Code

Switch to class-based interface#129

Code

Merged

cthoyt merged 97 commits intomasterbiopragmatics/pyobo:masterfrom classify-ontologiesbiopragmatics/pyobo:classify-ontologiesCopy head branch name to clipboardDec 16, 2021

+1,816-1,010

Commits

Commits on Nov 12, 2021

• Begin converting to class-based interface

  cthoyt

  committed
  44f1145

  Copy full SHA for 44f1145

• Add imports

  cthoyt

  committed
  c177ef1

  Copy full SHA for c177ef1

Commits on Nov 13, 2021

• Remove imports

  cthoyt

  committed
  6e1d0c2

  Copy full SHA for 6e1d0c2

• Generate ad-hoc class for OBO

  cthoyt

  committed
  9df3364

  Copy full SHA for 9df3364

• Merge branch 'master' into classify-ontologies

  cthoyt

  committed
  dba5f99

  Copy full SHA for dba5f99

Commits on Nov 14, 2021

• Update sgd.py

  cthoyt

  committed
  1c7acf6

  Copy full SHA for 1c7acf6

• Convert more getters

  cthoyt

  committed
  7898d34

  Copy full SHA for 7898d34

• Merge branch 'master' into classify-ontologies

  cthoyt

  committed
  e4fdcb5

  Copy full SHA for e4fdcb5

• Update UMLS

  cthoyt

  committed
  8a2c0db

  Copy full SHA for 8a2c0db

• Add class resolver

  cthoyt

  committed
  ab9be60

  Copy full SHA for ab9be60

• Update GWAS Central

  cthoyt

  committed
  3dd7bfa

  Copy full SHA for 3dd7bfa

• Update flybase and imports for hgnc/mgi

  cthoyt

  committed
  53598e6

  Copy full SHA for 53598e6

• Remove fraunhofer resource

  cthoyt

  committed
  562fd15

  Copy full SHA for 562fd15

• Update more resources

  cthoyt

  committed
  a9cd59d

  Copy full SHA for a9cd59d

• Update several more getters

  cthoyt

  committed
  b77c350

  Copy full SHA for b77c350

• Update sgd.py

  cthoyt

  committed
  4ce0855

  Copy full SHA for 4ce0855

• Upgrade famplex

  Show description for 7102d43
  cthoyt

  committed
  7102d43

  Copy full SHA for 7102d43

• Upgrade interpro

  cthoyt

  committed
  4ef15a7

  Copy full SHA for 4ef15a7

• Add docs

  cthoyt

  committed
  27f8dcb

  Copy full SHA for 27f8dcb

• Add docs

  cthoyt

  committed
  dab82fe

  Copy full SHA for dab82fe

Commits on Nov 15, 2021

• More updates

  cthoyt

  committed
  79dbca3

  Copy full SHA for 79dbca3

• Add more getters

  cthoyt

  committed
  61ccf63

  Copy full SHA for 61ccf63

• Save on failure to look up in bioregistry

  cthoyt

  committed
  2d53adf

  Copy full SHA for 2d53adf

• Update more getters

  cthoyt

  committed
  e7c1079

  Copy full SHA for e7c1079

• Finish remaining getters

  cthoyt

  committed
  ee6af3b

  Copy full SHA for ee6af3b

• Clean up docstrings

  cthoyt

  committed
  51e14d1

  Copy full SHA for 51e14d1

• Use bioversions for getting ITIS version

  cthoyt

  committed
  8ae0f87

  Copy full SHA for 8ae0f87

• Update selventa nomenclatures

  cthoyt

  committed
  c5448ef

  Copy full SHA for c5448ef

• MyPy fixes

  cthoyt

  committed
  de3e6d5

  Copy full SHA for de3e6d5

• Pass linting

  cthoyt

  committed
  1c69e13

  Copy full SHA for 1c69e13

• Update setup.cfg

  cthoyt

  committed
  e87b3de

  Copy full SHA for e87b3de

