def _get_bioentries(self, biodb_name, start=0, limit=10):
"""Retreive bioentries associated with the database.
"""
start = int(request.params.get('start', start))
limit = int(request.params.get('limit', limit))
biosql_db = BioSeqDatabase.open_database()
try:
biodb = biosql_db[biodb_name]
except KeyError:
return []
biodb = biodb.get_biodatabase()
return biodb.bioentries[start:start+limit]
def genbank_upload(self, *args, **kwargs):
# XXX hack for os.linesep not being present; where did it go?
os.linesep = "\n"
biodb_name = config.get("biosql_biodb_name")
biosql_db = BioSeqDatabase.open_database()
try:
biodb = biosql_db[biodb_name]
except KeyError:
biodb = biosql_db.new_database(biodb_name)
handle = request.params['upload_file'].file
biodb.load(SeqIO.parse(handle, "genbank"))
handle.close()
response.headers['content-type'] = 'text/javascript'
return json.dumps(dict())