Code

Omnipath processor#1158

Code

Merged

bgyori merged 100 commits intosorgerlab:mastersorgerlab/indra:masterfrom kkaris:omnipath_processorkkaris/indra:omnipath_processorCopy head branch name to clipboardAug 24, 2020

+392-8

Commits

Commits on Aug 20, 2020

• Initial commit of Omnipath PTM query

  

  johnbachman

  authored and

  bgyori

  committed
  c3eaa06

  Copy full SHA for c3eaa06

• Add func to hgnc_client to get db_refs from hgnc name

  

  johnbachman

  authored and

  bgyori

  committed
  c4bb529

  Copy full SHA for c4bb529

• Get mod statements from omnipath

  

  johnbachman

  authored and

  bgyori

  committed
  2dc97c7

  Copy full SHA for 2dc97c7

• Add docs to funcs

  

  johnbachman

  authored and

  bgyori

  committed
  f1ea514

  Copy full SHA for f1ea514

• Build statements for other mod types

  

  johnbachman

  authored and

  bgyori

  committed
  91395c3

  Copy full SHA for 91395c3

• Move omnipath_client to sources

  

  johnbachman

  authored and

  bgyori

  committed
  a21bb52

  Copy full SHA for a21bb52

• Add function to get receptor-ligand interactions

  

  kkaris

  authored and

  bgyori

  committed
  fdd3897

  Copy full SHA for fdd3897

• WIP Add prototype generator of rec-lig statements

  

  kkaris

  authored and

  bgyori

  committed
  e2492f2

  Copy full SHA for e2492f2

• Formatting

  

  kkaris

  authored and

  bgyori

  committed
  3935b28

  Copy full SHA for 3935b28

• Better docstring

  

  kkaris

  authored and

  bgyori

  committed
  f248842

  Copy full SHA for f248842

• Get agents contained in op complex string

  

  kkaris

  authored and

  bgyori

  committed
  39cf353

  Copy full SHA for 39cf353

• Handle more cases of up_id_strings

  

  kkaris

  authored and

  bgyori

  committed
  8298e4c

  Copy full SHA for 8298e4c

• Add helper for making text refs

  

  kkaris

  authored and

  bgyori

  committed
  e83667f

  Copy full SHA for e83667f

• Use PyPath instead of web client

  

  kkaris

  authored and

  bgyori

  committed
  13c7e56

  Copy full SHA for 13c7e56

• Manually rebase api.py

  

  kkaris

  authored and

  bgyori

  committed
  65a7263

  Copy full SHA for 65a7263

• Manually rebase omnipath_processor

  

  kkaris

  authored and

  bgyori

  committed
  705046d

  Copy full SHA for 705046d

• Re-rename omnipath_client -> processor

  

  kkaris

  authored and

  bgyori

  committed
  59aba06

  Copy full SHA for 59aba06

• Update init

  

  kkaris

  authored and

  bgyori

  committed
  4a34e24

  Copy full SHA for 4a34e24

• Update with new classes

  

  kkaris

  authored and

  bgyori

  committed
  b2ef37a

  Copy full SHA for b2ef37a

• Clean up imports, global scope variables

  

  kkaris

  authored and

  bgyori

  committed
  d60b554

  Copy full SHA for d60b554

• Fix docstring, add function to delete cache

  

  kkaris

  authored and

  bgyori

  committed
  7aae009

  Copy full SHA for 7aae009

• Improve hidden method description

  

  kkaris

  authored and

  bgyori

  committed
  29077a8

  Copy full SHA for 29077a8

• Add more annotations

  

  kkaris

  authored and

  bgyori

  committed
  2c328ae

  Copy full SHA for 2c328ae

• Only add cellphonedb info for cellphonedb stmts

  

  kkaris

  authored and

  bgyori

  committed
  80891ae

  Copy full SHA for 80891ae

• Comments, info, docstrings

  

  kkaris

  authored and

  bgyori

  committed
  21203f0

  Copy full SHA for 21203f0

• Add check if pypath can be loaded

  

  kkaris

  authored and

  bgyori

  committed
  1ff1a54

  Copy full SHA for 1ff1a54

• Inform user PyPath is not available

  

  kkaris

  authored and

  bgyori

  committed
  5c74b2e

  Copy full SHA for 5c74b2e

• Bubble up the api functions to __init__

  

  kkaris

  authored and

  bgyori

  committed
  d141209

  Copy full SHA for d141209

• Try import in processor

  

  kkaris

  authored and

  bgyori

  committed
  ecd9d9b

  Copy full SHA for ecd9d9b

• Bubble up processors in __init__

  

  kkaris

  authored and

  bgyori

  committed
  6b8062b

  Copy full SHA for 6b8062b

• Add pypath to extras_require in setup.py

  

  kkaris

  authored and

  bgyori

  committed
  e0d844e

  Copy full SHA for e0d844e

• Add omnipath to packages, format list

  

