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.

requested review from @henrik

assigned to @florian

added 3 commits

• 600603ba - ENH: Automatically replace all column keys by custom definitions
• dc1aebc5 - ENH: Addapt upload sample script to configurable column names
• c0d0740d - ENH: Add sample postprocessing

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added 1 commit

• fe4d2ca4 - DOC: Add a brief description of customizations to the README

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• 9f0ecc0e - MAINT: Remove geomar specific time properties

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• 6615797a - ENH: Make get_person customizable in sample upload

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• 0cadc8df - ENH: Remove GEOMAR-specific date treatment

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• 57ef07b1 - MAINT: Also remove timezones from special treatment

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• 421f0ee2 - WIP: Add treatment for events

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• 7e29c2d6 - WIP: Remove unused properties and recordtypes
• c20672a6 - FIX: Use correct label names
• 9e577d31 - FIX: Add missing custom label header name

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added 1 commit

• 6cde3c31 - ENH: Use separate event-adding module

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added 2 commits

• c1a64649 - ENH: Use correct datamodel in sample registration
• 16ab9c3d - MAINT: Remove more unused GEOMAR entities from datamodel

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• 206daaef - ENH: Move adding of special sample properties to separate module

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• 5fa73e89 - ENH: Use correct datamodel in special tretment lists

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• 0fbb980a - MAINT: Remove unused GEOMAR specail property functions

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• 1a9e1857 - ENH: Add separate module for container identification

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• 7d04de0c - ENH: Add special properties treatment for samples

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• 29dc4b42 - EN: Also support parent/child samples
• dbb061c0 - ENH: Add position treatment to events
• 3d636dab - ENH: Define identifiables

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• a447505b - ENH: Add event to sample

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• e8009701 - WIP: Remove some entries from sample exporter

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• 232ea812 - ENH: Add start/end time treatment

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added 2 commits

• 77930b32 - FIX: Typos
• 092be437 - ENH: Add separate getter for devices, too

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• 84933ee0 - ENH: Add missing event properties

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• 7a4660dd - ENH: Use configurable server URL in sample export
• 8f7beb3f - ENH: Adapt sample export to new data model

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• bded836d - FIX: Correct exporter list

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resolved all threads

marked this merge request as ready

marked the checklist item Reference related issues as completed

marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed

marked the checklist item Up-to-date JSON schema (or not necessary) as completed

marked the checklist item Appropriate user and developer documentation (or not necessary) as completed

marked the checklist item Annotations in code (Gitlab comments) as completed

resolved all threads

added 1 commit

• 399fda02 - MAINT: Remove debugging output

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• 292fed5a - WIP: new dump; make data model consistent

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Only try to set the converter if none is set in DATAYPTE_DEFINITIONS

added 1 commit

• 715a8085 - FIX: in consistencies in csv treatment

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marked the checklist item I understand the intent of this MR as completed

marked the checklist item All automated tests pass as completed

marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed