def load_ontology(ontology_file):
nex_session = get_session()
source_to_id = dict([(x.display_name, x.source_id)
for x in nex_session.query(Source).all()])
obiid_to_obi = dict([(x.obiid, x) for x in nex_session.query(Obi).all()])
term_to_ro_id = dict([(x.display_name, x.ro_id)
for x in nex_session.query(Ro).all()])
obi_id_to_parent = {}
for x in nex_session.query(ObiRelation).all():
parents = []
if x.child_id in obi_id_to_parent:
parents = obi_id_to_parent[x.child_id]
parents.append(x.parent_id)
obi_id_to_parent[x.child_id] = parents
####################################
fw = open(log_file, "w")
is_sgd_term = {}
data = read_owl(ontology_file, ontology)
[update_log,
to_delete_list] = load_new_data(nex_session, data, source_to_id,
obiid_to_obi, term_to_ro_id['is a'],
obi_id_to_parent, fw)
write_summary_and_send_email(fw, update_log, to_delete_list)
nex_session.close()
fw.close()
def load_ontology(ontology_file):
nex_session = get_session()
log.info(str(datetime.now()))
log.info("Getting data from database...")
source_to_id = dict([(x.display_name, x.source_id)
for x in nex_session.query(Source).all()])
chebiid_to_chebi = dict([(x.chebiid, x)
for x in nex_session.query(Chebi).all()])
chebi_id_to_alias = {}
for x in nex_session.query(ChebiAlia).all():
if x.alias_type in ['PharmGKB ID', 'YeastPathway ID']:
continue
aliases = []
if x.chebi_id in chebi_id_to_alias:
aliases = chebi_id_to_alias[x.chebi_id]
aliases.append((x.display_name, x.alias_type))
chebi_id_to_alias[x.chebi_id] = aliases
####################################
fw = open(log_file, "w")
log.info("Reading data from ontology file...")
is_3_star_term = {}
data = read_owl(ontology_file, ontology, is_3_star_term)
log.info("Updating chebi ontology data in the database...")
[update_log, to_delete_list,
term_name_changed] = load_new_data(nex_session, data, source_to_id,
chebiid_to_chebi, chebi_id_to_alias,
is_3_star_term, fw)
log.info("Writing loading summary...")
write_summary_and_send_email(fw, update_log, to_delete_list,
term_name_changed)
nex_session.close()
fw.close()
log.info(str(datetime.now()))
log.info("Done!\n\n")
def load_ontology(ontology_file):
nex_session = get_session()
source_to_id = dict([(x.display_name, x.source_id)
for x in nex_session.query(Source).all()])
taxid_to_taxonomy = dict([(x.taxid, x)
for x in nex_session.query(Taxonomy).all()])
term_to_ro_id = dict([(x.display_name, x.ro_id)
for x in nex_session.query(Ro).all()])
taxonomy_id_to_alias = {}
for x in nex_session.query(TaxonomyAlia).all():
aliases = []
if x.taxonomy_id in taxonomy_id_to_alias:
aliases = taxonomy_id_to_alias[x.taxonomy_id]
aliases.append((x.display_name, x.alias_type))
taxonomy_id_to_alias[x.taxonomy_id] = aliases
taxonomy_id_to_parent = {}
for x in nex_session.query(TaxonomyRelation).all():
parents = []
if x.child_id in taxonomy_id_to_parent:
parents = taxonomy_id_to_parent[x.child_id]
parents.append(x.parent_id)
taxonomy_id_to_parent[x.child_id] = parents
####################################
fw = open(log_file, "w")
[filtered_set,
id_to_rank] = children_for_taxonomy_ancestor(ontology_file, ancestor)
## total 1037 in the filtered set
## print "COUNT=", len(filtered_set)
data = read_owl(ontology_file, ontology)
[update_log, to_delete_list
] = load_new_data(nex_session, data, source_to_id, taxid_to_taxonomy,
term_to_ro_id['is a'], taxonomy_id_to_alias,
