def update(moldb_id):
"""Update a molecular database.
Request: {
archived: {true/false}
description - database description
full_name - full database name
link - public database URL
citation - database citation string
}
Response: {
status - success or error type
data?: {
id - unique int id
name
version
}
errors? - list of database import errors
}
"""
params = None
try:
params = body_to_json(bottle.request)
logger.info(
f'Updating molecular database. ID: {moldb_id}. Params: {params}')
moldb = molecular_db.update(moldb_id, **params)
return make_response(OK, data=moldb.to_dict())
except Exception:
logger.exception(f'Server error. ID: {moldb_id}. Params: {params}')
return make_response(INTERNAL_ERROR)
def delete(moldb_id):
"""Delete the molecular database and all associated jobs."""
try:
logger.info(f'Deleting molecular database. ID: {moldb_id}')
molecular_db.delete(moldb_id)
return make_response(OK)
except Exception:
logger.exception(f'Server error. ID: {moldb_id}')
return make_response(INTERNAL_ERROR)
def generate(ion, instr, res_power, at_mz, charge):
try:
pattern = isotopic_pattern.generate(ion, instr, res_power, at_mz,
charge)
return make_response(OK, data=pattern)
except Exception as e:
logger.warning(
f'({ion}, {instr}, {res_power}, {at_mz}, {charge}) - {e}')
return make_response(INTERNAL_ERROR)
def create():
"""Create a molecular database and import molecules.
Request: {
name - short database name
version - database version, any string
group_id - UUID of group database belongs to
user_id - UUID of user database create to
is_public - database search results visible to everybody
file_path - S3 path to database import file (s3://bucket/path)
description - database description
full_name - full database name
link - public database URL
citation - database citation string
}
Response: {
status - success or error type
data?: {
id - unique int id
name
version
}
errors? - list of database import errors
}
"""
params = None
try:
params = body_to_json(bottle.request)
logger.info(f'Creating molecular database. Params: {params}')
required_fields = [
'name', 'version', 'group_id', 'user_id', 'file_path'
]
if not all(field in params for field in required_fields):
return make_response(
WRONG_PARAMETERS,
errors=[f'Required fields: {required_fields}'])
moldb = molecular_db.create(**params)
return make_response(OK, data=moldb.to_dict())
except psycopg2.errors.UniqueViolation: # pylint: disable=no-member
logger.exception(f'Database already exists. Params: {params}')
return make_response(ALREADY_EXISTS)
except molecular_db.MalformedCSV as e:
logger.exception(f'Malformed CSV file. Params: {params}')
return make_response(MALFORMED_CSV, error=e.message)
except molecular_db.BadData as e:
logger.exception(
f'Bad data in CSV file: {e.message}, {e.errors} Params: {params}')
return make_response(BAD_DATA,
error='Bad data in CSV file',
details=e.errors)
except Exception:
logger.exception(f'Server error. Params: {params}')
return make_response(INTERNAL_ERROR)
def root():
return make_response(OK)