def upload(self, db):
"""Upload the content for this dataset into the database."""
dbid = self._check_reference(db)
stmts = self._get_statements()
# Raise any validity issues with statements as exceptions here
# to avoid uploading invalid content.
for stmt in stmts:
assert_valid_statement(stmt)
insert_db_stmts(db, stmts, dbid)
return
def update(self, db):
"""Add any new statements that may have come into the dataset."""
dbid = self._check_reference(db, can_create=False)
if dbid is None:
raise ValueError("This knowledge base has not yet been "
"registered.")
existing_keys = set(db.select_all([db.RawStatements.mk_hash,
db.RawStatements.source_hash],
db.RawStatements.db_info_id == dbid))
stmts = self._get_statements()
filtered_stmts = [s for s in stmts
if (s.get_hash(), s.evidence[0].get_source_hash())
not in existing_keys]
insert_db_stmts(db, filtered_stmts, dbid)
return
def test_simple_db_insert():
db = get_temp_db()
db._clear(force=True)
stmts = [
Phosphorylation(Agent('MEK', db_refs={'FPLX': 'MEK'}),
Agent('ERK', db_refs={'FPLX': 'ERK'}),
evidence=Evidence(source_api='test')),
Complex([Agent(n, db_refs={'FPLX': n}) for n in ('MEK', 'ERK')],
evidence=Evidence(source_api='test'))
]
dbid = db.insert(db.DBInfo, db_name='test', source_api='tester')
insert_db_stmts(db, stmts, dbid)
db_stmts = db.select_all(db.RawStatements)
db_agents = db.select_all(db.RawAgents)
assert len(db_stmts) == 2, len(db_stmts)
assert len(db_agents) == 8, len(db_agents)
db.session.close()
def upload(self, db):
"""Upload the content for this dataset into the database."""
dbid = self._check_reference(db)
stmts = self._get_statements()
insert_db_stmts(db, stmts, dbid)
return