  kkaris

  authored and

  bgyori

  committed
  16057be

  Copy full SHA for 16057be

• Make warning more informative

  

  kkaris

  authored and

  bgyori

  committed
  c809c7d

  Copy full SHA for c809c7d

• Update imports, test general web api

  

  kkaris

  authored and

  bgyori

  committed
  a8601d8

  Copy full SHA for a8601d8

• Add mods test

  

  kkaris

  authored and

  bgyori

  committed
  b760c4a

  Copy full SHA for b760c4a

• Test import PyPath

  

  kkaris

  authored and

  bgyori

  committed
  05cc18f

  Copy full SHA for 05cc18f

• Start test for ligand-receptor processor

  

  kkaris

  authored and

  bgyori

  committed
  e11046f

  Copy full SHA for e11046f

• Update docstring, fix args bug

  

  kkaris

  authored and

  bgyori

  committed
  5cd47f9

  Copy full SHA for 5cd47f9

• Add more tests for ligand-receptor

  

  kkaris

  authored and

  bgyori

  committed
  0eccf07

  Copy full SHA for 0eccf07

• Fix bug testing web api

  

  kkaris

  authored and

  bgyori

  committed
  a9628a7

  Copy full SHA for a9628a7

• Update travis with PyPath dependencies

  

  kkaris

  authored and

  bgyori

  committed
  e77103f

  Copy full SHA for e77103f

• Sudo all setup commands for igraph

  

  kkaris

  authored and

  bgyori

  committed
  a60e287

  Copy full SHA for a60e287

• Add dependency url for PyPath

  

  kkaris

  authored and

  bgyori

  committed
  3f5790e

  Copy full SHA for 3f5790e

• Try listing pypath as installable from github

  

  kkaris

  authored and

  bgyori

  committed
  ba2daef

  Copy full SHA for ba2daef

• Try explicit pip-install for pypath

  

  kkaris

  authored and

  bgyori

  committed
  502dabf

  Copy full SHA for 502dabf

• Add dependency for pycurl

  

  kkaris

  authored and

  bgyori

  committed
  0f9e435

  Copy full SHA for 0f9e435

• Add more import tests for pypath

  

  kkaris

  authored and

  bgyori

  committed
  fea1e55

  Copy full SHA for fea1e55

• Fix libigraph.so.0 linking issue

  

  kkaris

  authored and

  bgyori

  committed
  67a5455

  Copy full SHA for 67a5455

• Try hpmr as test instead of cellphonedb

  

  kkaris

  authored and

  bgyori

  committed
  cea2b5d

  Copy full SHA for cea2b5d

• Mark PyPyPath test as no-travis

  

  kkaris

  authored and

  bgyori

  committed
  054237f

  Copy full SHA for 054237f

• Catch import errors in pypath network test

  

  kkaris

  authored and

  bgyori

  committed
  79d252f

  Copy full SHA for 79d252f

• Test stmts were produced

  

  kkaris

  authored and

  bgyori

  committed
  443f405

  Copy full SHA for 443f405

• Revert to one class, move preprocessing to api.py

  

  kkaris

  authored and

  bgyori

  committed
  41c753c

  Copy full SHA for 41c753c

• Comments, docstrings

  

  kkaris

  authored and

  bgyori

  committed
  d41f40b

  Copy full SHA for d41f40b

• Fix bug in _delete_cache

  

  kkaris

  authored and

  bgyori

  committed
  4db186f

  Copy full SHA for 4db186f

• Update tests

  

  kkaris

  authored and

  bgyori

  committed
  7a4483e

  Copy full SHA for 7a4483e

• Update __init__

  

  kkaris

  authored and

  bgyori

  committed
  b72c728

  Copy full SHA for b72c728

• Add comments

  

  kkaris

  authored and

  bgyori

  committed
  dc70526

  Copy full SHA for dc70526

• Add helper getting interactions

  

  kkaris

  authored and

  bgyori

  committed
  b8c3787

  Copy full SHA for b8c3787

• WIP First pass at new json format

  

  kkaris

  authored and

  bgyori

  committed
  0dd266c

  Copy full SHA for 0dd266c

• Remove pypath dependencies and functions

  

  kkaris

  authored and

  bgyori

  committed
  9de7699

  Copy full SHA for 9de7699

• Put info in annotations

  

  kkaris

  authored and

  bgyori

  committed
  1e98867

  Copy full SHA for 1e98867

• Build single stmt with multiple evidences

  

  kkaris

  authored and

  bgyori

  committed
  a56ed97

  Copy full SHA for a56ed97

• Update exposed functions

  

  kkaris

  authored and

  bgyori

  committed
  1605d50

  Copy full SHA for 1605d50

• Count skips instead of logging

  

  kkaris

  authored and

  bgyori

  committed
  600ab58

  Copy full SHA for 600ab58

• Update fields, remove genesymbols

  

