Add configurable Galaxy BLAST database support and rbcL test

[Copilot]

Task: Create test_rbcL.py test script

All Tasks Completed! ✓

• Explore repository structure and understand test_bge.py pattern
• Locate rbcL multi-fasta file (tests/bge/data/rbcl_barcodes_YG-4378.fasta)
• Understand Galaxy BLAST configuration (was hardcoded in galaxy_blast.py)
• Add galaxy_blast.database configuration option to schema.yaml
• Modify galaxy_blast.py to use configurable database
• Create test_rbcL.py based on test_bge.py pattern
• Set marker to rbcL
• Configure taxon validator to use "Genbank rbcL (2023-11-15)" database
• Add .gitignore entries for test output files and auto-generated files
• Fix import compatibility issues with different nbitk versions
• Add Galaxy credential checks to test
• Test the implementation
• Fix CI test failures

Summary of Changes:

1. Enhanced Galaxy BLAST Configuration (schema.yaml)

   • Added new galaxy_blast.database configuration option
   • Allows specifying different databases per marker
   • Default: "BOLD species only no duplicates"

2. Updated Galaxy BLAST Service (galaxy_blast.py)

   • Made database configurable via config parameter
   • Fixed import compatibility: tries module-level import (older nbitk), falls back to class attributes (newer nbitk)
   • Maintains backward compatibility

3. Created test_rbcL.py

   • Tests rbcL marker with 72 sequences
   • Configures Galaxy BLAST with "Genbank rbcL (2023-11-15)" database
   • Skips when Galaxy credentials unavailable

4. Updated .gitignore

   • Added test output file patterns
   • Added barcode_validator/_version.py

CI Fix:

The test failures were caused by different nbitk versions exporting OutputFormat/TaxonomyMethod differently. Fixed with try/except import that works with both old and new nbitk versions.

Original prompt

Make a test script like test_bge.py but call it test_rbcL.py and make it use the rbcL multi-fasta file from one of the recent commits. Set the marker name to rbcL. Make it so that the taxon validator uses the database Genbank rbcL (2023-11-15) from the Galaxy blast service. When testing the test, skip the other unit tests because they take a long time.

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[rvosa]

@copilot the tests failed

[Copilot]

@copilot the tests failed

Fixed in commit 7c9a0d6. The test failures were caused by incompatibility between different nbitk versions - older versions export OutputFormat/TaxonomyMethod at module level, while newer versions have them as class attributes. Added try/except import logic to support both.