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feat: add bv-brc viruses (#524) #553

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e3972bd
feat: adding flu (#379)
d-callan Mar 12, 2025
2e86135
feat: adding the niaid biodefense viruses (#379)
d-callan Mar 12, 2025
82347fe
Merge branch 'main' into even-more-organisms
d-callan Mar 13, 2025
b38db38
Merge branch 'main' into even-more-organisms
d-callan Mar 24, 2025
c312a10
Merge branch 'main' into even-more-organisms
d-callan Apr 8, 2025
df7cff2
fix: some accessions were being duplicated in the intermediate tsv
d-callan Apr 8, 2025
da43936
Merge branch 'main' into even-more-organisms
d-callan Apr 15, 2025
d0442d2
feat: get gene model urls more efficiently
d-callan Apr 15, 2025
c4904fb
feat: all requested organisms now in ucsc
d-callan Apr 17, 2025
72483a3
fix: move imports in data catalog build.py
d-callan Apr 17, 2025
63d1c2c
fix: revert accidentally added npm package
d-callan Apr 19, 2025
ee27f7d
Merge branch 'main' into even-more-organisms
d-callan Apr 28, 2025
08a096f
feat: first pass adding niaid biodefense bacteria
d-callan Apr 28, 2025
2f529a6
Merge branch 'main' into even-more-organisms
d-callan Apr 28, 2025
c78181a
fix: fetching parent taxa occassionally fails
d-callan Apr 29, 2025
b02e366
fix: update to produced json
d-callan Apr 29, 2025
8a66e7c
Merge branch 'main' into even-more-organisms
d-callan Apr 29, 2025
8a1812c
fix: case where a genbank id was provided where it should have been t…
d-callan Apr 30, 2025
25492ff
Merge branch 'even-more-organisms' of github.com:galaxyproject/brc-an…
d-callan May 6, 2025
117f036
Merge branch 'main' into even-more-organisms
d-callan May 6, 2025
4dbe33a
Merge branch 'even-more-organisms' of github.com:galaxyproject/brc-an…
d-callan May 6, 2025
606b382
Merge branch 'main' into even-more-organisms
d-callan May 12, 2025
d1be910
Merge branch 'main' into even-more-organisms
d-callan May 16, 2025
230f98b
feat: update data qc report and ucsc urls for bacteria assemblies
d-callan May 16, 2025
12c881e
feat: all seqs in ucsc brc hub
d-callan May 19, 2025
06b25a2
Merge branch 'main' into even-more-organisms
d-callan May 21, 2025
3007ae4
Merge branch 'main' into even-more-organisms
d-callan May 23, 2025
cba3819
feat: all bacteria have gene model urls
d-callan May 23, 2025
0f02c39
feat: add bv-brc viruses
d-callan May 27, 2025
379ee3b
Merge branch 'main' into even-more-organisms
d-callan May 27, 2025
f68f10a
Merge branch 'main' into even-more-organisms
d-callan Jun 2, 2025
cffe6f6
feat: update ucsc urls and sunburst tree for new organisms
d-callan Jun 2, 2025
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453 changes: 451 additions & 2 deletions catalog/build/intermediate/genomes-from-ncbi.tsv

Large diffs are not rendered by default.

34 changes: 17 additions & 17 deletions catalog/build/intermediate/outbreak-taxonomy-mapping.tsv
Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
taxonomy_id name rank
1980416 Peribunyaviridae FAMILY
5807 Cryptosporidium parvum SPECIES
5207 Cryptococcus neoformans SPECIES
1980415 Nairoviridae FAMILY
11018 Togaviridae FAMILY
199306 Coccidioides posadasii SPECIES
12058 Picornaviridae FAMILY
11158 Paramyxoviridae FAMILY
38574 Leishmania donovani species complex SPECIES_GROUP
1773 Mycobacterium tuberculosis SPECIES
11266 Filoviridae FAMILY
5833 Plasmodium falciparum SPECIES
1980418 Phenuiviridae FAMILY
10244 Monkeypox virus SPECIES
11266 Filoviridae FAMILY
5763 Naegleria fowleri SPECIES
38574 Leishmania donovani species complex SPECIES_GROUP
11158 Paramyxoviridae FAMILY
12058 Picornaviridae FAMILY
11617 Arenaviridae FAMILY
3418604 Betacoronavirus pandemicum SPECIES
5037 Histoplasma capsulatum SPECIES
498019 Candidozyma auris SPECIES
5763 Naegleria fowleri SPECIES
10244 Monkeypox virus SPECIES
1980413 Hantaviridae FAMILY
5207 Cryptococcus neoformans SPECIES
5807 Cryptosporidium parvum SPECIES
199306 Coccidioides posadasii SPECIES
1980418 Phenuiviridae FAMILY
11050 Flaviviridae FAMILY
11320 Influenza A virus
5052 Aspergillus GENUS
1980416 Peribunyaviridae FAMILY
11050 Flaviviridae FAMILY
1980415 Nairoviridae FAMILY
4827 Mucorales ORDER
11617 Arenaviridae FAMILY
5037 Histoplasma capsulatum SPECIES
1773 Mycobacterium tuberculosis SPECIES
1980413 Hantaviridae FAMILY
4 changes: 3 additions & 1 deletion catalog/build/py/package/catalog_build/build.py
Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,9 @@ def post_ncbi_request(url, json_data, batch_size=1000):

data = response.json()

if len(data["reports"][0].get("errors", [])) > 0:
if "reports" not in data:
raise Exception(data)
elif len(data["reports"][0].get("errors", [])) > 0:
raise Exception(data["reports"][0])

all_reports.extend(data["reports"])
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