From 3e8bf3c4e72ca035f98142b3dc153de0a8e9d6a1 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <nuwan.ag@gmail.com>
Date: Fri, 18 Aug 2017 21:20:27 +0530
Subject: [PATCH] Moved genomespace token to environment variable

---
 tools/genomespace/genomespace_exporter.py  |  9 ++++++---
 tools/genomespace/genomespace_exporter.xml | 13 ++++++++-----
 tools/genomespace/genomespace_importer.py  |  5 +++--
 tools/genomespace/genomespace_push.xml     | 10 +++++++---
 4 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/tools/genomespace/genomespace_exporter.py b/tools/genomespace/genomespace_exporter.py
index 494c2a5e198..bca99e5e009 100644
--- a/tools/genomespace/genomespace_exporter.py
+++ b/tools/genomespace/genomespace_exporter.py
@@ -1,11 +1,13 @@
 import argparse
 import binascii
+import os
 import sys
 
 from genomespaceclient import GenomeSpaceClient
 
 
 def upload_to_genomespace(token, input_file, target_url):
+    token = token or os.environ.get('GS_TOKEN')
     gs_client = GenomeSpaceClient(token=token)
     gs_client.copy(input_file, target_url)
     print("File successfully copied.")
@@ -13,12 +15,13 @@ def upload_to_genomespace(token, input_file, target_url):
 
 def process_args(args):
     parser = argparse.ArgumentParser()
-    parser.add_argument('-t', '--token', type=str,
-                        help="GenomeSpace auth token", required=True)
     parser.add_argument('-i', '--input_file', type=str,
                         help="File to export", required=True)
     parser.add_argument('-o', '--target_url', type=str,
                         help="GenomeSpace output target folder location", required=True)
+    parser.add_argument('-t', '--token', type=str,
+                        help="Optional OpenID/GenomeSpace token if not passed in as part of the URL as URLs^Token."
+                        " If none, the environment variable GS_TOKEN will be respected.", required=False)
 
     args = parser.parse_args(args[1:])
     return args
@@ -26,7 +29,7 @@ def process_args(args):
 
 def main():
     args = process_args(sys.argv)
-    upload_to_genomespace(binascii.unhexlify(args.token).decode('utf-8'),
+    upload_to_genomespace(args.token,
                           binascii.unhexlify(args.input_file).decode('utf-8'),
                           binascii.unhexlify(args.target_url).decode('utf-8'))
 
diff --git a/tools/genomespace/genomespace_exporter.xml b/tools/genomespace/genomespace_exporter.xml
index 83aca4e326e..899eb9241ca 100644
--- a/tools/genomespace/genomespace_exporter.xml
+++ b/tools/genomespace/genomespace_exporter.xml
@@ -1,14 +1,18 @@
 <?xml version="1.0"?>
 <tool name="GenomeSpace Exporter" id="genomespace_exporter" version="0.0.5">
     <description> - send data to GenomeSpace</description>
+    <environment_variables>
+        <environment_variable name="GS_TOKEN">
+            #set $token = $genomespace_browser.split('^')[1] or $__user__.preferences.get('genomespace_token', None)
+            #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID or select a valid folder via the GenomeSpace browse dialog.')
+            $token
+        </environment_variable>
+    </environment_variables>
     <command>python $__tool_directory__/genomespace_exporter.py
         #set $target_folder = $genomespace_browser.split('^')[0]
-        #set $token = $genomespace_browser.split('^')[1] if '^' in $genomespace_browser and $genomespace_browser.split('^')[1] else $__user__.preferences.get('genomespace_token', None)
-        
         #assert $target_folder, Exception('You must select a valid target folder.')
-        #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID or select a valid folder via the GenomeSpace browse dialog.')
+        
         #import binascii
-        --token '${ binascii.hexlify(str(token).encode("utf-8")) }'
         --input_file '${ binascii.hexlify(str($input1).encode("utf8")) }'
         #if $filename:
         --target_url '${ binascii.hexlify(str($target_folder + "/" + str($filename)).encode("utf8") ) }'
@@ -18,7 +22,6 @@
     </command>
     <inputs>
         <param format="data" name="input1" type="data" label="Send this dataset to GenomeSpace" />
-        <param name="base_url" type="baseurl" />
         <!-- If using this tool through bioblend, the genomespace_browser parameter should contain the path to the GenomeSpaceFile + the security token
              separated by a ^ as follows: GenomeSpaceFilePath^Token -->
         <param name="genomespace_browser" type="genomespacefile" label="Choose Target Directory" select_type="FOLDER" />
diff --git a/tools/genomespace/genomespace_importer.py b/tools/genomespace/genomespace_importer.py
index 8201bd5392a..f6851a69aa2 100644
--- a/tools/genomespace/genomespace_importer.py
+++ b/tools/genomespace/genomespace_importer.py
@@ -244,7 +244,8 @@ def process_args(args):
     parser.add_argument('-c', '--data_conf', type=str,
                         help="Galaxy data types conf file for mapping file types", required=True)
     parser.add_argument('-t', '--token', type=str,
-                        help="Optional OpenID/GenomeSpace token if not passed in as part of the URL as URLs^Token", required=False)
+                        help="Optional OpenID/GenomeSpace token if not passed in as part of the URL as URLs^Token."
+                        " If none, the environment variable GS_TOKEN will be respected.", required=False)
 
     args = parser.parse_args(args[1:])
     return args
@@ -252,7 +253,7 @@ def process_args(args):
 
 def main():
     args = process_args(sys.argv)
-    download_from_genomespace_importer(args.json_parameter_file, args.galaxy_root, args.data_conf, args.token)
+    download_from_genomespace_importer(args.json_parameter_file, args.galaxy_root, args.data_conf, args.token or os.environ.get("GS_TOKEN"))
 
 
 if __name__ == "__main__":
diff --git a/tools/genomespace/genomespace_push.xml b/tools/genomespace/genomespace_push.xml
index 6c079f46a53..e1a431c3247 100644
--- a/tools/genomespace/genomespace_push.xml
+++ b/tools/genomespace/genomespace_push.xml
@@ -1,16 +1,20 @@
 <?xml version="1.0"?>
 <tool name="GenomeSpace Push" id="genomespace_push"  tool_type="data_source" force_history_refresh="True" hidden="True" display_interface="False" require_login="True" version="0.0.1">
     <description> - Push data from GenomeSpace to Galaxy</description>
+    <environment_variables>
+        <environment_variable name="GS_TOKEN">
+            #set $token = $__user__.preferences.get( 'genomespace_token', None )
+            #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID or select a valid file via the GenomeSpace browse dialog.' )
+            $token
+        </environment_variable>
+    </environment_variables>
     <command interpreter="python">genomespace_importer.py
         #set $input_file = $URL.split("^")[0] if "^" in $URL else $URL
-        #set $token = $__user__.preferences.get( 'genomespace_token', None )
 
         #assert $input_file, Exception( 'You must select a valid input file.' )
-        #assert $token, Exception( 'Invalid token. You must be logged into GenomeSpace through OpenID or select a valid file via the GenomeSpace browse dialog.' )
         --json_parameter_file '${output_file1}'
         --galaxy_root $__root_dir__
         --data_conf $__datatypes_config__
-        --token '${token}'
     </command>
     <!-- If using this tool through bioblend, the URL parameter should contain a comma separated list of GenomeSpace URLs -->
     <inputs check_values="False">