Feature #41 | Fix - physical sample draft fields get lost after saving

[gabrielakuhn]

Summary

When save a physical sample as a draft or submitting it to review, some fields get lost after saving because of 2 reasons: cache was not invalidating the correct and some data were not persistent.

Changes

web: Fix physical sample draft fields lost after saving

• src/djehuty/web/database.py: Correct cache prefixes invalidated on
  physical sample update, remove a redundant second run of the update and
  persist the deposit and publish agreement on update.
• src/djehuty/web/wsgi.py: Persist the alternate identifier and the deposit
  and publish agreement when saving a physical sample draft.
• src/djehuty/web/resources/sparql_templates/update_physical_sample_draft.sparql:
  Update the deposit and publish agreement triples.
• src/djehuty/web/resources/sparql_templates/physical-samples.sparql: Return
  the deposit and publish agreement of a physical sample.
• src/djehuty/web/resources/static/js/edit-physical-sample.js: Send the
  deposit and publish agreement when saving a draft.
• src/djehuty/web/resources/html_templates/depositor/edit-physical-sample.html:
  Show the agreement checkboxes pre-filled from the saved draft and keep
  them visible but read-only when it is under review.

Approval Checklist

• I agree to follow Djehuty's code of conduct.
• I have read and I have follow the code contribution workflow.
• Code style and conventions were respected.
• Documentation has been updated where needed (README, docs, or examples).
• Review approved by at least one maintainer.
• Merge readiness (PR is squashed into a single commit and follows the commit template).

**Issue Reference **

Part of #41

Notes

Branch forked from wip-feat-41-igsn-issued-date

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 16.33%. Comparing base (b682cd4) to head (9803a48).

Additional details and impacted files

@@              Coverage Diff              @@
##           feat-41/igsn     #131   +/-   ##
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  Coverage         16.33%   16.33%           
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  Files                21       21           
  Lines             11447    11447           
  Branches           2246     2246           
=============================================
  Hits               1870     1870           
  Misses             9386     9386           
  Partials            191      191           

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[kairoaraujo]

Check if caught it correct, please.

[kairoaraujo]

this makes the agreements writable on draft-save but it doesn't check the review state, and the template already disables these checkboxes under review. So an API caller can still flip the agreements back to false on an under-review sample. We could skip just these two params when its under review so the backend matches the UI?