"Sampling Person": extract_person,
"PI": extract_person,
@@ -402,14 +393,14 @@ IGNORE_KEYS = [
# Additional list of keys to be ignored when extracting parent sample information
IGNORE_KEYS_PARENT = IGNORE_KEYS + [
- "BIS ID",
+ "LinkAhead ID",
]
# List of columns to be exported although they are not known to or ignored by
# the import.
ADDITIONAL_EXPORTS = [
- "BIS URL",
- "Parent BIS ID",
+ "LinkAhead URL",
+ "Parent LinkAhead ID",
"Storage chain",
]
@@ -540,25 +531,25 @@ def to_csv(samples):
def retrieve_samples(data):
container = []
not_found = []
- for bis_id in data:
- if isinstance(bis_id, int):
+ for eid in data:
+ if isinstance(eid, int):
try:
container.append(
- cached_get_entity_by(query=f"FIND RECORD SAMPLE WITH id='{bis_id}'"))
+ cached_get_entity_by(query=f"FIND RECORD SAMPLE WITH id='{eid}'"))
except EmptyUniqueQueryError as e:
# we want to warn about these
- not_found.append(bis_id)
+ not_found.append(eid)
else:
found_at_least_one_in_range = False
- for next_bis_id in bis_id:
+ for next_eid in eid:
try:
container.append(
- cached_get_entity_by(query=f"FIND RECORD Sample WITH id='{next_bis_id}'"))
+ cached_get_entity_by(query=f"FIND RECORD Sample WITH id='{next_eid}'"))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
pass
if not found_at_least_one_in_range:
- not_found.append(f"{bis_id.start}-{bis_id.stop-1}")
+ not_found.append(f"{eid.start}-{eid.stop-1}")
return container, not_found
@@ -626,19 +617,6 @@ def main():
logger.info("Removing empty columns from export")
no_empty_columns = True
- if "from_date" in form_data:
- # Inserted after ...
- data = [el.id for el in db.execute_query(
- "SELECT id FROM sample WHICH REFERENCES A SourceEvent "
- "WHICH HAS AN IGSN AND "
- f"(WHICH WAS INSERTED SINCE {form_data['from_date']})")
- ]
- # ... + update after
- data += [el.id for el in db.execute_query(
- "SELECT id FROM sample WHICH REFERENCES A SourceEvent "
- "WHICH HAS AN IGSN AND "
- f"(WHICH WAS UPDATED SINCE {form_data['from_date']})")
- ]
elif "query_string" in form_data and form_data["query_string"]:
query_string = form_data["query_string"]
if not query_string.lower().startswith("find ") and not query_string.lower().startswith("select "):
@@ -657,11 +635,11 @@ def main():
)
return
else:
- if not form_data["bis_ids"]:
+ if not form_data["ids"]:
logger.error(
"Please specify the samples to be exported either by query or by id(s).")
return
- tmp = form_data["bis_ids"].split(",")
+ tmp = form_data["ids"].split(",")
data = []
for d in tmp:
if "-" in d:
--
GitLab
From 8f7beb3fd5b053b474d6a33c10d92f63ecbcfff1 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 17 Feb 2025 18:13:53 +0100
Subject: [PATCH 59/63] ENH: Adapt sample export to new data model
---
.../scripting/bin/export_sample_csv.py | 278 ++++++++----------
.../bin/sample_helpers/default_constants.yml | 1 +
...mple_registration_get_person_identifier.py | 5 +
.../sample_upload_column_definitions.py | 16 +-
4 files changed, 143 insertions(+), 157 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
index 41ca25f..169575a 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
@@ -42,8 +42,10 @@ from bis_utils import (create_email_with_link_text,
get_options_row, send_mail_with_defaults)
from export_container_csv import (generate_label_text,
extract_storage_chain as container_storage_chain)
+from sample_helpers.sample_registration_get_person_identifier import get_person_identifier_from_rec
from sample_helpers.sample_upload_column_definitions import (
- DATATYPE_DEFINITIONS, SPECIAL_TREATMENT_SAMPLE as SPECIAL_TREATMENT)
+ DATATYPE_DEFINITIONS, SPECIAL_TREATMENT_SAMPLE as
+ SPECIAL_TREATMENT, use_custom_names)
from sample_helpers.utils import (CONSTANTS, get_column_header_name,
get_entity_name)
@@ -126,7 +128,7 @@ def extract_value_as_list(record, key):
def extract_storage_id(record, key):
- return extract_value_as_list(record, "Container")
+ return extract_value_as_list(record, get_entity_name("container_rt"))
def extract_pdf_id(record, key):
@@ -134,19 +136,20 @@ def extract_pdf_id(record, key):
return prop.value if prop is not None else None
-def extract_storage_container_label(record, key):
- ids = extract_value_as_list(record, "Container")
- return retrieve_values(ids, 'BIS Label')
-
-
-def extract_nagoya_case_number(record, key):
- ids = extract_value_as_list(record, "NagoyaCase")
- return retrieve_values(ids, key)
-
-
def extract_person(record, key):
ids = extract_value_as_list(record, key)
- return retrieve_values(ids, 'Abbreviation')
+ person_recs = [cached_record(i) for i in ids]
+ return [get_person_identifier_from_rec(r) for r in person_recs]
+
+
+def extract_event_responsible(record_key):
+ evt = retrieve_event(record)
+ if len(evt) == 0:
+ return None
+ elif len(evt) > 1:
+ logger.debug(f"Sample {record.id} references more than one event.")
+ return None
+ return extract_person(evt[0], get_entity_name("responsible_person_event"))
def extract_parent_sample(record, key):
@@ -161,51 +164,14 @@ def extract_reference_name(record, key):
for i in ids if i is not None]
-def retrieve_source_event(record):
- ids = extract_value_as_list(record, 'SourceEvent')
- if record.get_property("SourceEvent") is None:
+def retrieve_event(record):
+ ids = extract_value_as_list(record, get_entity_name("event_rt"))
+ if record.get_property(get_entity_name("event_rt")) is None:
# there are cases where this property is named "Event"
ids = extract_value_as_list(record, 'Event')
return [cached_record(i) for i in ids]
-def retrieve_gear(record):
- ids = [e.get_property("Gear").value for e in retrieve_source_event(record)
- if e.get_property("Gear") is not None]
- return [cached_query(f"SELECT 'parent', 'Configuration' FROM ENTITY WITH id = '{i}'", unique=True) for i in ids]
-
-
-def extract_gear(record, key):
- return [e.get_parents()[0].name for e in retrieve_gear(record)]
-
-
-def extract_gear_configuration(record, key):
- return [e.get_property("Configuration").value for e in
- retrieve_gear(record)
- if e.get_property("Configuration") is not None]
-
-
-def extract_date_time(record, p):
- if p.lower() == "time start" or p.lower() == "time stop":
- # these are attached to the source event directly
- return [e.get_property(p).value for e in retrieve_source_event(record) if
- e.get_property(p) is not None and e.get_property(p).value is not None]
- else:
- return extract_value_as_list(record, p)
-
-
-def extract_station_number(record, key):
- source_ev = retrieve_source_event(record)
- return [e.get_property(key).value for e in source_ev if
- e.get_property(key) is not None]
-
-
-def extract_station_id(record, key):
- source_ev = retrieve_source_event(record)
- return [e.get_property(key).value for e in source_ev if
- e.get_property(key) is not None]
-
-
def retrieve_positions(source_ev):
pos_ids = extract_value_as_list(source_ev, "Position")
return [cached_record(i) for i in pos_ids]
@@ -217,7 +183,7 @@ def has_parent(r, par):
def extract_position(record, position, component):
- source_evs = retrieve_source_event(record)
+ source_evs = retrieve_event(record)
result = []
for ev in source_evs:
_pos = [pos for pos in retrieve_positions(ev)]
@@ -234,83 +200,108 @@ def extract_position(record, position, component):
return [pos.get_property(component).value for pos in result if pos.get_property(component) is not None]
+def extract_ele_start(record, key):
+ return extract_position(record, get_entity_name("StartPosition"), get_entity_name("elevation"))
+
+
+def extract_ele_stop(record, key):
+ return extract_position(record, get_enum_value("StopPosition"), get_entity_name("elevation"))
+
+
def extract_lat_start(record, key):
- return extract_position(record, "StartPosition", "Latitude")
+ return extract_position(record, get_entity_name("StartPosition"), get_entity_name("latitude"))
def extract_lat_stop(record, key):
- return extract_position(record, "StopPosition", "Latitude")
+ return extract_position(record, get_enum_value("StopPosition"), get_entity_name("latitude"))
def extract_lng_start(record, key):
- return extract_position(record, "StartPosition", "Longitude")
+ return extract_position(record, get_entity_name("StartPosition"), get_entity_name("longitude"))
def extract_lng_stop(record, key):
- return extract_position(record, "StopPosition", "Longitude")
+ return extract_position(record, get_entity_name("StopPosition"), get_entity_name("longitude"))
-def extract_sampling_depth_start(record, key):
- return extract_position(record, "StartPosition", "Sampling depth")
+def extract_linkahead_url(record, key):
+ # base_uri = db.get_config().get("Connection", "url")
+ base_uri = get_config_setting("public_host_url")
+ return urllib.parse.urljoin(base_uri, f"Entity/{record.id}")
-def extract_sampling_depth_stop(record, key):
- return extract_position(record, "StopPosition", "Sampling depth")
+def extract_doi(record, key):
+ source_evs = retrieve_event(record)
+ if len(source_evs) > 1:
+ logger.error(
+ f"Sample {record.id} references more than one event so no unique DOI can be exported.")
+ return None
+ elif len(source_evs) == 0:
+ return None
+ ev = source_evs[0]
+ return ev.get_property(get_entity_name("igsn_doi_prop")).value if ev.get_property("igsn_doi_prop") is not None else None
-def extract_water_depth_start(record, key):
- return extract_position(record, "StartPosition", "Water depth")
+def _extract_event_prop(record, key, ref=False):
+ evt = retrieve_event(record)
+ if len(evt) == 0:
+ return None
+ elif len(evt) > 1:
+ logger.debug(f"Sample {record.id} references more than one event.")
+ return None
-def extract_water_depth_stop(record, key):
- return extract_position(record, "StopPosition", "Water depth")
+ if ref:
+ return extract_reference_name(evt[0], key)
+ return extract_value_as_list(evt[0], key)
-def extract_source_event_name(record, key):
- return [e.name for e in retrieve_source_event(record)]
+def extract_biome(record, key):
-def extract_hol(record, key):
- source_ev = retrieve_source_event(record)
- return [e.get_property(key).value for e in source_ev if
- e.get_property(key) is not None]
+ return _extract_event_prop(record, get_entity_name("Biome"), ref=True)
-def extract_bis_url(record, key):
- # base_uri = db.get_config().get("Connection", "url")
- base_uri = get_config_setting("public_host_url")
- return urllib.parse.urljoin(base_uri, f"Entity/{record.id}")
+def extract_campaign(record, key):
+ return _extract_event_prop(record, get_entity_name("Campaign"), ref=True)
-def extract_igsn(record, key):
- source_evs = retrieve_source_event(record)
- if len(source_evs) > 1:
- logger.error(
- f"Sample {record.id} references more than one SourceEvent so no unique IGSN can be exported.")
- return None
- elif len(source_evs) == 0:
- return None
- ev = source_evs[0]
- return ev.get_property(key).value if ev.get_property(key) is not None else None
+def extract_device(record, key):
-def extract_doi(record, key):
- source_evs = retrieve_source_event(record)
- if len(source_evs) > 1:
- logger.error(
- f"Sample {record.id} references more than one SourceEvent so no unique DOI can be exported.")
