ENH: Move adding of special sample properties to separate module

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():

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 .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