Source code for indra.sources.eidos.api

__all__ = ['_run_eidos_on_text', 'process_text_bio',
           'process_json_bio', 'process_json_bio_entities',
           'process_text_bio_entities', 'eidos_reader',
           'initialize_reader']

import json
import logging
from indra.sources.eidos import client as eidos_client
from .bio_processor import EidosBioProcessor

logger = logging.getLogger(__name__)


try:
    # For text reading
    from .reader import EidosReader
    eidos_reader = EidosReader()
except Exception as e:
    logger.warning('Could not instantiate Eidos reader, local reading '
                   'will not be available.')
    eidos_reader = None


def _run_eidos_on_text(text, save_json='eidos_output.json',
                       webservice=None):
    if not webservice:
        if eidos_reader is None:
            logger.error('Eidos reader is not available.')
            return None
        json_dict = eidos_reader.process_text(text)
    else:
        if webservice.endswith('/'):
            webservice = webservice[:-1]
        json_dict = eidos_client.process_text(text, webservice=webservice)
    if json_dict and save_json:
        with open(save_json, 'wt') as fh:
            json.dump(json_dict, fh, indent=2)
    return json_dict


[docs]def process_text_bio(text, save_json='eidos_output.json', webservice=None, grounder=None): """Return an EidosProcessor by processing the given text. This constructs a reader object via Java and extracts mentions from the text. It then serializes the mentions into JSON and processes the result with process_json. Parameters ---------- text : str The text to be processed. save_json : Optional[str] The name of a file in which to dump the JSON output of Eidos. webservice : Optional[str] An Eidos reader web service URL to send the request to. If None, the reading is assumed to be done with the Eidos JAR rather than via a web service. Default: None grounder : Optional[function] A function which takes a text and an optional context as argument and returns a dict of groundings. Returns ------- ep : EidosProcessor An EidosProcessor containing the extracted INDRA Statements in its statements attribute. """ json_dict = _run_eidos_on_text(text, save_json, webservice) if json_dict: return process_json_bio(json_dict, grounder=grounder) return None
[docs]def process_json_bio(json_dict, grounder=None): """Return EidosProcessor with grounded Activation/Inhibition statements. Parameters ---------- json_dict : dict The JSON-LD dict to be processed. grounder : Optional[function] A function which takes a text and an optional context as argument and returns a dict of groundings. Returns ------- ep : EidosProcessor A EidosProcessor containing the extracted INDRA Statements in its statements attribute. """ from indra.sources.eidos.bio_processor import EidosBioProcessor ep = EidosBioProcessor(json_dict, grounder=grounder) ep.extract_statements() return ep
[docs]def process_json_bio_entities(json_dict, grounder=None): """Return INDRA Agents grounded to biological ontologies extracted from Eidos JSON-LD. Parameters ---------- json_dict : dict The JSON-LD dict to be processed. grounder : Optional[function] A function which takes a text and an optional context as argument and returns a dict of groundings. Returns ------- list of indra.statements.Agent A list of INDRA Agents which are derived from concepts extracted by Eidos from text. """ from .bio_processor import get_agent_bio if not json_dict: return [] ep = EidosBioProcessor(json_dict, grounder=grounder) ep.extract_causal_relations() ep.extract_events() events = ep.get_all_events() agents = [] for event in events: context = event.evidence[0].text agent = get_agent_bio(event.concept, context=context, grounder=grounder) agents.append(agent) return agents
[docs]def process_text_bio_entities(text, webservice=None, grounder=None): """Return INDRA Agents grounded to biological ontologies extracted from text. Parameters ---------- text : str Text to be processed. webservice : Optional[str] An Eidos reader web service URL to send the request to. If None, the reading is assumed to be done with the Eidos JAR rather than via a web service. Default: None grounder : Optional[function] A function which takes a text and an optional context as argument and returns a dict of groundings. Returns ------- list of indra.statements.Agent A list of INDRA Agents which are derived from concepts extracted by Eidos from text. """ json_dict = _run_eidos_on_text(text, None, webservice=webservice) return process_json_bio_entities(json_dict, grounder=grounder)
[docs]def initialize_reader(): """Instantiate an Eidos reader for fast subsequent reading.""" eidos_reader.process_text('')