- return None
- elif len(source_evs) == 0:
- return None
- ev = source_evs[0]
- return ev.get_property("DOI").value if ev.get_property("DOI") is not None else None
+ return _extract_event_prop(record, get_entity_name("Device"), ref=True)
+
+
+def extract_end_date(record, key):
+
+ return _extract_event_prop(record, get_entity_name("end_date_prop"))
+
+
+def extract_level(record, key):
+
+ return _extract_event_prop(record, get_entity_name("level"))
+
+
+def extract_sphere(record, key):
+
+ return _extract_event_prop(record, get_entity_name("Sphere"), ref=True)
+
+
+def extract_locality_descr(record, key):
+
+ return _extract_event_prop(record, get_entity_name("locality_description_prop"))
+
+
+def extract_locality_name(record, key):
+
+ return _extract_event_prop(record, get_entity_name("locality_name_prop"))
def extract_storage_chain(record, key):
- if record.get_property("Container") is not None and record.get_property("Container").value:
+ if record.get_property(get_entity_name("container_rt")) is not None and record.get_property(get_entity_name("container_rt")).value:
- cont_id = record.get_property("Container").value
+ cont_id = record.get_property(get_entity_name("container_rt")).value
if isinstance(cont_id, list):
if len(cont_id) > 1:
logger.debug(f"Sample {record.id} has multiple containers.")
@@ -327,7 +318,7 @@ def extract_storage_chain(record, key):
def extract_event_url(record, key):
- events = retrieve_source_event(record)
+ events = retrieve_event(record)
if not events:
return None
if len(events) == 1:
@@ -337,72 +328,61 @@ def extract_event_url(record, key):
# must include all keys from SPECIAL_TREATMENT
-EXTRACTORS = {
- "BIS ID": lambda record, key: record.id,
- "Parent BIS ID": extract_parent_sample,
- "AphiaID": default_find,
- "Collection": extract_reference_name,
+EXTRACTORS = use_custom_names({
+ "entity_id": lambda record, key: record.id,
"Main User": extract_person,
- "Sampling Person": extract_person,
- "PI": extract_person,
- "Person": extract_person,
- "Gear": extract_gear,
- "Gear configuration": extract_gear_configuration,
+ "Biome": extract_biome,
+ "Campaign": extract_campaign,
+ "Collector": extract_person,
+ "Curator": extract_person,
+ "Device": extract_device,
+ "Elevation start": extract_ele_start,
+ "Elevation stop": extract_ele_stop,
+ "Embargo": default_find,
+ "End date": extract_end_date,
"Latitude start": extract_lat_start,
- "Longitude start": extract_lng_start,
- "Storage ID": extract_storage_id,
- "Nagoya case number": extract_nagoya_case_number,
- "PDFReport": extract_pdf_id,
- "Subevent": extract_source_event_name,
- "Station ID": extract_station_id,
- "Station number": extract_station_number,
- "Sampling depth start": extract_sampling_depth_start,
- "Sampling depth stop": extract_sampling_depth_stop,
- "Water depth start": extract_water_depth_start,
- "Water depth stop": extract_water_depth_stop,
"Latitude stop": extract_lat_stop,
+ "Level": extract_level,
+ "LinkAhead URL": extract_linkahead_url,
+ "Longitude start": extract_lng_start,
"Longitude stop": extract_lng_stop,
- "Storage chain": extract_storage_chain,
- "Storage Container Label": extract_storage_container_label,
- "Hol": extract_hol,
+ "PDFReport": extract_pdf_id,
"Sampling method": default_find,
- # "Publications": TODO never used
- # "NCBI BioProject": TODO never used
- # "NCBI BioSample": TODO never used
- # "NCBI Accession": TODO never used
- "BIS URL": extract_bis_url,
- "IGSN": extract_igsn,
- "IGSN URL": extract_doi,
- "Sphere": default_find,
- "URL SourceEvent": extract_event_url,
-}
-
-REVERSE_COLUMN_CONVERTER = {
- "Collection": collection_value,
- "PI": person_value,
- "Person": person_value,
-}
+ "Sphere": extract_sphere,
+ "Start date": extract_end_date,
+ "Storage ID": extract_storage_id,
+ "Storage chain": extract_storage_chain,
+ "URL Event": extract_event_url,
+ "igsn_doi_prop": extract_doi,
+ "locality_description_prop": extract_locality_descr,
+ "locality_name_prop": extract_locality_name,
+ "parent_sample_prop": extract_parent_sample,
+ "responsible_person_event": extract_event_responsible
+})
+
+REVERSE_COLUMN_CONVERTER = use_custom_names({
+})
# List of sample properties to be ignored because they are treated
# otherwise. Similar, but not identical to SPECIAL TREATMENT.
-IGNORE_KEYS = [
- "Parent Sample",
- "Container",
- "Event",
-]
+IGNORE_KEYS = use_custom_names([
+ "parent_sample_prop",
+ "container_rt",
+ "event_rt",
+])
# Additional list of keys to be ignored when extracting parent sample information
-IGNORE_KEYS_PARENT = IGNORE_KEYS + [
- "LinkAhead ID",
-]
+IGNORE_KEYS_PARENT = IGNORE_KEYS + use_custom_names([
+ "entity_id",
+])
# List of columns to be exported although they are not known to or ignored by
# the import.
-ADDITIONAL_EXPORTS = [
+ADDITIONAL_EXPORTS = use_custom_names([
"LinkAhead URL",
"Parent LinkAhead ID",
"Storage chain",
-]
+])
def extract_value(r, e):
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index c7f1baa..f752180 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -24,6 +24,7 @@ csv_column_names:
locality_description_prop: "Locality description"
locality_name_prop: "Locality name"
responsible_person_event: "Event responsible"
+ parent_sample_prop: "Parent LinkAhead ID"
csv_column_descriptions:
LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
index 329dc3d..396bf0e 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
@@ -26,6 +26,11 @@ def get_person_identifier(form_data: dict) -> str:
"""
person_rec = db.cached.cached_get_entity_by(eid=form_data["responsible_person"])
+
+ return get_person_identifier_from_rec(person_rec)
+
+
+def get_person_identifier_from_rec(person_rec: db.Record) -> str:
# Use abbreviation if present
if (person_rec.get_property(get_entity_name("abbreviation_prop")) is not None and
person_rec.get_property(get_entity_name("abbreviation_prop")).value):
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index d6a62cb..3912595 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -43,7 +43,7 @@ def _embargo_converter(text: str):
f"The embargo should be either a date in YYYY-MM-DD format, or 'true'/'yes' or 'false'/'no', but is {text}.")
-def _use_custom_names(definition: Union[list, dict]):
+def use_custom_names(definition: Union[list, dict]):
"""Replace names in list or dict keys by custom names with
`utils.get_column_header_name`.
@@ -56,7 +56,7 @@ def _use_custom_names(definition: Union[list, dict]):
raise ValueError(f"Expected dict or list, but got {type(definition)}.")
-DATATYPE_DEFINITIONS = _use_custom_names({
+DATATYPE_DEFINITIONS = use_custom_names({
"Campaign": str,
"Elevation start": float,
"Elevation stop": float,
@@ -75,16 +75,16 @@ DATATYPE_DEFINITIONS = _use_custom_names({
# Obligatory columns: Must exist and must not be empty
# Must exist
-OBLIGATORY_COLUMNS = _use_custom_names([
+OBLIGATORY_COLUMNS = use_custom_names([
"entity_id",
])
-OBLIGATORY_COLUMNS_CHILD = _use_custom_names([
+OBLIGATORY_COLUMNS_CHILD = use_custom_names([
"entity_id",
"Parent LinkAhead ID",
])
-COLUMN_CONVERTER = _use_custom_names({
+COLUMN_CONVERTER = use_custom_names({
"Collector": semicolon_separated_list,
"Curator": semicolon_separated_list,
"Embargo": _embargo_converter,
@@ -92,7 +92,7 @@ COLUMN_CONVERTER = _use_custom_names({
"Sphere": semicolon_separated_list,
})
-SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
+SPECIAL_TREATMENT_SAMPLE = use_custom_names([
"Biome",
"Campaign",
"Collector",
@@ -102,7 +102,7 @@ SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"Elevation stop",
"Embargo",
"End date",
- "Event responsible",
+ "responsible_person_event",
"igsn_doi_prop",
"Latitude start",
"Latitude stop",
@@ -120,7 +120,7 @@ SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
"entity_id",
])
-IGNORED_COLUMN_NAMES_SAMPLE = _use_custom_names([
+IGNORED_COLUMN_NAMES_SAMPLE = use_custom_names([
"LinkAhead URL",
"Parent Sample",
"Storage chain",
--
GitLab
From bded836dbeb2c7a64cb57c72ea0e65d46cb8387b Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 17 Feb 2025 18:49:07 +0100
Subject: [PATCH 60/63] FIX: Correct exporter list
---
.../scripting/bin/export_sample_csv.py | 20 +++++++++++++------
.../sample_upload_column_definitions.py | 8 +++++---
2 files changed, 19 insertions(+), 9 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
index 169575a..7311fc1 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
@@ -75,7 +75,10 @@ def cached_query(query, unique=False):
def reverse_semicolon_separated_list(value):
if isinstance(value, list):
- return ";".join([str(val) for val in value if val is not None])
+ ret_str = ";".join([str(val) for val in value if val is not None])
+ if ',' in ret_str:
+ ret_str = f"\"{ret_str}\""
+ return ret_str
else:
return value
@@ -168,7 +171,7 @@ def retrieve_event(record):
ids = extract_value_as_list(record, get_entity_name("event_rt"))
if record.get_property(get_entity_name("event_rt")) is None:
# there are cases where this property is named "Event"
- ids = extract_value_as_list(record, 'Event')
+ ids = extract_value_as_list(record, get_entity_name("event_rt"))
return [cached_record(i) for i in ids]
@@ -205,7 +208,7 @@ def extract_ele_start(record, key):
def extract_ele_stop(record, key):
- return extract_position(record, get_enum_value("StopPosition"), get_entity_name("elevation"))
+ return extract_position(record, get_entity_name("StopPosition"), get_entity_name("elevation"))
def extract_lat_start(record, key):
@@ -213,7 +216,7 @@ def extract_lat_start(record, key):
def extract_lat_stop(record, key):
- return extract_position(record, get_enum_value("StopPosition"), get_entity_name("latitude"))
+ return extract_position(record, get_entity_name("StopPosition"), get_entity_name("latitude"))
def extract_lng_start(record, key):
@@ -277,6 +280,11 @@ def extract_end_date(record, key):
return _extract_event_prop(record, get_entity_name("end_date_prop"))
+def extract_start_date(record, key):
+
+ return _extract_event_prop(record, get_entity_name("start_date_prop"))
+
+
def extract_level(record, key):
return _extract_event_prop(record, get_entity_name("level"))
