Mercurial > repos > yating-l > gonramp_apollo_tools

annotate jbrowsehubToApollo.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 1da8b9042af4
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 util.Reader import Reader
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10 from util.Logger import Logger
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13 def main(argv):
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14 parser = argparse.ArgumentParser(description='Upload a hub to display on Apollo.')
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15 parser.add_argument('-j', '--data_json', help='JSON file containing the metadata of the inputs')
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16 parser.add_argument('-o', '--output', help='HTML output')
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18 # Get the args passed in parameter
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19 args = parser.parse_args()
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20 json_inputs_data = args.data_json
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21 outputFile = args.output
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23 ##Parse JSON file with Reader
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24 reader = Reader(json_inputs_data)
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26 # Begin init variables
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27 extra_files_path = reader.getExtFilesPath()
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28 jbrowse_hub = reader.getJBrowseHubDir()
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29 #user_email = reader.getUserEmail()
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30 species_name = reader.getSpeciesName()
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31 #apollo_host = reader.getApolloHost()
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32 apollo_port = reader.getPortNum()
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33 apollo_host = "http://localhost:"+ apollo_port + "/apollo"
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34 #apollo_host = "http://localhost:8080/apollo"
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35 #apollo_user = reader.getApolloUser()
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36 apollo_admin_user = reader.getAdminUser()
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37 toolDirectory = reader.getToolDir()
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38 debug_mode = reader.getDebugMode()
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39 action = reader.getAction()
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41 #### Logging management ####
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42 # If we are in Debug mode, also print in stdout the debug dump
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43 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
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44 log.setup_logging()
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46 logging.info("#### JBrowsehub To Apollo: Start to %s JBrowse Hub to Apollo instance: %s #### ", action, apollo_host)
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47 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
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48
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49 # Set up apollo
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50 apollo = ApolloInstance(apollo_host, apollo_admin_user, toolDirectory)
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51 jbrowse_hub_dir = _getHubDir(jbrowse_hub)
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52 apollo.manageApolloOrganism(species_name, jbrowse_hub_dir, action)
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53 outHtml(outputFile, apollo_host, species_name, action)
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55 logging.info('#### JBrowsehub To Apollo: Congratulation! JBrowse Hub is uploaded! ####\n')
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57 def _getHubDir(extra_files_path):
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58 for root, dirs, files in os.walk(extra_files_path):
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59 for name in files:
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60 if name == "trackList.json":
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61 logging.debug("JBrowse hub directory: %s", root)
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62 return root
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63 logging.error("Cannot find jbrowsehub")
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64 exit(-1)
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65
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66 def outHtml(outputFile, host_name, species_name, action):
0
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67 with open(outputFile, 'w') as htmlfile:
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68 if action == "add":
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69 htmlstr = 'The Organism "%s" is added on Apollo: <br>' % species_name
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70 elif action == "overwrite":
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71 htmlstr = 'The Organism "%s" is overwritten on Apollo: <br>' % species_name
0
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72 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
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73 htmlstr += jbrowse_hub
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74 htmlfile.write(htmlstr)
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75
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76 if __name__ == "__main__":
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77 main(sys.argv)