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erikhuckerikhuck
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Merge pull request #222 from MoseleyBioinformaticsLab/conv
Conv
2 parents 302b55f + 33694a7 commit 7b918eb

15 files changed

Lines changed: 79602 additions & 73508 deletions

‎dev/test.sh‎

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source .env/bin/activate || source .env/Scripts/activate # Windows has Scripts instead of bin
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python3 -m pytest dev --cov --cov-branch --cov-report=term-missing
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python3 -m pytest dev --cov --cov-branch --cov-report=term-missing -x

‎dev/test_data/all-brite-entry-ids.txt‎

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@@ -2,10 +2,11 @@ br:br08901
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br:br08902
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br:br08904
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br:br08906
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br:br08907
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br:br08908
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br:ko00001
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br:ko00002
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br:ko00003
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br:br08907
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br:ko01000
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br:ko01001
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br:ko01009
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br:br08201
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br:br08202
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br:br08204
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br:br08203
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br:br08303
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br:br08302
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br:br08301
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br:br08313
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br:br08312
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br:br08304
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br:br08305
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br:br08331
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br:br08332
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br:br08020
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br:br08012
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br:br08110
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br:br08111
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br:br08203
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br:br08210
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br:br08081
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br:br08082
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br:br08083
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br:br08084
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br:br08319
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br:br08329
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br:br08318
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br:br08333
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br:br08308
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br:br08406
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br:br08416
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br:br08442
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br:br08431
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br:br08431
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br:br08622
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br:br08606
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br:br08608
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br:br08623

‎dev/test_data/brite-entries/br_br08431.txt‎

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<title>KEGG DISEASE: Carbohydrates in viral infections</title>
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<link rel="stylesheet" href="/css/kegg20.css">
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<script src="/kegg/js/colorid.js"></script>
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<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
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</head>
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<body onload="colorid();">

‎dev/test_data/brite-entries/br_br08902.txt‎

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+C Br number
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!
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APathway and Brite
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B Pathway maps
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B Pathway
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C br08901 KEGG pathway maps
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B Brite files
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B Brite
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C br08902 BRITE hierarchy files
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C br08904 BRITE table files
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C br08906 BRITE binary relation files
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B Network
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C br08907 KEGG network variation maps
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B Taxonomy
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C br08908 Taxonomy files
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AGenes and Proteins
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B Orthologs, modules and networks
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B Orthologs and modules
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C ko00001 KEGG Orthology (KO)
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C ko00002 KEGG modules
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C ko00003 KEGG reaction modules
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C br08907 KEGG networks
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B Protein families: metabolism
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C ko01000 Enzymes
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C ko01001 Protein kinases
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C ko03310 Nuclear receptors
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C ko04040 Ion channels
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C ko04031 GTP-binding proteins
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C ko04052 Cytokines and growth factors
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C ko04052 Cytokines and neuropeptides
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C ko04515 Cell adhesion molecules
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C ko04090 CD molecules
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C ko01504 Antimicrobial resistance genes
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C br08201 Enzymatic reactions
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C br08202 IUBMB reaction hierarchy
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C br08204 Reaction class
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C br08203 Glycosyltransferase reactions
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ADrugs
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B Drug classifications
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C br08303 Anatomical Therapeutic Chemical (ATC) classification
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C br08312 Risk category of Japanese OTC drugs
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C br08304 Traditional Chinese Medicine in Japan
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C br08305 Crude drugs
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C br08331 Animal drugs in Japan
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B Drug information
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C br08330 Drug groups
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C br08332 Drug classes
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C br08410 ICD-10 International Classification of Diseases
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C br08420 ICD-O-3 International Classification of Diseases for Oncology
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AOrganisms and Viruses
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B Taxonomy
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B KEGG taxonomy
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C br08601 KEGG organisms
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B NCBI taxonomy
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C br08610 KEGG organisms in the NCBI taxonomy
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C br08611 KEGG organisms in taxonomic ranks
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C br08612 KEGG organisms: animals
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C br08615 KEGG organisms: protists
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C br08620 KEGG viruses in the NCBI taxonomy
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C br08621 KEGG viruses in taxonomic ranks
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B Organism information
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B Organism and virus information
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C br08605 Plant pathogens
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!
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#
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#Last updated: July 10, 2023
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#Last updated: June 9, 2025
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#&raquo; Japanese version

dev/test_data/brite-entries/pull-results.json renamed to dev/test_data/brite-entries/pull-results.tmp.json

File renamed without changes.

‎dev/test_data/ddi-output.txt‎

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D00100 D00564 CI,P unclassified
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D00109 D00564 P unclassified
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D00564 D00100 CI,P unclassified
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D00564 D00109 P unclassified
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dr:D00100 dr:D00564 CI,P unclassified
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dr:D00109 dr:D00564 P unclassified
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dr:D00564 dr:D00100 CI,P unclassified
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dr:D00564 dr:D00109 P unclassified

‎dev/test_data/drug-entry-ids.txt‎

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dr:D12467
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dr:D13073
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dr:D13086
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dr:D13099
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dr:D13114
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dr:D13123

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