@@ -349,7 +357,7 @@ EXTRACTORS = use_custom_names({
"PDFReport": extract_pdf_id,
"Sampling method": default_find,
"Sphere": extract_sphere,
- "Start date": extract_end_date,
+ "Start date": extract_start_date,
"Storage ID": extract_storage_id,
"Storage chain": extract_storage_chain,
"URL Event": extract_event_url,
@@ -380,7 +388,7 @@ IGNORE_KEYS_PARENT = IGNORE_KEYS + use_custom_names([
# the import.
ADDITIONAL_EXPORTS = use_custom_names([
"LinkAhead URL",
- "Parent LinkAhead ID",
+ "parent_sample_prop",
"Storage chain",
])
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 3912595..9347ad4 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -57,20 +57,22 @@ def use_custom_names(definition: Union[list, dict]):
DATATYPE_DEFINITIONS = use_custom_names({
+ "entity_id": str,
+ "Main User": str,
"Campaign": str,
"Elevation start": float,
"Elevation stop": float,
+ "End date": str,
"Latitude start": float,
"Latitude stop": float,
"Longitude start": float,
"Longitude stop": float,
- "Main User": str,
"PI": str,
"Parent LinkAhead ID": str,
"SampleMethod": str,
"SampleType": str,
+ "Start Date": str,
"Storage ID": str,
- "entity_id": str,
})
# Obligatory columns: Must exist and must not be empty
@@ -113,7 +115,7 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
"Longitude stop",
"Main User",
"PDFReport",
- "Parent Linkahead ID",
+ "parent_sample_prop",
"Sphere",
"Start date",
"Storage ID",
--
GitLab
From 399fda02c5e34880279ab88aec902055639b2967 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 11 Mar 2025 16:12:40 +0100
Subject: [PATCH 61/63] MAINT: Remove debugging output
---
.../caosdb-server/scripting/bin/crawl_sample_data_async.py | 1 -
1 file changed, 1 deletion(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index f3fff6d..ace23ee 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -176,7 +176,6 @@ def update_sample_records(data, htmluserlog_public):
# Samples might need additional post processing
samples = post_process_samples(samples, data)
- logger.info(samples)
synchroize(samples, additional_property_ents, htmluserlog_public)
--
GitLab
From 292fed5ab5fe5c4d8bc1299b0acf3656680dc674 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Tue, 11 Mar 2025 16:21:21 +0100
Subject: [PATCH 62/63] WIP: new dump; make data model consistent
---
README.md | 122 +
.../sample-management-datamodel.yml | 17 +-
.../ext/js/ext_sample_reference_resolver.js | 1 +
.../sample_upload_column_definitions.py | 2 +-
.../scripting/bin/upload_sample_template.py | 25 +-
...5-03-11T15:15:22.815622880+00:00.dump.sql} | 2822 +++++++----------
.../caosroot.2025-03-11T16151741706122.tar.gz | Bin 0 -> 126 bytes
.../custom/other/restore/caosroot.tar.gz | Bin 124 -> 0 bytes
8 files changed, 1257 insertions(+), 1732 deletions(-)
rename test-profile/custom/other/restore/{caosdb.dump.sql => caosdb.2025-03-11T15:15:22.815622880+00:00.dump.sql} (76%)
create mode 100644 test-profile/custom/other/restore/caosroot.2025-03-11T16151741706122.tar.gz
delete mode 100644 test-profile/custom/other/restore/caosroot.tar.gz
diff --git a/README.md b/README.md
index ff11a58..724f519 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,68 @@ This module contains the custom code for sample management like it is
used in GEOMAR's [Biosample Information System
BIS](https://biosamples.geomar.de/).
+## Features
+### Sample Registration
+Samples have unique identifiers (Sample ID) that can be used to persistently
+identify them. The Sample ID can for example be printed as QR Code and used to
+label the physical samples.
+
+Since online access to LinkAhead might not be available during sampling,
+Samples can be registered in advance in order to generate the Sample IDs. This
+allows to print labels for future samples and also allows to download a CSV
+template that can be filled with information about the sample for later import
+into LinkAhead.
+
+Registration is available via the menu in the webinterface "Sample
+Management" -> "Register new Sample"
+
+The CSV Template that is generated always has a set of required columns and
+possibly additional columns that can be selected during the registration. The
+set of columns can be stored for later use via the `RegisterSampleTemplates`.
+Such a template can be created using the "Create sample template" menu entry.
+
+### Sample Update
+Via the menu in the webinterface "Sample Management" -> "Upload Sample template"
+you can upload a CSV template that was created via the registration detailed
+above (or via the export, see below). This updates existing Sample Records
+according to the data contained in the CSV file. This upload possibly creates
+new Records like Events which are related to the updated Samples.
+
+**Important**: Note, that this will override the information of updated samples
+in the server and thus can possibly cause data loss if changes in LinkAhead are
+not reflected in the uploaded file.
+
+### Child Samples
+A Sample can reference another Sample as `Parent sample` to indicate, that the
+sample originated form the other one. If a sample has such a reference, we
+call it a child sample and the referenced sample a parent sample.
+A lot of information is the same
+for both child and parent Sample and this information is not duplicated but it
+is only referenced by the parent Sample.
+
+This implies that child samples are treated differently thatn parent samples
+during the upload of CSV templates: Some information that is obligatory for
+parent sample are not needed for child samples. There for you can create a
+different CSV template for child samples via the "Register new child sample"
+menu entry.
+
+### Container Registration
+Containers have a unique identifier (Container ID) that can be used to
+persistently identify them. The Container ID can for example be printed as QR
+Code and used to label physical containers.
+
+The "Register new Container" menu entry under "Storage Management" allows to
+create new Container Records with the respective IDs. In this process also
+information on Container Type, Size and parent Containers are incorporated.
+
+### Container Update
+You can upload filled CSV templates to update the information about Containers
+stored in LinkAhead
+
+### Container Export
+You can create a filled CSV template with the information about Containers as
+it is currently stored in LinkAhead.
+
## Usage
**TODO**: Add explanations, screenshots, ec. to explain the sample
@@ -59,6 +121,66 @@ arguments and returns the list of post processed samples.
There is a pre-configured `test-profile` that you can use for testing
this repository.
+
+## Data Model
+This module requires a certain data model in order to work. However, the exact
+names of RecordTypes and Properties can be configured. Below, we will use the
+default names but also reference the variable names of `constants.yml` that
+allow to change those.
+
+### Sample (`variable missing`)
+This is the central RecordType for the sample management and used to represent
+samples of various types
+
+#### `Parent_Sample` (`$parent_sample_prop`)
+references the sample from which the sample at hand originated (for example by
+cutting the parent sample into multiple pieces0
+
+#### `Main User`
+references the person that mainly works with this sample
+
+#### `PI`
+references the person that is the responsible principle investigator (PI)
+
+### Event (`$event_rt`)
+A sampling event. Each sample reference the event where it was created.
+
+#### Position (`var missing`)
+The position (e.g. of an Event) that is defined via longituted, latitude and
+possibly elevation
+#### "Biome"
+#### "Campaign"
+#### "Device"
+#### "EventType"
+#### "igsn_doi_prop"
+#### "level"
+#### "locality_description_prop"
+#### "locality_name_prop"
+#### "Sphere"
+
+### Person (`variable missing`)
+a natural person
+
+#### `first_name` (`$first_name_prop`)
+#### `last_name` (`$last_name_prop`)
+#### `abbreviation` (`$abbreviation_prop`)
+
+### `Container` (`$container_rt`)
+a physical container that contains Samples and/or other Containers
+
+####`Child_Container` (`$child_container_prop`)
+references Containers that are contained in the Container at hand
+
+#### `container_label` (`$container_label_prop`)
+#### `Container size` (`$container_size_prop`)
+#### `ContainerType` (`$containertype_rt`)
+#### `custom_label` (`$custom_label_prop`)
+
+#### `Responsible_Person` (`$responsible_person_event`)
+references the person that is responsilbe for this sample, e.g. the PI
+
+### `RegisterSampleTemplates` (missing var)
+
## Further Reading
Please refer to the [official documentation](https://docs.indiscale.com/caosdb-deploy/) for more information.
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index 04b74cc..4d12dc6 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -48,8 +48,9 @@ ContainerType:
Abbreviation:
ConditionType:
- inherit_from_recommended:
- - ControlledRecordtype
+ inherit_from_obligatory:
+ - ControlledRecordType
+
StorageCondition:
recommended_properties:
ConditionType:
@@ -64,7 +65,7 @@ Container:
container_label:
description: A standardized label for a container
datatype: TEXT
- Child container:
+ Child_Container:
datatype: LIST<Container>
Container size:
description: The size of the container, e.g. number of spaces or dimension
@@ -82,7 +83,7 @@ Sample:
recommended_properties:
Container:
SampleType:
- Parent sample:
+ Parent_Sample:
datatype: Sample
Main User:
datatype: Person
@@ -149,12 +150,12 @@ EventType:
- ControlledRecordType
Biome:
- inherit_from_recommended:
- - ControlledRecordtype
+ inherit_from_obligatory:
+ - ControlledRecordType
Device:
- inherit_from_recommended:
- - ControlledRecordtype
+ inherit_from_obligatory:
+ - ControlledRecordType
Event:
recommended_properties:
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
index ec82f14..d237d62 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
@@ -1,4 +1,5 @@
var sample_management_reference_resolver = new function (getEntityID, getEntityName, getParents, getProperty, query) {
+ // TODO note explicitly what data model assumptions are made here
const lastname_prop_name = "last_name";
const firstname_prop_name = "first_name";
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 9347ad4..5535863 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -71,7 +71,7 @@ DATATYPE_DEFINITIONS = use_custom_names({
"Parent LinkAhead ID": str,
"SampleMethod": str,
"SampleType": str,
- "Start Date": str,
+ "Start date": str,
"Storage ID": str,
})
diff --git a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
index 4551b35..7160007 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
@@ -156,19 +156,20 @@ def main():
property_name = eprop.name
if property_name in SPECIAL_TREATMENT_SAMPLE:
continue
- if db.apiutils.is_reference(eprop):
- rt = db.get_entity_by_id(eprop.id)
- if len(rt.properties) == 1:
- converter = _get_converter_from_property_datatype(rt.properties[0].datatype)
- elif len(rt.properties) == 1:
- converter = str
+ if property_name not in DATATYPE_DEFINITIONS:
+ if db.apiutils.is_reference(eprop):
+ rt = db.get_entity_by_id(eprop.id)
+ if len(rt.properties) == 1:
+ converter = _get_converter_from_property_datatype(rt.properties[0].datatype)
+ elif len(rt.properties) < 1:
+ converter = str
+ else:
+ converter = None
else:
- converter = None
- else:
- converter = _get_converter_from_property_datatype(eprop.datatype)
- if converter is None:
- continue
- DATATYPE_DEFINITIONS[property_name] = converter
+ converter = _get_converter_from_property_datatype(eprop.datatype)
+ if converter is None:
+ continue
+ DATATYPE_DEFINITIONS[property_name] = converter
