Source code for indra.sources.omnipath.api

import logging
import requests
from .processor import OmniPathProcessor

logger = logging.getLogger(__name__)

op_url = ''

[docs]def process_from_web(): """Query the OmniPath web API and return an OmniPathProcessor. Returns ------- OmniPathProcessor An OmniPathProcessor object which contains a list of extracted INDRA Statements in its statements attribute. """ ptm_json = _get_modifications() ligrec_json = _get_interactions() op = OmniPathProcessor(ptm_json=ptm_json, ligrec_json=ligrec_json) op.process_ptm_mods() op.process_ligrec_interactions() return op
def _get_modifications(): """Get all PTMs from Omnipath in JSON format. Returns ------- JSON content for PTMs. """ params = {'format': 'json', 'fields': ['curation_effort', 'isoforms', 'references', 'resources', 'sources']} ptm_url = '%s/ptms' % op_url res = requests.get(ptm_url, params=params) if not res.status_code == 200 or not res.text: return None else: return res.json() def _get_interactions(datasets=None): """Wrapper for calling the omnipath interactions API See full list of query options here: Parameters ---------- datasets A list of dataset names. Options are: dorothea, kinaseextra, ligrecextra, lncrna_mrna, mirnatarget, omnipath, pathwayextra, tf_mirna, tf_target, tfregulons Default: 'ligrecextra' Returns ------- dict json of database request """ interactions_url = '%s/interactions' % op_url params = { 'fields': ['curation_effort', 'entity_type', 'references', 'resources', 'sources', 'type'], 'format': 'json', 'datasets': datasets or ['ligrecextra'] } res = requests.get(interactions_url, params=params) res.raise_for_status() return res.json()