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.

models_and_helper_scripts/sample-management-datamodel.yml

 #
-#
-# Copyright (C) 2024 IndiScale <info@indiscale.com>
-# Copyright (C) 2024 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+# Copyright (C) 2024-2025 IndiScale <info@indiscale.com>
+# Copyright (C) 2024-2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Affero General Public License as
@@ -26,34 +25,21 @@ ControlledRecordType:
 Responsible:
   inherit_from_obligatory:
     - ControlledRecordType
-  obligatory_properties:
+  recommended_properties:
     Abbreviation:
-      description: An abbreviation for this entity that is used for creating BIS labels
-      datatype: TEXT
-ResearchDivision:
-  inherit_from_obligatory:
-    - Responsible
-  obligatory_properties:
-    German name:
-      description: A german name for an entitiy. This can be used in queries since it is an alias.
+      description: An abbreviation for this entity that is used for identification purposes
       datatype: TEXT
-ResearchUnit:
-  inherit_from_obligatory:
-    - Responsible
-  obligatory_properties:
-    German name:
-    ResearchDivision:
 Person:
-  inherit_from_obligatory:
+  inherit_from_recommended:
     - Responsible
   obligatory_properties:
-    First name:
+    first_name:
       datatype: TEXT
-    Last name:
+    last_name:
       datatype: TEXT
+  recommended_properties:
     Email:
       datatype: TEXT
-    ResearchUnit:
 
 ContainerType:
   inherit_from_obligatory:
@@ -61,63 +47,59 @@ ContainerType:
   obligatory_properties:
     Abbreviation:
 
+ConditionType:
+    inherit_from_obligatory:
+      - ControlledRecordType
+
+StorageCondition:
+  recommended_properties:
+    ConditionType:
+    condition_value:
+      datatype: TEXT
+
 Container:
   obligatory_properties:
     Responsible:
     ContainerType:
-    BIS Label:
-      description: A standardized label for a container in BIS.
-      datatype: TEXT
   suggested_properties:
-    Child container:
+    container_label:
+      description: A standardized label for a container
+      datatype: TEXT
+    Child_Container:
       datatype: LIST<Container>
     Container size:
       description: The size of the container, e.g. number of spaces or dimension
       datatype: TEXT
-    Custom label:
-      description: A custom label for a container that doesn't have to follow the BIS labeling guidelines.
+    custom_label:
+      description: A custom label for a container that doesn't have to follow the automatic labeling guidelines.
       datatype: TEXT
     Container Contents:
       datatype: TEXT
     PI:
       datatype: Person
+    StorageCondition:
 
 Sample:
   recommended_properties:
-    NagoyaCase:
     Container:
-    FunctionalGroup:
     SampleType:
-    Parent sample:
+    Parent_sample:
       datatype: Sample
-    Sampling Person:
-      datatype: Person
     Main User:
       datatype: Person
-  suggested_properties:
-    Custom ID:
-      datatype: LIST<TEXT>
-    Publications:
-      description: DOIs of publications related to this sample.
-      datatype: LIST<TEXT>
-    NCBI BioProject:
-      datatype: LIST<TEXT>
-    NCBI BioSample:
-      datatype: LIST<TEXT>
-    NCBI Accession:
-      datatype: LIST<TEXT>
-    Sampling method:
-      description: A short description of the sampling methodology used for this sample.
-      datatype: TEXT
-    Notes:
+    Collector:
+      datatype: LIST(Person)
+    Curator:
+      datatype: LIST(Person)
+    Device:
+    material_left:
+      datatype: BOOLEAN
+    Event:
+    SampleMethod:
+    nagoya_link:
       datatype: TEXT
-    Time sampled start:
-      datatype: DATETIME
-    Time sampled stop:
-      datatype: DATETIME
-    AphiaID:
-      description: An ID for this taxon that allows to uniquely identify it on http://www.marinespecies.org.
-      datatype: INTEGER
+    nagoya_relevance:
+      datatype: BOOLEAN
 
