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/bis_utils.py

@@ -32,57 +32,10 @@ from caosadvancedtools.serverside.helper import send_mail
 from caoscrawler.config import get_config_setting
 from linkahead import get_entity_by_name
 
+from sample_helpers.sample_upload_column_definitions import (
+    IGNORED_COLUMN_NAMES_SAMPLE, SPECIAL_TREATMENT_SAMPLE)
 from sample_helpers.utils import CONSTANTS
 
-SPECIAL_TREATMENT_SAMPLE = [
-    "BIS ID",
-    "Collection",
-    "Date collected start",
-    "Date collected stop",
-    "Date sampled start",
-    "Date sampled stop",
-    "Gear configuration",
-    "Gear",
-    "Hol",
-    "Latitude start",
-    "Latitude stop",
-    "Longitude start",
-    "Longitude stop",
-    "Main User",
-    "Nagoya case number",
-    "PDFReport",
-    "PI",
-    "Parent BIS ID",
-    "Person",
-    "Sampling Person",
-    "Sampling depth start",
-    "Sampling depth stop",
-    "Sphere",
-    "Station ID",
-    "Station number",
-    "Storage Container Label",
-    "Storage ID",
-    "Subevent",
-    "Time collected start",
-    "Time collected stop",
-    "Time sampled start",
-    "Time sampled stop",
-    "Timezone",
-    "Water depth start",
-    "Water depth stop",
-]
-
-IGNORED_COLUMN_NAMES_SAMPLE = [
-    "BIS URL",
-    "Date",
-    "IGSN URL",
-    "IGSN",  # TODO This will be relevant for external IGSNs in the future.
-    "Parent Sample",
-    "Sampling depth",
-    "Storage chain",
-    "Water depth",
-]
-
 
 COLUMN_DESCRIPTIONS = CONSTANTS["csv_column_descriptions"]