required=False,
default=None,
help='Gemma username')
cliParser.add_argument('-p',
required=False,
default=None,
help='Gemma password')
cliParser.add_argument('-o', required=False, default=None, help='Output file')
cliOpts = cliParser.parse_args()
# Declaring Global Flags and Paths
valUser = None
valPassword = None
taxonCol = ['human', 'mouse']
outputFile = 'metaOutput.tsv'
globalTimer = ElapseTime()
if (cliOpts.u != None and cliOpts.p != None):
valUser = cliOpts.u
valPassword = cliOpts.p
if (cliOpts.o != None):
outputFile = cliOpts.o
# Start Spring Session and Service Declarations
sx = SpringSupport(valUser, valPassword)
taxonService = sx.getBean('taxonService')
expressionExperimentService = sx.getBean('expressionExperimentService')
bioMaterialService = sx.getBean('bioMaterialService')
edwUtils = ExpressionDataWriterUtils(
) # not sure what this is. General utilities I guess
cliParser.add_argument('-c',
required=False,
default=False,
action='store_true',
help='Clear data cache')
cliParser.add_argument('-n',
required=False,
default=None,
type=int,
help='Download N entries; integer-type')
cliOpts = cliParser.parse_args()
# Declaring Global Variables
os.chdir('{0}/GeoData/GSE/'.format(os.getenv('DL_CACHE_DIR')))
ftpPath = '/geo/series/'
globalTimer = ElapseTime()
print(globalTimer.getBeginStamp())
# ------------------------------ MAIN ------------------------------
# Clear Cache
if cliOpts.c:
print('Emptying Cache [-c flag]')
cacheFiles = os.listdir()
for everyFile in cacheFiles:
os.remove(everyFile)
# Print Limit
if cliOpts.n is not None:
print('Entry Limit: {0} [-n flag]'.format(cliOpts.n))
# Parse FTP Directory (Multi-Step to Avoid Timeout)
cliParser.add_argument('-u',
required=False,
default=None,
help='Gemma username')
cliParser.add_argument('-p',
required=False,
default=None,
help='Gemma password')
cliOpts = cliParser.parse_args()
# Declaring Global Flags and Paths
valUser = None
valPassword = None
taxonCol = ['human', 'mouse']
globalTimer = ElapseTime()
if (cliOpts.u != None and cliOpts.p != None):
valUser = cliOpts.u
valPassword = cliOpts.p
# Start Spring Session and Service Declarations
sx = SpringSupport(valUser, valPassword)
taxonService = sx.getBean('taxonService')
expressionExperimentService = sx.getBean('expressionExperimentService')
bioMaterialService = sx.getBean('bioMaterialService')
edwUtils = ExpressionDataWriterUtils(
) # not sure what this is. General utilities I guess
print('')