diff jbrowsehubToApollo.py @ 0:ce4f91831680 draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowsehubToApollo.py	Fri Feb 16 10:57:13 2018 -0500
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+import os
+import sys
+import argparse
+import json
+import logging
+import socket
+from apollo.ApolloInstance import ApolloInstance
+from util.Reader import Reader
+from util.Logger import Logger
+
+
+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
+    extra_files_path = reader.getExtFilesPath()
+    jbrowse_hub = reader.getJBrowseHubDir()
+    #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()
+    debug_mode = reader.getDebugMode()
+    action = reader.getAction()
+
+    #### 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("#### JBrowsehub To Apollo: Start to %s JBrowse Hub to Apollo instance: %s #### ", action, 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(jbrowse_hub)
+    apollo.manageApolloOrganism(species_name, jbrowse_hub_dir, action)  
+    outHtml(outputFile, apollo_host, species_name, action)
+
+    logging.info('#### JBrowsehub To Apollo: Congratulation! JBrowse Hub is uploaded! ####\n')
+    
+def _getHubDir(extra_files_path):
+    for root, dirs, files in os.walk(extra_files_path):
+        for name in files:
+            if name == "trackList.json":
+                logging.debug("JBrowse hub directory: %s", root)
+                return root
+    logging.error("Cannot find jbrowsehub")
+    exit(-1)
+
+def outHtml(outputFile, host_name, species_name, action):
+    with open(outputFile, 'w') as htmlfile:
+        if action == "add":
+            htmlstr = 'The Organism "%s" is added on Apollo: <br>' % species_name
+        elif action == "overwrite":
+            htmlstr = 'The Organism "%s" is overwritten on Apollo: <br>' % species_name
+        jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
+        htmlstr += jbrowse_hub
+        htmlfile.write(htmlstr)     
+
+if __name__ == "__main__":
+    main(sys.argv)
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