From 5f6f92c32ca5b222e78162e93474b81a829e22eb Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 7 Mar 2013 11:16:53 -0600
Subject: [PATCH 1/8] select2 fixes for workflow running.

---
 templates/webapps/galaxy/workflow/run.mako | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/templates/webapps/galaxy/workflow/run.mako b/templates/webapps/galaxy/workflow/run.mako
index dfdccdce0e6..ad033070466 100644
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -8,7 +8,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "libs/jquery/jquery.autocomplete" )}
+    ${h.js( "libs/jquery/select2" )}
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){
@@ -40,12 +40,12 @@
                         select.val($('option:last', select).val());
                     }
                     select.closest('.form-row').children('label').children('span.mode-icon').hide();
-                    select.removeAttr('multiple').removeAttr('size');
+                    select.removeAttr('multiple').select2().removeAttr('size');
                     placeholder = 'type to filter';
                 } else {
                     $('.multiinput', select.closest('.form-row')).removeClass('disabled');
                     select.closest('.form-row').children('label').children('span.mode-icon').show();
-                    select.attr('multiple', 'multiple').attr('size', 8);
+                    select.attr('multiple', 'multiple').select2().attr('size', 8);
                     placeholder = 'type to filter, [enter] to select all';
                 }
                 $('input.multiinput-filter', select.parent()).attr(
@@ -79,7 +79,7 @@
             $("#new_history_cbx").click(function(){
                 $("#new_history_input").toggle(this.checked);
             });
-            $('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').each(function(i, s) {
+            $('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').select2().each(function(i, s) {
                 var select = $(s);
                 var new_width = Math.max(200, select.width()) + 20;
                 // Find the label for this element.

From 5a1fbd832bc7c93cc479d3348eb82da09abb6dc7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 7 Mar 2013 13:42:11 -0600
Subject: [PATCH 2/8] Abstract away logic for updating select boxes. For
 multiple select boxes set closeOnSelect to false, this vastly reduces the
 clicking required to select many items.

---
 static/scripts/galaxy.base.js              | 12 +++++++++---
 templates/webapps/galaxy/workflow/run.mako |  6 +++---
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js
index bdcd123f66e..838577b6587 100644
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -239,6 +239,14 @@ function naturalSort(a, b) {
     return 0;
 }
 
+$.fn.refresh_select2 = function() {
+    var select_elt = $(this);
+    var options = { width: "resolve",
+                    closeOnSelect: !select_elt.is("[MULTIPLE]"),
+                  };
+    return select_elt.select2( options );
+}
+
 // Replace select box with a text input box + autocomplete.
 function replace_big_select_inputs(min_length, max_length, select_elts) {
     // To do replace, the select2 plugin must be loaded.
@@ -276,9 +284,7 @@ function replace_big_select_inputs(min_length, max_length, select_elts) {
          *
          * - should we still sort dbkey fields here? 
          */
-        
-        select_elt.select2( { width: "resolve" } );
-
+        select_elt.refresh_select2();
     });
 }
 
diff --git a/templates/webapps/galaxy/workflow/run.mako b/templates/webapps/galaxy/workflow/run.mako
index ad033070466..eb8def9e38e 100644
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -40,12 +40,12 @@
                         select.val($('option:last', select).val());
                     }
                     select.closest('.form-row').children('label').children('span.mode-icon').hide();
-                    select.removeAttr('multiple').select2().removeAttr('size');
+                    select.removeAttr('multiple').refresh_select2().removeAttr('size');
                     placeholder = 'type to filter';
                 } else {
                     $('.multiinput', select.closest('.form-row')).removeClass('disabled');
                     select.closest('.form-row').children('label').children('span.mode-icon').show();
-                    select.attr('multiple', 'multiple').select2().attr('size', 8);
+                    select.attr('multiple', 'multiple').refresh_select2().attr('size', 8);
                     placeholder = 'type to filter, [enter] to select all';
                 }
                 $('input.multiinput-filter', select.parent()).attr(
@@ -79,7 +79,7 @@
             $("#new_history_cbx").click(function(){
                 $("#new_history_input").toggle(this.checked);
             });
-            $('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').select2().each(function(i, s) {
+            $('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').refresh_select2().each(function(i, s) {
                 var select = $(s);
                 var new_width = Math.max(200, select.width()) + 20;
                 // Find the label for this element.

