Feature #41 | Creating physical samples config support and edit form

[gabrielakuhn]

Attention

This branch is in wip. I am currently removing all the all physical-sample class and property
insertions from this branch to add later in the migrations.

Summary

Add physical samples to djehuty

This adds a new type of output you can deposit in the repository, physical samples.
Depositors get a new "Physical samples" area in their dashboard where they can create, edit, and delete sample drafts. This also creates a the edit form which lets you fill in all the
physical-samples metadata

Also adds a config for the IGSN to later integrate with Datacite.

Nothing here changes the existing dataset or collection flows; it all sits side by side.

Changes
web: Implement physical samples with metadata editing and IGSN config

• src/djehuty/web/database.py: Add physical_samples getter and
  insert/update/delete procedures, plus creators, dates and related
  resource sub-record getters and add helpers.
• src/djehuty/web/wsgi.py: Add UI endpoints to list, create, edit and
  delete physical samples, and API endpoints for creators, dates,
  related resources, tags, categories and reordering.
• src/djehuty/web/formatter.py: Add record formatters for physical
  samples, dates and related resources.
• src/djehuty/web/ui.py: Parse the IGSN API configuration from the
  configuration file.
• src/djehuty/web/config/runtime.py: Add IGSN settings and expose
  supports_igsn as a property derived from the prefix.
• src/Makefile.am: Register the new physical sample templates, SPARQL
  queries and edit-physical-sample.js in the resource list.
• src/djehuty/web/resources/html_templates/depositor/physical-samples.html:
  Add the page listing a depositor's physical samples.
• src/djehuty/web/resources/html_templates/depositor/edit-physical-sample.html:
  Add the physical sample metadata edit form.
• src/djehuty/web/resources/html_templates/depositor/dashboard.html: Add
  a physical samples entry to the dashboard.
• src/djehuty/web/resources/html_templates/depositor/my-data.html: Add a
  link to the physical samples page.
• src/djehuty/web/resources/html_templates/depositor/my-collections.html:
  Add a link to the physical samples page.
• src/djehuty/web/resources/static/js/edit-physical-sample.js: Add the
  client-side logic for editing physical samples, including creators,
  dates, related resources, keywords and categories.
• src/djehuty/web/resources/static/css/form.css: Adjust form styling.
• src/djehuty/web/resources/sparql_templates/physical-samples.sparql:
  Add query to retrieve physical samples.
• src/djehuty/web/resources/sparql_templates/physical_sample_creators.sparql:
  Add query to retrieve physical sample creators.
• src/djehuty/web/resources/sparql_templates/physical_sample_dates.sparql:
  Add query to retrieve physical sample dates.
• src/djehuty/web/resources/sparql_templates/physical_sample_related_resources.sparql:
  Add query to retrieve physical sample related resources.
• src/djehuty/web/resources/sparql_templates/initiate_creator_for_physical_sample.sparql:
  Add query to create a creator for a physical sample.
• src/djehuty/web/resources/sparql_templates/initiate_date_for_physical_sample.sparql:
  Add query to create a date for a physical sample.
• src/djehuty/web/resources/sparql_templates/initiate_related_resource_for_physical_sample.sparql:
  Add query to create a related resource for a physical sample.
• src/djehuty/web/resources/sparql_templates/update_physical_sample_draft.sparql:
  Add query to update a physical sample draft.
• src/djehuty/web/resources/sparql_templates/delete_physical_sample_draft.sparql:
  Add query to delete a physical sample draft.
• src/djehuty/web/resources/sparql_templates/update_authors_order.sparql:
  Generalise the author reorder query to accept a predicate.

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

Is part of issue #41

Screenshots (optional)

User dashboard:

Physical Samples dashboard:

Physical Samples registration form

Note

• This is a very big PR (sorry) it should be better spitted from the beginning.
• It was forked from a previous wip.
• There is still more work coming that are splinted in other branches including tests.

[codecov]

Codecov Report

❌ Patch coverage is 9.53545% with 370 lines in your changes missing coverage. Please review.
✅ Project coverage is 16.83%. Comparing base (dee251c) to head (bcbca9f).

Files with missing lines	Patch %	Lines
src/djehuty/web/wsgi.py	5.73%	263 Missing ⚠️
src/djehuty/web/database.py	10.09%	98 Missing ⚠️
src/djehuty/web/ui.py	37.50%	4 Missing and 1 partial ⚠️
src/djehuty/web/formatter.py	50.00%	3 Missing ⚠️
src/djehuty/web/config/runtime.py	85.71%	1 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff                @@
##           feat-41/igsn     #118      +/-   ##
================================================
- Coverage         17.13%   16.83%   -0.31%     
================================================
  Files                21       21              
  Lines             10212    10617     +405     
  Branches           1977     2064      +87     
================================================
+ Hits               1750     1787      +37     
- Misses             8279     8646     +367     
- Partials            183      184       +1     

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[kairoaraujo]

Hi @gabrielakuhn I'm leaving few comments on this round.
I'm planning do a second round in the database and sparql

[kairoaraujo]

Sorry, I have some small comments :)

[kairoaraujo]

LGTM, I assume you will rebase the others after merged

[gabrielakuhn]

LGTM, I assume you will rebase the others after merged

Thanks! Yes, will do that.