elif object_version_number and object_id:
contig_set = ws_client.get_objects([{"workspace":workspace_name,"objid":object_id, "ver":object_version_number}])[0]
else:
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]
logger.info("getting info {0}".format(ws_object_name))
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("_")
try:
ws_client = biokbase.workspace.client.Workspace('https://ci.kbase.us/services/ws')
except Exception,e:
raise Exception("Could not create workspace client")
if object_type in ("SingleEnd"):
print "entering if"
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']
print shock_id
if shock_id is None:
raise Exception("There was not shock id found.")
try:
script_utils.download_file_from_shock(logger, shock_service_url, shock_id, working_directory, token)
except Exception,e:
print e
raise Exception( "Unable to download shock file , {0}".format(e))
logger.info("Conversion completed.")
elif object_type in ("PairedEnd"):
paired_end_library = ws_client.get_objects([{'workspace':workspace_name,'name':object_name}])[0]['data']
shock_id1 = None
shock_id2 = None
if "handle_1" in paired_end_library and "id" in paired_end_library['handle']:
shock_id1 = paired_end_library['handle_1']['id']
if shock_id1 is None:
raise Exception("Handle1 there was not shock id found.")
if "handle_2" in paired_end_library and "id" in paired_end_library['handle']:
shock_id2 = paired_end_library['handle_2']['id']
print "entering if"
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']
print shock_id
if shock_id is None:
raise Exception("There was not shock id found.")
try:
script_utils.download_file_from_shock(logger, shock_service_url,
shock_id, working_directory,
token)
except Exception, e:
print e
raise Exception("Unable to download shock file , {0}".format(e))
logger.info("Conversion completed.")
elif object_type in ("PairedEnd"):
paired_end_library = ws_client.get_objects([{
'workspace': workspace_name,
'name': object_name
}])[0]['data']
shock_id1 = None
shock_id2 = None
if "handle_1" in paired_end_library and "id" in paired_end_library[
'handle']:
