Mercurial > repos > yating-l > gonramp_apollo_tools

comparison 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
comparison
equal deleted inserted replaced
1:78af01d73add 2:4be6fcac4bf2
23 ##Parse JSON file with Reader 23 ##Parse JSON file with Reader
24 reader = Reader(json_inputs_data) 24 reader = Reader(json_inputs_data)
25 25
26 # Begin init variables 26 # Begin init variables
27 extra_files_path = reader.getExtFilesPath() 27 extra_files_path = reader.getExtFilesPath()
28 jbrowse_hub = reader.getJBrowseHubDir()
28 #user_email = reader.getUserEmail() 29 #user_email = reader.getUserEmail()
29 species_name = reader.getSpeciesName() 30 species_name = reader.getSpeciesName()
30 #apollo_host = reader.getApolloHost() 31 #apollo_host = reader.getApolloHost()
31 apollo_port = reader.getPortNum() 32 apollo_port = reader.getPortNum()
32 apollo_host = "http://localhost:"+ apollo_port + "/apollo" 33 apollo_host = "http://localhost:"+ apollo_port + "/apollo"
33 #apollo_host = "http://localhost:8080/apollo" 34 #apollo_host = "http://localhost:8080/apollo"
34 #apollo_user = reader.getApolloUser() 35 #apollo_user = reader.getApolloUser()
35 apollo_admin_user = reader.getAdminUser() 36 apollo_admin_user = reader.getAdminUser()
36 toolDirectory = reader.getToolDir() 37 toolDirectory = reader.getToolDir()
37 #jbrowse_hub = reader.getJBrowseHubDir()
38 debug_mode = reader.getDebugMode() 38 debug_mode = reader.getDebugMode()
39 action = reader.getAction() 39 action = reader.getAction()
40 40
41 #### Logging management #### 41 #### Logging management ####
42 # If we are in Debug mode, also print in stdout the debug dump 42 # If we are in Debug mode, also print in stdout the debug dump
43 log = Logger(tool_directory=toolDirectory, debug=debug_mode) 43 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
44 log.setup_logging() 44 log.setup_logging()
45 45
46 <<<<<<< HEAD
47 logging.info("#### JBrowsehub To Apollo: Start to %s JBrowse Hub to Apollo instance: %s #### ", action, apollo_host) 46 logging.info("#### JBrowsehub To Apollo: Start to %s JBrowse Hub to Apollo instance: %s #### ", action, apollo_host)
48 =======
49 logging.info("#### JBrowseArchiveCreator: Start to %s JBrowse Hub to Apollo instance: %s #### ", action, apollo_host)
50 >>>>>>> 8b9a3b41d4dd4689764592d278ec2d67f67fbca4
51 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args)) 47 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
52 48
53 # Set up apollo 49 # Set up apollo
54 apollo = ApolloInstance(apollo_host, apollo_admin_user, toolDirectory) 50 apollo = ApolloInstance(apollo_host, apollo_admin_user, toolDirectory)
55 jbrowse_hub_dir = _getHubDir(extra_files_path) 51 jbrowse_hub_dir = _getHubDir(jbrowse_hub)
56 <<<<<<< HEAD
57 apollo.manageApolloOrganism(species_name, jbrowse_hub_dir, action) 52 apollo.manageApolloOrganism(species_name, jbrowse_hub_dir, action)
58 ======= 53 outHtml(outputFile, apollo_host, species_name, action)
59 apollo.loadHubToApollo(species_name, jbrowse_hub_dir, action)
60 >>>>>>> 8b9a3b41d4dd4689764592d278ec2d67f67fbca4
61 outHtml(outputFile, apollo_host, species_name)
62 54
63 logging.info('#### JBrowsehub To Apollo: Congratulation! JBrowse Hub is uploaded! ####\n') 55 logging.info('#### JBrowsehub To Apollo: Congratulation! JBrowse Hub is uploaded! ####\n')
64 56
65 def _getHubDir(extra_files_path): 57 def _getHubDir(extra_files_path):
66 for root, dirs, files in os.walk(extra_files_path): 58 for root, dirs, files in os.walk(extra_files_path):
69 logging.debug("JBrowse hub directory: %s", root) 61 logging.debug("JBrowse hub directory: %s", root)
70 return root 62 return root
71 logging.error("Cannot find jbrowsehub") 63 logging.error("Cannot find jbrowsehub")
72 exit(-1) 64 exit(-1)
73 65
74 def outHtml(outputFile, host_name, species_name): 66 def outHtml(outputFile, host_name, species_name, action):
75 with open(outputFile, 'w') as htmlfile: 67 with open(outputFile, 'w') as htmlfile:
76 htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % species_name 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
77 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name 72 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
78 htmlstr += jbrowse_hub 73 htmlstr += jbrowse_hub
79 htmlfile.write(htmlstr) 74 htmlfile.write(htmlstr)
80 75
81 if __name__ == "__main__": 76 if __name__ == "__main__":