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/caosdb-webui/src/ext/js/ext_samplemanagement.js

@@ -35,6+35,6 @@
         ".CSV",
         "application/csv",
         "text/csv",
     ];
     const required_column_names = [
         "LinkAhead ID",
         "Main User",
         "Latitude start",
         "Longitude start",
-	"Elevation start",
-        "Collection",
-        "PI",
+        "Elevation start",
         "Storage ID",
-        "Nagoya case number",
-        "Sample container",
-        "Fixation",
-        "StorageTemperature",
-        "SampleType",
-        "SampleTypeSpecific",
-        "Sphere",
-        "Sample Context",
+        "Device"
     ];
     const requiredColumnNamesChildren = [
         "LinkAhead ID",
-        "Date sampled start",
-        "Fixation",
         "Main User",
         "Parent LinkAhead ID",
-        "Sample Context",
-        "Sample container",
         "SampleType",
-        "SampleTypeSpecific",
-        "Sphere",
         "Storage ID",
-        "StorageTemperature",
     ];
     const non_sample_rt_column_names = [
-        "Platform",
+        "Biome",
         "Campaign",
-        "Station ID",
-        "Station number",
-        "Subevent",
-        "Hol",
-        "Sampling depth start",
-        "Sampling depth stop",
-        "Water depth start",
-        "Water depth stop",
+        "Start date",
+        "End date",
+        "IGSN DOI",
+        "Level",
+        "Locality description",
+        "Locality name",
+        "Sphere",
+        "Event responsible",
         "Latitude stop",
         "Longitude stop",
-	"Elevation stop",
-        "Taxonomic group/Species",
-        "AphiaID",
-        "On-board sampleID",
-        "Extraction ID",
-        "Duplicate number",
-        "Other fixations",
-        "Notes / remarks",
-        "Forlmaldehyde_box",
-        "OSIS URL",
-        "Ecotaxa URL",
+        "Elevation stop",
         "PDFReport",
-        "Parent LinkAhead ID"
-    ]
+        "Parent LinkAhead ID",
+    ];
     const allColumnNames = non_sample_rt_column_names.concat(requiredColumnNamesChildren).concat(required_column_names);
 
     const unused_property_names = [
-        'Container',
-        'Event',
         "Main User",
         'NagoyaCase',
-        "Parent Sample",
-        "Person",
+        "Parent_Sample",
     ]
 
     const upload_sample_template_form_config = {