import itertools
import statistics
from datetime import datetime
from collections import defaultdict
import indra.tools.assemble_corpus as ac
from indra.pipeline import register_pipeline
from indra.statements import Influence, Association, Event
from indra.statements.concept import get_sorted_compositional_groundings
from indra_world.sources.eidos.client import reground_texts
from .matches import *
from .refinement import *
logger = logging.getLogger(__name__)
register_pipeline(datetime)
@register_pipeline
def get_expanded_events_influences(stmts):
"""Return a list of all standalone events from a list of statements."""
events_influences = []
for stmt_orig in stmts:
stmt = copy.deepcopy(stmt_orig)
if isinstance(stmt, Influence):
for member in [stmt.subj, stmt.obj]:
member.evidence = stmt.evidence[:]
# Remove the context since it may be for the other member
for ev in member.evidence:
ev.context = None
events_influences.append(member)
from indra.pipeline import AssemblyPipeline, register_pipeline
from indra.tools.assemble_corpus import filter_grounded_only
from indra_db.client.principal.curation import get_curations
from emmaa.priors import SearchTerm
from emmaa.readers.aws_reader import read_pmid_search_terms
from emmaa.readers.db_client_reader import read_db_pmid_search_terms, \
read_db_doi_search_terms
from emmaa.readers.elsevier_eidos_reader import \
read_elsevier_eidos_search_terms
from emmaa.util import make_date_str, find_latest_s3_file, strip_out_date, \
EMMAA_BUCKET_NAME, find_nth_latest_s3_file, load_pickle_from_s3, \
save_pickle_to_s3, load_json_from_s3, save_json_to_s3
from emmaa.statements import to_emmaa_stmts
logger = logging.getLogger(__name__)
register_pipeline(get_curations)
class EmmaaModel(object):
""""Represents an EMMAA model.
Parameters
----------
name : str
The name of the model.
config : dict
A configuration dict that is typically loaded from a YAML file.
Attributes
----------
name : str