 
 Collection:
@@ -154,65 +136,54 @@ NagoyaCase:
 
 Position:
   obligatory_properties:
-    Latitude:
+    latitude:
       datatype: DOUBLE
       unit: °
-    Longitude:
+    longitude:
       datatype: DOUBLE
       unit: °
-  recommended_properties:
-    Water depth:
-      description: The depth of the water in meters as a positive value
-      datatype: DOUBLE
-      unit: m
-    Sampling depth:
-      description: The depth in meters where the sampling took place as a positive value
+    elevation:
       datatype: DOUBLE
-      unit: m
 
-FunctionalGroup:
+EventType:
   inherit_from_obligatory:
     - ControlledRecordType
 
-Gear:
+Biome:
+  inherit_from_obligatory:
+    - ControlledRecordType
+
+Device:
   inherit_from_obligatory:
     - ControlledRecordType
-  recommended_properties:
-    Configuration:
-      datatype: TEXT
 
 Event:
-  obligatory_properties:
-    Gear:
   recommended_properties:
-    Time start:
+    Parent_Event:
+      datatype: Event
+    Biome:
+    Campaign:
+    Device:
+    Position:
+      datatype: LIST(Position)
+    start_date:
       description: The date and time the event started.
       datatype: DATETIME
-  suggested_properties:
-    Time stop:
+    end_date:
       description: The date and time the event ended.
       datatype: DATETIME
-
-SourceEvent:
-  inherit_from_suggested:
-    - Event
-  obligatory_properties:
-    Position:
-      datatype: LIST<Position>
-    Gear:
-  recommended_properties:
-    Hol:
+    EventType:
+    igsn_doi:
       datatype: TEXT
-    Station Number:
+    level:
       datatype: TEXT
-    IGSN:
+    locality_description:
       datatype: TEXT
-    DOI:
-      datatype: TEXT
-  suggested_properties:
-    Station ID:
-      description: The name/identifier of a station where regular sampling activity takes place.
+    locality_name:
       datatype: TEXT
+    Sphere:
+    Responsible_Person:
+      datatype: LIST(Person)
 
 Platform:
   inherit_from_obligatory:
@@ -222,9 +193,10 @@ SampleType:
   inherit_from_obligatory:
     - ControlledRecordType
 
-SampleTypeSpecific:
-  inherit_from_obligatory:
-    - ControlledRecordType
+SampleMethod:
+  recommended_properties:
+    Parent_SampleMethod:
+      datatype: SampleMethod
 
 StartPosition:
   inherit_from_obligatory:
@@ -239,25 +211,6 @@ RegisterSampleTemplate:
     column_names:
       datatype: LIST<TEXT>
 
-MeshPoreSize:
-  inherit_from_obligatory:
-    - ControlledRecordType
-  recommended_properties:
-    enumValue:
-      datatype: TEXT
-
-Fixation:
-  inherit_from_obligatory:
-    - ControlledRecordType
-  recommended_properties:
-    enumValue:
-
-StorageTemperature:
-  inherit_from_obligatory:
-    - ControlledRecordType
-  recommended_properties:
-    enumValue:
-
 Campaign:
   inherit_from_obligatory:
     - ControlledRecordType
@@ -267,27 +220,7 @@ Sphere:
   inherit_from_obligatory:
     - ControlledRecordType
 
-Sample context:
-  inherit_from_obligatory:
-    - ControlledRecordType
-
 PDFReport:
   inherit_from_obligatory:
     - ControlledRecordType
   description: PDF files which contain reports and additional information about samples, collections, or containers
-
-commonGermanName:
-  inherit_from_obligatory:
-    - ControlledRecordType
-
-commonEnglishName:
-  inherit_from_obligatory:
-    - ControlledRecordType
-
-Taxonomic group/Species:
-  inherit_from_obligatory:
-    - ControlledRecordType
-
-Sample container:
-  inherit_from_obligatory:
-    - ControlledRecordType