if sample.get_importance(property_name) == db.OBLIGATORY:
# This is only needed if the sample is not a child sample
OBLIGATORY_COLUMNS.append(property_name)
diff --git a/test-profile/custom/other/restore/caosdb.dump.sql b/test-profile/custom/other/restore/caosdb.2025-03-11T15:15:22.815622880+00:00.dump.sql
similarity index 76%
rename from test-profile/custom/other/restore/caosdb.dump.sql
rename to test-profile/custom/other/restore/caosdb.2025-03-11T15:15:22.815622880+00:00.dump.sql
index 3dac867..de206c4 100644
--- a/test-profile/custom/other/restore/caosdb.dump.sql
+++ b/test-profile/custom/other/restore/caosdb.2025-03-11T15:15:22.815622880+00:00.dump.sql
@@ -2,7 +2,7 @@
--
-- Host: sqldb Database: caosdb
-- ------------------------------------------------------
--- Server version 10.11.9-MariaDB-ubu2204
+-- Server version 11.4.5-MariaDB-ubu2404
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -36,7 +36,7 @@ CREATE TABLE `archive_collection_type` (
CONSTRAINT `archive_collection_type_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_collection_type_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_collection_type_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -46,9 +46,10 @@ CREATE TABLE `archive_collection_type` (
LOCK TABLES `archive_collection_type` WRITE;
/*!40000 ALTER TABLE `archive_collection_type` DISABLE KEYS */;
INSERT INTO `archive_collection_type` VALUES
-(0,153,177,'LIST',1),
-(0,153,177,'LIST',2),
-(0,153,177,'LIST',3);
+(0,0,113,'LIST',1),
+(0,192,162,'LIST',1),
+(0,194,162,'LIST',1),
+(0,196,162,'LIST',1);
/*!40000 ALTER TABLE `archive_collection_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -75,7 +76,7 @@ CREATE TABLE `archive_data_type` (
CONSTRAINT `archive_data_type_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_data_type_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_data_type_ibfk_4` FOREIGN KEY (`datatype`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -85,55 +86,14 @@ CREATE TABLE `archive_data_type` (
LOCK TABLES `archive_data_type` WRITE;
/*!40000 ALTER TABLE `archive_data_type` DISABLE KEYS */;
INSERT INTO `archive_data_type` VALUES
-(0,0,144,13,1),
-(0,0,144,13,2),
-(0,0,144,13,3),
-(0,0,145,13,1),
-(0,0,145,13,2),
-(0,0,145,13,3),
-(0,0,146,13,1),
-(0,0,146,13,2),
-(0,0,146,13,3),
-(0,0,147,13,1),
-(0,0,147,13,2),
-(0,0,147,13,3),
-(0,0,102,14,1),
-(0,0,107,14,1),
-(0,0,108,14,1),
-(0,0,114,14,1),
-(0,111,177,101,1),
-(0,111,177,101,2),
-(0,111,177,101,3),
-(0,111,178,110,1),
-(0,111,178,110,2),
-(0,111,178,110,3),
-(0,136,177,110,1),
-(0,136,177,110,2),
-(0,136,177,110,3),
-(0,118,178,111,1),
-(0,118,178,111,2),
-(0,118,178,111,3),
-(0,118,177,119,1),
-(0,118,177,119,2),
-(0,118,177,119,3),
-(0,118,179,120,1),
-(0,118,179,120,2),
-(0,118,179,120,3),
-(0,118,180,121,1),
-(0,118,180,121,2),
-(0,118,180,121,3),
-(0,119,178,138,1),
-(0,119,178,138,2),
-(0,119,178,138,3),
-(0,153,177,143,1),
-(0,153,177,143,2),
-(0,153,177,143,3),
-(0,150,177,148,1),
-(0,150,177,148,2),
-(0,150,177,148,3),
-(0,153,178,148,1),
-(0,153,178,148,2),
-(0,153,178,148,3);
+(0,0,113,111,1),
+(0,0,120,118,1),
+(0,192,163,124,1),
+(0,194,163,124,1),
+(0,196,163,124,1),
+(0,192,162,139,1),
+(0,194,162,139,1),
+(0,196,162,139,1);
/*!40000 ALTER TABLE `archive_data_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -159,7 +119,7 @@ CREATE TABLE `archive_date_data` (
CONSTRAINT `archive_date_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_date_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_date_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -168,6 +128,13 @@ CREATE TABLE `archive_date_data` (
LOCK TABLES `archive_date_data` WRITE;
/*!40000 ALTER TABLE `archive_date_data` DISABLE KEYS */;
+INSERT INTO `archive_date_data` VALUES
+(0,196,147,20231220,'FIX',2,1),
+(0,196,148,20231220,'FIX',3,1),
+(0,194,147,20231220,'FIX',2,1),
+(0,194,148,20231220,'FIX',3,1),
+(0,192,147,20231220,'FIX',2,1),
+(0,192,148,20231220,'FIX',3,1);
/*!40000 ALTER TABLE `archive_date_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -194,7 +161,7 @@ CREATE TABLE `archive_datetime_data` (
CONSTRAINT `archive_datetime_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_datetime_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_datetime_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -217,7 +184,7 @@ CREATE TABLE `archive_desc_overrides` (
`domain_id` int(10) unsigned NOT NULL,
`entity_id` int(10) unsigned NOT NULL,
`property_id` int(10) unsigned NOT NULL,
- `description` text NOT NULL,
+ `description` mediumtext NOT NULL,
`_iversion` int(10) unsigned NOT NULL,
UNIQUE KEY `archive_desc_overrides-d-e-p-v` (`domain_id`,`entity_id`,`property_id`,`_iversion`),
KEY `domain_id` (`domain_id`,`entity_id`,`_iversion`),
@@ -227,7 +194,7 @@ CREATE TABLE `archive_desc_overrides` (
CONSTRAINT `archive_desc_overrides_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_desc_overrides_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_desc_overrides_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -262,7 +229,7 @@ CREATE TABLE `archive_double_data` (
CONSTRAINT `archive_double_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_double_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_double_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -283,7 +250,7 @@ DROP TABLE IF EXISTS `archive_entities`;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `archive_entities` (
`id` int(10) unsigned NOT NULL,
- `description` text DEFAULT NULL,
+ `description` mediumtext DEFAULT NULL,
`role` enum('RECORDTYPE','RECORD','FILE','_REPLACEMENT','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE') NOT NULL,
`acl` int(10) unsigned DEFAULT NULL,
`_iversion` int(10) unsigned NOT NULL,
@@ -291,7 +258,7 @@ CREATE TABLE `archive_entities` (
KEY `acl` (`acl`),
CONSTRAINT `archive_entities_ibfk_1` FOREIGN KEY (`id`, `_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE,
CONSTRAINT `archive_entities_ibfk_2` FOREIGN KEY (`acl`) REFERENCES `entity_acl` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -301,68 +268,18 @@ CREATE TABLE `archive_entities` (
LOCK TABLES `archive_entities` WRITE;
/*!40000 ALTER TABLE `archive_entities` DISABLE KEYS */;
INSERT INTO `archive_entities` VALUES
-(101,NULL,'RECORDTYPE',2,1),
-(102,'An abbreviation for this entity that is used for creating BIS labels','PROPERTY',2,1),
-(106,NULL,'RECORDTYPE',2,1),
-(106,NULL,'RECORDTYPE',2,2),
-(106,NULL,'RECORDTYPE',2,3),
-(107,NULL,'PROPERTY',2,1),
-(108,NULL,'PROPERTY',2,1),
-(110,NULL,'RECORDTYPE',2,1),
-(111,NULL,'RECORDTYPE',2,1),
-(111,NULL,'RECORDTYPE',2,2),
-(111,NULL,'RECORDTYPE',2,3),
-(114,'A custom label for a container that doesn\'t have to follow the BIS labeling guidelines.','PROPERTY',2,1),
-(118,NULL,'RECORDTYPE',2,1),
-(118,NULL,'RECORDTYPE',2,2),
-(118,NULL,'RECORDTYPE',2,3),
-(119,NULL,'RECORDTYPE',2,1),
-(119,NULL,'RECORDTYPE',2,2),
-(119,NULL,'RECORDTYPE',2,3),
-(136,NULL,'RECORDTYPE',2,1),
-(136,NULL,'RECORDTYPE',2,2),
-(136,NULL,'RECORDTYPE',2,3),
-(143,NULL,'RECORDTYPE',2,1),
-(143,NULL,'RECORDTYPE',2,2),
-(143,NULL,'RECORDTYPE',2,3),
-(144,'The depth of the water in meters as a positive value','PROPERTY',2,1),
-(144,'The depth of the water in meters as a positive value','PROPERTY',2,2),
-(144,'The depth of the water in meters as a positive value','PROPERTY',2,3),
-(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,1),
-(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,2),
-(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2,3),
-(146,NULL,'PROPERTY',2,1),
-(146,NULL,'PROPERTY',2,2),
-(146,NULL,'PROPERTY',2,3),
-(147,NULL,'PROPERTY',2,1),
-(147,NULL,'PROPERTY',2,2),
-(147,NULL,'PROPERTY',2,3),
-(150,NULL,'RECORDTYPE',2,1),
-(150,NULL,'RECORDTYPE',2,2),
-(150,NULL,'RECORDTYPE',2,3),
-(153,NULL,'RECORDTYPE',2,1),
-(153,NULL,'RECORDTYPE',2,2),
-(153,NULL,'RECORDTYPE',2,3),
-(161,NULL,'RECORDTYPE',2,1),
-(161,NULL,'RECORDTYPE',2,2),
-(161,NULL,'RECORDTYPE',2,3),
-(162,NULL,'RECORDTYPE',2,1),
-(162,NULL,'RECORDTYPE',2,2),
-(162,NULL,'RECORDTYPE',2,3),
-(188,NULL,'RECORD',2,1),
-(188,NULL,'RECORD',2,2),
+(113,NULL,'PROPERTY',2,1),
+(120,NULL,'PROPERTY',2,1),
+(184,NULL,'RECORD',2,1),
+(185,NULL,'RECORD',2,1),
+(186,NULL,'RECORD',2,1),
+(187,NULL,'RECORD',2,1),
+(189,NULL,'RECORD',2,1),
+(190,NULL,'RECORD',2,1),
+(191,NULL,'RECORD',2,1),
(192,NULL,'RECORD',2,1),
-(193,NULL,'RECORD',2,1),
-(193,NULL,'RECORD',3,2),
-(193,NULL,'RECORD',3,3),
(194,NULL,'RECORD',2,1),
-(195,NULL,'RECORD',2,1),
-(195,NULL,'RECORD',3,2),
-(195,NULL,'RECORD',3,3),
-(196,NULL,'RECORD',2,1),
-(197,NULL,'RECORD',2,1),
-(197,NULL,'RECORD',3,2),
-(198,NULL,'RECORD',2,1);
+(196,NULL,'RECORD',2,1);
/*!40000 ALTER TABLE `archive_entities` ENABLE KEYS */;
UNLOCK TABLES;
@@ -388,7 +305,7 @@ CREATE TABLE `archive_enum_data` (
CONSTRAINT `archive_enum_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_enum_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_enum_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -409,13 +326,13 @@ DROP TABLE IF EXISTS `archive_files`;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `archive_files` (
`file_id` int(10) unsigned NOT NULL,
- `path` text NOT NULL,
+ `path` mediumtext NOT NULL,
`size` bigint(20) unsigned NOT NULL,
`hash` binary(64) DEFAULT NULL,
`_iversion` int(10) unsigned NOT NULL,
PRIMARY KEY (`file_id`,`_iversion`),
CONSTRAINT `archive_files_ibfk_1` FOREIGN KEY (`file_id`, `_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -450,7 +367,7 @@ CREATE TABLE `archive_integer_data` (
CONSTRAINT `archive_integer_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_integer_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_integer_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -460,9 +377,7 @@ CREATE TABLE `archive_integer_data` (
LOCK TABLES `archive_integer_data` WRITE;
/*!40000 ALTER TABLE `archive_integer_data` DISABLE KEYS */;
INSERT INTO `archive_integer_data` VALUES
-(0,192,137,1,'FIX',0,1,NULL),
-(0,194,137,1,'FIX',0,1,NULL),
-(0,196,137,1,'FIX',0,1,NULL);
+(0,187,162,1,'FIX',0,1,NULL);
/*!40000 ALTER TABLE `archive_integer_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -482,7 +397,7 @@ CREATE TABLE `archive_isa` (
KEY `child` (`child`,`child_iversion`),
CONSTRAINT `archive_isa_ibfk_1` FOREIGN KEY (`parent`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_isa_ibfk_2` FOREIGN KEY (`child`, `child_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -492,41 +407,16 @@ CREATE TABLE `archive_isa` (
LOCK TABLES `archive_isa` WRITE;
/*!40000 ALTER TABLE `archive_isa` DISABLE KEYS */;
INSERT INTO `archive_isa` VALUES
-(188,1,100,0),
-(188,1,101,0),
-(188,1,106,1),
-(193,1,111,1),
-(192,1,136,1),
-(195,1,111,1),
-(193,2,111,1),
-(194,1,136,1),
-(197,1,111,1),
-(195,2,111,1),
-(196,1,136,1),
-(198,1,118,1),
-(106,1,100,0),
-(106,1,101,1),
-(153,1,150,1),
-(161,1,143,1),
-(162,1,143,1),
-(193,3,111,1),
-(195,3,111,1),
-(197,2,111,1),
-(101,1,100,1),
-(106,2,100,0),
-(106,2,101,1),
-(110,1,100,1),
-(153,2,150,1),
-(161,2,143,1),
-(162,2,143,1),
-(188,2,100,0),
-(188,2,101,0),
-(188,2,106,1),
-(106,3,100,0),
-(106,3,101,1),
-(153,3,150,1),
-(161,3,143,1),
-(162,3,143,1);
+(187,1,131,1),
+(191,1,111,1),
+(190,1,111,1),
+(189,1,111,1),
+(186,1,118,1),
+(185,1,118,1),
+(184,1,118,1),
+(196,1,126,1),
+(194,1,126,1),
+(192,1,126,1);
/*!40000 ALTER TABLE `archive_isa` ENABLE KEYS */;
UNLOCK TABLES;
@@ -553,7 +443,7 @@ CREATE TABLE `archive_name_data` (
CONSTRAINT `archive_name_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -563,63 +453,11 @@ CREATE TABLE `archive_name_data` (
LOCK TABLES `archive_name_data` WRITE;
/*!40000 ALTER TABLE `archive_name_data` DISABLE KEYS */;
