def convert(
workspace_service_url,
shock_service_url,
handle_service_url,
workspace_name,
object_name,
working_directory,
level=logging.INFO,
logger=None,
):
"""
Converts KBaseAssembly.SingleEndLibrary to a Fasta file of assembledDNA.
Args:
workspace_service_url : A url for the KBase Workspace service
shock_service_url: A url for the KBase SHOCK service.
handle_service_url: A url for the KBase Handle Service.
workspace_name : Name of the workspace
object_name : Name of the object in the workspace
working_directory : The working directory for where the output file should be stored.
level: Logging level, defaults to logging.INFO.
"""
if not os.path.isdir(args.working_directory):
raise Exception("The working directory does not exist {0} does not exist".format(working_directory))
md5 = None
if logger is None:
logger = script_utils.getStderrLogger(__file__)
logger.info("Starting conversion of KBaseAssembly.SingleEndLibrary to FASTA.")
token = os.environ.get("KB_AUTH_TOKEN")
logger.info("Gathering information.")
ws_client = biokbase.workspace.client.Workspace("https://kbase.us/services/ws")
single_end_library = ws_client.get_objects([{"workspace": workspace_name, "name": object_name}])[0]["data"]
shock_id = None
if "handle" in single_end_library and "id" in single_end_library["handle"]:
shock_id = single_end_library["handle"]["id"]
if shock_id is None:
raise Exception("There was not shock id found.")
# if "handle" in ws_object and "remote_md5" in single_end_library['handle']:
# md5 = single_end_library['handle']['remote_md5']
script_utils.download_file_from_shock(logger, shock_service_url, shock_id, working_directory, token)
logger.info("Conversion completed.")
def convert(workspace_service_url, shock_service_url, handle_service_url, workspace_name, object_name, working_directory, level=logging.INFO, logger=None):
"""
Converts KBaseAssembly.SingleEndLibrary to a Fasta file of assembledDNA.
Args:
workspace_service_url : A url for the KBase Workspace service
shock_service_url: A url for the KBase SHOCK service.
handle_service_url: A url for the KBase Handle Service.
workspace_name : Name of the workspace
object_name : Name of the object in the workspace
working_directory : The working directory for where the output file should be stored.
level: Logging level, defaults to logging.INFO.
"""
if not os.path.isdir(args.working_directory):
raise Exception("The working directory does not exist {0} does not exist".format(working_directory))
md5 = None
if logger is None:
logger = script_utils.getStderrLogger(__file__)
logger.info("Starting conversion of KBaseAssembly.SingleEndLibrary to FASTA.")
token = os.environ.get('KB_AUTH_TOKEN')
logger.info("Gathering information.")
ws_client = biokbase.workspace.client.Workspace('https://kbase.us/services/ws')
single_end_library = ws_client.get_objects([{'workspace':workspace_name,'name':object_name}])[0]['data']
shock_id = None
if "handle" in single_end_library and "id" in single_end_library['handle']:
shock_id = single_end_library['handle']['id']
if shock_id is None:
raise Exception("There was not shock id found.")
# if "handle" in ws_object and "remote_md5" in single_end_library['handle']:
# md5 = single_end_library['handle']['remote_md5']
script_utils.download_file_from_shock(logger, shock_service_url, shock_id, working_directory, token)
logger.info("Conversion completed.")
"objid": object_id
}])[0]
except Exception, e:
logger.exception(
"Unable to retrieve workspace object from {0}:{1}.".format(
workspace_service_url, workspace_name))
logger.exception(e)
raise
shock_id = None
if "fasta_ref" in contig_set["data"]:
shock_id = contig_set["data"]["fasta_ref"]
logger.info("Retrieving data from Shock.")
script_utils.download_file_from_shock(
logger=logger,
shock_service_url=shock_service_url,
shock_id=shock_id,
directory=working_directory,
token=token)
else:
ws_object_name = contig_set["info"][1]
valid_chars = "-_.(){0}{1}".format(string.ascii_letters, string.digits)
temp_file_name = ""
filename_chars = list()
for character in ws_object_name:
if character in valid_chars:
filename_chars.append(character)
else:
filename_chars.append("_")
if len(filename_chars) == 0:
contig_set = ws_client.get_objects([{"workspace": workspace_name, "objid": object_id}])[0]
except Exception, e:
logger.exception(
"Unable to retrieve workspace object from {0}:{1}.".format(workspace_service_url, workspace_name)
)
logger.exception(e)
raise
shock_id = None
if "fasta_ref" in contig_set["data"]:
shock_id = contig_set["data"]["fasta_ref"]
logger.info("Retrieving data from Shock.")
script_utils.download_file_from_shock(
logger=logger,
shock_service_url=shock_service_url,
shock_id=shock_id,
directory=working_directory,
token=token,
)
else:
ws_object_name = contig_set["info"][1]
valid_chars = "-_.(){0}{1}".format(string.ascii_letters, string.digits)
temp_file_name = ""
filename_chars = list()
for character in ws_object_name:
if character in valid_chars:
filename_chars.append(character)
else:
filename_chars.append("_")