From a1e6b1e8b2848aa8aa67898f250100528a21bba6 Mon Sep 17 00:00:00 2001
From: Dave Bouvier <dave@bx.psu.edu>
Date: Wed, 27 Mar 2013 11:20:39 -0400
Subject: [PATCH 3/8] Change install and test script to never set do_not_test =
 True.

---
 .../functional_tests.py                                      | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/test/install_and_test_tool_shed_repositories/functional_tests.py b/test/install_and_test_tool_shed_repositories/functional_tests.py
index 3b11eed2226..ba56471afea 100644
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -281,8 +281,7 @@ def json_from_url( url ):
 
 def register_test_result( url, metadata_id, test_results_dict, tests_passed=False ):
     '''
-    Set do_not_test = True if the repository fails functional tests. Set do_not_test = False
-    if the repository passes functional tests, so that the repository will always be re-tested
+    This script should never set do_not_test = True, because the repositories should always be re-tested
     against the most recent code.
     '''
     params = {}
@@ -291,7 +290,7 @@ def register_test_result( url, metadata_id, test_results_dict, tests_passed=Fals
         params[ 'do_not_test' ] = 'false'
     else:
         params[ 'tools_functionally_correct' ] = 'false'
-        params[ 'do_not_test' ] = 'true'
+        params[ 'do_not_test' ] = 'false'
     params[ 'tool_test_errors' ] = test_results_dict
     return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False )
 

From fd46d149aced7c9644852a762760fe46b5230aaa Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 Mar 2013 14:26:38 -0400
Subject: [PATCH 4/8] Jobs: Fix job finish() to only set state after
 reconciling all outputs.  This will allow us to eliminate
 force_history_refresh in the new history panel.  Slight import cleanup.

---
 lib/galaxy/jobs/__init__.py | 54 +++++++++++++++++--------------------
 1 file changed, 25 insertions(+), 29 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index eb2d7cfd2c7..6466a7b4826 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2,24 +2,22 @@
 Support for running a tool in Galaxy via an internal job management system
 """
 
-import os
-import sys
-import pwd
-import time
 import copy
-import random
-import logging
 import datetime
+import logging
+import os
+import pwd
+import random
+import re
+import shutil
+import subprocess
+import sys
 import threading
 import traceback
-import subprocess
 
 import galaxy
 from galaxy import util, model
 from galaxy.util.bunch import Bunch
-from galaxy.datatypes.tabular import *
-from galaxy.datatypes.interval import *
-# tabular/interval imports appear to be unused.  Clean up?
 from galaxy.datatypes import metadata
 from galaxy.util.json import from_json_string
 from galaxy.util.expressions import ExpressionContext
@@ -882,13 +880,16 @@ class JobWrapper( object ):
             return self.fail( job.info, stderr=stderr, stdout=stdout, exit_code=tool_exit_code )
 
         # Check the tool's stdout, stderr, and exit code for errors, but only
-        # if the job has not already been marked as having an error. 
+        # if the job has not already been marked as having an error.
         # The job's stdout and stderr will be set accordingly.
+
+        # We set final_job_state to use for dataset management, but *don't* set
+        # job.state until after dataset collection to prevent history issues
         if job.states.ERROR != job.state:
             if ( self.check_tool_output( stdout, stderr, tool_exit_code, job )):
-                job.state = job.states.OK
+                final_job_state = job.states.OK
             else:
-                job.state = job.states.ERROR
+                final_job_state = job.states.ERROR
 
         if self.version_string_cmd:
             version_filename = self.get_version_string_path()
@@ -908,9 +909,11 @@ class JobWrapper( object ):
                     if os.path.exists( dataset_path.real_path ) and os.stat( dataset_path.real_path ).st_size > 0:
                         log.warning( "finish(): %s not found, but %s is not empty, so it will be used instead" % ( dataset_path.false_path, dataset_path.real_path ) )
                     else:
+                        # Prior to fail we need to set job.state
+                        job.state = final_job_state
                         return self.fail( "Job %s's output dataset(s) could not be read" % job.id )
+
         job_context = ExpressionContext( dict( stdout = job.stdout, stderr = job.stderr ) )
-        job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None )
 