INSERT INTO `archive_name_data` VALUES
-(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,1),
-(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,1),
-(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,2),
-(0,197,20,'fad_mru_myn_2025_fri_1','FIX',0,1),
-(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,2),
-(0,106,20,'Person','FIX',0,1),
-(0,111,20,'Container','FIX',0,1),
-(0,118,20,'Sample','FIX',0,1),
-(0,119,20,'NagoyaCase','FIX',0,1),
-(0,136,20,'LabelCounter','FIX',0,1),
-(0,143,20,'Position','FIX',0,1),
-(0,144,20,'Water depth','FIX',0,1),
-(0,145,20,'Sampling depth','FIX',0,1),
-(0,146,20,'Latitude','FIX',0,1),
-(0,147,20,'Longitude','FIX',0,1),
-(0,150,20,'Event','FIX',0,1),
-(0,153,20,'SourceEvent','FIX',0,1),
-(0,161,20,'StartPosition','FIX',0,1),
-(0,162,20,'StopPosition','FIX',0,1),
-(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,3),
-(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,3),
-(0,197,20,'fad_mru_myn_2025_fri_1','FIX',0,2),
-(0,101,20,'Responsible','FIX',0,1),
-(0,102,20,'Abbreviation','FIX',0,1),
-(0,106,20,'Person','FIX',0,2),
-(0,110,20,'ContainerType','FIX',0,1),
-(0,111,20,'Container','FIX',0,2),
-(0,114,20,'Custom label','FIX',0,1),
-(0,118,20,'Sample','FIX',0,2),
-(0,119,20,'NagoyaCase','FIX',0,2),
-(0,136,20,'LabelCounter','FIX',0,2),
-(0,143,20,'Position','FIX',0,2),
-(0,144,20,'Water depth','FIX',0,2),
-(0,145,20,'Sampling depth','FIX',0,2),
-(0,146,20,'Latitude','FIX',0,2),
-(0,147,20,'Longitude','FIX',0,2),
-(0,150,20,'Event','FIX',0,2),
-(0,153,20,'SourceEvent','FIX',0,2),
-(0,161,20,'StartPosition','FIX',0,2),
-(0,162,20,'StopPosition','FIX',0,2),
-(0,188,20,'My Name','FIX',0,2),
-(0,107,20,'First name','FIX',0,1),
-(0,108,20,'Last name','FIX',0,1),
-(0,106,20,'Person','FIX',0,3),
-(0,111,20,'Container','FIX',0,3),
-(0,118,20,'Sample','FIX',0,3),
-(0,119,20,'NagoyaCase','FIX',0,3),
-(0,136,20,'LabelCounter','FIX',0,3),
-(0,143,20,'Position','FIX',0,3),
-(0,144,20,'Water depth','FIX',0,3),
-(0,145,20,'Sampling depth','FIX',0,3),
-(0,146,20,'Latitude','FIX',0,3),
-(0,147,20,'Longitude','FIX',0,3),
-(0,150,20,'Event','FIX',0,3),
-(0,153,20,'SourceEvent','FIX',0,3),
-(0,161,20,'StartPosition','FIX',0,3),
-(0,162,20,'StopPosition','FIX',0,3);
+(0,113,20,'Child container','FIX',0,1),
+(0,191,20,'MM_sb_3','FIX',0,1),
+(0,190,20,'MM_sb_2','FIX',0,1),
+(0,189,20,'MM_sb_1','FIX',0,1),
+(0,120,20,'Parent sample','FIX',0,1);
/*!40000 ALTER TABLE `archive_name_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -644,7 +482,7 @@ CREATE TABLE `archive_name_overrides` (
CONSTRAINT `archive_name_overrides_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_overrides_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_overrides_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -654,14 +492,7 @@ CREATE TABLE `archive_name_overrides` (
LOCK TABLES `archive_name_overrides` WRITE;
/*!40000 ALTER TABLE `archive_name_overrides` DISABLE KEYS */;
INSERT INTO `archive_name_overrides` VALUES
-(0,193,177,'BIS label',1),
-(0,193,177,'BIS label',2),
-(0,193,177,'BIS label',3),
-(0,195,177,'BIS label',1),
-(0,195,177,'BIS label',2),
-(0,195,177,'BIS label',3),
-(0,197,177,'BIS label',1),
-(0,197,177,'BIS label',2);
+(0,187,162,'counter',1);
/*!40000 ALTER TABLE `archive_name_overrides` ENABLE KEYS */;
UNLOCK TABLES;
@@ -686,7 +517,7 @@ CREATE TABLE `archive_null_data` (
CONSTRAINT `archive_null_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_null_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_null_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -696,182 +527,9 @@ CREATE TABLE `archive_null_data` (
LOCK TABLES `archive_null_data` WRITE;
/*!40000 ALTER TABLE `archive_null_data` DISABLE KEYS */;
INSERT INTO `archive_null_data` VALUES
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/*!40000 ALTER TABLE `archive_null_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -884,11 +542,11 @@ DROP TABLE IF EXISTS `archive_query_template_def`;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `archive_query_template_def` (
`id` int(10) unsigned NOT NULL,
- `definition` mediumtext NOT NULL,
+ `definition` longtext NOT NULL,
`_iversion` int(10) unsigned NOT NULL,
PRIMARY KEY (`id`,`_iversion`),
CONSTRAINT `archive_query_template_def_ibfk_1` FOREIGN KEY (`id`, `_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -925,7 +583,7 @@ CREATE TABLE `archive_reference_data` (
CONSTRAINT `archive_reference_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_reference_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_reference_data_ibfk_4` FOREIGN KEY (`value`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -935,90 +593,32 @@ CREATE TABLE `archive_reference_data` (
LOCK TABLES `archive_reference_data` WRITE;
/*!40000 ALTER TABLE `archive_reference_data` DISABLE KEYS */;
INSERT INTO `archive_reference_data` VALUES
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+(0,187,132,162,NULL,'REPLACEMENT',0,1),
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+(0,194,139,162,NULL,'REPLACEMENT',0,1),
+(0,194,163,177,NULL,'FIX',0,1),
+(0,194,124,163,NULL,'REPLACEMENT',1,1),
+(0,192,162,193,NULL,'FIX',0,1),
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+(0,192,163,177,NULL,'FIX',0,1),
+(0,192,124,163,NULL,'REPLACEMENT',1,1);
/*!40000 ALTER TABLE `archive_reference_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1033,7 +633,7 @@ CREATE TABLE `archive_text_data` (
`domain_id` int(10) unsigned NOT NULL,
`entity_id` int(10) unsigned NOT NULL,
`property_id` int(10) unsigned NOT NULL,
- `value` text NOT NULL,
+ `value` mediumtext NOT NULL,
`status` enum('OBLIGATORY','RECOMMENDED','SUGGESTED','FIX') NOT NULL,
`pidx` int(10) unsigned NOT NULL,
`_iversion` int(10) unsigned NOT NULL,
@@ -1044,7 +644,7 @@ CREATE TABLE `archive_text_data` (
CONSTRAINT `archive_text_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_text_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_text_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1054,66 +654,9 @@ CREATE TABLE `archive_text_data` (
LOCK TABLES `archive_text_data` WRITE;
/*!40000 ALTER TABLE `archive_text_data` DISABLE KEYS */;
INSERT INTO `archive_text_data` VALUES
-(0,188,107,'My','FIX',0,1),
-(0,188,102,'myn','FIX',1,1),
-(0,188,108,'Name','FIX',2,1),
-(0,188,109,'my.name@example.com','FIX',3,1),
-(0,193,113,'20 rooms','FIX',2,1),
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-(0,195,113,'30 m²','FIX',2,1),
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-(0,193,113,'20 rooms','FIX',2,2),
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-(0,197,113,'300 l','FIX',2,1),
-(0,197,177,'fad_mru_myn_2025_fri_1','FIX',0,1),
-(0,195,113,'30 m²','FIX',2,2),
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-(0,193,113,'20 rooms','FIX',2,3),
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-(0,195,113,'30 m²','FIX',2,3),
-(0,195,177,'fad_mru_myn_2025_rom_1','FIX',0,3),
-(0,197,113,'300 l','FIX',2,2),
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-(0,188,107,'My','FIX',0,2),
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/*!40000 ALTER TABLE `archive_text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1136,7 +679,7 @@ CREATE TABLE `collection_type` (
CONSTRAINT `collection_type_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `collection_type_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `collection_type_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1146,16 +689,19 @@ CREATE TABLE `collection_type` (
LOCK TABLES `collection_type` WRITE;
/*!40000 ALTER TABLE `collection_type` DISABLE KEYS */;
INSERT INTO `collection_type` VALUES
-(0,0,112,'LIST'),
-(0,0,125,'LIST'),
-(0,0,126,'LIST'),
-(0,0,127,'LIST'),
-(0,0,128,'LIST'),
-(0,0,129,'LIST'),
-(0,0,141,'LIST'),
-(0,0,164,'LIST'),
-(0,153,177,'LIST'),
-(0,210,178,'LIST');
+(0,0,113,'LIST'),
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+(0,0,154,'LIST'),
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+(0,126,165,'LIST'),
+(0,189,163,'LIST'),
+(0,190,163,'LIST'),
+(0,191,163,'LIST'),
+(0,192,162,'LIST'),
+(0,194,162,'LIST'),
+(0,196,162,'LIST');
/*!40000 ALTER TABLE `collection_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1180,7 +726,7 @@ CREATE TABLE `data_type` (
CONSTRAINT `datatype_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `datatype_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`),
CONSTRAINT `datatype_forkey_type` FOREIGN KEY (`datatype`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1190,68 +736,77 @@ CREATE TABLE `data_type` (
LOCK TABLES `data_type` WRITE;
/*!40000 ALTER TABLE `data_type` DISABLE KEYS */;
INSERT INTO `data_type` VALUES
-(0,0,134,12),
-(0,0,137,12),
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+(0,126,163,146),
+(0,126,167,153);
/*!40000 ALTER TABLE `data_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1275,7 +830,7 @@ CREATE TABLE `date_data` (
CONSTRAINT `date_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `date_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `date_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1285,7 +840,12 @@ CREATE TABLE `date_data` (
LOCK TABLES `date_data` WRITE;
/*!40000 ALTER TABLE `date_data` DISABLE KEYS */;
INSERT INTO `date_data` VALUES
-(0,210,151,20250101,'FIX',0);
+(0,196,147,20231220,'FIX',2),
+(0,196,148,20231220,'FIX',3),
+(0,194,147,20231220,'FIX',2),
+(0,194,148,20231220,'FIX',3),
+(0,192,147,20231220,'FIX',2),
+(0,192,148,20231220,'FIX',3);
/*!40000 ALTER TABLE `date_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1310,7 +870,7 @@ CREATE TABLE `datetime_data` (
CONSTRAINT `dat_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dat_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dat_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1341,7 +901,7 @@ CREATE TABLE `desc_overrides` (
CONSTRAINT `desc_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `desc_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `desc_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1374,7 +934,7 @@ CREATE TABLE `double_data` (
CONSTRAINT `dou_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dou_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dou_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1384,8 +944,13 @@ CREATE TABLE `double_data` (
LOCK TABLES `double_data` WRITE;
/*!40000 ALTER TABLE `double_data` DISABLE KEYS */;
INSERT INTO `double_data` VALUES
-(0,211,146,1.1,'FIX',0,-1941227323),
-(0,211,147,1.2,'FIX',1,-1941227323);
+(0,193,140,13.2,'FIX',0,-1941227323),
+(0,193,141,1,'FIX',1,-1941227323),
+(0,195,140,14,'FIX',0,-1941227323),
+(0,195,141,2,'FIX',1,-1941227323),
+(0,195,142,23,'FIX',2,NULL),
+(0,197,140,16.3,'FIX',0,-1941227323),
+(0,197,141,3,'FIX',1,-1941227323);
/*!40000 ALTER TABLE `double_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1404,7 +969,7 @@ CREATE TABLE `entities` (
PRIMARY KEY (`id`),
KEY `entity_entity_acl` (`acl`),
CONSTRAINT `entity_entity_acl` FOREIGN KEY (`acl`) REFERENCES `entity_acl` (`id`)
-) ENGINE=InnoDB AUTO_INCREMENT=213 DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB AUTO_INCREMENT=198 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1435,111 +1000,100 @@ INSERT INTO `entities` VALUES
(100,'Abstract type to denote that a RecordType is controlled, i.e.,\nthat no new Records of this type may be created during\nsample/container upload. Add this type as a parent to any\nRecordType you want to be controlled.\n','RECORDTYPE',2),
(101,NULL,'RECORDTYPE',2),
(102,'An abbreviation for this entity that is used for identification purposes','PROPERTY',2),
-(104,'A german name for an entitiy. This can be used in queries since it is an alias.','PROPERTY',2),
