def update_gosupportevidence(nex_session, annotation_id, gosupport,
annotation_id_to_support_evidences, date_created,
created_by, annotation_type,
annotation_update_log, fw):
key_to_support = {}
if annotation_id in annotation_id_to_support_evidences:
key_to_support = annotation_id_to_support_evidences[annotation_id]
groups = gosupport.split('|')
seen_this_group = {}
group_id = 0
for group in groups:
if group in seen_this_group:
continue
seen_this_group[group] = 1
if group.startswith('With:Not_supplied'):
break
dbxref_ids = group.split(',')
group_id = group_id + 1
seen_this_id = {}
for dbxref_id in dbxref_ids:
if dbxref_id in seen_this_id:
continue
seen_this_id[dbxref_id] = 1
if dbxref_id.startswith('EcoGene:') or dbxref_id.startswith(
'UniPathway:'):
continue
link = get_go_extension_link(dbxref_id)
if link.startswith('Unknown'):
print("Unknown ID: ", dbxref_id)
continue
evidence_type = 'with'
if dbxref_id.startswith('GO:'):
evidence_type = 'from'
key = (group_id, evidence_type, dbxref_id)
if key in key_to_support:
# print "GO supporting evidence ", key, " is in the database"
x = key_to_support.pop(key)
if x.obj_url != link:
x.obj_url = link
nex_session.add(x)
nex_session.flush()
else:
# print "NEW GO supporting evidence ", key
thisSupport = Gosupportingevidence(annotation_id=annotation_id,
group_id=group_id,
dbxref_id=dbxref_id,
obj_url=link,
evidence_type=evidence_type,
date_created=date_created,
created_by=created_by)
fw.write("NEW GOSUPPORTINGEVIDENCE: key=" + str(key) + "\n")
nex_session.add(thisSupport)
key = (annotation_type, 'supportevidence_added')
annotation_update_log[key] = annotation_update_log[key] + 1
to_be_deleted = list(key_to_support.values())
for row in to_be_deleted:
# print "DELETE GO supporting evidence ", row.annotation_id, row.group_id, row.evidence_type, row.dbxref_id
fw.write("DELETE GOSUPPORTINGEVIDENCE: row=" + str(row) + "\n")
nex_session.delete(row)
key = (annotation_type, 'supportevidence_deleted')
annotation_update_log[key] = annotation_update_log[key] + 1
nex_session.commit()
def update_goextension(nex_session, annotation_id, goextension,
annotation_id_to_extensions, date_created, created_by,
annotation_type, annotation_update_log, fw):
key_to_extension = {}
if annotation_id in annotation_id_to_extensions:
key_to_extension = annotation_id_to_extensions[annotation_id]
groups = goextension.split('|')
seen_this_group = {}
group_id = 0
for group in groups:
if group in seen_this_group:
continue
seen_this_group[group] = 1
members = group.split(',')
group_id = group_id + 1
seen_this_member = {}
for member in members:
if member in seen_this_member:
continue
seen_this_member[member] = 1
pieces = member.split('(')
role = pieces[0].replace('_', ' ')
ro_id = get_relation_to_ro_id(role)
if ro_id is None:
print(role, " is not in RO table.")
continue
dbxref_id = pieces[1][:-1]
if dbxref_id.startswith('EcoGene:') or dbxref_id.startswith(
'UniPathway:'):
continue
link = get_go_extension_link(dbxref_id)
if link.startswith('Unknown'):
if dbxref_id.startswith('IntAct:'):
continue
else:
print("Unknown ID: ", dbxref_id)
continue
key = (group_id, ro_id, dbxref_id)
if key in key_to_extension:
# print "GO extension ", key, " is in the database."
x = key_to_extension.pop(key)
if x.obj_url != link:
x.obj_url = link
nex_session.add(x)
nex_session.flush()
else:
# print "NEW GO extension ", key
thisExtension = Goextension(annotation_id=annotation_id,
group_id=group_id,
dbxref_id=dbxref_id,
obj_url=link,
ro_id=ro_id,
date_created=date_created,
created_by=created_by)
fw.write("NEW GOEXTENSION: key=" + str(key) + "\n")
nex_session.add(thisExtension)
key = (annotation_type, 'extension_added')
annotation_update_log[key] = annotation_update_log[key] + 1
to_be_deleted = list(key_to_extension.values())
for row in to_be_deleted:
# print "DELETE GO extension: ", row.annotation_id, row.group_id, row.ro_id, row.dbxref_id
fw.write("DELETE GOEXTENSION: row=" + str(row) + "\n")
nex_session.delete(row)
key = (annotation_type, 'extension_deleted')
annotation_update_log[key] = annotation_update_log[key] + 1
nex_session.commit()