• Update test_struct.py

  cthoyt

  committed
  fb6f95e

  Copy full SHA for fb6f95e

Commits on Nov 16, 2021

• Merge branch 'master' into classify-ontologies

  cthoyt

  committed
  fb670b9

  Copy full SHA for fb670b9

• Version the ec2go mapping

  cthoyt

  committed
  c138285

  Copy full SHA for c138285

• Cleanup

  cthoyt

  committed
  2f795c5

  Copy full SHA for 2f795c5

• Update CLI

  cthoyt

  committed
  ca7f2ad

  Copy full SHA for ca7f2ad

• Better error on missing version

  cthoyt

  committed
  ce7062a

  Copy full SHA for ce7062a

• Update mirbase family processing

  cthoyt

  committed
  580ea60

  Copy full SHA for 580ea60

Commits on Nov 19, 2021

• Better use of version for GWAS Central studies

  cthoyt

  committed
  b15c362

  Copy full SHA for b15c362

• Fix handling of missing GWAS Central Phenotype descriptions

  cthoyt

  committed
  af591b3

  Copy full SHA for af591b3

• Fix setting constant version

  cthoyt

  committed
  3f28143

  Copy full SHA for 3f28143

• Safer usage of bioversions

  cthoyt

  committed
  d7a3545

  Copy full SHA for d7a3545

• Update relations.py

  cthoyt

  committed
  b6b942c

  Copy full SHA for b6b942c

• Update ccle.py

  cthoyt

  committed
  7b6b81f

  Copy full SHA for 7b6b81f

Commits on Nov 22, 2021

• Improve logging

  cthoyt

  committed
  9ef540a

  Copy full SHA for 9ef540a

• Fix version lookup

  cthoyt

  committed
  0ce41aa

  Copy full SHA for 0ce41aa

• Remove unused classvars

  cthoyt

  committed
  ad3c3db

  Copy full SHA for ad3c3db

• Allow drugbank missing descriptions

  cthoyt

  committed
  6aa88af

  Copy full SHA for 6aa88af

• Fix drugcentral download

  cthoyt

  committed
  10bb20a

  Copy full SHA for 10bb20a

• Fix ITIS unpacking

  cthoyt

  committed
  78f8fd2

  Copy full SHA for 78f8fd2

• Normalize datatypes

  cthoyt

  committed
  c8ec088

  Copy full SHA for c8ec088

• Fix RGD download

  cthoyt

  committed
  0ad7434

  Copy full SHA for 0ad7434

• Update UMLS download and version getter

  cthoyt

  committed
  efaeed6

  Copy full SHA for efaeed6

• Remove FIXMEs

  cthoyt

  committed
  a24e64b

  Copy full SHA for a24e64b

• Update version tags

  cthoyt

  committed
  b3ee487

  Copy full SHA for b3ee487

• Update wikipathways.py

  cthoyt

  committed
  7461f8d

  Copy full SHA for 7461f8d

• More version fixes

  cthoyt

  committed
  693ca73

  Copy full SHA for 693ca73

• Update flybase.py

  cthoyt

  committed
  1eb35f8

  Copy full SHA for 1eb35f8

• More cleanup and annotate static resources

  cthoyt

  committed
  6c7cd9a

  Copy full SHA for 6c7cd9a

• Skip loading ontologies that don't have their own terms

  cthoyt

  committed
  f1b6962

  Copy full SHA for f1b6962

• Fix type checking

  cthoyt

  committed
  3367eb9

  Copy full SHA for 3367eb9

• Fix passing date and version to ad hoc ontology

  cthoyt

  committed
  71b8f46

  Copy full SHA for 71b8f46

• Fix GWAS central versions

  cthoyt

  committed
  765bc0f

  Copy full SHA for 765bc0f

Commits on Nov 24, 2021

• Update reader.py

  cthoyt

  committed
  b4e456d

