def insert_abstract(nex_session, pmid, reference_id, record, source_id, journal_abbrev, journal_title, issn_print):
text = record.get('AB', '')
if text == '':
return
x = Referencedocument(document_type = 'Abstract',
source_id = source_id,
reference_id = reference_id,
text = text,
html = link_gene_names(text, {}, nex_session),
created_by = CREATED_BY)
nex_session.add(x)
entries = create_bibentry(pmid, record, journal_abbrev, journal_title, issn_print)
y = Referencedocument(document_type = 'Medline',
source_id = source_id,
reference_id = reference_id,
text = '\n'.join([key + ' - ' + str(value) for key, value in entries if value is not None]),
html = '\n'.join([key + ' - ' + str(value) for key, value in entries if value is not None]),
created_by = CREATED_BY)
nex_session.add(y)
nex_session.flush()
nex_session.refresh(x)
def update_abstract(nex_session, fw, pmid, reference_id, abstract, abstract_db,
source_id, update_log, updated_pmids):
if abstract is None or abstract == "" or len(abstract) < 10:
return
if abstract == abstract_db:
return
update_log['abstract'] = update_log['abstract'] + 1
if pmid not in updated_pmids:
updated_pmids.append(pmid)
if abstract_db is None:
x = Referencedocument(document_type='Abstract',
source_id=source_id,
reference_id=reference_id,
text=abstract,
html=link_gene_names(abstract, {}, nex_session),
created_by=CREATED_BY)
nex_session.add(x)
nex_session.commit()
fw.write("PMID:" + str(pmid) +
": new abstract added.\nNew abstract: " + abstract + "\n")
else:
nex_session.query(Referencedocument).filter_by(
reference_id=reference_id).update({
'text':
abstract,
'html':
link_gene_names(abstract, {}, nex_session)
})
nex_session.commit()
fw.write("PMID=" + str(pmid) +
": the abstract is updated.\nNew abstract: " + abstract +
"\nOld abstract: " + abstract_db + "\n\n")
def update_abstract(nex_session, fw, pmid, reference_id, abstract,
abstract_db):
if abstract is None or abstract == "" or len(abstract) < 10:
return
if abstract == abstract_db or abstract_db is None:
return
nex_session.query(Referencedocument).filter_by(
reference_id=reference_id).update({
'text':
abstract,
'html':
link_gene_names(abstract, {}, nex_session)
})
nex_session.commit()