[galaxy-commits] commit/galaxy-central: 5 new changesets

16 Mar 2015

5 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/9f40ff3e3fe1/
Changeset:   9f40ff3e3fe1
Branch:      stable
User:        natefoo
Date:        2015-03-17 02:34:24+00:00
Summary:     Merge release_15.03
Affected #:  26 files

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 client/galaxy/scripts/mvc/history/history-model.js

--- a/client/galaxy/scripts/mvc/history/history-model.js
+++ b/client/galaxy/scripts/mvc/history/history-model.js
@@ -208,7 +208,7 @@
     /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */
     purge : function( options ){
         if( this.get( 'purged' ) ){ return jQuery.when(); }
-        return this.save( { purged: true }, options );
+        return this.save( { deleted: true, purged: true }, options );
     },
     /** save this history, _Mark_ing it as undeleted */
     undelete : function( options ){

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -667,11 +667,20 @@
         # need to make different keys for them, since ids can overlap
         return "%s_%d" % ( dataset.__class__.__name__, dataset.id )
 
-    def setup_external_metadata( self, datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None,
-                                 output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, kwds=None ):
+    def setup_external_metadata( self, datasets, sa_session, exec_dir=None,
+                                 tmp_dir=None, dataset_files_path=None,
+                                 output_fnames=None, config_root=None,
+                                 config_file=None, datatypes_config=None,
+                                 job_metadata=None, compute_tmp_dir=None,
+                                 include_command=True, kwds=None ):
         kwds = kwds or {}
         if tmp_dir is None:
             tmp_dir = MetadataTempFile.tmp_dir
+        else:
+            MetadataTempFile.tmp_dir = tmp_dir
+
+        if not os.path.exists(tmp_dir):
+            os.makedirs(tmp_dir)
 
         # path is calculated for Galaxy, may be different on compute - rewrite
         # for the compute server.
@@ -687,8 +696,8 @@
             def __get_filename_override():
                 if output_fnames:
                     for dataset_path in output_fnames:
-                        if dataset_path.false_path and dataset_path.real_path == metadata_files.dataset.file_name:
-                            return dataset_path.false_path
+                        if dataset_path.real_path == metadata_files.dataset.file_name:
+                            return dataset_path.false_path or dataset_path.real_path
                 return ""
             line = "%s,%s,%s,%s,%s,%s" % (
                 metadata_path_on_compute(metadata_files.filename_in),
@@ -761,8 +770,18 @@
                 sa_session.add( metadata_files )
                 sa_session.flush()
             metadata_files_list.append( metadata_files )
-        #return command required to build
-        return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, compute_tmp_dir or tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
+        args = "%s %s %s" % ( datatypes_config,
+                              job_metadata,
+                              " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
+        if include_command:
+            #return command required to build
+            fd, fp = tempfile.mkstemp( suffix='.py', dir = tmp_dir, prefix = "set_metadata_" )
+            metadata_script_file = abspath( fp )
+            os.fdopen( fd, 'w' ).write( 'from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()' )
+            return "python %s %s" % ( metadata_path_on_compute(metadata_script_file), args )
+        else:
+            # return args to galaxy_ext.metadata.set_metadata required to build
+            return args
 
     def external_metadata_set_successfully( self, dataset, sa_session ):
         metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -653,12 +653,15 @@
                   <requirement type="package">samtools</requirement></requirements><action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
-              <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command>
+              <command>python $set_metadata $__SET_EXTERNAL_METADATA_COMMAND_LINE__</command><inputs><param format="data" name="input1" type="data" label="File to set metadata on."/><param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/><param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/></inputs>
+              <configfiles>
+                <configfile name="set_metadata">from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()</configfile>
+              </configfiles></tool>
             """
         tmp_name = tempfile.NamedTemporaryFile()

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -831,8 +831,7 @@
 
         self.command_line, self.extra_filenames = tool_evaluator.build()
         # FIXME: for now, tools get Galaxy's lib dir in their path
-        if self.command_line and self.command_line.startswith( 'python' ):
-            self.galaxy_lib_dir = os.path.abspath( "lib" )  # cwd = galaxy root
+        self.galaxy_lib_dir = os.path.abspath( "lib" )  # cwd = galaxy root
         # Shell fragment to inject dependencies
         self.dependency_shell_commands = self.tool.build_dependency_shell_commands()
         # We need command_line persisted to the db in order for Galaxy to re-queue the job

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/jobs/actions/post.py
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -156,7 +156,7 @@
             #      "replace" option so you can replace a portion of the name,
             #      support multiple #{name} in one rename action...
 
-            if new_name.find("#{") > -1:
+            while new_name.find("#{") > -1:
                 to_be_replaced = ""
                 #  This assumes a single instance of #{variable} will exist
                 start_pos = new_name.find("#{") + 2

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/jobs/command_factory.py
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -145,7 +145,7 @@
     metadata_command = metadata_command.strip()
     if metadata_command:
         commands_builder.capture_return_code()
-        commands_builder.append_command("cd %s; %s" % (exec_dir, metadata_command))
+        commands_builder.append_command(metadata_command)
 
 
 def __copy_if_exists_command(work_dir_output):

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -680,6 +680,9 @@
         except Empty:
             pass
         for job, error_msg in jobs_to_check:
+            if job.state != job.states.DELETED_NEW and job.finished:
+                log.debug('Job %s already finished, not deleting or stopping', job.id)
+                continue
             final_state = job.states.DELETED
             if error_msg is not None:
                 final_state = job.states.ERROR

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/managers/hdas.py
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -156,11 +156,12 @@
         self.dataset_manager.error_unless_dataset_purge_allowed( trans, hda )
         super( HDAManager, self ).purge( trans, hda, flush=flush )
 
-        # signal to stop the creating job?
         if hda.creating_job_associations:
             job = hda.creating_job_associations[0].job
-            job.mark_deleted( self.app.config.track_jobs_in_database )
-            self.app.job_manager.job_stop_queue.put( job.id )
+            if not job.finished:
+                # signal to stop the creating job
+                job.mark_deleted( self.app.config.track_jobs_in_database )
+                self.app.job_manager.job_stop_queue.put( job.id )
 
         # more importantly, purge dataset as well
         if hda.dataset.user_can_purge:

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/metadata
--- /dev/null
+++ b/lib/galaxy/metadata
@@ -0,0 +1,1 @@
+../galaxy_ext/metadata
\ No newline at end of file

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -517,6 +517,9 @@
         """
         Mark this job as deleted, and mark any output datasets as discarded.
         """
+        if self.finished:
+            # Do not modify the state/outputs of jobs that are already terminal
+            return
         if track_jobs_in_database:
             self.state = Job.states.DELETED_NEW
         else:

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/objectstore/__init__.py
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -392,39 +392,39 @@
         super(NestedObjectStore, self).shutdown()
 
     def exists(self, obj, **kwargs):
-        return self.__call_method('exists', obj, False, False, **kwargs)
+        return self._call_method('exists', obj, False, False, **kwargs)
 
     def file_ready(self, obj, **kwargs):
-        return self.__call_method('file_ready', obj, False, False, **kwargs)
+        return self._call_method('file_ready', obj, False, False, **kwargs)
 
     def create(self, obj, **kwargs):
         random.choice(self.backends.values()).create(obj, **kwargs)
 
     def empty(self, obj, **kwargs):
-        return self.__call_method('empty', obj, True, False, **kwargs)
+        return self._call_method('empty', obj, True, False, **kwargs)
 
     def size(self, obj, **kwargs):
-        return self.__call_method('size', obj, 0, False, **kwargs)
+        return self._call_method('size', obj, 0, False, **kwargs)
 
     def delete(self, obj, **kwargs):
-        return self.__call_method('delete', obj, False, False, **kwargs)
+        return self._call_method('delete', obj, False, False, **kwargs)
 
     def get_data(self, obj, **kwargs):
-        return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('get_data', obj, ObjectNotFound, True, **kwargs)
 
     def get_filename(self, obj, **kwargs):
-        return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
 
     def update_from_file(self, obj, **kwargs):
         if kwargs.get('create', False):
             self.create(obj, **kwargs)
             kwargs['create'] = False
-        return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
 
     def get_object_url(self, obj, **kwargs):
-        return self.__call_method('get_object_url', obj, None, False, **kwargs)
+        return self._call_method('get_object_url', obj, None, False, **kwargs)
 
-    def __call_method(self, method, obj, default, default_is_exception, **kwargs):
+    def _call_method(self, method, obj, default, default_is_exception, **kwargs):
         """
         Check all children object stores for the first one with the dataset
         """
@@ -432,7 +432,7 @@
             if store.exists(obj, **kwargs):
                 return store.__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
-            raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s'
+            raise default( 'objectstore, _call_method failed: %s on %s, kwargs: %s'
                 % ( method, str( obj ), str( kwargs ) ) )
         else:
             return default
@@ -535,12 +535,12 @@
                 log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id))
             self.backends[obj.object_store_id].create(obj, **kwargs)
 
-    def __call_method(self, method, obj, default, default_is_exception, **kwargs):
+    def _call_method(self, method, obj, default, default_is_exception, **kwargs):
         object_store_id = self.__get_store_id_for(obj, **kwargs)
         if object_store_id is not None:
             return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
-            raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s'
+            raise default( 'objectstore, _call_method failed: %s on %s, kwargs: %s'
                 % ( method, str( obj ), str( kwargs ) ) )
         else:
             return default

