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/scripting/bin/sample_helpers/sample_upload_get_event.py

@@ -32,7 +32,8 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
     """
 
     _perform_sanity_checks(sample, data)
-    event = db.Record().add_parent(get_entity_name("event_rt"))
+    event_rt = db.get_entity_by_name(get_entity_name("event_rt"), role="RECORDTYPE")
+    event = db.Record().add_parent(event_rt)
 
     # We performed the sanity checks so we can assume that if the
     # Start/Stop Latitude exists, all start/stop data exist.
@@ -57,6 +58,8 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
 
     # TODO: Start/end date, remaining event props
 
+    sample = update_property(sample, event_rt.id, event)
+    
     return sample