def get_json(name, seqid=None, update=False, inter=False, strict=False):
"""
Attempts to return a JSON formatted data based on a name.
"""
# Data is an existing path to a file.
if os.path.isfile(name):
data = jsonrec.parse_file(name, seqid=seqid)
return data
# Not a local file, attempt to resolve to storage.
# Report as not found if update is requested.
if update:
return None
# The JSON representation of the data.
json_name = resolve_fname(name=name, format="json")
# GenBank representation of the data.
gbk_name = resolve_fname(name=name, format="gb")
# Found the JSON representation of the file.
if os.path.isfile(json_name):
logger.info(f"found {json_name}")
data = read_json_file(json_name)
return data
# No JSON file but there is a genbank file.
if os.path.isfile(gbk_name):
logger.info(f"found {gbk_name}")
data = jsonrec.parse_file(fname=gbk_name, seqid=seqid)
data = save_json_file(fname=json_name, data=data)
return data
# If not found and interactive mode create a JSON from the name itself.
if inter:
data = jsonrec.make_jsonrec(seq=name, seqid=seqid)
return data
# At this point the data was not found
if strict:
utils.error(f"data not found: {name}")
return None
def get_json(name, seqid=None, inter=False, strict=False):
"""
Attempts to return a JSON formatted data based on a name.
"""
# Data is an existing path to a JSON file.
if os.path.isfile(name):
try:
data = jsonrec.parse_file(name, seqid=seqid)
except Exception as exc:
logger.error(f"JSON parsing error for file {name}: {exc}")
sys.exit(-1)
return data
# The JSON representation of the data.
json_name = resolve_fname(name=name, format="json")
# GenBank representation of the data.
gbk_name = resolve_fname(name=name, format="gb")
# Found the JSON representation of the file.
if os.path.isfile(json_name):
logger.info(f"found {json_name}")
data = read_json_file(json_name)
return data
# There is no JSON file but there is a GenBank file.
if os.path.isfile(gbk_name):
logger.info(f"found {gbk_name}")
data = jsonrec.parse_file(fname=gbk_name, seqid=seqid)
data = save_json_file(fname=json_name, data=data)
return data
# Interactive input, make JSON from name
if inter:
data = jsonrec.make_jsonrec(name, seqid=seqid)
return data
# Raise error if in strict mode
if strict:
utils.error(f"data not found: {name}")
return None