ENH: Add separate getter for devices, too

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)
 
 

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:

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

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",

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

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:

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
 
 

sample-management-custom/caosdb-server/scripting/home/identifiables.yml

 ControlledRecordType:
   - name
 Event:
-  - Device
   - start_date
   - Position
 SampleType: