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annotate apolloUserManager.py @ 2:4be6fcac4bf2 draft default tip

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
author yating-l
date Wed, 29 Nov 2017 15:39:32 -0500
parents 78af01d73add
children
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1 #!/usr/bin/env python
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2 import os
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3 import sys
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4 import argparse
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5 import json
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6 import logging
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7 import socket
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8 from apollo.ApolloInstance import ApolloInstance
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9 from apollo.ApolloUser import ApolloUser
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10 from util.Reader import Reader
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11 from util.Logger import Logger
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14 def main(argv):
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15 parser = argparse.ArgumentParser(description='Upload a hub to display on Apollo.')
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16 parser.add_argument('-j', '--data_json', help='JSON file containing the metadata of the inputs')
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17 parser.add_argument('-o', '--output', help='HTML output')
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19 # Get the args passed in parameter
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20 args = parser.parse_args()
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21 json_inputs_data = args.data_json
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22 outputFile = args.output
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24 ##Parse JSON file with Reader
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25 reader = Reader(json_inputs_data)
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27 # Begin init variables
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29 apollo_port = reader.getPortNum()
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30 apollo_host = "http://localhost:"+ apollo_port + "/apollo"
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31 apollo_admin_user = reader.getAdminUser()
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32 toolDirectory = reader.getToolDir()
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33 extra_files_path = reader.getExtFilesPath()
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34 debug_mode = reader.getDebugMode()
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35 operations_dictionary = reader.getOperationList()
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40 #### Logging management ####
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41 # If we are in Debug mode, also print in stdout the debug dump
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42 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
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43 log.setup_logging()
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45 logging.info("#### Apollo User Manager: Start on Apollo instance: %s #### ", apollo_host)
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46 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
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48 # Set up apollo
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49 apollo = ApolloInstance(apollo_host, apollo_admin_user, toolDirectory)
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50 apollo.manageApolloUser(operations_dictionary)
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51 outHtml(outputFile, apollo_host)
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52 logging.info('#### Apollo User Manager: Congratulation! ####\n')
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54 def outHtml(outputFile, host_name):
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55 with open(outputFile, 'w') as htmlfile:
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56 htmlstr = 'The Apollo User Manager has done with operations on Apollo: <br>'
4be6fcac4bf2 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
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57 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
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58 htmlstr += jbrowse_hub
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59 htmlfile.write(htmlstr)
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62 if __name__ == "__main__":
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63 main(sys.argv)