  Copy full SHA for b4e456d

Commits on Nov 30, 2021

• Update ccle.py

  cthoyt

  committed
  3b6caac

  Copy full SHA for 3b6caac

• Update reactome.py

  cthoyt

  committed
  89b8416

  Copy full SHA for 89b8416

• Update reader.py

  cthoyt

  committed
  c9139b5

  Copy full SHA for c9139b5

• Update getters.py

  cthoyt

  committed
  143c45b

  Copy full SHA for 143c45b

• Update metadata.py

  cthoyt

  committed
  f0c285e

  Copy full SHA for f0c285e

• Reorganize cleanup function

  cthoyt

  committed
  dc65d27

  Copy full SHA for dc65d27

• Keep deprecation status

  cthoyt

  committed
  b6a0466

  Copy full SHA for b6a0466

• Protect against uncleaned data versions

  cthoyt

  committed
  50d0174

  Copy full SHA for 50d0174

• Add additional broken ontology

  cthoyt

  committed
  eea0096

  Copy full SHA for eea0096

Commits on Dec 1, 2021

• Update metaregistry.json

  cthoyt

  committed
  3e9a824

  Copy full SHA for 3e9a824

• Update metaregistry.json

  cthoyt

  committed
  b076c24

  Copy full SHA for b076c24

Commits on Dec 7, 2021

• Update version handling

  cthoyt

  committed
  57ef3cf

  Copy full SHA for 57ef3cf

• Update metaregistry.json

  cthoyt

  committed
  be8a5aa

  Copy full SHA for be8a5aa

• Update database.py

  cthoyt

  committed
  e4d76a2

  Copy full SHA for e4d76a2

Commits on Dec 8, 2021

• More metadata updates

  cthoyt

  committed
  6aa9f25

  Copy full SHA for 6aa9f25

• More restrictions

  cthoyt

  committed
  1596fd2

  Copy full SHA for 1596fd2

• Don't fail for missing prefixs in deprecated ontologies

  cthoyt

  committed
  4ed7231

  Copy full SHA for 4ed7231

• More updates

  cthoyt

  committed
  867a228

  Copy full SHA for 867a228

• Update reader.py

  cthoyt

  committed
  96afdd2

  Copy full SHA for 96afdd2

• Update metaregistry.json

  cthoyt

  committed
  ddcb616

  Copy full SHA for ddcb616

• Merge branch 'master' into classify-ontologies

  cthoyt

  committed
  18d0b9e

  Copy full SHA for 18d0b9e

• Merge branch 'master' into classify-ontologies

  cthoyt

  committed
  736e307

  Copy full SHA for 736e307

• Cleanup

  cthoyt

  committed
  209ebb9

  Copy full SHA for 209ebb9

• Merge branch 'master' into classify-ontologies

  cthoyt

  committed
  cdee491

  Copy full SHA for cdee491

• Update path.py

  cthoyt

  committed
  794bb19

  Copy full SHA for 794bb19

• Update setup.cfg

  cthoyt

  committed
  d29d45a

  Copy full SHA for d29d45a

Commits on Dec 14, 2021

• Update metaregistry.json

  cthoyt

  committed
  b7ca7d0

  Copy full SHA for b7ca7d0

• Update version handling

  cthoyt

  committed
  6e9fd67

  Copy full SHA for 6e9fd67

• Update getters.py

  cthoyt

  committed
  25189cb

  Copy full SHA for 25189cb

• Update setup.cfg

  cthoyt

  committed
  998d9fa

  Copy full SHA for 998d9fa

Commits on Dec 16, 2021

• Handle bad content

  cthoyt

  committed
  6e5d100

  Copy full SHA for 6e5d100

• Ensure new version of pystow

  cthoyt

  committed
  7712faa

  Copy full SHA for 7712faa

• Fix versions

  cthoyt

  committed
  b5d3066

  Copy full SHA for b5d3066