  kkaris

  authored and

  bgyori

  committed
  0220f79

  Copy full SHA for 0220f79

• Replace ; with , in docstring

  

  kkaris

  authored and

  bgyori

  committed
  84e3d55

  Copy full SHA for 84e3d55

• Add description to docstring

  

  kkaris

  authored and

  bgyori

  committed
  2b092a8

  Copy full SHA for 2b092a8

• Skip of protmapper is only source

  

  kkaris

  authored and

  bgyori

  committed
  d05e464

  Copy full SHA for d05e464

• Remove unused code

  

  kkaris

  authored and

  bgyori

  committed
  13aa147

  Copy full SHA for 13aa147

• Remove unused fields, update docstring

  

  kkaris

  authored and

  bgyori

  committed
  d218b02

  Copy full SHA for d218b02

• Add test for ligrec from web

  

  kkaris

  authored and

  bgyori

  committed
  cfa7666

  Copy full SHA for cfa7666

• Update ptm processing

  

  kkaris

  authored and

  bgyori

  committed
  0d30be8

  Copy full SHA for 0d30be8

• Set source_db as source_sub_id in annotations

  

  kkaris

  authored and

  bgyori

  committed
  3e9089d

  Copy full SHA for 3e9089d

• Remove unused imports in omnipath processor

  

  kkaris

  authored and

  bgyori

  committed
  080f47b

  Copy full SHA for 080f47b

• Remove pypath and dependencies from setup.py

  

  kkaris

  authored and

  bgyori

  committed
  4821636

  Copy full SHA for 4821636

• Remove docstring overflow

  

  kkaris

  authored and

  bgyori

  committed
  a6d80a3

  Copy full SHA for a6d80a3

• Rename helper method

  

  kkaris

  authored and

  bgyori

  committed
  5c58d36

  Copy full SHA for 5c58d36

• Log count of bad pmids (len>8)

  

  kkaris

  authored and

  bgyori

  committed
  409c371

  Copy full SHA for 409c371

• Add bound condition regulations

  

  kkaris

  authored and

  bgyori

  committed
  5e150ce

  Copy full SHA for 5e150ce

• Add docstring for process_from_web

  

  kkaris

  authored and

  bgyori

  committed
  0ceca9e

  Copy full SHA for 0ceca9e

• Add omnipath to docs

  

  kkaris

  authored and

  bgyori

  committed
  85528bb

  Copy full SHA for 85528bb

• Remove pypath dependencies in travis config

  

  kkaris

  authored and

  bgyori

  committed
  b56702c

  Copy full SHA for b56702c

• Add sources/omnipath/index.rst

  

  kkaris

  authored and

  bgyori

  committed
  8c3d2ef

  Copy full SHA for 8c3d2ef

• Reverse removed newline

  

  kkaris

  authored and

  bgyori

  committed
  b08c3a5

  Copy full SHA for b08c3a5

• Fix grammar

  

  kkaris

  authored and

  bgyori

  committed
  0a58335

  Copy full SHA for 0a58335

• Write short blurb about module and its usage

  

  kkaris

  authored and

  bgyori

  committed
  4b10355

  Copy full SHA for 4b10355

• Standardize logger name

  

  kkaris

  authored and

  bgyori

  committed
  5dacf51

  Copy full SHA for 5dacf51

• Directly use name standardization

  

  kkaris

  authored and

  bgyori

  committed
  61f9260

  Copy full SHA for 61f9260

• Do not initialize the processing from init

  

  kkaris

  authored and

  bgyori

  committed
  59266c7

  Copy full SHA for 59266c7

• Initialize agent name with up_id as safeguard

  

  kkaris

  authored and

  bgyori

  committed
  6464daa

  Copy full SHA for 6464daa

• Switch to ontology standardizing in tests

  

  kkaris

  authored and

  bgyori

  committed
  8ece227

  Copy full SHA for 8ece227

• Add omnipath to list of sources in README

  

  kkaris

  authored and

  bgyori

  committed
  45fa569

  Copy full SHA for 45fa569

• Add skips for already known sources

  

  kkaris

  authored and

  bgyori

  committed
  8f9713c

  Copy full SHA for 8f9713c

• Remove logger warning

  

  kkaris

  authored and

  bgyori

  committed
  82a13df

  Copy full SHA for 82a13df

• Add omnipath to belief json

  bgyori

  committed
  74acab5

  Copy full SHA for 74acab5

• Add omnipath to HTML assembler

  bgyori

  committed
  943b66d

  Copy full SHA for 943b66d

• Remove print

  bgyori

  committed
  59e3a0a

  Copy full SHA for 59e3a0a

• Touch up documentation

  bgyori

  committed
  087987e

  Copy full SHA for 087987e

Commits on Aug 24, 2020

• Add omnipath test UP ids

  kkaris

  committed
  fd5cef4

  Copy full SHA for fd5cef4