Adapt to model and backend changes

[manulera]

Issue #562

---

Note

Update frontend to use repository_id/coordinates-based source schema with new repository metadata, add strict URL param validation for genome coordinates, and refresh tests and example files.

• Frontend:
  • Schema migration: Switch sources to repository_id + coordinates (e.g., formatSequenceLocationString) instead of sequence_accession/start/end/strand; remove repository_name usage.
  • Repository abstraction: Add repositoryMetadata and refactor repository UI to use source type (e.g., NCBISequenceSource, AddgeneIdSource); update request endpoints to use slugs.
  • Genome coordinates:
    • Validate URL params (numeric start/end, strand ∈ {1, -1}, start>0, `end>start}); show specific error alerts.
    • New GenomeCoordinatesMessage rendering using coordinates and repository_id.
  • Manually typed source: Change POST payload to nested { source, sequence } structure.
  • Utilities: Add formatSequenceLocationString helper.
• Tests (Cypress):
  • Add/adjust checks for genome coordinate URL errors and display (.. formatting; strand validation); update alert selector path.
• Examples/Data:
  • Bump schema_version to 0.4.9 and update example JSONs to new fields (repository_id, coordinates); remove repository_name entries and update SnapGene/GenBank fields accordingly.

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[manulera]

Related to OpenCloning/OpenCloning_backend#383

[cursor]

Bug: URL strand parameter not converted to number before comparison

The strand value from URL parameters is a string (e.g., '-1' or '1'), but formatSequenceLocationString compares it against the number -1 with strict equality. Since '-1' !== -1, the complement format will never be generated for negative strand sequences loaded from URL parameters. The strand value needs to be converted to a number (e.g., Number(strand)) before being passed to formatSequenceLocationString.

 

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.39%. Comparing base (92e27aa) to head (ea0e120).
⚠️ Report is 2 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #563      +/-   ##
==========================================
+ Coverage   82.32%   82.39%   +0.06%     
==========================================
  Files         176      177       +1     
  Lines        6157     6181      +24     
  Branches     1319     1328       +9     
==========================================
+ Hits         5069     5093      +24     
  Misses       1088     1088              

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