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2587,11 +2587,9 @@
         hda_source_dict = {} # Mapping from HDA in history to source HDAs.
         for hda in history.datasets:
             source_hda = hda.copied_from_history_dataset_association
-            while source_hda:#should this check library datasets as well?
-                #FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
-                #but is still less than perfect when eg individual datasets are copied between histories
-                if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
-                    hda_source_dict[ source_hda ] = hda
+            while source_hda:
+                if source_hda.dataset.id not in hda_source_dict or source_hda.hid == hda.hid:
+                    hda_source_dict[ source_hda.dataset.id ] = hda
                 source_hda = source_hda.copied_from_history_dataset_association
 
         # Ditto for dataset collections.
@@ -2599,8 +2597,8 @@
         for hdca in history.dataset_collections:
             source_hdca = hdca.copied_from_history_dataset_collection_association
             while source_hdca:
-                if source_hdca not in hdca_source_dict or source_hdca.hid == hdca.hid:
-                    hdca_source_dict[ source_hdca ] = hdca
+                if source_hdca.collection.id not in hdca_source_dict or source_hdca.hid == hdca.hid:
+                    hdca_source_dict[ source_hdca.collection.id ] = hdca
                 source_hdca = source_hdca.copied_from_history_dataset_collection_association
 
         # Unpack unvalidated values to strings, they'll be validated when the
@@ -2619,17 +2617,21 @@
                 if isinstance(value,list):
                     values = []
                     for val in value:
-                        if is_hashable( val ):
-                            if val in history.datasets:
+                        if isinstance(val, trans.app.model.HistoryDatasetAssociation):
+                            if val.dataset.id in hda_source_dict:
+                                values.append( hda_source_dict[ val.dataset.id ] )
+                            else:
                                 values.append( val )
-                            elif val in hda_source_dict:
-                                values.append( hda_source_dict[ val ])
                     return values
-                if is_hashable( value ) and value not in history.datasets and value in hda_source_dict:
-                    return hda_source_dict[ value ]
+                if isinstance(value, trans.app.model.HistoryDatasetAssociation):
+                    if value.dataset.id in hda_source_dict:
+                        return hda_source_dict[ value.dataset.id ]
+                if isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation):
+                    if value.collection.id in hdca_source_dict:
+                        return hdca_source_dict[ value.collection.id ]
             elif isinstance( input, DataCollectionToolParameter ):
-                if is_hashable( value ) and value not in history.dataset_collections and value in hdca_source_dict:
-                    return hdca_source_dict[ value ]
+                if value.collection.id in hdca_source_dict:
+                    return hdca_source_dict[ value.collection.id ]
         visit_input_values( tool_inputs, params, rerun_callback )
 
     def _compare_tool_version( self, trans, job ):

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/tools/actions/metadata.py
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -1,11 +1,15 @@
+import logging
+
 from __init__ import ToolAction
 from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
 from galaxy.util.odict import odict
 from galaxy.util.json import dumps
+from galaxy.jobs.datasets import DatasetPath
 
-import logging
+
 log = logging.getLogger( __name__ )
 
+
 class SetMetadataToolAction( ToolAction ):
     """Tool action used for setting external metadata on an existing dataset"""
 
@@ -65,17 +69,21 @@
         #add parameters to job_parameter table
         # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)?
         incoming[ '__ORIGINAL_DATASET_STATE__' ] = dataset.state
+        input_paths = [DatasetPath( dataset.id, real_path=dataset.file_name, mutable=False )]
+        app.object_store.create(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
+        job_working_dir = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
         external_metadata_wrapper = JobExternalOutputMetadataWrapper( job )
         cmd_line = external_metadata_wrapper.setup_external_metadata( dataset,
                                                                       sa_session,
                                                                       exec_dir = None,
-                                                                      tmp_dir = app.config.new_file_path,
+                                                                      tmp_dir = job_working_dir,
                                                                       dataset_files_path = app.model.Dataset.file_path,
-                                                                      output_fnames = None,
+                                                                      output_fnames = input_paths,
                                                                       config_root = app.config.root,
                                                                       config_file = app.config.config_file,
                                                                       datatypes_config = app.datatypes_registry.integrated_datatypes_configs,
                                                                       job_metadata = None,
+                                                                      include_command = False,
                                                                       kwds = { 'overwrite' : overwrite } )
         incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line
         for name, value in tool.params_to_strings( incoming, app ).iteritems():

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/tools/imp_exp/__init__.py
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -17,12 +17,15 @@
         <tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history"><type class="ExportHistoryTool" module="galaxy.tools"/><action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/>
-          <command>$__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command>
+          <command>python $export_history $__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command><inputs><param name="__HISTORY_TO_EXPORT__" type="hidden"/><param name="compress" type="boolean"/><param name="__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__" type="hidden"/></inputs>
+          <configfiles>
+            <configfile name="export_history">from galaxy.tools.imp_exp.export_history import main; main()</configfile>
+          </configfiles><outputs><data format="gzip" name="output_file"/></outputs>
@@ -530,11 +533,9 @@
         options = ""
         if jeha.compressed:
             options = "-G"
-        return "python %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ),
-                                           "lib/galaxy/tools/imp_exp/export_history.py" ),
-                                           options, history_attrs_filename,
-                                           datasets_attrs_filename,
-                                           jobs_attrs_filename )
+        return "%s %s %s %s" % ( options, history_attrs_filename,
+                                 datasets_attrs_filename,
+                                 jobs_attrs_filename )
 
     def cleanup_after_job( self, db_session ):
         """ Remove temporary directory and attribute files generated during setup for this job. """

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/tools/imp_exp/export_history.py
--- a/lib/galaxy/tools/imp_exp/export_history.py
+++ b/lib/galaxy/tools/imp_exp/export_history.py
@@ -70,7 +70,7 @@
     except Exception, e:
         return 'Error creating history archive: %s' % str( e ), sys.stderr
 
-if __name__ == "__main__":
+def main():
     # Parse command line.
     parser = optparse.OptionParser()
     parser.add_option( '-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.' )
@@ -81,3 +81,6 @@
     # Create archive.
     status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip )
     print status
+
+if __name__ == "__main__":
+    main()

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/version.py
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,1 +1,3 @@
 VERSION_MAJOR = "15.03"
+VERSION_MINOR = "1"
+VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/webapps/galaxy/api/users.py
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -105,7 +105,7 @@
         POST /api/users
         Creates a new Galaxy user.
         """
-        if not trans.app.config.allow_user_creation:
+        if not trans.app.config.allow_user_creation and not trans.user_is_admin():
             raise exceptions.ConfigDoesNotAllowException( 'User creation is not allowed in this Galaxy instance' )
         if trans.app.config.use_remote_user and trans.user_is_admin():
             user = trans.get_or_create_remote_user( remote_user_email=payload['remote_user_email'] )

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/webapps/galaxy/controllers/history.py
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -359,6 +359,15 @@
                     history.purged = True
                     self.sa_session.add( history )
                     self.sa_session.flush()
+                for hda in history.datasets:
+                    # Not all datasets have jobs associated with them (e.g., datasets imported from libraries).
+                    if hda.creating_job_associations:
+                        # HDA has associated job, so try marking it deleted.
+                        job = hda.creating_job_associations[0].job
+                        if job.history_id == history.id and not job.finished:
+                            # No need to check other outputs since the job's parent history is this history
+                            job.mark_deleted( trans.app.config.track_jobs_in_database )
+                            trans.app.job_manager.job_stop_queue.put( job.id )
         trans.sa_session.flush()
         if n_deleted:
             part = "Deleted %d %s" % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) )
@@ -1125,7 +1134,7 @@
             if hda.creating_job_associations:
                 # HDA has associated job, so try marking it deleted.
                 job = hda.creating_job_associations[0].job
-                if job.history_id == history.id and job.state in [ trans.app.model.Job.states.QUEUED, trans.app.model.Job.states.RUNNING, trans.app.model.Job.states.NEW ]:
+                if job.history_id == history.id and not job.finished:
                     # No need to check other outputs since the job's parent history is this history
                     job.mark_deleted( trans.app.config.track_jobs_in_database )
                     trans.app.job_manager.job_stop_queue.put( job.id )
@@ -1224,33 +1233,28 @@
             # Use current history.
             history = trans.history
             id = trans.security.encode_id( history.id )
-
         if not history:
             return trans.show_error_message( "This history does not exist or you cannot export this history." )
-
-        #
         # If history has already been exported and it has not changed since export, stream it.
-        #
         jeha = history.latest_export
         if jeha and jeha.up_to_date:
             if jeha.ready:
                 if preview:
                     url = url_for( controller='history', action="export_archive", id=id, qualified=True )
-                    return trans.show_message( "History Ready: '%(n)s'. Use this link to download \
-                                                the archive or import it to another Galaxy server: \
-                                                <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) )
+                    return trans.show_message( "History Ready: '%(n)s'. Use this link to download "
+                                               "the archive or import it to another Galaxy server: "
+                                               "<a href='%(u)s'>%(u)s</a>" % ( { 'n': history.name, 'u': url } ) )
                 else:
                     return self.serve_ready_history_export( trans, jeha )
             elif jeha.preparing:
-                return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" \
-                        % ( { 'n' : history.name, 's' : url_for( controller='history', action="export_archive", id=id, qualified=True ) } ) )
-
+                return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>"
+                                           % ( { 'n': history.name, 's': url_for( controller='history', action="export_archive", id=id, qualified=True ) } ) )
         self.queue_history_export( trans, history, gzip=gzip, include_hidden=include_hidden, include_deleted=include_deleted )
         url = url_for( controller='history', action="export_archive", id=id, qualified=True )
-        return trans.show_message( "Exporting History '%(n)s'. Use this link to download \
-                                    the archive or import it to another Galaxy server: \
-                                    <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) )
-        #TODO: used in this file and index.mako
+        return trans.show_message( "Exporting History '%(n)s'. You will need to <a href='%(share)s'>make this history 'accessible'</a> in order to import this to another galaxy sever. <br/>"
+                                   "Use this link to download the archive or import it to another Galaxy server: "
+                                   "<a href='%(u)s'>%(u)s</a>" % ( { 'share': url_for(controller='history', action='sharing'), 'n': history.name, 'u': url } ) )
+        # TODO: used in this file and index.mako
 
     @web.expose
     @web.json

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1,6 +1,7 @@
 import base64
 import httplib
 import json
+import logging
 import os
 import sgmllib
 import urllib2
@@ -41,6 +42,8 @@
 from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING
 from markupsafe import escape
 
+log = logging.getLogger( __name__ )
+
 
 class StoredWorkflowListGrid( grids.Grid ):
 
@@ -895,8 +898,9 @@
                     data = json.loads( workflow_data )
                 except Exception, e:
                     data = None
-                    message = "The data content does not appear to be a Galaxy workflow.<br/>Exception: %s" % str( e )
+                    message = "The data content does not appear to be a Galaxy workflow."
                     status = 'error'
+                    log.exception("Error importing workflow.")
                 if data:
                     # Create workflow if possible.  If a required tool is not available in the local
                     # Galaxy instance, the tool information will be available in the step_dict.