         for dataset_assoc in job.output_datasets + job.output_library_datasets:
             context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset )
@@ -926,10 +929,7 @@ class JobWrapper( object ):
                 # Update (non-library) job output datasets through the object store
                 if dataset not in job.output_library_datasets:
                     self.app.object_store.update_from_file(dataset.dataset, create=True)
-                # TODO: The context['stderr'] holds stderr's contents. An error
-                # only really occurs if the job also has an error. So check the
-                # job's state:
-                if job.states.ERROR == job.state:
+                if job.states.ERROR == final_job_state:
                     dataset.blurb = "error"
                     dataset.mark_unhidden()
                 elif dataset.has_data():
@@ -945,13 +945,7 @@ class JobWrapper( object ):
                      ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) \
                        and self.app.config.retry_metadata_internally ):
                         dataset.datatype.set_meta( dataset, overwrite = False ) #call datatype.set_meta directly for the initial set_meta call during dataset creation
-                    # TODO: The context['stderr'] used to indicate that there
-                    # was an error. Now we must rely on the job's state instead;
-                    # that indicates whether the tool relied on stderr to indicate
-                    # the state or whether the tool used exit codes and regular
-                    # expressions to do so. So we use 
-                    # job.state == job.states.ERROR to replace this same test.
-                    elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and job.states.ERROR != job.state: 
+                    elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and job.states.ERROR != final_job_state: 
                         dataset._state = model.Dataset.states.FAILED_METADATA
                     else:
                         #load metadata from file
@@ -981,10 +975,7 @@ class JobWrapper( object ):
                     if dataset.ext == 'auto':
                         dataset.extension = 'txt'
                 self.sa_session.add( dataset )
-            # TODO: job.states.ERROR == job.state now replaces checking
-            # stderr for a problem:
-            #if context['stderr']:
-            if job.states.ERROR == job.state:
+            if job.states.ERROR == final_job_state:
                 log.debug( "setting dataset state to ERROR" )
                 # TODO: This is where the state is being set to error. Change it!
                 dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
@@ -1054,7 +1045,12 @@ class JobWrapper( object ):
         # fix permissions
         for path in [ dp.real_path for dp in self.get_mutable_output_fnames() ]:
             util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
+
+        # Finally set the job state.  This should only happen *after* all
+        # dataset creation, and will allow us to eliminate force_history_refresh.
+        job.state = final_job_state
         self.sa_session.flush()
+
         log.debug( 'job %d ended' % self.job_id )
         if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ):
             self.cleanup()

From 1c2ffbd58c019b72f5a087896597328765d0136d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 Mar 2013 14:27:14 -0400
Subject: [PATCH 5/8] Strip whitespace in jobs/__init__.py

---
 lib/galaxy/jobs/__init__.py | 90 ++++++++++++++++++-------------------
 1 file changed, 45 insertions(+), 45 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 6466a7b4826..090eb335a01 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -84,7 +84,7 @@ class JobToolConfiguration( Bunch ):
 
 class JobConfiguration( object ):
     """A parser and interface to advanced job management features.
-    
+
     These features are configured in the job configuration, by default, ``job_conf.xml``
     """
     DEFAULT_NWORKERS = 4
@@ -609,7 +609,7 @@ class JobWrapper( object ):
 
         Calling this method for the first time causes the dynamic runner to do
         its calculation, if any.
-        
+
         :returns: ``JobDestination``
         """
         return self.job_runner_mapper.get_job_destination(self.params)
@@ -673,7 +673,7 @@ class JobWrapper( object ):
             special = self.sa_session.query( model.GenomeIndexToolData ).filter_by( job=job ).first()
         if special:
             out_data[ "output_file" ] = FakeDatasetAssociation( dataset=special.dataset )
-            
+
         # These can be passed on the command line if wanted as $__user_*__
         if job.history and job.history.user:
             user_id = '%d' % job.history.user.id
@@ -777,11 +777,11 @@ class JobWrapper( object ):
             if ( len( stdout ) > 32768 ):
                 stdout = stdout[:32768]
                 log.info( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id )
-            job.stdout = stdout 
+            job.stdout = stdout
             if ( len( stderr ) > 32768 ):
                 stderr = stderr[:32768]
                 log.info( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id )
-            job.stderr = stderr  
+            job.stderr = stderr
             # Let the exit code be Null if one is not provided:
             if ( exit_code != None ):
                 job.exit_code = exit_code
@@ -863,7 +863,7 @@ class JobWrapper( object ):
         self.sa_session.expunge_all()
         job = self.get_job()
 
