def main(argv):
parser = argparse.ArgumentParser(
description='Upload a hub to display on Apollo.')
parser.add_argument('-j',
'--data_json',
help='JSON file containing the metadata of the inputs')
parser.add_argument('-o', '--output', help='HTML output')
#parser.add_argument('-e', '--extra_file_path', help='Extra file path for generated jbrowse hub')
#parser.add_argument('-d', '--jbrowsehub', help='Name of the HTML summarizing the content of the JBrowse Hub Archive')
# Get the args passed in parameter
args = parser.parse_args()
json_inputs_data = args.data_json
outputFile = args.output
#outputFile = args.jbrowsehub
##Parse JSON file with Reader
reader = Reader(json_inputs_data)
# Begin init variables
extra_files_path = reader.getExtFilesPath()
#user_email = reader.getUserEmail()
species_name = reader.getSpeciesName()
#apollo_host = reader.getApolloHost()
apollo_port = reader.getPortNum()
apollo_host = "http://localhost:" + apollo_port + "/apollo"
#apollo_host = "http://localhost:8080/apollo"
#apollo_user = reader.getApolloUser()
apollo_admin_user = reader.getAdminUser()
toolDirectory = reader.getToolDir()
#jbrowse_hub = reader.getJBrowseHubDir()
debug_mode = reader.getDebugMode()
#### Logging management ####
# If we are in Debug mode, also print in stdout the debug dump
log = Logger(tool_directory=toolDirectory,
debug=debug_mode,
extra_files_path=extra_files_path)
log.setup_logging()
logging.info(
"#### JBrowseArchiveCreator: Start to upload JBrowse Hub to Apollo instance: %s #### ",
apollo_host)
logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
# Set up apollo
apollo = ApolloInstance(apollo_host, apollo_admin_user, toolDirectory)
jbrowse_hub_dir = _getHubDir(extra_files_path)
apollo.loadHubToApollo(apollo_admin_user,
species_name,
jbrowse_hub_dir,
admin=True)
outHtml(outputFile, apollo_host, species_name)
logging.info(
'#### JBrowseArchiveCreator: Congratulation! JBrowse Hub is uploaded! ####\n'
)
def main(argv):
parser = argparse.ArgumentParser(description='Upload a hub to display on Apollo.')
parser.add_argument('-j', '--data_json', help='JSON file containing the metadata of the inputs')
parser.add_argument('-o', '--output', help='HTML output')
# Get the args passed in parameter
args = parser.parse_args()
json_inputs_data = args.data_json
outputFile = args.output
##Parse JSON file with Reader
reader = Reader(json_inputs_data)
# Begin init variables
apollo_port = reader.getPortNum()
apollo_host = "http://localhost:"+ apollo_port + "/apollo"
apollo_admin_user = reader.getAdminUser()
toolDirectory = reader.getToolDir()
extra_files_path = reader.getExtFilesPath()
debug_mode = reader.getDebugMode()
operations_dictionary = reader.getOperationList()
#### Logging management ####
# If we are in Debug mode, also print in stdout the debug dump
log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
log.setup_logging()
logging.info("#### Apollo User Manager: Start on Apollo instance: %s #### ", apollo_host)
logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
# Set up apollo
apollo = ApolloInstance(apollo_host, apollo_admin_user, toolDirectory)
apollo.manageApolloUser(operations_dictionary)
outHtml(outputFile, apollo_host)
logging.info('#### Apollo User Manager: Congratulation! ####\n')
def main(argv):
parser = argparse.ArgumentParser(
description='Create a hub to display in jbrowse.')
parser.add_argument('-j',
'--data_json',
help='JSON file containing the metadata of the inputs')
parser.add_argument(
'-o',
'--output',
help=
'Name of the HTML summarizing the content of the JBrowse Hub Archive')
# Get the args passed in parameter
args = parser.parse_args()
json_inputs_data = args.data_json
outputFile = args.output
##Parse JSON file with Reader
reader = Reader(json_inputs_data)
# Begin init variables
extra_files_path = reader.getExtFilesPath()
toolDirectory = reader.getToolDir()
#outputFile = reader.getOutputDir()
user_email = reader.getUserEmail()
reference_genome = reader.getRefGenome()
debug_mode = reader.getDebugMode()
track_type = reader.getTrackType()
#### Logging management ####
# If we are in Debug mode, also print in stdout the debug dump
log = Logger(tool_directory=toolDirectory,
debug=debug_mode,
extra_files_path=extra_files_path)
log.setup_logging()
logging.info('#### JBrowseArchiveCreator: Start ####\n')
logging.debug('---- Welcome in JBrowseArchiveCreator Debug Mode ----\n')
logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
#### END Logging management ####
# Create the Track Hub folder
logging.info(
'#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n')
trackHub = TrackHub(reference_genome, outputFile, extra_files_path,
toolDirectory, track_type)
# Create Ordered Dictionary to add the tracks in the tool form order
logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n')
all_datatype_dictionary = reader.getTracksData()
all_datatype_ordered_dictionary = collections.OrderedDict(
all_datatype_dictionary)
logging.debug("----- End of all_datatype_dictionary processing -----")
#logging.debug("all_datatype_ordered_dictionary are: %s", json.dumps(all_datatype_ordered_dictionary))
logging.info(
'#### JBrowseArchiveCreator: Adding tracks to Track Hub ####\n')
logging.debug("----- Beginning of Track adding processing -----")
for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
trackHub.addTrack(datatypeObject.track.track_db)
logging.debug("----- End of Track adding processing -----")
# We terminate the process and so create a HTML file summarizing all the files
logging.info('#### JBrowseArchiveCreator: Creating the HTML file ####\n')
trackHub.terminate(debug_mode)
logging.debug('---- End of JBrowseArchiveCreator Debug Mode: Bye! ----\n')
logging.info(
'#### JBrowseArchiveCreator: Congratulation! Assembly Hub is created! ####\n'
)
sys.exit(0)