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy_ext/__init__.py
--- /dev/null
+++ b/lib/galaxy_ext/__init__.py
@@ -0,0 +1,4 @@
+""" Package for things which are loaded from outside Galaxy and which we can be
+sure will not conflict with the `galaxy` namespace, which may be provided by
+other packages (e.g. galaxy_ops in the toolshed).
+"""

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy_ext/metadata/__init__.py
--- /dev/null
+++ b/lib/galaxy_ext/metadata/__init__.py
@@ -0,0 +1,2 @@
+""" Work with Galaxy metadata
+"""

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 lib/galaxy_ext/metadata/set_metadata.py
--- /dev/null
+++ b/lib/galaxy_ext/metadata/set_metadata.py
@@ -0,0 +1,125 @@
+"""
+Execute an external process to set_meta() on a provided list of pickled datasets.
+
+This was formerly scripts/set_metadata.py and expects these arguments:
+
+    %prog datatypes_conf.xml job_metadata_file metadata_in,metadata_kwds,metadata_out,metadata_results_code,output_filename_override,metadata_override...
+
+Galaxy should be importable on sys.path and output_filename_override should be
+set to the path of the dataset on which metadata is being set
+(output_filename_override could previously be left empty and the path would be
+constructed automatically).
+"""
+
+import logging
+logging.basicConfig()
+log = logging.getLogger( __name__ )
+
+import cPickle
+import json
+import os
+import sys
+
+# ensure supported version
+assert sys.version_info[:2] >= ( 2, 6 ) and sys.version_info[:2] <= ( 2, 7 ), 'Python version must be 2.6 or 2.7, this is: %s' % sys.version
+
+# insert *this* galaxy before all others on sys.path
+new_path = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
+sys.path.insert( 0, new_path )
+
+from galaxy import eggs
+import pkg_resources
+import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
+galaxy.model.Job()  # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
+from galaxy.util import stringify_dictionary_keys
+from sqlalchemy.orm import clear_mappers
+
+
+def set_meta_with_tool_provided( dataset_instance, file_dict, set_meta_kwds ):
+    # This method is somewhat odd, in that we set the metadata attributes from tool,
+    # then call set_meta, then set metadata attributes from tool again.
+    # This is intentional due to interplay of overwrite kwd, the fact that some metadata
+    # parameters may rely on the values of others, and that we are accepting the
+    # values provided by the tool as Truth. 
+    for metadata_name, metadata_value in file_dict.get( 'metadata', {} ).iteritems():
+        setattr( dataset_instance.metadata, metadata_name, metadata_value )
+    dataset_instance.datatype.set_meta( dataset_instance, **set_meta_kwds )
+    for metadata_name, metadata_value in file_dict.get( 'metadata', {} ).iteritems():
+        setattr( dataset_instance.metadata, metadata_name, metadata_value )
+
+def set_metadata():
+    # locate galaxy_root for loading datatypes
+    galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir))
+    galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tool_job_working_directory = os.path.abspath(os.getcwd())
+
+    # Set up datatypes registry
+    datatypes_config = sys.argv.pop( 1 )
+    datatypes_registry = galaxy.datatypes.registry.Registry()
+    datatypes_registry.load_datatypes( root_dir=galaxy_root, config=datatypes_config )
+    galaxy.model.set_datatypes_registry( datatypes_registry )
+
+    job_metadata = sys.argv.pop( 1 )
+    existing_job_metadata_dict = {}
+    new_job_metadata_dict = {}
+    if job_metadata != "None" and os.path.exists( job_metadata ):
+        for line in open( job_metadata, 'r' ):
+            try:
+                line = stringify_dictionary_keys( json.loads( line ) )
+                if line['type'] == 'dataset':
+                    existing_job_metadata_dict[ line['dataset_id'] ] = line
+                elif line['type'] == 'new_primary_dataset':
+                    new_job_metadata_dict[ line[ 'filename' ] ] = line
+            except:
+                continue
+
+    for filenames in sys.argv[1:]:
+        fields = filenames.split( ',' )
+        filename_in = fields.pop( 0 )
+        filename_kwds = fields.pop( 0 )
+        filename_out = fields.pop( 0 )
+        filename_results_code = fields.pop( 0 )
+        dataset_filename_override = fields.pop( 0 )
+        # Need to be careful with the way that these parameters are populated from the filename splitting,
+        # because if a job is running when the server is updated, any existing external metadata command-lines
+        #will not have info about the newly added override_metadata file
+        if fields:
+            override_metadata = fields.pop( 0 )
+        else:
+            override_metadata = None
+        set_meta_kwds = stringify_dictionary_keys( json.load( open( filename_kwds ) ) )  # load kwds; need to ensure our keywords are not unicode
+        try:
+            dataset = cPickle.load( open( filename_in ) )  # load DatasetInstance
+            dataset.dataset.external_filename = dataset_filename_override
+            files_path = os.path.abspath(os.path.join( tool_job_working_directory, "dataset_%s_files" % (dataset.dataset.id) ))
+            dataset.dataset.external_extra_files_path = files_path
+            if dataset.dataset.id in existing_job_metadata_dict:
+                dataset.extension = existing_job_metadata_dict[ dataset.dataset.id ].get( 'ext', dataset.extension )
+            # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
+            if override_metadata:
+                override_metadata = json.load( open( override_metadata ) )
+                for metadata_name, metadata_file_override in override_metadata:
+                    if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
+                        metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
+                    setattr( dataset.metadata, metadata_name, metadata_file_override )
+            file_dict = existing_job_metadata_dict.get( dataset.dataset.id, {} )
+            set_meta_with_tool_provided( dataset, file_dict, set_meta_kwds )
+            dataset.metadata.to_JSON_dict( filename_out )  # write out results of set_meta
+            json.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) )  # setting metadata has succeeded
+        except Exception, e:
+            json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) )  # setting metadata has failed somehow
+
+    for i, ( filename, file_dict ) in enumerate( new_job_metadata_dict.iteritems(), start=1 ):
+        new_dataset = galaxy.model.Dataset( id=-i, external_filename=os.path.join( tool_job_working_directory, file_dict[ 'filename' ] ) )
+        extra_files = file_dict.get( 'extra_files', None )
+        if extra_files is not None:
+            new_dataset._extra_files_path = os.path.join( tool_job_working_directory, extra_files )
+        new_dataset.state = new_dataset.states.OK
+        new_dataset_instance = galaxy.model.HistoryDatasetAssociation( id=-i, dataset=new_dataset, extension=file_dict.get( 'ext', 'data' ) )
+        set_meta_with_tool_provided( new_dataset_instance, file_dict, set_meta_kwds )
+        file_dict[ 'metadata' ] = json.loads( new_dataset_instance.metadata.to_JSON_dict() ) #storing metadata in external form, need to turn back into dict, then later jsonify
+    if existing_job_metadata_dict or new_job_metadata_dict:
+        with open( job_metadata, 'wb' ) as job_metadata_fh:
+            for value in existing_job_metadata_dict.values() + new_job_metadata_dict.values():
+                job_metadata_fh.write( "%s\n" % ( json.dumps( value ) ) )
+
+    clear_mappers()

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 static/scripts/mvc/history/history-model.js
--- a/static/scripts/mvc/history/history-model.js
+++ b/static/scripts/mvc/history/history-model.js
@@ -208,7 +208,7 @@
     /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */
     purge : function( options ){
         if( this.get( 'purged' ) ){ return jQuery.when(); }
-        return this.save( { purged: true }, options );
+        return this.save( { deleted: true, purged: true }, options );
     },
     /** save this history, _Mark_ing it as undeleted */
     undelete : function( options ){

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 static/scripts/packed/mvc/history/history-model.js
--- a/static/scripts/packed/mvc/history/history-model.js
+++ b/static/scripts/packed/mvc/history/history-model.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}});
\ No newline at end of file
+define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}});
\ No newline at end of file

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 templates/webapps/galaxy/workflow/run.mako
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -513,7 +513,7 @@
     <div class="metadataFormTitle">Workflow Parameters</div><div class="metadataFormBody">
     %for parm in wf_parms:
-        <div class='form-row'><label style='width:100px;'>${parm}<input style="border:2px solid ${wf_parms[parm]};border-left-width:8px;" type="text" class='wf_parm_input ptag_${parm}' name="wf_parm|${parm}" value=""/></label></div>
+        <div class='form-row'><label>${parm}<br/><input size=40 style="border:2px solid ${wf_parms[parm]};border-left-width:8px;" type="text" class='wf_parm_input ptag_${parm}' name="wf_parm|${parm}" value=""/></label></div>
     %endfor
     </div></div>

diff -r db72e1534441c03d2d60616bacfee5bf4ebc66cc -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 test/unit/jobs/test_command_factory.py
--- a/test/unit/jobs/test_command_factory.py
+++ b/test/unit/jobs/test_command_factory.py
@@ -72,7 +72,7 @@
         self.include_metadata = True
         self.include_work_dir_outputs = False
         self.job_wrapper.metadata_line = TEST_METADATA_LINE
-        expected_command = '%s; return_code=$?; cd %s; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, getcwd(), TEST_METADATA_LINE)
+        expected_command = '%s; return_code=$?; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, TEST_METADATA_LINE)
         self.__assert_command_is( expected_command )
 
     def test_empty_metadata(self):


https://bitbucket.org/galaxy/galaxy-central/commits/128373c02e90/
Changeset:   128373c02e90
Branch:      stable
User:        natefoo
Date:        2015-03-17 02:35:28+00:00
Summary:     Added tag v15.03.1 for changeset 9f40ff3e3fe1
Affected #:  1 file

diff -r 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 -r 128373c02e907d1256299d40e184fabb6dfb4bae .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -25,3 +25,4 @@
 5cdf5dc395f16f47e88a5567775dcd21b4906f08 latest_2015.01.13
 738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03
 18e0d31267acda451743fcf1a09ac04fe8681d8f latest_15.03
+9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1


https://bitbucket.org/galaxy/galaxy-central/commits/28113eeee212/
Changeset:   28113eeee212
Branch:      stable
User:        natefoo
Date:        2015-03-17 02:38:27+00:00
Summary:     Update tag latest_15.03 for changeset 9f40ff3e3fe1
Affected #:  1 file

diff -r 128373c02e907d1256299d40e184fabb6dfb4bae -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -24,5 +24,5 @@
 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13
 5cdf5dc395f16f47e88a5567775dcd21b4906f08 latest_2015.01.13
 738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03
-18e0d31267acda451743fcf1a09ac04fe8681d8f latest_15.03
 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1
+9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 latest_15.03


https://bitbucket.org/galaxy/galaxy-central/commits/708cab19708d/
Changeset:   708cab19708d
User:        natefoo
Date:        2015-03-17 02:49:15+00:00
Summary:     Merge v15.03 to default
Affected #:  200 files

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -22,4 +22,4 @@
 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
 782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06
 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13
-d677cb314dccedd8743eba26f1d446cdf97ebf16 latest_2015.01.13
+5cdf5dc395f16f47e88a5567775dcd21b4906f08 latest_2015.01.13

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a CONTRIBUTING.md
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -25,24 +25,27 @@
 
 ## How to Contribute
 
-* If you are new to Git - please check out the very useful tutorials on the [GitHub training hub](https://training.github.com/kit/)
+* If you are new to Mercurial - please check out this [official
+  tutorial](http://mercurial.selenic.com/wiki/Tutorial)
 
-* Make sure you have a free [GitHub account](https://github.com/)
+* Make sure you have a free [Bitbucket
+  account](https://bitbucket.org/account/signup/)
 
-* Fork the galaxy repository on
-  [GitHub](https://github.com/galaxyproject/galaxy) to make your changes.
-  (While many Galaxy instances track
-  [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist), active development
-  happens in the galaxy GitHub repository and this is where pull requests
-  should be made).
+* Fork the galaxy-central repository on
+  [Bitbucket](https://bitbucket.org/galaxy/galaxy-central/fork) to
+  make your changes. (Many Galaxy instances target
+  [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist) - but active
+  development happens on galaxy-central and this is where pull
+  requests should be made).
 
-* Choose the correct branch to develop your changes against.
+* Choose the correct Mercurial branch to develop your changes against.
 
-  * Additions to the code base should be pushed to the `dev` branch (`git
-    checkout dev`).
+  * Additions to the code base should be pushed to the `default`
+    branch (`hg checkout default`).
 
-  * Most bug fixes to previously release components (things in galaxy-dist)
-    should be made against the `master` branch (`git checkout master`).
+  * Most bug fixes to previously release components (things in
+    galaxy-dist) should be pushed to the `stable` branch (`hg checkout
+    stable`).
 
   * Serious security problems should not be fixed via pull request -
     please responsibly disclose these by e-mailing them (with or
@@ -73,9 +76,9 @@
   with these changes. You pull request message should include:
 
    * A description of why the change should be made.
-
+   
    * A description of implementation of the change.
-
+   
    * A description of how to test the change.
 
 ## Ideas

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a README.rst
--- a/README.rst
+++ /dev/null
@@ -1,80 +0,0 @@
-.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target=galaxyLogoTrimmed.png
-   :alt: Galaxy Logo
-
-The latest information about Galaxy is always available via the Galaxy
-website: `http://galaxyproject.org/ <http://galaxyproject.org/>`__
-
-Galaxy Quickstart
-=================
-
-Galaxy requires Python 2.6 or 2.7. To check your python version, run:
-
-.. code:: console
-
-    $ python -V
-    Python 2.7.3
-
-Start Galaxy:
-
-.. code:: console
-
-    $ sh run.sh
-
-Once Galaxy completes startup, you should be able to view Galaxy in your
-browser at:
-
-http://localhost:8080
-
-You may wish to make changes from the default configuration. This can be
-done in the ``config/galaxy.ini`` file. Tools can be either installed
-from the Tool Shed or added manually. For details please see the Galaxy
-wiki:
-
-https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
-
-Not all dependencies are included for the tools provided in the sample
-``tool_conf.xml``. A full list of external dependencies is available at:
-
-https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
-
-Issues
-======
-
-Issues can be submitted to trello via the `galaxyproject
-website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy
-Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__
-
-
-Galaxy Development
-==================
-
-Galaxy welcomes new development! There is extensive documentation on developing
-with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__.
-
-Source Repository
------------------
-
-Galaxy development has moved to `Github
-<https://github.com/galaxyproject/galaxy>`__.
-
-**Developers** should develop against the ``dev`` branch in the Github
-repository.
-
-**Deployers** can continue to pull Galaxy changes from Bitbucket without
-interruption. Alternatively, deployers can track the ``master`` branch in
-Github.
-
-Syncing a Fork
---------------
-
-If you fork Galaxy to work on it, you may be interested in keeping your copy
-up to date with respect to the main repository. Github has `good documentation
-<https://help.github.com/articles/syncing-a-fork/>`__ on this.
-
-.. code:: console
-
-    $ git remote add upstream https://github.com/galaxyproject/galaxy
-    $ git fetch upstream
-    $ git checkout dev
-    $ git merge upstream/dev
-

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a README.txt
--- /dev/null
+++ b/README.txt
@@ -0,0 +1,34 @@
+GALAXY
+======
+http://galaxyproject.org/
+
+The latest information about Galaxy is always available via the Galaxy
+website above.
+
+HOW TO START
+============
+Galaxy requires Python 2.6 or 2.7. To check your python version, run:
+
+% python -V
+Python 2.7.3
+
+Start Galaxy:
+
+% sh run.sh
+
+Once Galaxy completes startup, you should be able to view Galaxy in your
+browser at:
+
+http://localhost:8080
+
+You may wish to make changes from the default configuration. This can be done
+in the config/galaxy.ini file. Tools can be either installed from the Tool Shed
+or added manually. For details please see the Galaxy wiki: 
+
+https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
+
+
+Not all dependencies are included for the tools provided in the sample
+tool_conf.xml. A full list of external dependencies is available at:
+
+https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/mvc/base-mvc.js
--- a/client/galaxy/scripts/mvc/base-mvc.js
+++ b/client/galaxy/scripts/mvc/base-mvc.js
@@ -94,7 +94,7 @@
         if( !options.silent ){
             model.trigger( 'request', model, {}, options );
         }
-        var returned = {};
+        var returned;
         switch( method ){
             case 'create'   : returned = this._create( model ); break;
             case 'read'     : returned = this._read( model );   break;
@@ -111,19 +111,9 @@
 
     /** set storage to the stringified item */
     _create : function( model ){
-        try {
-            var json = model.toJSON(),
-                set = sessionStorage.setItem( model.id, JSON.stringify( json ) );
-            return ( set === null )?( set ):( json );
-        // DOMException is thrown in Safari if in private browsing mode and sessionStorage is attempted:
-        // http://stackoverflow.com/questions/14555347
-        // TODO: this could probably use a more general soln - like detecting priv. mode + safari => non-ajaxing Model
-        } catch( err ){
-            if( !( ( err instanceof DOMException ) && ( navigator.userAgent.indexOf("Safari") > -1 ) ) ){
-                throw err;
-            }
-        }
-        return null;
+        var json = model.toJSON(),
+            set = sessionStorage.setItem( model.id, JSON.stringify( json ) );
+        return ( set === null )?( set ):( json );
     },
 
     /** read and parse json from storage */

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/mvc/tools.js
--- a/client/galaxy/scripts/mvc/tools.js
+++ b/client/galaxy/scripts/mvc/tools.js
@@ -386,14 +386,12 @@
         $("#search-spinner").show();
         var self = this;
         this.timer = setTimeout(function () {
-            // log the search to analytics
-            ga( 'send', 'pageview', galaxy_config.root + '?q=' + q );
             $.get(self.attributes.search_url, { query: q }, function (data) {
                 self.set("results", data);
                 $("#search-spinner").hide();
                 $("#search-clear-btn").show();
             }, "json" );
-        }, 400 );
+        }, 200 );
     },
 
     clear_search: function() {

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/mvc/tools/tools-content.js
--- /dev/null
+++ b/client/galaxy/scripts/mvc/tools/tools-content.js
@@ -0,0 +1,55 @@
+define(['utils/utils'], function(Utils){
+    return Backbone.Model.extend({
+        // initialize
+        initialize: function(app) {
+            this.summary = {};
+        },
+        
+        /** Add new content elements
+        */
+        add: function(content_list) {
+            // add/update content in summary list
+            for (var i in content_list) {
+                for (var j in content_list[i]) {
+                    var c = content_list[i][j];
+                    this.summary[c.id + '_' + c.src] = c;
+                }
+            }
+        },
+        
+        /** Returns matched content from summary.
+        */
+        get: function(options) {
+            return _.findWhere(this.summary, options) || {};
+        },
+        
+        /** Get details of a content by id.
+        */
+        getDetails: function(options) {
+            // check id
+            if (!options.id || options.id === 'null') {
+                options.success && options.success();
+                return;
+            }
+            
+            // create url
+            var api_url = this.base_url + '/datasets/' + options.id;
+            if (options.src == 'hdca') {
+                api_url = this.base_url + '/dataset_collections/' + options.id;
+            }
+            
+            // request details
+            Utils.get({
+                url     : api_url,
+                success : function(response) {
+                    options.success && options.success(response);
+                },
+                error   : function(response) {
+                    options.success && options.success();
+                    console.debug('tools-content::getDetails() - Ajax request for content failed.');
+                    console.debug(response);
+                }
+            });
+        }
+    });
+});
\ No newline at end of file

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/mvc/tools/tools-form-base.js
--- a/client/galaxy/scripts/mvc/tools/tools-form-base.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js
@@ -3,9 +3,9 @@
 */
 define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
         'mvc/citation/citation-model', 'mvc/citation/citation-view',
-        'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-section', 'mvc/tools/tools-tree'],
+        'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-content', 'mvc/tools/tools-section', 'mvc/tools/tools-tree'],
     function(Utils, Deferred, Portlet, Ui, CitationModel, CitationView,
-             Tools, ToolTemplate, ToolSection, ToolTree) {
+             Tools, ToolTemplate, ToolContent, ToolSection, ToolTree) {
 
     // create form view
     return Backbone.View.extend({
@@ -83,8 +83,8 @@
             // creates a tree/json data structure from the input form
             this.tree = new ToolTree(this);
 
-            // keeps track of history items
-            this.history = {};
+            // request history content and build form
+            this.content = new ToolContent(this);
 
             // update model data
             self.options.inputs = options && options.inputs;

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -157,4 +157,4 @@
     }
 });
 
-});
+});
\ No newline at end of file

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/mvc/tools/tools-select-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-select-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js
@@ -179,7 +179,6 @@
     /** Update content selector */
     update: function(options) {
         // update a particular select field
-        var self = this;
         function _update(field, options) {
             if (field) {
                 // identify available options
@@ -190,8 +189,6 @@
                         label: item.hid + ': ' + item.name,
                         value: item.id
                     });
-                    // backup to local history
-                    self.app.history[item.id + '_' + item.src] = item;
                 }
                 // update field
                 field.update(select_options);
@@ -202,6 +199,9 @@
         _update(this.select_single, options.hda);
         _update(this.select_multiple, options.hda);
         _update(this.select_collection, options.hdca);
+
+        // add to content list
+        this.app.content.add(options);
     },
 
     /** Return the currently selected dataset values */
@@ -266,7 +266,7 @@
 
         // append to dataset ids
         for (var i in id_list) {
-            var details = _.findWhere(this.app.history, {
+            var details = this.app.content.get({
                 id  : id_list[i],
                 src : this.list[this.current].type
             });
@@ -312,7 +312,7 @@
     /** Assists in identifying the batch mode */
     _batch: function() {
         if (this.current == 'collection') {
-            var hdca = _.findWhere(this.app.history, {
+            var hdca = this.app.content.get({
                 id  : this._select().value(),
                 src : 'hdca'
             });

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/templates/compiled/panel_section.js
--- a/client/galaxy/scripts/templates/compiled/panel_section.js
+++ b/client/galaxy/scripts/templates/compiled/panel_section.js
@@ -1,14 +1,13 @@
 (function() {
   var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
 templates['panel_section'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
-    var helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
-
+  var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression;
   return "<div class=\"toolSectionTitle\" id=\"title_"
-    + alias3(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"id","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper)))
     + "\">\n    <a href=\"javascript:void(0)\"><span>"
-    + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
     + "</span></a>\n</div>\n<div id=\""
-    + alias3(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"id","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper)))
     + "\" class=\"toolSectionBody\" style=\"display: none; \">\n    <div class=\"toolSectionBg\"></div>\n<div>";
 },"useData":true});
 })();
\ No newline at end of file

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/templates/compiled/tool_form.js
--- a/client/galaxy/scripts/templates/compiled/tool_form.js
+++ b/client/galaxy/scripts/templates/compiled/tool_form.js
@@ -1,28 +1,26 @@
 (function() {
   var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
 templates['tool_form'] = template({"1":function(depth0,helpers,partials,data) {
-    var stack1, helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
-
-  return "        <div class=\"form-row\">\n            <label for=\""
-    + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+  var stack1, helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression, buffer = "        <div class=\"form-row\">\n            <label for=\""
+    + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
     + "\">"
-    + alias3(((helper = (helper = helpers.label || (depth0 != null ? depth0.label : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"label","hash":{},"data":data}) : helper)))
-    + ":</label>\n            <div class=\"form-row-input\">\n                "
-    + ((stack1 = ((helper = (helper = helpers.html || (depth0 != null ? depth0.html : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"html","hash":{},"data":data}) : helper))) != null ? stack1 : "")
-    + "\n            </div>\n            <div class=\"toolParamHelp\" style=\"clear: both;\">\n                "
-    + alias3(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"help","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.label || (depth0 != null ? depth0.label : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"label","hash":{},"data":data}) : helper)))
+    + ":</label>\n            <div class=\"form-row-input\">\n                ";
+  stack1 = ((helper = (helper = helpers.html || (depth0 != null ? depth0.html : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"html","hash":{},"data":data}) : helper));
+  if (stack1 != null) { buffer += stack1; }
+  return buffer + "\n            </div>\n            <div class=\"toolParamHelp\" style=\"clear: both;\">\n                "
+    + escapeExpression(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"help","hash":{},"data":data}) : helper)))
     + "\n            </div>\n            <div style=\"clear: both;\"></div>\n        </div>\n";
 },"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
-    var stack1, helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
-
-  return "<div class=\"toolFormTitle\">"
-    + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+  var stack1, helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression, buffer = "<div class=\"toolFormTitle\">"
+    + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
     + " (version "
-    + alias3(((helper = (helper = helpers.version || (depth0 != null ? depth0.version : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"version","hash":{},"data":data}) : helper)))
-    + ")</div>\n    <div class=\"toolFormBody\">\n"
-    + ((stack1 = helpers.each.call(depth0,(depth0 != null ? depth0.inputs : depth0),{"name":"each","hash":{},"fn":this.program(1, data, 0),"inverse":this.noop,"data":data})) != null ? stack1 : "")
-    + "    </div>\n    <div class=\"form-row form-actions\">\n    <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n    <div class=\"toolHelpBody\">"
-    + alias3(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"help","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.version || (depth0 != null ? depth0.version : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"version","hash":{},"data":data}) : helper)))
+    + ")</div>\n    <div class=\"toolFormBody\">\n";
+  stack1 = helpers.each.call(depth0, (depth0 != null ? depth0.inputs : depth0), {"name":"each","hash":{},"fn":this.program(1, data),"inverse":this.noop,"data":data});
+  if (stack1 != null) { buffer += stack1; }
+  return buffer + "    </div>\n    <div class=\"form-row form-actions\">\n    <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n    <div class=\"toolHelpBody\">"
+    + escapeExpression(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"help","hash":{},"data":data}) : helper)))
     + "</div>\n</div>";
 },"useData":true});
 })();
\ No newline at end of file

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/templates/compiled/tool_link.js
--- a/client/galaxy/scripts/templates/compiled/tool_link.js
+++ b/client/galaxy/scripts/templates/compiled/tool_link.js
@@ -1,19 +1,18 @@
 (function() {
   var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
 templates['tool_link'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
-    var helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
-
+  var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression;
   return "<a class=\""
-    + alias3(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"id","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper)))
     + " tool-link\" href=\""
-    + alias3(((helper = (helper = helpers.link || (depth0 != null ? depth0.link : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"link","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.link || (depth0 != null ? depth0.link : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"link","hash":{},"data":data}) : helper)))
     + "\" target=\""
-    + alias3(((helper = (helper = helpers.target || (depth0 != null ? depth0.target : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"target","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.target || (depth0 != null ? depth0.target : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"target","hash":{},"data":data}) : helper)))
     + "\" minsizehint=\""
-    + alias3(((helper = (helper = helpers.min_width || (depth0 != null ? depth0.min_width : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"min_width","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.min_width || (depth0 != null ? depth0.min_width : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"min_width","hash":{},"data":data}) : helper)))
     + "\">"
-    + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+    + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
     + "</a> "
-    + alias3(((helper = (helper = helpers.description || (depth0 != null ? depth0.description : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"description","hash":{},"data":data}) : helper)));
+    + escapeExpression(((helper = (helper = helpers.description || (depth0 != null ? depth0.description : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"description","hash":{},"data":data}) : helper)));
 },"useData":true});
 })();
\ No newline at end of file