-        # TODO: After failing here, consider returning from the function. 
+        # TODO: After failing here, consider returning from the function.
         try:
             self.reclaim_ownership()
         except:
@@ -945,7 +945,7 @@ class JobWrapper( object ):
                      ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) \
                        and self.app.config.retry_metadata_internally ):
                         dataset.datatype.set_meta( dataset, overwrite = False ) #call datatype.set_meta directly for the initial set_meta call during dataset creation
-                    elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and job.states.ERROR != final_job_state: 
+                    elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and job.states.ERROR != final_job_state:
                         dataset._state = model.Dataset.states.FAILED_METADATA
                     else:
                         #load metadata from file
@@ -1006,7 +1006,7 @@ class JobWrapper( object ):
         job.stderr = job.stderr[:32768]
         # The exit code will be null if there is no exit code to be set.
         # This is so that we don't assign an exit code, such as 0, that
-        # is either incorrect or has the wrong semantics. 
+        # is either incorrect or has the wrong semantics.
         if None != tool_exit_code:
             job.exit_code = tool_exit_code
         # custom post process setup
@@ -1058,26 +1058,26 @@ class JobWrapper( object ):
     def check_tool_output( self, stdout, stderr, tool_exit_code, job ):
         """
         Check the output of a tool - given the stdout, stderr, and the tool's
-        exit code, return True if the tool exited succesfully and False 
+        exit code, return True if the tool exited succesfully and False
         otherwise. No exceptions should be thrown. If this code encounters
         an exception, it returns True so that the workflow can continue;
-        otherwise, a bug in this code could halt workflow progress. 
+        otherwise, a bug in this code could halt workflow progress.
         Note that, if the tool did not define any exit code handling or
         any stdio/stderr handling, then it reverts back to previous behavior:
         if stderr contains anything, then False is returned.
         Note that the job id is just for messages.
         """
-        # By default, the tool succeeded. This covers the case where the code 
+        # By default, the tool succeeded. This covers the case where the code
         # has a bug but the tool was ok, and it lets a workflow continue.
-        success = True 
+        success = True
 
         try:
-            # Check exit codes and match regular expressions against stdout and 
+            # Check exit codes and match regular expressions against stdout and
             # stderr if this tool was configured to do so.
             # If there is a regular expression for scanning stdout/stderr,
-            # then we assume that the tool writer overwrote the default 
+            # then we assume that the tool writer overwrote the default
             # behavior of just setting an error if there is *anything* on
-            # stderr. 
+            # stderr.
             if ( len( self.tool.stdio_regexes ) > 0 or
                  len( self.tool.stdio_exit_codes ) > 0 ):
                 # Check the exit code ranges in the order in which
@@ -1088,9 +1088,9 @@ class JobWrapper( object ):
                 max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR
                 if tool_exit_code != None:
                     for stdio_exit_code in self.tool.stdio_exit_codes:
-                        if ( tool_exit_code >= stdio_exit_code.range_start and 
+                        if ( tool_exit_code >= stdio_exit_code.range_start and
                              tool_exit_code <= stdio_exit_code.range_end ):
-                            # Tack on a generic description of the code 
+                            # Tack on a generic description of the code
                             # plus a specific code description. For example,
                             # this might prepend "Job 42: Warning (Out of Memory)\n".
                             code_desc = stdio_exit_code.desc
@@ -1102,21 +1102,21 @@ class JobWrapper( object ):
                                          code_desc ) )
                             log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) )
                             stderr = tool_msg + "\n" + stderr
-                            max_error_level = max( max_error_level, 
+                            max_error_level = max( max_error_level,
                                                    stdio_exit_code.error_level )
-                            if ( max_error_level >= 
+                            if ( max_error_level >=
                                  galaxy.tools.StdioErrorLevel.FATAL ):
                                 break
-    
+
                 if max_error_level < galaxy.tools.StdioErrorLevel.FATAL:
                     # We'll examine every regex. Each regex specifies whether
-                    # it is to be run on stdout, stderr, or both. (It is 
+                    # it is to be run on stdout, stderr, or both. (It is
                     # possible for neither stdout nor stderr to be scanned,
                     # but those regexes won't be used.) We record the highest
                     # error level, which are currently "warning" and "fatal".
                     # If fatal, then we set the job's state to ERROR.
                     # If warning, then we still set the job's state to OK
-                    # but include a message. We'll do this if we haven't seen 
+                    # but include a message. We'll do this if we haven't seen
                     # a fatal error yet
                     for regex in self.tool.stdio_regexes:
                         # If ( this regex should be matched against stdout )
@@ -1126,16 +1126,16 @@ class JobWrapper( object ):
                         # Repeat the stdout stuff for stderr.
                         # TODO: Collapse this into a single function.
                         if ( regex.stdout_match ):
-                            regex_match = re.search( regex.match, stdout, 
+                            regex_match = re.search( regex.match, stdout,
                                                      re.IGNORECASE )
                             if ( regex_match ):
                                 rexmsg = self.regex_err_msg( regex_match, regex)
-                                log.info( "Job %s: %s" 
+                                log.info( "Job %s: %s"
                                         % ( job.get_id_tag(), rexmsg ) )
                                 stdout = rexmsg + "\n" + stdout
-                                max_error_level = max( max_error_level, 
+                                max_error_level = max( max_error_level,
                                                        regex.error_level )
-                                if ( max_error_level >= 
+                                if ( max_error_level >=
                                      galaxy.tools.StdioErrorLevel.FATAL ):
                                     break
 
