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.

README.md

@@ -29,6 +29,31 @@ instance's data model (e.g., by [synchronizing with the LinkAhead
 advanced user
 tools](https://docs.indiscale.com//caosdb-advanced-user-tools/yaml_interface.html)).
 
+## Customization
+
+The sample management module can be customized by overwriting
+indivdual code and config files by using files of the same name and
+with the same relative path in your LinkAhead profile's custom
+directory.  E.g., if you want to overwrite how sample entities are post-processed in the sample upload, you overwrite
+
+```
+sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
+```
+
+from this repository by a
+
+```
+profile/custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
+```
+
+in your server profile. When doing so, it is important that in your
+custom file, you use the exact same function names, signatures, and
+return types as in the original file. In our example, the custom
+`sample_upload_post_processing.py` needs to contain a
+`post_process_samples` that takes the samples and the csv data as
+arguments and returns the list of post processed samples.
+
+
 ## Testing
 
 There is a pre-configured `test-profile` that you can use for testing