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/utils.py

@@ -3,6 +3,8 @@ import yaml
 
 from pathlib import Path
 
+import linkahead as db
+
 with open(os.path.join(Path(__file__).parent, "default_constants.yml")) as yaml_file:
     CONSTANTS = yaml.safe_load(yaml_file)
 
@@ -26,3 +28,39 @@ def get_column_header_name(name: str):
         return CONSTANTS["csv_column_names"][name]
 
     return get_entity_name(name)
+
+
+def update_property(entity: db.Record, property_id: int, value, property_name="", datatype=None):
+    """
+    Set the property of an entity.
+
+    If the entity already has the property, just the value is set.
+    Else, the property is added to the entity
+    """
+    # TODO: Replace by assure_property_is etc.
+
+    # If the value in the spreadsheet is empty (nan)
+    if ((isinstance(value, list) and len(value) == 0)
+            or (not isinstance(value, list) and pd.isna(value))):
+        # Remove the property from te Entity if it has it
+        try:
+            entity.get_properties().get_by_name(property_name)
+            entity.remove_property(property_name)
+        except KeyError:
+            pass
+        return entity
+    if entity.get_property(property_id) is None:
+        if datatype:
+            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