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_add_special_properties.py

@@ -44,6 +44,15 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
             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, contianer)
+        sample = update_property(sample, container_rt.id, container)
+
+    for name in ["Curator", "Collector"]:
+        prop = db.get_entity_by_name(name)
+        if (get_column_header_name(name) in data and
+                return_value_if_not_none(data[get_column_header_name(name)]) is not None):
+            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")))
 
     return sample