-(106,NULL,'RECORDTYPE',2),
-(107,NULL,'PROPERTY',2),
-(108,NULL,'PROPERTY',2),
-(109,NULL,'PROPERTY',2),
-(110,NULL,'RECORDTYPE',2),
+(103,NULL,'RECORDTYPE',2),
+(104,NULL,'PROPERTY',2),
+(105,NULL,'PROPERTY',2),
+(106,NULL,'PROPERTY',2),
+(107,NULL,'RECORDTYPE',2),
+(108,NULL,'RECORDTYPE',2),
+(109,NULL,'RECORDTYPE',2),
+(110,NULL,'PROPERTY',2),
(111,NULL,'RECORDTYPE',2),
-(112,NULL,'PROPERTY',2),
-(113,'The size of the container, e.g. number of spaces or dimension','PROPERTY',2),
-(114,'A custom label for a container that doesn\'t have to follow the automatic labeling guidelines.','PROPERTY',2),
-(115,NULL,'PROPERTY',2),
+(112,'A standardized label for a container','PROPERTY',2),
+(113,NULL,'PROPERTY',2),
+(114,'The size of the container, e.g. number of spaces or dimension','PROPERTY',2),
+(115,'A custom label for a container that doesn\'t have to follow the automatic labeling guidelines.','PROPERTY',2),
(116,NULL,'PROPERTY',2),
+(117,NULL,'PROPERTY',2),
(118,NULL,'RECORDTYPE',2),
(119,NULL,'RECORDTYPE',2),
-(120,NULL,'RECORDTYPE',2),
-(121,NULL,'RECORDTYPE',2),
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(122,NULL,'PROPERTY',2),
(123,NULL,'PROPERTY',2),
-(124,NULL,'PROPERTY',2),
+(124,NULL,'RECORDTYPE',2),
(125,NULL,'PROPERTY',2),
-(126,'DOIs of publications related to this sample.','PROPERTY',2),
-(127,NULL,'PROPERTY',2),
+(126,NULL,'RECORDTYPE',2),
+(127,NULL,'RECORDTYPE',2),
(128,NULL,'PROPERTY',2),
(129,NULL,'PROPERTY',2),
-(130,'A short description of the sampling methodology used for this sample.','PROPERTY',2),
-(131,NULL,'PROPERTY',2),
+(130,NULL,'RECORDTYPE',2),
+(131,NULL,'RECORDTYPE',2),
(132,NULL,'PROPERTY',2),
-(133,NULL,'PROPERTY',2),
-(134,'An ID for this taxon that allows to uniquely identify it on http://www.marinespecies.org.','PROPERTY',2),
+(133,NULL,'RECORDTYPE',2),
+(134,'The Marine Regions Geographic Identifier, i.e. a PID (Persistent Identifier) for a geographic region on https://www.marineregions.org','PROPERTY',2),
(135,NULL,'RECORDTYPE',2),
-(136,NULL,'RECORDTYPE',2),
+(136,'A link to the Nagoya documents (or an indication where to find the documents).','PROPERTY',2),
(137,NULL,'PROPERTY',2),
-(138,NULL,'RECORDTYPE',2),
-(139,'The Marine Regions Geographic Identifier, i.e. a PID (Persistent Identifier) for a geographic region on https://www.marineregions.org','PROPERTY',2),
-(140,'A link to the Nagoya documents (or an indication where to find the documents).','PROPERTY',2),
+(138,'An identifier for nagoya cases. This is managed by the Nagoya-Coordinator and should be taken care of before sampling.','PROPERTY',2),
+(139,NULL,'RECORDTYPE',2),
+(140,NULL,'PROPERTY',2),
(141,NULL,'PROPERTY',2),
-(142,'An identifier for nagoya cases. This is managed by the Nagoya-Coordinator and should be taken care of before sampling.','PROPERTY',2),
+(142,NULL,'PROPERTY',2),
(143,NULL,'RECORDTYPE',2),
-(144,'The depth of the water in meters as a positive value','PROPERTY',2),
-(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2),
-(146,NULL,'PROPERTY',2),
-(147,NULL,'PROPERTY',2),
-(148,NULL,'RECORDTYPE',2),
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+(145,NULL,'PROPERTY',2),
+(146,'Cruise name or leg description','RECORDTYPE',2),
+(147,'The date and time the event started.','PROPERTY',2),
+(148,'The date and time the event ended.','PROPERTY',2),
(149,NULL,'PROPERTY',2),
-(150,NULL,'RECORDTYPE',2),
-(151,'The date and time the event started.','PROPERTY',2),
-(152,'The date and time the event ended.','PROPERTY',2),
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(153,NULL,'RECORDTYPE',2),
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-(155,NULL,'PROPERTY',2),
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(156,NULL,'PROPERTY',2),
-(157,NULL,'PROPERTY',2),
-(158,'The name/identifier of a station where regular sampling activity takes place.','PROPERTY',2),
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+(158,NULL,'RECORDTYPE',2),
(159,NULL,'RECORDTYPE',2),
-(160,NULL,'RECORDTYPE',2),
-(161,NULL,'RECORDTYPE',2),
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-(170,NULL,'RECORDTYPE',2),
-(171,NULL,'RECORDTYPE',2),
-(172,'PDF files which contain reports and additional information about samples, collections, or containers','RECORDTYPE',2),
-(173,NULL,'RECORDTYPE',2),
-(174,NULL,'RECORDTYPE',2),
-(175,NULL,'RECORDTYPE',2),
-(176,NULL,'RECORDTYPE',2),
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-(178,NULL,'_REPLACEMENT',0),
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-(181,NULL,'_REPLACEMENT',0),
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(194,NULL,'RECORD',2),
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(196,NULL,'RECORD',2),
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-(209,NULL,'RECORD',2),
-(210,NULL,'RECORD',2),
-(211,NULL,'RECORD',2),
-(212,'A standardized label for a container','PROPERTY',2);
+(197,NULL,'RECORD',2);
/*!40000 ALTER TABLE `entities` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1555,7 +1109,7 @@ CREATE TABLE `entity_acl` (
`acl` varbinary(65525) NOT NULL,
PRIMARY KEY (`id`),
KEY `entity_acl_acl` (`acl`(3072))
-) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB AUTO_INCREMENT=3 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1566,8 +1120,7 @@ LOCK TABLES `entity_acl` WRITE;
/*!40000 ALTER TABLE `entity_acl` DISABLE KEYS */;
INSERT INTO `entity_acl` VALUES
(0,''),
-(2,'[{\"realm\":\"PAM\",\"bitSet\":536608371,\"username\":\"admin\"}]'),
-(3,'[{\"role\":\"Stock Manager\",\"bitSet\":1},{\"realm\":\"PAM\",\"bitSet\":536608371,\"username\":\"admin\"}]');
+(2,'[{\"realm\":\"PAM\",\"bitSet\":536608371,\"username\":\"admin\"}]');
/*!40000 ALTER TABLE `entity_acl` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1614,7 +1167,9 @@ INSERT INTO `entity_ids` VALUES
('102',100),
('103',101),
('104',102),
+('105',103),
('106',104),
+('107',105),
('108',106),
('109',107),
('110',108),
@@ -1626,6 +1181,7 @@ INSERT INTO `entity_ids` VALUES
('116',114),
('117',115),
('118',116),
+('119',117),
('120',118),
('121',119),
('122',120),
@@ -1670,46 +1226,34 @@ INSERT INTO `entity_ids` VALUES
('161',159),
('162',160),
('163',161),
-('164',162),
-('165',163),
-('166',164),
-('167',165),
-('168',166),
-('169',167),
-('170',168),
-('171',169),
-('172',170),
-('173',171),
-('174',172),
-('175',173),
-('176',174),
-('177',175),
-('178',176),
-('181',188),
-('182',189),
-('183',190),
-('184',191),
-('185',192),
-('186',193),
-('187',194),
-('188',195),
-('189',196),
-('190',197),
-('191',198),
-('192',199),
-('193',200),
-('194',201),
-('195',202),
-('196',203),
-('197',204),
-('198',205),
-('199',206),
-('200',207),
-('201',208),
-('202',209),
-('203',210),
-('204',211),
-('205',212);
+('164',169),
+('165',170),
+('166',171),
+('167',172),
+('168',173),
+('169',174),
+('170',175),
+('171',176),
+('172',177),
+('173',178),
+('174',179),
+('175',180),
+('176',181),
+('177',182),
+('178',183),
+('179',184),
+('180',185),
+('181',186),
+('182',187),
+('184',189),
+('185',190),
+('186',191),
+('187',192),
+('188',193),
+('189',194),
+('190',195),
+('191',196),
+('192',197);
/*!40000 ALTER TABLE `entity_ids` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1732,7 +1276,7 @@ CREATE TABLE `entity_version` (
KEY `srid` (`srid`),
CONSTRAINT `entity_version_ibfk_1` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `entity_version_ibfk_2` FOREIGN KEY (`srid`) REFERENCES `transactions` (`srid`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1760,167 +1304,108 @@ INSERT INTO `entity_version` VALUES
(20,NULL,'9030ad4b0f91c832ddb4a7c9d9b090c1f035b1d3',1,NULL,'cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e'),
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UNLOCK TABLES;
@@ -1944,7 +1429,7 @@ CREATE TABLE `enum_data` (
CONSTRAINT `enum_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `enum_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `enum_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1967,7 +1452,7 @@ CREATE TABLE `feature_config` (
`_key` varchar(255) NOT NULL,
`_value` varchar(255) DEFAULT NULL,
PRIMARY KEY (`_key`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
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@@ -1996,7 +1481,7 @@ CREATE TABLE `files` (
`checked_timestamp` bigint(20) NOT NULL DEFAULT 0,
PRIMARY KEY (`file_id`),
CONSTRAINT `fil_file_id_entity` FOREIGN KEY (`file_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -2029,7 +1514,7 @@ CREATE TABLE `integer_data` (
CONSTRAINT `int_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `int_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `int_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
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LOCK TABLES `integer_data` WRITE;
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UNLOCK TABLES;
@@ -2060,7 +1543,7 @@ CREATE TABLE `isa_cache` (
KEY `isa_cache_parent_entity` (`parent`),
CONSTRAINT `isa_cache_child_entity` FOREIGN KEY (`child`) REFERENCES `entities` (`id`),
CONSTRAINT `isa_cache_parent_entity` FOREIGN KEY (`parent`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
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UNLOCK TABLES;
@@ -2162,7 +1638,7 @@ CREATE TABLE `name_data` (
CONSTRAINT `name_data_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_data_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_data_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
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@@ -2193,93 +1669,80 @@ INSERT INTO `name_data` VALUES
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(0,101,20,'Responsible','FIX',0),
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UNLOCK TABLES;
@@ -2302,7 +1765,7 @@ CREATE TABLE `name_overrides` (
CONSTRAINT `name_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
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LOCK TABLES `name_overrides` WRITE;
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INSERT INTO `name_overrides` VALUES
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UNLOCK TABLES;
@@ -2335,7 +1798,7 @@ CREATE TABLE `null_data` (
CONSTRAINT `null_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `null_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `null_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
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PRIMARY KEY (`principal`)
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CONSTRAINT `perm_name_roles` FOREIGN KEY (`role`) REFERENCES `roles` (`name`)
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CONSTRAINT `query_template_def_ibfk_1` FOREIGN KEY (`id`) REFERENCES `entities` (`id`)
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CONSTRAINT `reference_data_ibfk_1` FOREIGN KEY (`value`, `value_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`)
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PRIMARY KEY (`name`)
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CONSTRAINT `str_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `str_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
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-('Update','188','admin',1737542878,789000000,'PAM'),
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+('Insert','144','admin',1741701919,236000000,'PAM'),
+('Insert','145','admin',1741701919,236000000,'PAM'),
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+('Update','115','admin',1741702929,507000000,'PAM'),
+('Insert','184','admin',1741702954,287000000,'PAM'),
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+('Update','182','admin',1741702954,341000000,'PAM'),