@@ -1144,33 +1144,33 @@ class JobWrapper( object ):
                                                      re.IGNORECASE )
                             if ( regex_match ):
                                 rexmsg = self.regex_err_msg( regex_match, regex)
-                                log.info( "Job %s: %s" 
+                                log.info( "Job %s: %s"
                                         % ( job.get_id_tag(), rexmsg ) )
                                 stderr = rexmsg + "\n" + stderr
-                                max_error_level = max( max_error_level, 
+                                max_error_level = max( max_error_level,
                                                        regex.error_level )
-                                if ( max_error_level >= 
+                                if ( max_error_level >=
                                      galaxy.tools.StdioErrorLevel.FATAL ):
                                     break
-    
+
                 # If we encountered a fatal error, then we'll need to set the
                 # job state accordingly. Otherwise the job is ok:
                 if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL:
-                    success = False 
+                    success = False
                 else:
-                    success = True 
-    
+                    success = True
+
             # When there are no regular expressions and no exit codes to check,
             # default to the previous behavior: when there's anything on stderr
-            # the job has an error, and the job is ok otherwise. 
+            # the job has an error, and the job is ok otherwise.
             else:
-                # TODO: Add in the tool and job id: 
+                # TODO: Add in the tool and job id:
                 log.debug( "Tool did not define exit code or stdio handling; "
                          + "checking stderr for success" )
                 if stderr:
-                    success = False 
+                    success = False
                 else:
-                    success = True 
+                    success = True
 
         # On any exception, return True.
         except:
@@ -1178,7 +1178,7 @@ class JobWrapper( object ):
             log.warning( "Tool check encountered unexpected exception; "
                        + "assuming tool was successful: " + tb )
             success = True
-        
+
         # Store the modified stdout and stderr in the job:
         if None != job:
             job.stdout = stdout
@@ -1192,7 +1192,7 @@ class JobWrapper( object ):
         ToolStdioRegex regex object. The regex_match is a MatchObject
         that will contain the string matched on.
         """
-        # Get the description for the error level: 
+        # Get the description for the error level:
         err_msg = galaxy.tools.StdioErrorLevel.desc( regex.error_level ) + ": "
         # If there's a description for the regular expression, then use it.
         # Otherwise, we'll take the first 256 characters of the match.
@@ -1206,7 +1206,7 @@ class JobWrapper( object ):
             if mend - mstart > 256:
                 err_msg += match.string[ mstart : mstart+256 ] + "..."
             else:
-                err_msg += match.string[ mstart: mend ] 
+                err_msg += match.string[ mstart: mend ]
         return err_msg
 
     def cleanup( self ):
@@ -1485,7 +1485,7 @@ class TaskWrapper(JobWrapper):
         self.status = task.states.NEW
 
     def can_split( self ):
-        # Should the job handler split this job up? TaskWrapper should 
+        # Should the job handler split this job up? TaskWrapper should
         # always return False as the job has already been split.
         return False
 
@@ -1627,8 +1627,8 @@ class TaskWrapper(JobWrapper):
         the contents of the output files.
         """
         # This may have ended too soon
-        log.debug( 'task %s for job %d ended; exit code: %d' 
-                 % (self.task_id, self.job_id, 
+        log.debug( 'task %s for job %d ended; exit code: %d'
+                 % (self.task_id, self.job_id,
                     tool_exit_code if tool_exit_code != None else -256 ) )
         # default post job setup_external_metadata
         self.sa_session.expunge_all()
@@ -1643,12 +1643,12 @@ class TaskWrapper(JobWrapper):
             self.fail( task.info )
             return
 
-        # Check what the tool returned. If the stdout or stderr matched 
+        # Check what the tool returned. If the stdout or stderr matched
         # regular expressions that indicate errors, then set an error.
         # The same goes if the tool's exit code was in a given range.
         if ( self.check_tool_output( stdout, stderr, tool_exit_code, task ) ):
             task.state = task.states.OK
-        else: 
+        else:
             task.state = task.states.ERROR
 
         # Save stdout and stderr

From 44eb87b8c5aee867d1b9933207daa0d76d2bef51 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Wed, 27 Mar 2013 15:36:07 -0400
Subject: [PATCH 6/8] biostar: send encoded unique ID for user as username

---
 lib/galaxy/webapps/galaxy/controllers/biostar.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/biostar.py b/lib/galaxy/webapps/galaxy/controllers/biostar.py
index f625e49a968..a4eb36786d4 100644
--- a/lib/galaxy/webapps/galaxy/controllers/biostar.py
+++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py
@@ -72,14 +72,16 @@ class BiostarController( BaseUIController ):
         payload = dict( DEFAULT_PAYLOAD, **payload )
         # Do the best we can of providing user information for the payload
         if trans.user:
+            payload['username'] = "user-" + trans.security.encode_id( trans.user.id )
             payload['email'] = trans.user.email
             if trans.user.username:
-                payload['username'] = trans.user.username
                 payload['display_name'] = trans.user.username
             else:
-                payload['display_name'] = "Galaxy User"
+                payload['display_name'] = trans.user.email.split( "@" )[0]
         else:
-            payload['username'] = payload['display_name'] = "Anonymous Galaxy User %d" % trans.galaxy_session.id
+            encoded = trans.security.encode_id( trans.galaxy_session.id )
+            payload['username'] = "anon-" + encoded
+            payload['display_name'] = "Anonymous Galaxy User %d" % encoded[0:8]
         data, digest = encode_data( trans.app.config.biostar_key, payload )
         return trans.response.send_redirect( url_for( trans.app.config.biostar_url, data=data, digest=digest, name=trans.app.config.biostar_key_name, action=biostar_action ) )
 

From 65950caabd1676edccd1fcc1ceef9e58c55629a9 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Thu, 28 Mar 2013 12:38:35 -0400
Subject: [PATCH 7/8] biostar: open tool question link in new window/tab

---
 templates/webapps/galaxy/tool_form.mako | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
index 7d8d5e179dc..9bcfe54af3c 100644
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -73,7 +73,7 @@
             });
             $(this).append(select_link).append(" ").append(unselect_link);
         });
-        
+
         $(".add-librarydataset").live("click", function() {
             var link = $(this);
             $.ajax({
@@ -311,7 +311,7 @@
 
         %if trans.app.config.biostar_url:
             <!-- BioStar links -->
-            <span class="pull-right"><a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" target="galaxy_main" class="fa-icon-question-sign tooltip" data-original-title="Ask a question about this tool"></a></span>
+            <span class="pull-right"><a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" target="_blank" class="fa-icon-question-sign tooltip" data-original-title="Ask a question about this tool"></a></span>
             <!-- End of BioStar links -->
         %endif
         </div>

From fb6a186b335191059607203f5c6e3c7fa581c669 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Thu, 28 Mar 2013 12:40:44 -0400
Subject: [PATCH 8/8] biostar: do not fill in question title

---
 lib/galaxy/webapps/galaxy/controllers/biostar.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/biostar.py b/lib/galaxy/webapps/galaxy/controllers/biostar.py
index a4eb36786d4..8162a6c0672 100644
--- a/lib/galaxy/webapps/galaxy/controllers/biostar.py
+++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py
@@ -29,7 +29,7 @@ def slugify(text, delim=u'-'):
 # Biostar requires all keys to be present, so we start with a template
 DEFAULT_PAYLOAD = {
     'email': "",
-    'title': "Question about Galaxy",
+    'title': "",
     'tags': 'galaxy',
     'tool_name': '',
     'tool_version': '',
@@ -109,8 +109,7 @@ class BiostarController( BaseUIController ):
         if not tool:
             return error( "No tool found matching '%s'" % tool_id )
         # Tool specific information for payload
-        payload = { 'title': "Question about Galaxy tool '%s'" % tool.name,
-                    'tool_name': tool.name,
+        payload = { 'tool_name': tool.name,
                     'tool_version': tool.version,
                     'tool_id': tool.id,
                     'tags': 'galaxy ' + tag_for_tool( tool ) }