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/upload_sample_template.py

@@ -42,7 +42,7 @@ from caoscrawler.logging import configure_server_side_logging
 
 from bis_utils import (replace_entity_urls_by_ids,
                        SPECIAL_TREATMENT_SAMPLE, whitespace_cleanup_in_df)
-from sample_helpers.utils import CONSTANTS
+from sample_helpers.utils import CONSTANTS, get_column_header_name
 
 # suppress warning of diff function
 apilogger = logging.getLogger("linkahead.apiutils")
@@ -66,7 +66,7 @@ def get_parser():
 def _is_child_sample_table(filename):
     tmp_data = pd.read_csv(filename, sep=',')
     if 'Parent BIS ID' in tmp_data.columns:
-        return not tmp_data["Parent BIS ID"].isnull().all()
+        return not tmp_data[get_column_header_name("Parent LinkAhead ID")].isnull().all()
     return False
 
 
@@ -171,7 +171,8 @@ def main():
                 OBLIGATORY_COLUMNS.append(property_name)
         try:
             data = read_data_from_file(path)
-            data = replace_entity_urls_by_ids(data, ["BIS ID", "Storage ID", "Parent BIS ID"])
+            data = replace_entity_urls_by_ids(data, [get_column_header_name(name) for name in [
+                                              "entity_id", "Storage ID", "Parent LinkAhead ID"]])
             pickle_out = NamedTemporaryFile(delete=False, suffix=".pkl")
             data.to_pickle(pickle_out.name)
         except DataInconsistencyError as err: