def exists(self):
try:
options = dict(uuid=self.UUID)
result = db.select('work', options, where="work_id = $uuid")
return result.first()["work_id"] == self.UUID
except BaseException:
return False
def exists(self):
try:
where = "%s = $%s" % (self.table_name, self.table_name)
result = db.select(self.table_name, self.__dict__, where=where)
candidate = self.__dict__[self.table_name]
return result.first()[self.table_name] == candidate
except BaseException:
return False
def get(self, table_id=''):
"""Returns the list of samples in the table with the given ID
"""
con = db.get_engine(bind='summarization')
tbl = SummarizationGeneExpressionUtils.get_table_object(table_id)
values = []
try:
rows = con.execute(db.select([tbl.c.Sample]).distinct())
except SQLAlchemyError:
return BARUtils.error_exit('Internal server error'), 500
[values.append(row.Sample) for row in rows]
return BARUtils.success_exit(values)
def get(self, table_id='', user_string=''):
"""Returns all genes that contain a given string as part of their name
"""
con = db.get_engine(bind='summarization')
tbl = SummarizationGeneExpressionUtils.get_table_object(table_id)
values = []
try:
rows = con.execute(
db.select([tbl.c.Gene]).where(
tbl.c.Gene.contains(user_string)).distinct())
except SQLAlchemyError:
return BARUtils.error_exit('Internal server error'), 500
[values.append(row.Gene) for row in rows]
return BARUtils.success_exit(values)
def get(self, table_id=''):
"""Returns the list of genes in the table with the given ID
"""
key = request.headers.get('x-api-key')
if SummarizationGeneExpressionUtils.decrement_uses(key):
con = db.get_engine(bind='summarization')
tbl = SummarizationGeneExpressionUtils.get_table_object(table_id)
values = []
try:
rows = con.execute(db.select([tbl.c.Gene]).distinct())
except SQLAlchemyError:
return BARUtils.error_exit('Internal server error'), 500
[values.append(row.Gene) for row in rows]
return BARUtils.success_exit(values)
else:
return BARUtils.error_exit('Invalid API key')
def get(self):
"""
List of probes.
"""
session = config.session()
try:
query = select(session, request.args.getlist("show"),
self.SELECT_COLUMN_MAPPING,
self.SELECT_JOIN_MAPPING,
self.TABLE_JOINS).order_by(entity.Probe.name)
result = [probe._asdict() for probe in query.all()]
logging.info(result)
return result
finally:
session.commit()
def validate_api_key(key):
"""Checks if a given API key is in the Users database
:param key: The API key to be checked
"""
tbl = SummarizationGeneExpressionUtils.get_table_object('users')
con = db.get_engine(bind='summarization')
try:
row = con.execute(
db.select([tbl.c.uses_left
]).where(tbl.c.api_key == key)).first()
except SQLAlchemyError as e:
error = str(e.__dict__['orig'])
return error
if row is None:
return False
else:
if row.uses_left > 0:
return True
else:
return False
def get_all():
return db.select(UriScheme.table_name)
def get_all():
return db.select(WorkType.table_name)
def get_relatives(self, key):
where = {"parent_work_id": "child_work_id=$uuid",
"child_work_id": "parent_work_id=$uuid"}
options = dict(uuid=self.UUID)
return db.select('work_relation', options, what=key, where=where[key])
def get_identifiers(self):
options = dict(uuid=self.UUID)
uris = db.select('work_uri', options,
what="uri_scheme, uri_value, canonical",
where="work_id = $uuid")
return results_to_identifiers(uris)
def get_titles(self):
options = dict(uuid=self.UUID)
titles = db.select('work_title', options,
what="title", where="work_id = $uuid")
return [(x["title"]) for x in titles] if titles else []
def get_type(self):
options = dict(uuid=self.UUID)
result = db.select('work', options,
what="work_type", where="work_id = $uuid")
return result.first()["work_type"] if result else None
def get_all():
return db.select('title')
def get_from_email(email):
options = dict(email=email)
return db.select('account', options, where="email = $email")
def get_all():
try:
return db.select('measure')
except (Exception, psycopg2.DatabaseError) as error:
logger.error(error)
raise Error(FATAL)