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/templates/compiled/tool_search.js
--- a/client/galaxy/scripts/templates/compiled/tool_search.js
+++ b/client/galaxy/scripts/templates/compiled/tool_search.js
@@ -1,12 +1,11 @@
 (function() {
   var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
 templates['tool_search'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
-    var helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
-
-  return "<input type=\"text\" name=\"query\" placeholder=\""
-    + alias3(((helper = (helper = helpers.search_hint_string || (depth0 != null ? depth0.search_hint_string : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"search_hint_string","hash":{},"data":data}) : helper)))
+  var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression;
+  return "<input type=\"text\" name=\"query\" value=\""
+    + escapeExpression(((helper = (helper = helpers.search_hint_string || (depth0 != null ? depth0.search_hint_string : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"search_hint_string","hash":{},"data":data}) : helper)))
     + "\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<a id=\"search-clear-btn\" title=\"clear search (esc)\"></a>\n<img src=\""
-    + alias3(((helper = (helper = helpers.spinner_url || (depth0 != null ? depth0.spinner_url : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"spinner_url","hash":{},"data":data}) : helper)))
-    + "\" id=\"search-spinner\" class=\"search-spinner\"/>\n";
+    + escapeExpression(((helper = (helper = helpers.spinner_url || (depth0 != null ? depth0.spinner_url : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"spinner_url","hash":{},"data":data}) : helper)))
+    + "\" id=\"search-spinner\" class=\"search-spinner\"/>";
 },"useData":true});
 })();
\ No newline at end of file

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a client/galaxy/scripts/templates/tool_search.handlebars
--- a/client/galaxy/scripts/templates/tool_search.handlebars
+++ b/client/galaxy/scripts/templates/tool_search.handlebars
@@ -1,3 +1,3 @@
-<input type="text" name="query" placeholder="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" />
+<input type="text" name="query" value="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /><a id="search-clear-btn" title="clear search (esc)"></a>
-<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/>
+<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/>
\ No newline at end of file

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a config/auth_conf.xml.sample
--- a/config/auth_conf.xml.sample
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<auth>
-    <authenticator>
-        <type>localdb</type>
-        <options>
-            <allow-password-change>true</allow-password-change>
-        </options>
-    </authenticator>
-</auth>

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a config/demo_sequencer_wsgi.ini.sample
--- /dev/null
+++ b/config/demo_sequencer_wsgi.ini.sample
@@ -0,0 +1,66 @@
+# ---- HTTP Server ----------------------------------------------------------
+
+[server:main]
+
+use = egg:Paste#http
+port = 9011
+host = 0.0.0.0
+use_threadpool = true
+threadpool_workers = 10
+
+# ---- Galaxy Demo Sequencer Emulator Interface -------------------------------------------------
+
+[app:main]
+
+# Specifies the factory for the universe WSGI application
+paste.app_factory = galaxy.webapps.demo_sequencer.buildapp:app_factory
+log_level = DEBUG
+
+# Where dataset files are saved
+file_path = database/demo_sequencer_files
+# Temporary storage for additional datasets, this should be shared through the cluster
+new_file_path = database/tmp
+
+# Sequencer emulator actions
+sequencer_actions_config_file = %(here)s/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml
+
+# Session support (beaker)
+use_beaker_session = True
+session_type = memory
+session_data_dir = %(here)s/database/beaker_sessions
+session_key = galaxysessions
+session_secret = changethisinproduction
+
+# Galaxy session security
+id_secret = changethisinproductiontoo
+
+# Configuration for debugging middleware
+debug = true
+use_lint = false
+
+# NEVER enable this on a public site (even test or QA)
+# use_interactive = true
+
+# this should be a comma-separated list of valid Galaxy users
+#admin_users = test@bx.psu.edu
+
+# Force everyone to log in (disable anonymous access)
+require_login = False
+
+# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!)
+## use_heartbeat = True
+
+# Profiling middleware (cProfile based)
+## use_profile = True
+
+# Use the new iframe / javascript based layout
+use_new_layout = true
+
+# Serving static files (needed if running standalone)
+static_enabled = True
+static_cache_time = 360
+static_dir = %(here)s/static/
+static_images_dir = %(here)s/static/images
+static_favicon_dir = %(here)s/static/favicon.ico
+static_scripts_dir = %(here)s/static/scripts/
+static_style_dir = %(here)s/static/june_2007_style/blue

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -176,7 +176,7 @@
 # install from in the admin interface (.sample used if default does not exist).
 #tool_sheds_config_file = config/tool_sheds_conf.xml
 
-# Set to True to enable monitoring of tools and tool directories
+# Set to True to Enable monitoring of tools and tool directories
 # listed in any tool config file specified in tool_config_file option.
 # If changes are found, tools are automatically reloaded.  Watchdog (
 # https://pypi.python.org/pypi/watchdog ) must be installed and
@@ -184,7 +184,7 @@
 # which will attempt to watch tools if the watchdog library is available
 # but won't fail to load Galaxy if it is not and 'polling' which will use
 # a less efficient monitoring scheme that may work in wider range of scenarios
-# than the watchdog default.
+# then the watchdog default montiory.
 #watch_tools = False
 
 # Enable automatic polling of relative tool sheds to see if any updates
@@ -844,13 +844,8 @@
 #openid_config_file = config/openid_conf.xml
 #openid_consumer_cache_path = database/openid_consumer_cache
 
-# XML config file that allows the use of different authentication providers
-# (e.g. Active Directory) instead or in addition to local authentication
-# (.sample is used if default does not exist).
-#auth_config_file = config/auth_conf.xml
-
 # Optional list of email addresses of API users who can make calls on behalf of
-# other users.
+# other users
 #api_allow_run_as = None
 
 # Master key that allows many API admin actions to be used without actually

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a config/job_conf.xml.sample_advanced
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -427,15 +427,6 @@
             <param id="nativeSpecification">--mem-per-cpu=512</param><resubmit condition="memory_limit_reached" destination="bigmem" /></destination>
-        <!-- Any tag param in this file can be set using an environment variable or using
-             values from galaxy.ini using the from_environ and from_config attributes
-             repectively. The text of the param will still be used if that environment variable
-             or config value isn't set.
-        -->
-        <destination id="params_from_environment" runner="slurm">
-            <param id="nativeSpecification" from_environ="NATIVE_SPECIFICATION">--time=00:05:00 --nodes=1</param>
-            <param id="docker_enabled" from_config="use_docker">false</param>
-        </destination></destinations><resources default="default">

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a config/reports_wsgi.ini.sample
--- a/config/reports_wsgi.ini.sample
+++ b/config/reports_wsgi.ini.sample
@@ -8,37 +8,10 @@
 use_threadpool = true
 threadpool_workers = 10
 
-# ---- Filters --------------------------------------------------------------
-
-# Filters sit between Galaxy and the HTTP server.
-
-# These filters are disabled by default.  They can be enabled with
-# 'filter-with' in the [app:main] section below.
-
-# Define the proxy-prefix filter.
-[filter:proxy-prefix]
-use = egg:PasteDeploy#prefix
-prefix = /reports
-
 # ---- Galaxy Webapps Report Interface -------------------------------------------------
 
 [app:main]
 
-# -- Application and filtering
-
-# If running behind a proxy server and Galaxy is served from a subdirectory,
-# enable the proxy-prefix filter and set the prefix in the
-# [filter:proxy-prefix] section above.
-#filter-with = proxy-prefix
-
-# If proxy-prefix is enabled and you're running more than one Galaxy instance
-# behind one hostname, you will want to set this to the same path as the prefix
-# in the filter above.  This value becomes the "path" attribute set in the
-# cookie so the cookies from each instance will not clobber each other.
-#cookie_path = None
-
-# -- Report 
-
 # Specifies the factory for the universe WSGI application
 paste.app_factory = galaxy.webapps.reports.buildapp:app_factory
 log_level = DEBUG

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a cron/parse_builds.py
--- a/cron/parse_builds.py
+++ b/cron/parse_builds.py
@@ -2,7 +2,7 @@
 
 """
 Connects to the URL specified and outputs builds available at that
-DSN in tabular format.  UCSC Main gateway is used as default.
+DSN in tabular format.  USCS Test gateway is used as default.
 build   description
 """
 
@@ -10,10 +10,7 @@
 import urllib
 import xml.etree.ElementTree as ElementTree
 
-try:
-    URL = sys.argv[1]
-except IndexError:
-    URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
+URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
 
 def getbuilds(url):
     try:
@@ -31,7 +28,7 @@
         print "?\tunspecified (?)"
         sys.exit(1)
 
-    print "#Harvested from " + URL
+    print "#Harvested from http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
     print "?\tunspecified (?)"
     for dsn in tree:
         build = dsn.find("SOURCE").attrib['id']

