Omnipath processor#1158

Merged

bgyori merged 100 commits into

gyorilab:masterfrom

kkaris:omnipath_processor

Aug 24, 2020

Commits on Aug 20, 2020

Initial commit of Omnipath PTM query

johnbachman
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bgyori
committed
Add func to hgnc_client to get db_refs from hgnc name

johnbachman
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bgyori
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Get mod statements from omnipath

johnbachman
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bgyori
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Add docs to funcs

johnbachman
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bgyori
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Build statements for other mod types

johnbachman
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bgyori
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Move omnipath_client to sources

johnbachman
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bgyori
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Add function to get receptor-ligand interactions

kkaris
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bgyori
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WIP Add prototype generator of rec-lig statements

kkaris
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bgyori
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Formatting

kkaris
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Better docstring

kkaris
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Get agents contained in op complex string

kkaris
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bgyori
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Handle more cases of up_id_strings

kkaris
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bgyori
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Add helper for making text refs

kkaris
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Use PyPath instead of web client

kkaris
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bgyori
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Manually rebase api.py

kkaris
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Manually rebase omnipath_processor

kkaris
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bgyori
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Re-rename omnipath_client -> processor

kkaris
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bgyori
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Update init

kkaris
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bgyori
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Update with new classes

kkaris
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bgyori
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Clean up imports, global scope variables

kkaris
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bgyori
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Fix docstring, add function to delete cache

kkaris
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bgyori
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Improve hidden method description

kkaris
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bgyori
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Add more annotations

kkaris
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bgyori
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Only add cellphonedb info for cellphonedb stmts

kkaris
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bgyori
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Comments, info, docstrings

kkaris
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bgyori
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Add check if pypath can be loaded

kkaris
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bgyori
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Inform user PyPath is not available

kkaris
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bgyori
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Bubble up the api functions to __init__

kkaris
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bgyori
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Try import in processor

kkaris
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bgyori
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Bubble up processors in __init__

kkaris
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bgyori
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Add pypath to extras_require in setup.py

kkaris
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bgyori
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Add omnipath to packages, format list

kkaris
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bgyori
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Make warning more informative

kkaris
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bgyori
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Update imports, test general web api

kkaris
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bgyori
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Add mods test

kkaris
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bgyori
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Test import PyPath

kkaris
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bgyori
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Start test for ligand-receptor processor

kkaris
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bgyori
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Update docstring, fix args bug

kkaris
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bgyori
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Add more tests for ligand-receptor

kkaris
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bgyori
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Fix bug testing web api

kkaris
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bgyori
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Update travis with PyPath dependencies

kkaris
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bgyori
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Sudo all setup commands for igraph

kkaris
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bgyori
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Add dependency url for PyPath

kkaris
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bgyori
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Try listing pypath as installable from github

kkaris
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bgyori
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Try explicit pip-install for pypath

kkaris
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bgyori
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Add dependency for pycurl

kkaris
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bgyori
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Add more import tests for pypath

kkaris
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bgyori
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Fix libigraph.so.0 linking issue

kkaris
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bgyori
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Try hpmr as test instead of cellphonedb

kkaris
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bgyori
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Mark PyPyPath test as no-travis

kkaris
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bgyori
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Catch import errors in pypath network test

kkaris
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bgyori
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Test stmts were produced

kkaris
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bgyori
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Revert to one class, move preprocessing to api.py

kkaris
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bgyori
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Comments, docstrings

kkaris
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bgyori
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Fix bug in _delete_cache

kkaris
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bgyori
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Update tests

kkaris
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bgyori
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Update __init__

kkaris
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bgyori
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Add comments

kkaris
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bgyori
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Add helper getting interactions

kkaris
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bgyori
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WIP First pass at new json format

kkaris
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bgyori
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Remove pypath dependencies and functions

kkaris
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bgyori
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Put info in annotations

kkaris
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bgyori
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Build single stmt with multiple evidences

kkaris
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Update exposed functions

kkaris
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bgyori
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Count skips instead of logging

kkaris
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bgyori
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Update fields, remove genesymbols

kkaris
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bgyori
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Replace ; with , in docstring

kkaris
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bgyori
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Add description to docstring

kkaris
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Skip of protmapper is only source

kkaris
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bgyori
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Remove unused code

kkaris
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bgyori
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Remove unused fields, update docstring

kkaris
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bgyori
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Add test for ligrec from web

kkaris
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bgyori
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Update ptm processing

kkaris
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bgyori
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Set source_db as source_sub_id in annotations

kkaris
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bgyori
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Remove unused imports in omnipath processor

kkaris
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bgyori
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Remove pypath and dependencies from setup.py

kkaris
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bgyori
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Remove docstring overflow

kkaris
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bgyori
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Rename helper method

kkaris
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bgyori
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Log count of bad pmids (len>8)

kkaris
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bgyori
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Add bound condition regulations

kkaris
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bgyori
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Add docstring for process_from_web

kkaris
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Add omnipath to docs

kkaris
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bgyori
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Remove pypath dependencies in travis config

kkaris
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bgyori
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Add sources/omnipath/index.rst

kkaris
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bgyori
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Reverse removed newline

kkaris
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bgyori
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Fix grammar

kkaris
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bgyori
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Write short blurb about module and its usage

kkaris
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bgyori
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Standardize logger name

kkaris
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bgyori
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Directly use name standardization

kkaris
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bgyori
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Do not initialize the processing from init

kkaris
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bgyori
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Initialize agent name with up_id as safeguard

kkaris
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bgyori
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Switch to ontology standardizing in tests

kkaris
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bgyori
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Add omnipath to list of sources in README

kkaris
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bgyori
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Add skips for already known sources

kkaris
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bgyori
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Remove logger warning

kkaris
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bgyori
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Add omnipath to belief json
bgyori
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Add omnipath to HTML assembler
bgyori
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Remove print
bgyori
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Touch up documentation
bgyori
committed

Commits on Aug 24, 2020

Add omnipath test UP ids
kkaris
committed