# HG changeset patch
# User yating-l
# Date 1511891002 18000
# Node ID 78af01d73addd851833b057819c25a03ac856dbd
# Parent  1da8b9042af4895bea553a8c6d2dedeead085910
planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty

diff -r 1da8b9042af4 -r 78af01d73add apollo/ApolloInstance.py
--- a/apollo/ApolloInstance.py	Mon Nov 27 14:47:03 2017 -0500
+++ b/apollo/ApolloInstance.py	Tue Nov 28 12:43:22 2017 -0500
@@ -74,7 +74,7 @@
                 apollo_user.deleteApolloUser()
             elif operation == "add":
                 apollo_user.addApolloUserToGroup()
-            elif operation == "delete":
+            elif operation == "remove":
                 apollo_user.removeApolloUserFromeGroup()
 
     
diff -r 1da8b9042af4 -r 78af01d73add apollo/ApolloUser.py
--- a/apollo/ApolloUser.py	Mon Nov 27 14:47:03 2017 -0500
+++ b/apollo/ApolloUser.py	Tue Nov 28 12:43:22 2017 -0500
@@ -45,16 +45,16 @@
             self.logger.error("The %s format is not supported!", file_format)
         with open(filename, 'r') as f:
             lines = f.readlines()
-        headers = lines[0].rstrip().split(delimiter)
+        headers = lines[0].split(delimiter)
         users = []
         lines = lines[1:]
         for l in lines:
-            print l
             l = l.split(delimiter)
             info = dict()
             fields = len(l)
             for i in range(fields):
-                info[headers[i]] = l[i]
+                title = headers[i].rstrip()
+                info[title] = l[i].rstrip()
             users.append(info)
         return users
 
@@ -93,6 +93,6 @@
                         self.logger.error("Cannot find useremail in the text file, make sure you use the correct header, see README file for examples.")
                     if not 'group' in u:
                         self.logger.error("Cannot find group in the text file, make sure you use the correct header, see README file for examples.")
-                    subtools.arrow_add_to_group(u['group'], u['useremail'])
+                    subtools.arrow_remove_from_group(u['group'], u['useremail'])
                 
 
diff -r 1da8b9042af4 -r 78af01d73add apolloUserManager.py
--- a/apolloUserManager.py	Mon Nov 27 14:47:03 2017 -0500
+++ b/apolloUserManager.py	Tue Nov 28 12:43:22 2017 -0500
@@ -30,20 +30,16 @@
     apollo_host = "http://localhost:"+ apollo_port + "/apollo"
     apollo_admin_user = reader.getAdminUser()
     toolDirectory = reader.getToolDir()
+    extra_files_path = reader.getExtFilesPath()
     debug_mode = reader.getDebugMode()
-
     operations_dictionary = reader.getOperationList()
-    #OPERATIONS = ['create', 'delete', 'add', 'remove']
-    #create_user_list = reader.getOperationList("create")
-    #delete_user_list = reader.getOperationList("delete")
-    #remove_user_list = reader.getOperationList("remove")
-    #add_user_list = reader.getOperationList("add")
+    
 
     
         
     #### Logging management ####
     # If we are in Debug mode, also print in stdout the debug dump
-    log = Logger(tool_directory=toolDirectory, debug=debug_mode)
+    log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
     log.setup_logging()
 
     logging.info("#### Apollo User Manager: Start on Apollo instance: %s #### ", apollo_host)
@@ -54,9 +50,8 @@
     apollo.manageApolloUser(operations_dictionary)
     
     logging.info('#### Apollo User Manager: Congratulation! ####\n')
-    
 
-
+        
 
 if __name__ == "__main__":
     main(sys.argv)
\ No newline at end of file
diff -r 1da8b9042af4 -r 78af01d73add apolloUserManager.xml
--- a/apolloUserManager.xml	Mon Nov 27 14:47:03 2017 -0500
+++ b/apolloUserManager.xml	Tue Nov 28 12:43:22 2017 -0500
@@ -14,7 +14,7 @@
     </stdio>
 
     <command detect_errors="exit_code"><![CDATA[
-
+        mkdir -p $output.extra_files_path;
         ## Dump the tool parameters into a JSON file 
         python $json_file parameters.json;
         python $__tool_directory__/apolloUserManager.py --data_json parameters.json -o $output
@@ -92,6 +92,7 @@
 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
+#silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
 with open(file_path, 'w') as f:
@@ -236,7 +237,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="html" name="output" label="${tool.name}" />
+        <data format="txt" name="output" label="${tool.name} on ${on_string}" />
     </outputs>
 
     <help>
diff -r 1da8b9042af4 -r 78af01d73add logging.json
--- a/logging.json	Mon Nov 27 14:47:03 2017 -0500
+++ b/logging.json	Tue Nov 28 12:43:22 2017 -0500
@@ -20,6 +20,16 @@
             "level": "ERROR",
             "formatter": "simple",
             "stream": "ext://sys.stderr"
+        },
+
+        "debug_file_handler": {
+            "class": "logging.handlers.RotatingFileHandler",
+            "level": "DEBUG",
+            "formatter": "simple",
+            "filename": "__main__.log",
+            "maxBytes": 10485760,
+            "backupCount": 20,
+            "encoding": "utf8"
         }
     },
 
@@ -33,6 +43,6 @@
 
     "root": {
         "level": "DEBUG",
-        "handlers": ["console", "console_stderr"]
+        "handlers": ["console", "console_stderr", "debug_file_handler"]
     }
 }
\ No newline at end of file
diff -r 1da8b9042af4 -r 78af01d73add test-data/adduserstogroup.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adduserstogroup.csv	Tue Nov 28 12:43:22 2017 -0500
@@ -0,0 +1,4 @@
+useremail,group
+test1@apollo.com,Test A
+test2@apollo.com,Test A
+test3@apollo.com,Test B
\ No newline at end of file
diff -r 1da8b9042af4 -r 78af01d73add util/Logger.py
--- a/util/Logger.py	Mon Nov 27 14:47:03 2017 -0500
+++ b/util/Logger.py	Tue Nov 28 12:43:22 2017 -0500
@@ -32,6 +32,7 @@
                         config["handlers"][i]["filename"] = os.path.join(self.extra_files_path, config["handlers"][i]["filename"])
                 logging.config.dictConfig(config)
             else:
+                logging.config.dictConfig(config)
                 logging.warn("Extra files path is not set. The log files will exist at current working directory instead of final output folder")
         else:
             logging.basicConfig(level=default_level)