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst
@@ -0,0 +1,19 @@
+controllers Package
+===================
+
+:mod:`controllers` Package
+--------------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.controllers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`common` Module
+--------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.controllers.common
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst
@@ -0,0 +1,11 @@
+framework Package
+=================
+
+:mod:`framework` Package
+------------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.framework
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a doc/source/lib/galaxy.webapps.demo_sequencer.rst
--- /dev/null
+++ b/doc/source/lib/galaxy.webapps.demo_sequencer.rst
@@ -0,0 +1,51 @@
+demo_sequencer Package
+======================
+
+:mod:`demo_sequencer` Package
+-----------------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`app` Module
+-----------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.app
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`buildapp` Module
+----------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.buildapp
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`config` Module
+--------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`registry` Module
+----------------------
+
+.. automodule:: galaxy.webapps.demo_sequencer.registry
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+    galaxy.webapps.demo_sequencer.controllers
+    galaxy.webapps.demo_sequencer.framework
+

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a doc/source/lib/galaxy.webapps.rst
--- a/doc/source/lib/galaxy.webapps.rst
+++ b/doc/source/lib/galaxy.webapps.rst
@@ -15,6 +15,7 @@
 .. toctree::
 
     galaxy.webapps.community
+    galaxy.webapps.demo_sequencer
     galaxy.webapps.galaxy
     galaxy.webapps.reports
 

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -120,8 +120,6 @@
         else:
             self.openid_providers = OpenIDProviders()
         # Start the heartbeat process if configured and available
-        from galaxy import auth
-        self.auth_manager = auth.AuthManager( self )
         if self.config.use_heartbeat:
             from galaxy.util import heartbeat
             if heartbeat.Heartbeat:
@@ -166,11 +164,8 @@
         if self.heartbeat:
             self.heartbeat.shutdown()
         self.update_repository_manager.shutdown()
-        try:
+        if self.control_worker:
             self.control_worker.shutdown()
-        except AttributeError:
-            # There is no control_worker
-            pass
         try:
             # If the datatypes registry was persisted, attempt to
             # remove the temporary file in which it was written.

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ /dev/null
@@ -1,196 +0,0 @@
-"""
-Contains implementations of the authentication logic.
-"""
-
-from collections import namedtuple
-import xml.etree.ElementTree
-
-from galaxy.security.validate_user_input import validate_publicname
-
-from galaxy.util import (
-    string_as_bool,
-    string_as_bool_or_none,
-)
-
-from galaxy.util import plugin_config
-
-
-import logging
-log = logging.getLogger(__name__)
-
-# <auth>
-#     <authenticator>
-#         <type>activedirectory</type>
-#         <filter>'[username]'.endswith('@students.latrobe.edu.au')</filter>
-#         <options>
-#             <auto-register>True</auto-register>
-#             <server>ldap://STUDENTS.ltu.edu.au</server>
-#             [<search-filter>(&(objectClass=user)(mail={username}))</search-filter>
-#             <search-base>dc=STUDENTS,dc=ltu,dc=edu,dc=au</search-base>
-#             <search-user>jsmith</search-user>
-#             <search-password>mysecret</search-password>
-#             <search-fields>sAMAccountName</search-fields>]
-#             <bind-user>{sAMAccountName}@STUDENTS.ltu.edu.au</bind-user>
-#             <bind-password>{password}</bind-password>
-#             <auto-register-username>{sAMAccountName}</auto-register-username>
-#         </options>
-#     </authenticator>
-#     ...
-# </auth>
-
-
-class AuthManager(object):
-
-    def __init__(self, app):
-        self.__app = app
-        import galaxy.auth.providers
-        self.__plugins_dict = plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )
-        auth_config_file = app.config.auth_config_file
-        self.__init_authenticators(auth_config_file)
-
-    def __init_authenticators(self, auth_config_file):
-        # parse XML
-        ct = xml.etree.ElementTree.parse(auth_config_file)
-        conf_root = ct.getroot()
-
-        authenticators = []
-        # process authenticators
-        for auth_elem in conf_root.getchildren():
-            type_elem = auth_elem.find('type')
-            plugin = self.__plugins_dict.get(type_elem.text)()
-
-            # check filterelem
-            filter_elem = auth_elem.find('filter')
-            if filter_elem is not None:
-                filter_template = str(filter_elem.text)
-            else:
-                filter_template = None
-
-            # extract options
-            options_elem = auth_elem.find('options')
-            options = {}
-            if options_elem is not None:
-                for opt in options_elem:
-                    options[opt.tag] = opt.text
-            authenticator = Authenticator(
-                plugin=plugin,
-                filter_template=filter_template,
-                options=options,
-            )
-            authenticators.append(authenticator)
-        self.authenticators = authenticators
-
-    def check_registration_allowed(self, email, password):
-        """Checks if the provided email is allowed to register."""
-        message = ''
-        status = 'done'
-        for provider, options in self.active_authenticators(email, password):
-            allow_reg = _get_tri_state(options, 'allow-register', True)
-            if allow_reg is None:  # i.e. challenge
-                auth_result, msg = provider.authenticate(email, password, options)
-                if auth_result is True:
-                    break
-                if auth_result is None:
-                    message = 'Invalid email address or password'
-                    status = 'error'
-                    break
-            elif allow_reg is True:
-                break
-            elif allow_reg is False:
-                message = 'Account registration not required for your account.  Please simply login.'
-                status = 'error'
-                break
-        return message, status
-
-    def check_auto_registration(self, trans, email, password):
-        """
-        Checks the email/password using auth providers in order. If a match is
-        found, returns the 'auto-register' option for that provider.
-        """
-        for provider, options in self.active_authenticators(email, password):
-            if provider is None:
-                log.debug( "Unable to find module: %s" % options )
-            else:
-                auth_result, auto_username = provider.authenticate(email, password, options)
-                auto_username = str(auto_username).lower()
-                if auth_result is True:
-                    # make username unique
-                    if validate_publicname( trans, auto_username ) != '':
-                        i = 1
-                        while i <= 10:  # stop after 10 tries
-                            if validate_publicname( trans, "%s-%i" % (auto_username, i) ) == '':
-                                auto_username = "%s-%i" % (auto_username, i)
-                                break
-                            i += 1
-                        else:
-                            break  # end for loop if we can't make a unique username
-                    log.debug( "Email: %s, auto-register with username: %s" % (email, auto_username) )
-                    return (_get_bool(options, 'auto-register', False), auto_username)
-                elif auth_result is None:
-                    log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
-                    break  # end authentication (skip rest)
-        return (False, '')
-
-    def check_password(self, user, password):
-        """Checks the email/password using auth providers."""
-        for provider, options in self.active_authenticators(user.email, password):
-            if provider is None:
-                log.debug( "Unable to find module: %s" % options )
-            else:
-                auth_result = provider.authenticate_user(user, password, options)
-                if auth_result is True:
-                    return True  # accept user
-                elif auth_result is None:
-                    break  # end authentication (skip rest)
-        return False
-
-    def check_change_password(self, user, current_password):
-        """Checks that auth provider allows password changes and current_password
-        matches.
-        """
-        for provider, options in self.active_authenticators(user.email, current_password):
-            if provider is None:
-                log.debug( "Unable to find module: %s" % options )
-            else:
-                if _get_bool(options, "allow-password-change", False):
-                    auth_result = provider.authenticate_user(user, current_password, options)
-                    if auth_result is True:
-                        return (True, '')  # accept user
-                    elif auth_result is None:
-                        break  # end authentication (skip rest)
-                else:
-                    return (False, 'Password change not supported')
-        return (False, 'Invalid current password')
-
-    def active_authenticators(self, username, password):
-        """Yields AuthProvider instances for the provided configfile that match the
-        filters.
-        """
-        try:
-            for authenticator in self.authenticators:
-                filter_template = authenticator.filter_template
-                if filter_template:
-                    filter_str = filter_template.format(username=username, password=password)
-                    passed_filter = eval(filter_str, {"__builtins__": None}, {'str': str})
-                    if not passed_filter:
-                        continue  # skip to next
-                yield authenticator.plugin, authenticator.options
-        except Exception:
-            log.exception( "Active Authenticators Failure" )
-            raise
-
-Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
-
-
-def _get_bool(d, k, o):
-    if k in d:
-        return string_as_bool(d[k])
-    else:
-        return o
-
-
-def _get_tri_state(d, k, o):
-    if k in d:
-        return string_as_bool_or_none(d[k])
-    else:
-        return o

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/auth/providers/__init__.py
--- a/lib/galaxy/auth/providers/__init__.py
+++ /dev/null
@@ -1,56 +0,0 @@
-"""
-Created on 15/07/2014
-
-@author: Andrew Robinson
-"""
-
-import abc
-
-
-class AuthProvider(object):
-    """A base class for all Auth Providers."""
-    __metaclass__ = abc.ABCMeta
-
-    @abc.abstractproperty
-    def plugin_type(self):
-        """ Short string providing labelling this plugin """
-
-    @abc.abstractmethod
-    def authenticate(self, username, password, options):
-        """
-        Check that the username and password are correct.
-
-        NOTE: Used within auto-registration to check it is ok to register this
-        user.
-
-        :param  username: the users email address
-        :type   username: str
-        :param  password: the plain text password they typed
-        :type   password: str
-        :param  options: options provided in auth_config_file
-        :type   options: dict
-        :returns:   True: accept user, False: reject user and None: reject user
-            and don't try any other providers.  str is the username to register
-            with if accepting
-        :rtype:     (bool, str)
-        """
-
-    @abc.abstractmethod
-    def authenticate_user(self, user, password, options):
-        """
-        Same as authenticate() method, except an User object is provided instead
-        of a username.
-
-        NOTE: used on normal login to check authentication and update user
-        details if required.
-
-        :param  username: the users email address
-        :type   username: str
-        :param  password: the plain text password they typed
-        :type   password: str
-        :param  options: options provided in auth_config_file
-        :type   options: dict
-        :returns:   True: accept user, False: reject user and None: reject user
-            and don't try any other providers
-        :rtype:     bool
-        """

