Test to check validation works properly

[emiliorighi]

test_project/annotations.tsv — intentional test rows

Fixture TSV for exercising registry PR validation.

Row	assembly_accession	Purpose
1–2	GCA_048338725.1, GCA_044906185.1	Valid Ensembl pig annotations (from ensembl_annotations.tsv)
3	NOT_A_VALID_ACCESSION	Invalid accession format (not GCA_/GCF_)
4	GCA_963930625.1	Valid accession, unreachable URL (example.invalid)
5	GCA_048338725.1 (again)	Duplicate accession (row 1 repeated with a different URL)
6	GCA_040869115.1	Duplicate URL (reuses row 2’s access_url)
7	GCA_000820885.1	NCBI genomic GFF that fails tabix indexing

Tabix-failure row (row 7): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/820/885/GCA_000820885.1_KLDO_01/GCA_000820885.1_KLDO_01_genomic.gff.gz

[github-actions]

Registry validation

• New rows: 4 valid, 3 invalid
• Manifest issues: 0
• Duplicate assemblies (TSV files): 1
• Duplicate URLs (TSV files): 1
• Duplicate annotation files (MD5, TSV files): 1
• Duplicate files vs registry index: 0
• TSV header/parse errors: 0

Inline annotations on each failing row — open Files changed for details.
Updated on every push.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
Duplicate assembly_accession

• GCA_048338725.1 appears more than once; keep at most one row per assembly.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
Duplicate assembly_accession

• GCA_048338725.1 appears more than once; keep at most one row per assembly.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
Duplicate access_url

• https://ftp.ebi.ac.uk/pub/ensemblorganisms/Sus_scrofa/GCA_048338725.1/ensembl/geneset/2025_08/genes.gff3.gz appears more than once; each row must use a distinct URL.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
Duplicate access_url

• https://ftp.ebi.ac.uk/pub/ensemblorganisms/Sus_scrofa/GCA_044906185.1/ensembl/geneset/2025_08/genes.gff3.gz appears more than once; each row must use a distinct URL.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
Duplicate access_url

• https://ftp.ebi.ac.uk/pub/ensemblorganisms/Sus_scrofa/GCA_048338725.1/ensembl/geneset/2025_08/genes.gff3.gz appears more than once; each row must use a distinct URL.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
Duplicate annotation file (MD5)

• checksum 09a3ba67712292763cd684a8f5119fc4 appears more than once; each row must refer to a distinct annotation file.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
Duplicate annotation file (MD5)

• checksum 09a3ba67712292763cd684a8f5119fc4 appears more than once; each row must refer to a distinct annotation file.

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
NOT_A_VALID_ACCESSION

• assembly_accession format invalid (need GCA_/GCF_…): 'NOT_A_VALID_ACCESSION'

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_963930625.1

• download failed: HTTPSConnectionPool(host='example.invalid', port=443): Max retries exceeded with url: /nonexistent.gff3.gz (Caused by NameResolutionError("HTTPSConnection(host='example.invalid', port=443): Failed to resolve 'example.invalid' ([Errno -2] Name or service not known)"))

[github-actions]

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_000820885.1

• tabix pipeline: [E::hts_idx_push] Invalid record on sequence test #4: end 276483 < begin 276510
  tbx_index_build failed: /tmp/arv_h_6kpfbw0v/pipe.gff.gz