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+('Update','185','admin',1741703106,793000000,'PAM'),
+('Update','184','admin',1741703106,793000000,'PAM'),
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+('Insert','187','admin',1741704540,640000000,'PAM'),
+('Insert','188','admin',1741704540,640000000,'PAM'),
+('Insert','189','admin',1741704540,640000000,'PAM'),
+('Insert','190','admin',1741704540,640000000,'PAM'),
+('Insert','191','admin',1741704540,640000000,'PAM'),
+('Insert','192','admin',1741704540,640000000,'PAM'),
+('Update','181','admin',1741704540,693000000,'PAM'),
+('Update','180','admin',1741704540,693000000,'PAM'),
+('Update','179','admin',1741704540,693000000,'PAM'),
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+('Update','187','admin',1741705215,273000000,'PAM');
/*!40000 ALTER TABLE `transaction_log` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2911,7 +2332,7 @@ CREATE TABLE `transactions` (
`seconds` bigint(20) unsigned NOT NULL,
`nanos` int(10) unsigned NOT NULL,
PRIMARY KEY (`srid`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -2921,60 +2342,39 @@ CREATE TABLE `transactions` (
LOCK TABLES `transactions` WRITE;
/*!40000 ALTER TABLE `transactions` DISABLE KEYS */;
INSERT INTO `transactions` VALUES
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/*!40000 ALTER TABLE `transactions` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2993,7 +2393,7 @@ CREATE TABLE `units_lin_con` (
`b_divisor` int(11) NOT NULL,
`c` decimal(65,30) NOT NULL,
PRIMARY KEY (`signature_from`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -3021,7 +2421,7 @@ CREATE TABLE `user_info` (
PRIMARY KEY (`realm`,`name`),
KEY `subject_entity` (`entity`),
CONSTRAINT `subjects_ibfk_2` FOREIGN KEY (`entity`) REFERENCES `entity_ids` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -3049,7 +2449,7 @@ CREATE TABLE `user_roles` (
PRIMARY KEY (`realm`,`user`,`role`),
KEY `user_roles_ibfk_1` (`role`),
CONSTRAINT `user_roles_ibfk_1` FOREIGN KEY (`role`) REFERENCES `roles` (`name`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -3072,13 +2472,13 @@ UNLOCK TABLES;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `CaosDBVersion`() RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `CaosDBVersion`() RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
-RETURN 'v8.0.0' ;;
+RETURN 'v8.1.0' ;;
DELIMITER ;
/*!50003 SET sql_mode = @saved_sql_mode */ ;
/*!50003 SET character_set_client = @saved_cs_client */ ;
@@ -3090,11 +2490,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `constructDateTimeWhereClauseForColumn`(seconds_col VARCHAR(255), nanos_col VARCHAR(255), vDateTimeSecLow VARCHAR(255), vDateTimeNSLow VARCHAR(255), vDateTimeSecUpp VARCHAR(255), vDateTimeNSUpp VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `constructDateTimeWhereClauseForColumn`(seconds_col VARCHAR(255), nanos_col VARCHAR(255), vDateTimeSecLow VARCHAR(255), vDateTimeNSLow VARCHAR(255), vDateTimeSecUpp VARCHAR(255), vDateTimeNSUpp VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
@@ -3159,9 +2559,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `convert_unit`(unit_sig BIGINT, value DECIMAL(65,30)) RETURNS decimal(65,30)
DETERMINISTIC
@@ -3182,11 +2582,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getAggValueWhereClause`(entities VARCHAR(255), properties VARCHAR(255)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getAggValueWhereClause`(entities VARCHAR(255), properties VARCHAR(255)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
RETURN CONCAT(" EXISTS (SELECT 1 FROM `", entities, "` AS ent WHERE ent.id = subdata.entity_id LIMIT 1)", IF(properties IS NOT NULL AND properties != '', CONCAT(" AND EXISTS (SELECT 1 FROM `", properties, "` as props WHERE props.id = subdata.property_id LIMIT 1)"),''));
@@ -3202,11 +2602,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getDateTimeWhereClause`(vDateTime VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getDateTimeWhereClause`(vDateTime VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
DECLARE sep_loc INTEGER DEFAULT LOCATE('--',vDateTime);
@@ -3233,11 +2633,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getDateWhereClause`(vDateTimeDotNotation VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getDateWhereClause`(vDateTimeDotNotation VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
DECLARE isInterval INTEGER DEFAULT LOCATE('--',vDateTimeDotNotation);
@@ -3342,11 +2742,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getDoubleWhereClause`(value DOUBLE, unit_sig BIGINT, valueStdUnit DECIMAL(65,30), stdUnit_sig BIGINT, o CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getDoubleWhereClause`(value DOUBLE, unit_sig BIGINT, valueStdUnit DECIMAL(65,30), stdUnit_sig BIGINT, o CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
RETURN IF(unit_sig IS NULL AND value IS NOT NULL,
@@ -3367,9 +2767,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_head_relative`(EntityID VARCHAR(255),
HeadOffset INT UNSIGNED) RETURNS varbinary(255)
@@ -3402,9 +2802,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_head_version`(EntityID VARCHAR(255)) RETURNS varbinary(255)
READS SQL DATA
@@ -3422,9 +2822,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_iversion`(InternalEntityID INT UNSIGNED,
Version VARBINARY(255)) RETURNS int(10) unsigned
@@ -3448,9 +2848,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_primary_parent_version`(EntityID VARCHAR(255),
Version VARBINARY(255)) RETURNS varbinary(255)
@@ -3480,12 +2880,12 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_version_timestamp`(EntityID VARCHAR(255),
- Version VARBINARY(255)) RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+ Version VARBINARY(255)) RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
READS SQL DATA
BEGIN
DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
@@ -3511,9 +2911,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `is_feature_config`(_Key VARCHAR(255),
Expected VARCHAR(255)) RETURNS tinyint(1)
@@ -3534,12 +2934,12 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `makeStmt`(sourceSet VARCHAR(255), targetSet VARCHAR(255), data VARCHAR(20000),
- properties VARCHAR(20000), versioned BOOLEAN) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+ properties VARCHAR(20000), versioned BOOLEAN) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
NO SQL
BEGIN
IF sourceSet = "entities" AND versioned THEN
@@ -3592,9 +2992,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `standard_unit`(unit_sig BIGINT) RETURNS bigint(20)
DETERMINISTIC
@@ -3615,9 +3015,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `_get_head_iversion`(InternalEntityID INT UNSIGNED) RETURNS int(10) unsigned
READS SQL DATA
@@ -3645,9 +3045,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `_get_version`(InternalEntityID INT UNSIGNED,
IVersion INT UNSIGNED) RETURNS varbinary(255)
@@ -3670,9 +3070,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyBackReference`(in sourceSet VARCHAR(255), targetSet VARCHAR(255),
in propertiesTable VARCHAR(255), in entitiesTable VARCHAR(255), in subQuery BOOLEAN,
@@ -3851,9 +3251,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyIDFilter`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255),
in o CHAR(2), in EntityID VARCHAR(255), in agg CHAR(3), in versioned BOOLEAN)
@@ -3988,9 +3388,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyPOV`(in sourceSet VARCHAR(255),
in targetSet VARCHAR(255),
@@ -4293,9 +3693,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyRefPOV`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255),
in properties VARCHAR(255), in refs VARCHAR(255),
@@ -4333,9 +3733,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applySAT`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255), in loc MEDIUMTEXT, in op CHAR(5))
BEGIN
@@ -4362,9 +3762,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyTransactionFilter`(in sourceSet VARCHAR(255), targetSet VARCHAR(255), in transaction VARCHAR(255), in operator_u CHAR(2), in realm VARCHAR(255), in userName VARCHAR(255), in ilb BIGINT, in ilb_nanos INT UNSIGNED, in eub BIGINT, in eub_nanos INT UNSIGNED, in operator_t CHAR(2))
BEGIN
@@ -4404,9 +3804,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcComplementUnion`(in targetSet VARCHAR(255), in subResultSet VARCHAR(255), in universe VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -4444,9 +3844,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcDifference`(in resultSetTable VARCHAR(255), in diff VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -4471,9 +3871,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcIntersection`(in resultSetTable VARCHAR(255), in intersectWith VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -4506,9 +3906,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcUnion`(in targetSet VARCHAR(255), in sourceSet VARCHAR(255))
BEGIN
@@ -4529,9 +3929,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `cleanUpLinCon`()
BEGIN
@@ -4550,9 +3950,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `cleanUpQuery`()
BEGIN
@@ -4577,9 +3977,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `copyTable`(in fromTable VARCHAR(255), in toTable VARCHAR(255))
BEGIN
@@ -4600,9 +4000,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `createTmpTable`(out newTableName VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -4630,9 +4030,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `createTmpTable2`(out newTableName VARCHAR(255))
BEGIN
@@ -4656,9 +4056,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteEntity`(in EntityID VARCHAR(255))
BEGIN
@@ -4712,9 +4112,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteEntityProperties`(in EntityID VARCHAR(255))
BEGIN
@@ -4885,9 +4285,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteIsa`(IN InternalEntityID INT UNSIGNED)
BEGIN
@@ -4923,9 +4323,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteLinCon`(in sig BIGINT)
BEGIN
@@ -4944,9 +4344,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `entityACL`(out ACLID INT UNSIGNED, in ACLSTR VARBINARY(65525))
BEGIN
@@ -4967,9 +4367,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `finishNegationFilter`(in resultSetTable VARCHAR(255), in diff VARCHAR(255))
BEGIN
@@ -4986,9 +4386,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `finishSubProperty`(in sourceSet VARCHAR(255),in targetSet VARCHAR(255),
in list VARCHAR(255), in versioned BOOLEAN)
@@ -5014,9 +4414,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getChildren`(in tableName varchar(255), in versioned BOOLEAN)
BEGIN
@@ -5083,9 +4483,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getDependentEntities`(in EntityID VARCHAR(255))
BEGIN
@@ -5187,9 +4587,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getFileIdByPath`(in FilePath TEXT)
BEGIN
@@ -5208,9 +4608,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getIdByName`(in Name VARCHAR(255), in Role VARCHAR(255), in Lmt INT UNSIGNED)
BEGIN
@@ -5271,9 +4671,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `get_version_history`(
in EntityID VARCHAR(255))
@@ -5324,9 +4724,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initBackReference`(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255), in EntityID VARCHAR(255), in EntityName VARCHAR(255))
BEGIN
@@ -5382,9 +4782,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initDisjunctionFilter`(in versioned BOOLEAN)
BEGIN
@@ -5401,9 +4801,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initEmptyTargetSet`(in targetSet VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -5433,9 +4833,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initEntity`(in eid VARCHAR(255), in ename VARCHAR(255),
