def update_abstract(nex_session, fw, pmid, reference_id, record, abstract_db,
source_id):
abstract = record.get('AB', '')
if abstract == '':
return
if abstract and abstract == abstract_db:
return
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")
print("PMID:", pmid, ": new abstract added.")
print("New abstract:", abstract)
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")
print("PMID=", pmid, ": the abstract is updated.")
print("New abstract:", abstract)
print("Old abstract:", abstract_db)
def read_summary_file(nex_session, fw, summary_type, summary_file, log_file):
from util import link_gene_names
from models import Locusdbentity, Referencedbentity
name_to_dbentity = dict([(x.systematic_name, x) for x in nex_session.query(Locusdbentity).all()])
sgdid_to_dbentity_id = dict([(x.sgdid, x.dbentity_id) for x in nex_session.query(Locusdbentity).all()])
pmid_to_reference_id = dict([(x.pmid, x.dbentity_id) for x in nex_session.query(Referencedbentity).all()])
data = []
if summary_type == 'Phenotype':
f = open(summary_file, 'U')
for line in f:
pieces = line.strip().split('\t')
dbentity = name_to_dbentity.get(pieces[0])
if dbentity is None:
continue
data.append({'locus_id': dbentity.dbentity_id,
'text': pieces[1],
'html': link_gene_names(pieces[1], {dbentity.display_name, dbentity.format_name, dbentity.display_name + 'P', dbentity.format_name + 'P'}, nex_session),
'summary_type': summary_type,
'summary_order': 1 })
elif summary_type == 'Regulation':
f = open(summary_file, 'U')
for line in f:
pieces = line.strip().split('\t')
dbentity = name_to_dbentity.get(pieces[0])
if dbentity is None:
continue
references = []
pmid_list = pieces[3].replace(' ', '')
pmids = pmid_list.split('|')
order = 0
for pmid in pmids:
reference_id = pmid_to_reference_id.get(int(pmid))
if reference_id is None:
print "PMID=", pmid, " is not in the database"
continue
order = order + 1
references.append({'reference_id': reference_id, 'reference_order': order})
data.append({'locus_id': dbentity.dbentity_id,
'text': pieces[2],
'html': link_gene_names(pieces[2], {dbentity.display_name, dbentity.format_name, dbentity.display_name + 'P', dbentity.format_name + 'P'}, nex_session),
'summary_type': summary_type,
'summary_order': 1,
'references': references})
elif summary_type == 'Function':
f = open(summary_file, 'U')
for line in f:
pieces = line.split('\t')
if len(pieces) >= 8:
sgdid = pieces[8]
if sgdid.startswith('SGD:'):
dbentity_id = sgdid_to_dbentity_id.get(sgdid[4:])
if dbentity_id is None:
continue
functionSummary = [x[22:].strip() for x in pieces[9].split('|') if x.startswith('go_annotation_summary')]
if len(functionSummary) == 1:
data.append({'locus_id': dbentity_id,
'text': functionSummary[0],
'html': functionSummary[0],
'summary_type': summary_type,
'summary_order': 1})
else:
fw.write("Unknown summary_type: " + summary_type+ "\n")
exit()
return data
def read_summary_file(nex_session, fw, summary_type, summary_file_reader,
log_file, data_for_json):
from util import link_gene_names
from models import Locusdbentity, Referencedbentity
name_to_dbentity = dict([(x.systematic_name, x)
for x in nex_session.query(Locusdbentity).all()])
sgdid_to_dbentity_id = dict([
(x.sgdid, x.dbentity_id)
for x in nex_session.query(Locusdbentity).all()
])
pmid_to_reference_id = dict([
(x.pmid, x.dbentity_id)
for x in nex_session.query(Referencedbentity).all()
])
data = []
if summary_type == 'Phenotype_Regulation':
for pieces in summary_file_reader:
summary_type = pieces[1]
if summary_type in ['Phenotype', 'phenotype', 'PHENOTYPE']:
summary_type = 'Phenotype'
elif summary_type in ['Regulation', 'regulation', 'REGULATION']:
summary_type = 'Regulation'
dbentity = name_to_dbentity.get(pieces[0])
if dbentity is None:
data_for_json.append({
'category': 'locus',
'name': pieces[0],
'type': x['summary_type'] + ' summary',
'value': x['text'],
'tag': "unknown gene name"
})
continue
references = []
if len(pieces) > 3:
pmid_list = pieces[3].replace(' ', '')
pmids = pmid_list.split('|')
order = 0
for pmid in pmids:
reference_id = pmid_to_reference_id.get(int(pmid))
if reference_id is None:
print("PMID=", pmid, " is not in the database")
continue
order = order + 1
references.append({
'reference_id': reference_id,
'reference_order': order
})
data.append({
'locus_id':
dbentity.dbentity_id,
'text':
pieces[2],
'html':
link_gene_names(
pieces[2], {
dbentity.display_name, dbentity.format_name,
dbentity.display_name + 'P', dbentity.format_name + 'P'
}, nex_session),
'summary_type':
summary_type,
'summary_order':
1,
'references':
references,
'dbentity':
dbentity
})
elif summary_type == 'Function':
for pieces in summary_file_reader:
if len(pieces) >= 8:
sgdid = pieces[8]
if sgdid.startswith('SGD:'):
dbentity_id = sgdid_to_dbentity_id.get(sgdid[4:])
if dbentity_id is None:
continue
functionSummary = [
x[22:].strip() for x in pieces[9].split('|')
if x.startswith('go_annotation_summary')
]
if len(functionSummary) == 1:
data.append({
'locus_id': dbentity_id,
'text': functionSummary[0],
'html': functionSummary[0],
'summary_type': summary_type,
'summary_order': 1
})
else:
fw.write("Unknown summary_type: " + summary_type + "\n")
exit()
return data