ENH: Use correct datamodel in special tretment lists

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

@@ -57,115 +57,68 @@ def _use_custom_names(definition: Union[list, dict]):
 
 
 DATATYPE_DEFINITIONS = _use_custom_names({
-    "AphiaID": int,
-    "entity_id": str,
     "Campaign": str,
-    "Fixation": str,
-    "Gear configuration": str,
-    "Gear": str,
-    "Hol": int,
+    "Elevation start": float,
+    "Elevation stop": float,
     "Latitude start": float,
     "Latitude stop": float,
     "Longitude start": float,
     "Longitude stop": float,
     "Main User": str,
-    "Nagoya case number": str,
     "PI": str,
     "Parent LinkAhead ID": str,
-    "Platform": str,
-    "Sample Context": str,
-    "Sample container": str,
+    "SampleMethod": str,
     "SampleType": str,
-    "SampleTypeSpecific": str,
-    "Sampling Person": str,
-    "Sampling depth start": float,
-    "Sampling depth stop": float,
-    "Sampling method": str,
-    "Station ID": str,
-    "Station number": str,
-    "Storage Container Label": str,
     "Storage ID": str,
-    "StorageTemperature": str,
-    "Subevent": str,
-    "Water depth start": float,
-    "Water depth stop": float,
+    "entity_id": str,
 })
 
 # Obligatory columns: Must exist and must not be empty
 # Must exist
 OBLIGATORY_COLUMNS = _use_custom_names([
     "entity_id",
-    "Device",
-    "Latitude start",
-    "Longitude start",
-    "Main User",
-    "PI",
-    "Sample container",
-    "SampleType",
-    "Sphere",
-    "Storage ID",
-    "StorageTemperature",
 ])
 
 OBLIGATORY_COLUMNS_CHILD = _use_custom_names([
     "entity_id",
-    "Main User",
     "Parent LinkAhead ID",
-    "Sample container",
-    "SampleType",
-    "SampleTypeSpecific",
-    "Sphere",
-    "Storage ID",
-    "StorageTemperature",
 ])
 
 COLUMN_CONVERTER = _use_custom_names({
-    "Collection": semicolon_separated_list,
-    "Ecotaxa URL": semicolon_separated_list,
-    "NCBI Accession": semicolon_separated_list,
-    "NCBI BioProject": semicolon_separated_list,
-    "NCBI BioSample": semicolon_separated_list,
-    "OSIS URL": semicolon_separated_list,
+    "Collector": semicolon_separated_list,
+    "Curator": semicolon_separated_list,
     "Embargo": _embargo_converter,
-    "Publications": semicolon_separated_list,
+    "Event responsible": semicolon_separated_list,
     "Sphere": semicolon_separated_list,
 })
 
 SPECIAL_TREATMENT_SAMPLE = _use_custom_names([
-    "entity_id",
-    "Collection",
-    "Gear configuration",
-    "Gear",
-    "Hol",
+    "Biome",
+    "Campaign",
+    "Elevation start",
+    "Elevation stop",
+    "End date",
+    "Event responsible",
+    "IGSN DOI",
     "Latitude start",
     "Latitude stop",
+    "Level",
+    "Locality description",
+    "Locality name",
     "Longitude start",
     "Longitude stop",
     "Main User",
-    "Nagoya case number",
     "PDFReport",
-    "PI",
     "Parent Linkahead ID",
-    "Person",
-    "Sampling Person",
-    "Sampling depth start",
-    "Sampling depth stop",
     "Sphere",
-    "Station ID",
-    "Station number",
-    "Storage Container Label",
+    "Sphere",
+    "Start date",
     "Storage ID",
-    "Subevent",
-    "Water depth start",
-    "Water depth stop",
+    "entity_id",
 ])
 
 IGNORED_COLUMN_NAMES_SAMPLE = _use_custom_names([
     "LinkAhead URL",
-    "IGSN URL",
-    "IGSN",  # TODO This will be relevant for external IGSNs in the future.
     "Parent Sample",
-    "Sampling depth",
     "Storage chain",
-    "Water depth",
 ])