F awi sams

Summary

For #1 (closed). Removes the dependencies on the specifics of the GEOMAR data model and makes things more configurable.

Focus

A lot of functionality is moved into small Python modules in scripting/bin/sample_helpers. They should define a reasonable default behavior for the datamodel in models_and_helper_scripts/sample-management-datamodel.yml and the AWI SAMS datamodel, and should be overwritten by files of the same name in a server profile's custom directory for customization.

Test Environment

So far, only manual testing.

Do round trips for:

• Container registration, export, update
• Sample registration, export, update

Check List for the Author

Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab comments for the reviewer. They should guide the reviewer through the changes, explain your changes and also point out open questions. For further good practices have a look at our review guidelines

• All automated tests pass
• Reference related issues
• Up-to-date CHANGELOG.md (or not necessary)
• Up-to-date JSON schema (or not necessary)
• Appropriate user and developer documentation (or not necessary)
  • How do I use the software? Assume "stupid" users.
  • How do I develop or debug the software? Assume novice developers.
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md (or not necessary)
• Appropriate user and developer documentation (or not necessary)
• The test environment setup works and the intended behavior is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?

For further good practices have a look at our review guidelines.

sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py

+#
+# 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 .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
+
+
+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.
+
+    """
+
+    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")]))
+        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, 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, property_name=parent_sample_prop.name)
+
+    for name in ["Curator", "Collector"]:
+        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(
+                data[get_column_header_name(name)])]
+            sample = update_property(sample, prop.id, persons,
+                                     datatype=db.LIST(get_entity_name("Person")), property_name=prop.name)
+
+    return sample