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 ace23eef4c481fdc20057fce83ef44d4c45dbca5..f3fff6dd3469613378aa7c702d8d90f750694362 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 12edef83b5b463839429faabad5a22e6a543c621..119abc9c165507e9b33a7f69e3224017ba55e2f2 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 cb7ce01ba2e526bd68068daab685818d85959424..5c559d42f9e926303f2c2d94d0bb26e2c42d5d38 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 8384ed934c1449d7b27ca5d6681de95e6d723d6f..235d6949eb3153c6d1e4891cb5938242bda5f987 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 0000000000000000000000000000000000000000..08cf3f0ac5b3148361fc8517cdbcbabf6f48e63e
--- /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 39ca20439768eb1d0d371b4df89eca89acb8c135..7c762df32b703c26ef937bf76e0a3bafe4519e2a 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 c482eeee68360683d92332817fc8aaf5c75ccc38..d047e6bbfd6a39cae610526d17238d3675533447 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 01181ef3afa4701b08593090cd76bc2b4fbbf4a9..25a6e4a6a1f05dc4537c58dd97afb447b3ab4e60 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: