Mercurial > repos > yating-l > gonramp_apollo_tools

comparison jbrowsehubToApollo.py @ 0:ce4f91831680 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 Fri, 16 Feb 2018 10:57:13 -0500
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-1:000000000000 0:ce4f91831680
1 #!/usr/bin/env python
2 import os
3 import sys
4 import argparse
5 import json
6 import logging
7 import socket
8 from apollo.ApolloInstance import ApolloInstance
9 from util.Reader import Reader
10 from util.Logger import Logger
11
12
13 def main(argv):
14 parser = argparse.ArgumentParser(description='Upload a hub to display on Apollo.')
15 parser.add_argument('-j', '--data_json', help='JSON file containing the metadata of the inputs')
16 parser.add_argument('-o', '--output', help='HTML output')
17
18 # Get the args passed in parameter
19 args = parser.parse_args()
20 json_inputs_data = args.data_json
21 outputFile = args.output
22
23 ##Parse JSON file with Reader
24 reader = Reader(json_inputs_data)
25
26 # Begin init variables
27 extra_files_path = reader.getExtFilesPath()
28 jbrowse_hub = reader.getJBrowseHubDir()
29 #user_email = reader.getUserEmail()
30 species_name = reader.getSpeciesName()
31 #apollo_host = reader.getApolloHost()
32 apollo_port = reader.getPortNum()
33 apollo_host = "http://localhost:"+ apollo_port + "/apollo"
34 #apollo_host = "http://localhost:8080/apollo"
35 #apollo_user = reader.getApolloUser()
36 apollo_admin_user = reader.getAdminUser()
37 toolDirectory = reader.getToolDir()
38 debug_mode = reader.getDebugMode()
39 action = reader.getAction()
40
41 #### Logging management ####
42 # If we are in Debug mode, also print in stdout the debug dump
43 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
44 log.setup_logging()
45
46 logging.info("#### JBrowsehub To Apollo: Start to %s JBrowse Hub to Apollo instance: %s #### ", action, apollo_host)
47 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
48
49 # Set up apollo
50 apollo = ApolloInstance(apollo_host, apollo_admin_user, toolDirectory)
51 jbrowse_hub_dir = _getHubDir(jbrowse_hub)
52 apollo.manageApolloOrganism(species_name, jbrowse_hub_dir, action)
53 outHtml(outputFile, apollo_host, species_name, action)
54
55 logging.info('#### JBrowsehub To Apollo: Congratulation! JBrowse Hub is uploaded! ####\n')
56
57 def _getHubDir(extra_files_path):
58 for root, dirs, files in os.walk(extra_files_path):
59 for name in files:
60 if name == "trackList.json":
61 logging.debug("JBrowse hub directory: %s", root)
62 return root
63 logging.error("Cannot find jbrowsehub")
64 exit(-1)
65
66 def outHtml(outputFile, host_name, species_name, action):
67 with open(outputFile, 'w') as htmlfile:
68 if action == "add":
69 htmlstr = 'The Organism "%s" is added on Apollo: <br>' % species_name
70 elif action == "overwrite":
71 htmlstr = 'The Organism "%s" is overwritten on Apollo: <br>' % species_name
72 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
73 htmlstr += jbrowse_hub
74 htmlfile.write(htmlstr)
75
76 if __name__ == "__main__":
77 main(sys.argv)