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Merged
erikhuck merged 3 commits into from
Mar 19, 2026
Merged

Conv #222

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c5de352
Adds an add_glycans and add_drugs option to conv operations
erikhuck Feb 21, 2026
d496768
Merge branch 'dev' of https://github.com/MoseleyBioinformaticsLab/keg…
Feb 21, 2026
33694a7
Corrects tests and fixes bugs
erikhuck Mar 19, 2026
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2 changes: 1 addition & 1 deletion dev/test.sh
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@@ -1,2 +1,2 @@
source .env/bin/activate || source .env/Scripts/activate # Windows has Scripts instead of bin
python3 -m pytest dev --cov --cov-branch --cov-report=term-missing
python3 -m pytest dev --cov --cov-branch --cov-report=term-missing -x
22 changes: 18 additions & 4 deletions dev/test_data/all-brite-entry-ids.txt
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Expand Up @@ -2,10 +2,11 @@ br:br08901
br:br08902
br:br08904
br:br08906
br:br08907
br:br08908
br:ko00001
br:ko00002
br:ko00003
br:br08907
br:ko01000
br:ko01001
br:ko01009
Expand Down Expand Up @@ -74,15 +75,13 @@ br:br08120
br:br08201
br:br08202
br:br08204
br:br08203
br:br08303
br:br08302
br:br08301
br:br08313
br:br08312
br:br08304
br:br08305
br:br08331
br:br08330
br:br08332
br:br08310
Expand Down Expand Up @@ -127,16 +126,31 @@ br:br08011
br:br08020
br:br08012
br:br08110
br:br08111
br:br08203
br:br08210
br:br08081
br:br08082
br:br08083
br:br08084
br:br08319
br:br08329
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br:br08328
br:br08333
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br:br08406
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br:br08431
br:br08431
br:br08622
br:br08606
br:br08608
br:br08623
1 change: 0 additions & 1 deletion dev/test_data/brite-entries/br_br08431.txt
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Expand Up @@ -6,7 +6,6 @@
<title>KEGG DISEASE: Carbohydrates in viral infections</title>
<link rel="stylesheet" href="/css/kegg20.css">
<script src="/kegg/js/colorid.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
</head>

<body onload="colorid();">
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22 changes: 12 additions & 10 deletions dev/test_data/brite-entries/br_br08902.txt
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@@ -1,18 +1,21 @@
+C Br number
!
APathway and Brite
B Pathway maps
B Pathway
C br08901 KEGG pathway maps
B Brite files
B Brite
C br08902 BRITE hierarchy files
C br08904 BRITE table files
C br08906 BRITE binary relation files
B Network
C br08907 KEGG network variation maps
B Taxonomy
C br08908 Taxonomy files
AGenes and Proteins
B Orthologs, modules and networks
B Orthologs and modules
C ko00001 KEGG Orthology (KO)
C ko00002 KEGG modules
C ko00003 KEGG reaction modules
C br08907 KEGG networks
B Protein families: metabolism
C ko01000 Enzymes
C ko01001 Protein kinases
Expand Down Expand Up @@ -60,7 +63,7 @@ C ko04054 Pattern recognition receptors
C ko03310 Nuclear receptors
C ko04040 Ion channels
C ko04031 GTP-binding proteins
C ko04052 Cytokines and growth factors
C ko04052 Cytokines and neuropeptides
C ko04515 Cell adhesion molecules
C ko04090 CD molecules
C ko01504 Antimicrobial resistance genes
Expand Down Expand Up @@ -90,7 +93,6 @@ B Reactions
C br08201 Enzymatic reactions
C br08202 IUBMB reaction hierarchy
C br08204 Reaction class
C br08203 Glycosyltransferase reactions
ADrugs
B Drug classifications
C br08303 Anatomical Therapeutic Chemical (ATC) classification
Expand All @@ -100,7 +102,6 @@ C br08313 Classification of Japanese OTC drugs
C br08312 Risk category of Japanese OTC drugs
C br08304 Traditional Chinese Medicine in Japan
C br08305 Crude drugs
C br08331 Animal drugs in Japan
B Drug information
C br08330 Drug groups
C br08332 Drug classes
Expand All @@ -117,8 +118,9 @@ C br08411 ICD-11 International Classification of Diseases
C br08410 ICD-10 International Classification of Diseases
C br08420 ICD-O-3 International Classification of Diseases for Oncology
AOrganisms and Viruses
B Taxonomy
B KEGG taxonomy
C br08601 KEGG organisms
B NCBI taxonomy
C br08610 KEGG organisms in the NCBI taxonomy
C br08611 KEGG organisms in taxonomic ranks
C br08612 KEGG organisms: animals
Expand All @@ -127,9 +129,9 @@ C br08614 KEGG organisms: fungi
C br08615 KEGG organisms: protists
C br08620 KEGG viruses in the NCBI taxonomy
C br08621 KEGG viruses in taxonomic ranks
B Organism information
B Organism and virus information
C br08605 Plant pathogens
!
#
#Last updated: July 10, 2023
#Last updated: June 9, 2025
#&raquo; Japanese version
0 ...test_data/brite-entries/pull-results.json → ..._data/brite-entries/pull-results.tmp.json
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8 changes: 4 additions & 4 deletions dev/test_data/ddi-output.txt
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D00100 D00564 CI,P unclassified
D00109 D00564 P unclassified
D00564 D00100 CI,P unclassified
D00564 D00109 P unclassified
dr:D00100 dr:D00564 CI,P unclassified
dr:D00109 dr:D00564 P unclassified
dr:D00564 dr:D00100 CI,P unclassified
dr:D00564 dr:D00109 P unclassified
15 changes: 14 additions & 1 deletion dev/test_data/drug-entry-ids.txt
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Expand Up @@ -397,4 +397,17 @@ dr:D12423
dr:D12467
dr:D12559
dr:D12604
dr:D12646
dr:D12646
dr:D12742
dr:D12746
dr:D12796
dr:D12910
dr:D12938
dr:D12948
dr:D13009
dr:D13044
dr:D13073
dr:D13086
dr:D13099
dr:D13114
dr:D13123
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