ENH: Add separate module for container identification

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

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",

sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.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
+
+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}."
+            )