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] 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
--
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