def get_new_readings(self, date_limit=10):
"""Search new literature, read, and add to model statements"""
readers = self.reading_config.get('reader', ['indra_db_pmid'])
lit_sources = self.reading_config.get('literature_source', ['pubmed'])
if isinstance(lit_sources, str):
lit_sources = [lit_sources]
if isinstance(readers, str):
readers = [readers]
estmts = []
for lit_source, reader in zip(lit_sources, readers):
ids_to_terms = self.search_literature(lit_source, date_limit)
if reader == 'aws':
estmts += read_pmid_search_terms(ids_to_terms)
elif reader == 'indra_db_pmid':
estmts += read_db_pmid_search_terms(ids_to_terms)
elif reader == 'indra_db_doi':
estmts += read_db_doi_search_terms(ids_to_terms)
elif reader == 'elsevier_eidos':
estmts += read_elsevier_eidos_search_terms(ids_to_terms)
else:
raise ValueError('Unknown reader: %s' % reader)
logger.info('Got a total of %d new EMMAA Statements from reading' %
len(estmts))
self.extend_unique(estmts)
if self.reading_config.get('cord19_update'):
self.update_with_cord19()
def get_new_readings(self, date_limit=10):
"""Search new literature, read, and add to model statements"""
reader = self.reading_config.get('reader', 'indra_db')
ids_to_terms = self.search_literature(date_limit=date_limit)
if reader == 'aws':
estmts = read_pmid_search_terms(ids_to_terms)
elif reader == 'indra_db':
estmts = read_db_pmid_search_terms(ids_to_terms)
elif reader == 'elsevier_eidos':
estmts = read_elsevier_eidos_search_terms(ids_to_terms)
else:
raise ValueError('Unknown reader: %s' % reader)
self.extend_unique(estmts)
def get_new_readings(self, date_limit=10):
"""Search new literature, read, and add to model statements"""
readers = self.reading_config.get('reader', ['indra_db_pmid'])
lit_sources = self.reading_config.get('literature_source', ['pubmed'])
if isinstance(lit_sources, str):
lit_sources = [lit_sources]
if isinstance(readers, str):
readers = [readers]
# First get statements from literature and extend existing statements
# Some models are not updated from literature
if lit_sources is not None and readers is not None:
estmts = []
for lit_source, reader in zip(lit_sources, readers):
ids_to_terms = self.search_literature(lit_source, date_limit)
if reader == 'aws':
new_estmts = read_pmid_search_terms(ids_to_terms)
self.add_paper_ids(ids_to_terms.keys(), 'pmid')
elif reader == 'indra_db_pmid':
new_estmts = read_db_pmid_search_terms(ids_to_terms)
self.add_paper_ids(ids_to_terms.keys(), 'pmid')
elif reader == 'indra_db_doi':
new_estmts = read_db_doi_search_terms(ids_to_terms)
self.add_paper_ids(ids_to_terms.keys(), 'doi')
elif reader == 'elsevier_eidos':
new_estmts = read_elsevier_eidos_search_terms(ids_to_terms)
self.add_paper_ids(ids_to_terms.keys(), 'pii')
else:
raise ValueError('Unknown reader: %s' % reader)
estmts += new_estmts
logger.info('Got a total of %d new EMMAA Statements from reading' %
len(estmts))
self.extend_unique(estmts)
# The following methods get subsets of statements from other sources
# and overwrite existing statements
estmts = []
if self.reading_config.get('cord19_update'):
new_estmts = self.update_with_cord19(
self.reading_config['cord19_update'])
estmts += new_estmts
if self.reading_config.get('disease_map'):
new_estmts = self.update_from_disease_map(
self.reading_config['disease_map'])
estmts += new_estmts
if self.reading_config.get('other_files'):
new_estmts = self.update_from_files(
self.reading_config['other_files'])
estmts += new_estmts
if estmts:
self.stmts = estmts
self.eliminate_copies()
def get_new_readings(self, pmit_to_terms):
pmid_to_terms = self.search_literature(date_limit=10)
estmts = read_pmid_search_terms(pmid_to_terms)
self.extend_unique(estmts)