From 4d88ce03deaf237f9ec63481436a406a7de51fa8 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 9 Apr 2014 17:24:56 -0400
Subject: [PATCH] Improve handling of invalid/expired GenomeSpace tokens in
 GenomeSpace export tool.

---
 tools/genomespace/genomespace_exporter.py  | 29 +++++++++++-----------
 tools/genomespace/genomespace_exporter.xml |  8 ++++--
 2 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/tools/genomespace/genomespace_exporter.py b/tools/genomespace/genomespace_exporter.py
index b35ae9f2a33..ef92c0676c6 100644
--- a/tools/genomespace/genomespace_exporter.py
+++ b/tools/genomespace/genomespace_exporter.py
@@ -11,6 +11,7 @@ import optparse
 import os
 import urllib
 import urllib2
+from urlparse import urljoin
 
 log = logging.getLogger( "tools.genomespace.genomespace_exporter" )#( __name__ )
 
@@ -117,7 +118,7 @@ def get_genome_space_launch_apps( atm_url, url_opener, file_url, file_type ):
                 break
     return webtools
     
-def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, value=None, **kwd ):
+def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, value=None, base_url=None, **kwd ):
     if value:
         value = value[0]#single select, only 1 value
     def recurse_directory_dict( url_opener, cur_options, url ):
@@ -142,19 +143,19 @@ def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, va
     if trans and trans.user:
         username = trans.user.preferences.get( 'genomespace_username', None )
         token = trans.user.preferences.get( 'genomespace_token', None )
-        if None in ( username, token ):
-            return []
-        url_opener = get_cookie_opener( username, token )
-        genomespace_site_dict = get_genomespace_site_urls()[ genomespace_site ]
-        dm_url = genomespace_site_dict['dmServer']
-        #get export root directory
-        #directory_dict = get_default_directory( url_opener, dm_url ).get( 'directory', None ) #This directory contains shares and other items outside of the users home
-        directory_dict = get_personal_directory( url_opener, dm_url ).get( 'directory', None ) #Limit export list to only user's home dir
-        if directory_dict is None:
-            return []
-        #what directory to stuff this in
-        recurse_directory_dict( url_opener, rval, directory_dict.get( 'url' ) )
-    
+        if None not in ( username, token ):
+            url_opener = get_cookie_opener( username, token )
+            genomespace_site_dict = get_genomespace_site_urls()[ genomespace_site ]
+            dm_url = genomespace_site_dict['dmServer']
+            #get export root directory
+            #directory_dict = get_default_directory( url_opener, dm_url ).get( 'directory', None ) #This directory contains shares and other items outside of the users home
+            directory_dict = get_personal_directory( url_opener, dm_url ).get( 'directory', None ) #Limit export list to only user's home dir
+            if directory_dict is not None:
+                recurse_directory_dict( url_opener, rval, directory_dict.get( 'url' ) )
+    if not rval:
+        if not base_url:
+            base_url = '..'
+        rval = [ { 'name':'Your GenomeSpace token appears to be <strong>expired</strong>, please <a href="%s">reauthenticate</a>.' % ( urljoin( base_url, 'user/openid_auth?openid_provider=genomespace&amp;auto_associate=True' ) ), 'value': '', 'options':[], 'selected': False  } ]
     return rval
     
 
diff --git a/tools/genomespace/genomespace_exporter.xml b/tools/genomespace/genomespace_exporter.xml
index 508e856986e..344698e2baa 100644
--- a/tools/genomespace/genomespace_exporter.xml
+++ b/tools/genomespace/genomespace_exporter.xml
@@ -35,14 +35,18 @@
     <inputs>
         <param format="data" name="input1" type="data" label="Send this dataset to GenomeSpace" />
         <param name="base_url" type="baseurl" />
-        <param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" optional="True" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1 )" help="Leave blank to generate automatically"/>
+        <param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" optional="True" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1, base_url=base_url )" help="Leave blank to generate automatically"/>
         <param name="filename" type="text" size="80" help="Leave blank to generate automatically" />
     </inputs>
     <outputs>
         <data format="html" name="output_log" />
     </outputs>
     <help>
-       This Tool allows you to export data to GenomeSpace. You must have logged in using your GenomeSpace OpenID. You can associate your OpenID credentials under the User Preferences panel.
+This Tool allows you to export data to GenomeSpace. You must have logged in using your GenomeSpace OpenID. You can associate your OpenID credentials under the User Preferences panel.
+
+If you are having trouble with this tool, click here_ to refresh your GenomeSpace token before reporting errors.
+
+.. _here:  ${static_path}/../user/openid_auth?openid_provider=genomespace&amp;auto_associate=True
     </help>
     <options refresh="True"/>
     <code file="genomespace_exporter.py" />