in enameLike VARCHAR(255), in enameRegexp VARCHAR(255),
@@ -5569,9 +4969,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initPOVPropertiesTable`(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255), in sourceSet VARCHAR(255))
BEGIN
@@ -5651,9 +5051,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initPOVRefidsTable`(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255))
BEGIN
@@ -5680,9 +5080,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initQuery`(in versioned BOOLEAN)
BEGIN
@@ -5703,9 +5103,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initSubEntity`(in EntityID VARCHAR(255), in ename VARCHAR(255), in tableName VARCHAR(255))
BEGIN
@@ -5755,9 +5155,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initSubProperty`(in sourceSet VARCHAR(255), in propertiesTable VARCHAR(255), in refIdsTable VARCHAR(255))
BEGIN
@@ -5806,9 +5206,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntity`(in EntityID VARCHAR(255), in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
BEGIN
@@ -5860,9 +5260,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntityCollection`(in PropertyID VARCHAR(255), in Collection VARCHAR(255))
BEGIN
@@ -5884,9 +5284,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntityDataType`(in PropertyID VARCHAR(255), in DataTypeID VARCHAR(255))
BEGIN
@@ -5909,9 +5309,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntityProperty`(
in DomainID VARCHAR(255),
@@ -6051,9 +5451,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertIsa`(IN ChildID VARCHAR(255), IN ParentID VARCHAR(255))
insert_is_a_proc: BEGIN
@@ -6116,9 +5516,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertLinCon`(in signature_from BIGINT, in signature_to BIGINT, in a DECIMAL(65,30), in b_dividend BIGINT, in b_divisor BIGINT, in c DECIMAL(65,30))
BEGIN
@@ -6137,9 +5537,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insert_single_child_version`(
in InternalEntityID INT UNSIGNED,
@@ -6192,9 +5592,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `intersectTable`(in resultSetTable VARCHAR(255), in diff VARCHAR(255))
BEGIN
@@ -6215,9 +5615,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `isSubtype`(in ChildID VARCHAR(255), in ParentID VARCHAR(255))
BEGIN
@@ -6242,9 +5642,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `overrideDesc`(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in Description TEXT)
BEGIN
@@ -6261,9 +5661,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `overrideName`(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in Name VARCHAR(255))
BEGIN
@@ -6280,9 +5680,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `overrideType`(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in InternalDataTypeID INT UNSIGNED)
BEGIN
@@ -6299,9 +5699,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `raiseWarning`(in str VARCHAR(20000))
BEGIN
@@ -6318,9 +5718,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `registerReplacementIds`(in amount INT UNSIGNED)
BEGIN
@@ -6349,9 +5749,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `registerTempTableName`(out newTableName VARCHAR(255))
BEGIN
@@ -6397,9 +5797,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveEntity`(
in EntityID VARCHAR(255),
@@ -6555,9 +5955,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveEntityParents`(
in EntityID VARCHAR(255),
@@ -6636,9 +6036,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveEntityProperties`(
in DomainID VARCHAR(255),
@@ -6958,9 +6358,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveOverrides`(
in DomainID VARCHAR(255),
@@ -7153,9 +6553,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveQueryTemplateDef`(
in EntityID VARCHAR(255),
@@ -7208,9 +6608,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `setFileProperties`(
in EntityID VARCHAR(255),
@@ -7255,9 +6655,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `set_transaction`(
srid VARBINARY(255),
@@ -7282,9 +6682,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `showEntityAutoIncr`()
BEGIN
@@ -7306,9 +6706,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `updateEntity`(
in EntityID VARCHAR(255),
@@ -7420,9 +6820,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `updateLinCon`(in sig_from BIGINT, in sig_to BIGINT, in new_a DECIMAL(65,30), in new_b_dividend BIGINT, in new_b_divisor BIGINT, in new_c DECIMAL(65,30))
BEGIN
@@ -7444,4 +6844,4 @@ DELIMITER ;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
--- Dump completed on 2025-01-27 15:08:09
+-- Dump completed on 2025-03-11 15:15:22
diff --git a/test-profile/custom/other/restore/caosroot.2025-03-11T16151741706122.tar.gz b/test-profile/custom/other/restore/caosroot.2025-03-11T16151741706122.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..3318963c255112ead04d39119581dc5972ab58a6
GIT binary patch
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VdR~YPFtR?9F)gg#nn8ns0RZvPH5mW^
literal 0
HcmV?d00001
diff --git a/test-profile/custom/other/restore/caosroot.tar.gz b/test-profile/custom/other/restore/caosroot.tar.gz
deleted file mode 100644
index 63e35ca3beaa34a5406928fc902d002cac087289..0000000000000000000000000000000000000000
GIT binary patch
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S`7p8~mD%>tz5fgv3=9Ce88Y+$
--
GitLab
From 715a8085bf70962b6b12e7b49445161ff304550e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Wed, 12 Mar 2025 09:12:35 +0100
Subject: [PATCH 63/63] FIX: in consistencies in csv treatment
---
README.md | 15 ++++++++++++-
.../sample-management-datamodel.yml | 2 +-
.../src/ext/js/ext_samplemanagement.js | 5 ++++-
.../bin/sample_helpers/default_constants.yml | 2 +-
.../sample_upload_add_special_properties.py | 6 ++++++
.../sample_upload_column_definitions.py | 4 +++-
.../sample_upload_get_person.py | 21 +++++++++++++------
7 files changed, 44 insertions(+), 11 deletions(-)
diff --git a/README.md b/README.md
index 724f519..71abb5a 100644
--- a/README.md
+++ b/README.md
@@ -66,6 +66,19 @@ stored in LinkAhead
You can create a filled CSV template with the information about Containers as
it is currently stored in LinkAhead.
+### Extensibility
+The registration, update and export does not only work with RecordTypes and
+Properties that are defined within this module, but the data model can be
+extended by users of the system: Any Property that is added to the Sample
+RecordType can also be used within the workflow. Once an additional Property
+was added to the RecordType (say "width"), you can select a corresponding
+column during registration with the same name and also upload CSV templates
+that have this column. The Sample records will be created or updated to also
+have this ("width") column.
+
+If the Property that is added is a RecordType, it must be kind of an enum, i.e.
+it should be uniquely identified either by its name or by a sole property.
+
## Usage
**TODO**: Add explanations, screenshots, ec. to explain the sample
@@ -132,7 +145,7 @@ allow to change those.
This is the central RecordType for the sample management and used to represent
samples of various types
-#### `Parent_Sample` (`$parent_sample_prop`)
+#### `Parent_sample` (`$parent_sample_prop`)
references the sample from which the sample at hand originated (for example by
cutting the parent sample into multiple pieces0
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index 4d12dc6..aef3b68 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -83,7 +83,7 @@ Sample:
recommended_properties:
Container:
SampleType:
- Parent_Sample:
+ Parent_sample:
datatype: Sample
Main User:
datatype: Person
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index ba4dcb4..e8e46e0 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -42,6 +42,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"Latitude start",
"Longitude start",
"Elevation start",
+ "Start date",
"Storage ID",
"Device"
];
@@ -73,8 +74,10 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
const unused_property_names = [
"Main User",
+ "Event",
+ "Container",
'NagoyaCase',
- "Parent_Sample",
+ "Parent_sample",
]
const upload_sample_template_form_config = {
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index f752180..c575cb6 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -68,7 +68,7 @@ entity_names:
labelcounter_prop: counter
labelcounter_rt: LabelCounter
last_name_prop: last_name
- parent_sample_prop: Parent_Sample
+ parent_sample_prop: Parent_sample
responsible_rt: Responsible
start_date_prop: start_date
locality_description_prop: locality_description
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
index 5c559d4..9ec2fff 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -33,10 +33,16 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
"""
main_user_prop = db.get_entity_by_name(get_entity_name("Main User"))
+ pi_prop = db.get_entity_by_name(get_entity_name("PI"))
container_rt = db.get_entity_by_name(get_entity_name("container_rt"))
device_rt = db.get_entity_by_name(get_entity_name("Device"))
parent_sample_prop = db.get_entity_by_name(get_entity_name("parent_sample_prop"))
+ if (get_column_header_name("PI") in data and
+ return_value_if_not_none(data[get_column_header_name("PI")]) is not None):
+ pi_user = get_person(return_value_if_not_none(data[get_column_header_name("PI")]))
+ sample = update_property(sample, pi_prop.id, pi_user, property_name=pi_prop.name)
+
if (get_column_header_name("Main User") in data and
return_value_if_not_none(data[get_column_header_name("Main User")]) is not None):
main_user = get_person(return_value_if_not_none(data[get_column_header_name("Main User")]))
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 5535863..0584522 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -79,6 +79,7 @@ DATATYPE_DEFINITIONS = use_custom_names({
# Must exist
OBLIGATORY_COLUMNS = use_custom_names([
"entity_id",
+ "Start date",
])
OBLIGATORY_COLUMNS_CHILD = use_custom_names([
@@ -114,6 +115,7 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
"Longitude start",
"Longitude stop",
"Main User",
+ "PI",
"PDFReport",
"parent_sample_prop",
"Sphere",
@@ -124,6 +126,6 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
IGNORED_COLUMN_NAMES_SAMPLE = use_custom_names([
"LinkAhead URL",
- "Parent Sample",
+ "Parent_sample",
"Storage chain",
])
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
index 1872f62..3e94780 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
@@ -21,6 +21,7 @@ from caosadvancedtools.datainconsistency import DataInconsistencyError
from .utils import get_entity_name
+from linkahead.cached import cached_get_entity_by, cached_query as cquery
def get_person(text: str) -> db.Record:
"""Return the Person Record that is specifed as 'Main User' or
@@ -60,11 +61,19 @@ def _get_person_by_fullname(first_name: str, last_name: str) -> db.Record:
return res[0]
-def _get_person_by_id(eid: str) -> db.Record:
-
- try:
- return db.get_entity_by_id(eid, role=get_entity_name("Person"))
- except db.EmptyUniqueQueryError:
+def _get_person_by_id(ident: str) -> db.Record:
+ options = cquery(f"FIND '{get_entity_name('Person')}' WITH ID='{ident}' ")
+ if len(options)==1:
+ return options[0]
+ options = cquery(f"FIND '{get_entity_name('Person')}' WITH "
+ f"'{get_entity_name('abbreviation_prop')}'='{ident}' ")
+ if len(options) == 1:
+ return options[0]
+ elif len(options) == 0:
+ raise DataInconsistencyError(
+ f"Could not find a {get_entity_name('Person')} with ID {ident}."
+ )
+ else:
raise DataInconsistencyError(
- f"Could not find a {get_entity_name('Person')} with ID {eid}."
+ f"Found multiple {get_entity_name('Person')} with {get_entity_name('abbreviation_prop')}={ident}."
)
--
GitLab