taxonomy_id_to_parent, filtered_set, id_to_rank, fw)
write_summary_and_send_email(fw, update_log, to_delete_list)
nex_session.close()
fw.close()
def load_ontology(ontology_file):
nex_session = get_session()
source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()])
soid_to_so = dict([(x.soid, x) for x in nex_session.query(So).all()])
term_to_ro_id = dict([(x.display_name, x.ro_id) for x in nex_session.query(Ro).all()])
so_id_to_alias = {}
for x in nex_session.query(SoAlia).all():
aliases = []
if x.so_id in so_id_to_alias:
aliases = so_id_to_alias[x.so_id]
aliases.append((x.display_name, x.alias_type))
so_id_to_alias[x.so_id] = aliases
so_id_to_parent = {}
for x in nex_session.query(SoRelation).all():
parents = []
if x.child_id in so_id_to_parent:
parents = so_id_to_parent[x.child_id]
parents.append(x.parent_id)
so_id_to_parent[x.child_id] = parents
####################################
fw = open(log_file, "w")
is_sgd_term = {}
data = read_owl(ontology_file, ontology)
[update_log, to_delete_list] = load_new_data(nex_session, data,
source_to_id,
soid_to_so,
term_to_ro_id['is a'],
so_id_to_alias,
so_id_to_parent,
fw)
write_summary_and_send_email(fw, update_log, to_delete_list)
nex_session.close()
fw.close()
def load_ontology(ontology_file):
nex_session = get_session()
source_to_id = dict([(x.display_name, x.source_id)
for x in nex_session.query(Source).all()])
roid_to_ro = dict([(x.roid, x) for x in nex_session.query(Ro).all()])
fw = open(log_file, "w")
data = read_owl(ontology_file, ontology)
[update_log,
to_delete_list] = load_new_data(nex_session, data, source_to_id[src],
roid_to_ro, fw)
write_summary_and_send_email(fw, update_log, to_delete_list)
nex_session.close()
fw.close()
def load_ontology(ontology_file):
nex_session = get_session()
log.info(str(datetime.now()))
log.info("Getting data from database...")
source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()])
doid_to_disease = dict([(x.doid, x) for x in nex_session.query(Disease).all()])
term_to_ro_id = dict([(x.display_name, x.ro_id) for x in nex_session.query(Ro).all()])
edam_to_id = dict([(x.format_name, x.edam_id) for x in nex_session.query(Edam).all()])
disease_id_to_alias = {}
for x in nex_session.query(DiseaseAlias).all():
aliases = []
if x.disease_id in disease_id_to_alias:
aliases = disease_id_to_alias[x.disease_id]
aliases.append((x.display_name, x.alias_type))
disease_id_to_alias[x.disease_id] = aliases
disease_id_to_parent = {}
for x in nex_session.query(DiseaseRelation).all():
parents = []
if x.child_id in disease_id_to_parent:
parents = disease_id_to_parent[x.child_id]
parents.append(x.parent_id)
disease_id_to_parent[x.child_id] = parents
####################################
fw = open(log_file, "w")
log.info(str(datetime.now()))
log.info("Reading data from owl file...")
is_sgd_term = {}
data = read_owl(ontology_file, ontology)
log.info(str(datetime.now()))
log.info("Loading data into database...")
[update_log, to_delete_list] = load_new_data(nex_session, data,
source_to_id,
doid_to_disease,
term_to_ro_id['is a'],
disease_id_to_alias,
disease_id_to_parent,
fw)
# log.info("Uploading file to S3...")
# update_database_load_file_to_s3(nex_session, ontology_file, source_to_id, edam_to_id)
log.info("Writing loading summary...")
write_summary_and_send_email(fw, update_log, to_delete_list)
nex_session.close()
fw.close()
log.info(str(datetime.now()))
log.info("Done!\n\n")