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ /dev/null
@@ -1,97 +0,0 @@
-"""
-Created on 15/07/2014
-
-@author: Andrew Robinson
-"""
-
-from ..providers import AuthProvider
-
-import logging
-log = logging.getLogger(__name__)
-
-
-def _get_subs(d, k, vars, default=''):
-    if k in d:
-        return str(d[k]).format(**vars)
-    return str(default).format(**vars)
-
-
-class ActiveDirectory(AuthProvider):
-    """
-    Attempts to authenticate users against an Active Directory server.
-
-    If options include search-fields then it will attempt to search the AD for
-    those fields first.  After that it will bind to the AD with the username
-    (formatted as specified).
-    """
-    plugin_type = 'activedirectory'
-
-    def authenticate(self, username, password, options):
-        """
-        See abstract method documentation.
-        """
-        log.debug("Username: %s" % username)
-        log.debug("Options: %s" % options)
-
-        failure_mode = False  # reject but continue
-        if options.get('continue-on-failure', 'False') == 'False':
-            failure_mode = None  # reject and do not continue
-
-        try:
-            import ldap
-        except:
-            log.debug("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
-            return (failure_mode, '')
-
-        # do AD search (if required)
-        vars = {'username': username, 'password': password}
-        if 'search-fields' in options:
-            try:
-                # setup connection
-                ldap.set_option(ldap.OPT_REFERRALS, 0)
-                l = ldap.initialize(_get_subs(options, 'server', vars))
-                l.protocol_version = 3
-                l.simple_bind_s(_get_subs(options, 'search-user', vars), _get_subs(options, 'search-password', vars))
-                scope = ldap.SCOPE_SUBTREE
-
-                # setup search
-                attributes = map(lambda s: s.strip().format(**vars), options['search-fields'].split(','))
-                result = l.search(_get_subs(options, 'search-base', vars), scope, _get_subs(options, 'search-filter', vars), attributes)
-
-                # parse results
-                _, suser = l.result(result, 60)
-                _, attrs = suser[0]
-                log.debug(("AD Search attributes: %s" % attrs))
-                if hasattr(attrs, 'has_key'):
-                    for attr in attributes:
-                        if attr in attrs:
-                            vars[attr] = str(attrs[attr][0])
-                        else:
-                            vars[attr] = ""
-            except Exception:
-                log.exception('ACTIVEDIRECTORY Search Exception for User: %s' % username)
-                return (failure_mode, '')
-        # end search
-
-        # bind as user to check their credentials
-        try:
-            # setup connection
-            ldap.set_option(ldap.OPT_REFERRALS, 0)
-            l = ldap.initialize(_get_subs(options, 'server', vars))
-            l.protocol_version = 3
-            l.simple_bind_s(_get_subs(options, 'bind-user', vars), _get_subs(options, 'bind-password', vars))
-        except Exception:
-            log.exception('ACTIVEDIRECTORY Authenticate Exception for User %s' % username)
-            return (failure_mode, '')
-
-        log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
-        return (True, _get_subs(options, 'auto-register-username', vars))
-
-    def authenticate_user(self, user, password, options):
-        """
-        See abstract method documentation.
-        """
-        return self.authenticate(user.email, password, options)[0]
-
-
-__all__ = ['ActiveDirectory']

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/auth/providers/alwaysreject.py
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ /dev/null
@@ -1,33 +0,0 @@
-"""
-Created on 16/07/2014
-
-@author: Andrew Robinson
-"""
-
-from ..providers import AuthProvider
-
-import logging
-log = logging.getLogger(__name__)
-
-
-class AlwaysReject(AuthProvider):
-    """A simple authenticator that just accepts users (does not care about their
-    password).
-    """
-    plugin_type = 'alwaysreject'
-
-    def authenticate(self, username, password, options):
-        """
-        See abstract method documentation.
-        """
-        return (None, '')
-
-    def authenticate_user(self, user, password, options):
-        """
-        See abstract method documentation.
-        """
-        log.debug("User: %s, ALWAYSREJECT: None" % (user.email))
-        return None
-
-
-__all__ = ['AlwaysReject']

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/auth/providers/localdb.py
--- a/lib/galaxy/auth/providers/localdb.py
+++ /dev/null
@@ -1,31 +0,0 @@
-"""
-Created on 16/07/2014
-
-@author: Andrew Robinson
-"""
-
-from ..providers import AuthProvider
-import logging
-log = logging.getLogger(__name__)
-
-
-class LocalDB(AuthProvider):
-    """Authenticate users against the local Galaxy database (as per usual)."""
-    plugin_type = 'localdb'
-
-    def authenticate(self, username, password, options):
-        """
-        See abstract method documentation.
-        """
-        return (False, '')  # it can never auto-create based of localdb (chicken-egg)
-
-    def authenticate_user(self, user, password, options):
-        """
-        See abstract method documentation.
-        """
-        user_ok = user.check_password(password)
-        log.debug("User: %s, LOCALDB: %s" % (user.email, user_ok))
-        return user_ok
-
-
-__all__ = ['LocalDB']

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -462,7 +462,6 @@
         Backwards compatibility for config files moved to the config/ dir.
         """
         defaults = dict(
-            auth_config_file=[ 'config/auth_conf.xml', 'config/auth_conf.xml.sample' ],
             data_manager_config_file=[ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ],
             datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ],
             external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ],

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
--- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
+++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
@@ -52,7 +52,7 @@
                return missval
    if not missval:
        missval = 'N' # punt
-   f.close()
+   close(f)
    return missval
 
 def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
--- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
+++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
@@ -4,10 +4,7 @@
 # eg lped/eigen/fbat/snpmatrix all to pbed
 # and pbed to lped/eigen/fbat/snpmatrix ?
 # that's a lot of converters
-import os
-import subprocess
-import sys
-import time
+import sys,os,time,subprocess
 
 
 prog = os.path.split(sys.argv[0])[-1]
@@ -26,21 +23,23 @@
 <div class="document">
 """
 
-
 def timenow():
     """return current time as a string
     """
     return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
 
 
-def rgConv(inpedfilepath, outhtmlname, outfilepath, plink):
+def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):
     """
     """
-    basename = os.path.split(inpedfilepath)[-1]  # get basename
-    outroot = os.path.join(outfilepath, basename)
-    cl = '%s --noweb --bfile %s --recode --out %s ' % (plink, inpedfilepath, outroot)
-    p = subprocess.Popen(cl, shell=True, cwd=outfilepath)
-    p.wait()  # run plink
+
+    basename = os.path.split(inpedfilepath)[-1] # get basename
+    outroot = os.path.join(outfilepath,basename)
+    cl = '%s --noweb --bfile %s --recode --out %s ' % (plink,inpedfilepath,outroot)
+    p = subprocess.Popen(cl,shell=True,cwd=outfilepath)
+    retval = p.wait() # run plink
+
+
 
 
 def main():
@@ -53,7 +52,7 @@
     """
     nparm = 4
     if len(sys.argv) < nparm:
-        sys.stderr.write('PBED to LPED converter called with %s - needs %d parameters \n' % (sys.argv, nparm))
+        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (myname,sys.argv,nparm))
         sys.exit(1)
     inpedfilepath = sys.argv[1]
     outhtmlname = sys.argv[2]
@@ -63,18 +62,19 @@
     except:
         pass
     plink = sys.argv[4]
-    rgConv(inpedfilepath, outhtmlname, outfilepath, plink)
-    f = file(outhtmlname, 'w')
+    rgConv(inpedfilepath,outhtmlname,outfilepath,plink)
+    f = file(outhtmlname,'w')
     f.write(galhtmlprefix % prog)
     flist = os.listdir(outfilepath)
-    s = '## Rgenetics: http://bitbucket.org/rgalaxy Galaxy Tools %s %s' % (prog, timenow())  # becomes info
+    s = '## Rgenetics: http://bitbucket.org/rgalaxy Galaxy Tools %s %s' % (prog,timenow()) # becomes info
     print s
     f.write('<div>%s\n<ol>' % (s))
     for i, data in enumerate( flist ):
-        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1], os.path.split(data)[-1]))
+        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
     f.write("</div></body></html>")
     f.close()
 
 
+
 if __name__ == "__main__":
-    main()
+   main()

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/datatypes/dataproviders/dataset.py
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -465,8 +465,8 @@
     def __iter__( self ):
         for id_ in self.ids:
             yield {
-                'id': id_,
-                'seq': self.source[ id_ ]
+                'id'  : id_,
+                'seq' : self.source[ name ]
             }
 
 
@@ -690,7 +690,7 @@
     def __init__( self, dataset, **kwargs ):
         #TODO: as samtools
         raise NotImplementedError()
-        super( BcftoolsDataProvider, self ).__init__( dataset, **kwargs )
+        super( BCFDataProvider, self ).__init__( dataset, **kwargs )
 
 
 class BGzipTabixDataProvider( base.DataProvider ):

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/datatypes/display_applications/application.py
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -244,12 +244,12 @@
             link = DisplayApplicationLink.from_elem( link_elem, self )
             if link:
                 self.links[ link.id ] = link
-        try:
-            for dynamic_links in elem.findall( 'dynamic_links' ):
+        for dynamic_links in elem.findall( 'dynamic_links' ):
+            try:
                 for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
                     self.links[ link.id ] = link
-        except Exception, e:
-            log.error( "Error loading a set of Dynamic Display Application links: %s", e )
+            except Exception, e:
+                log.error( "Error loading a set of Dynamic Display Application links: %s", e )
     def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ):
         #returns a link object with data knowledge to generate links
         self._check_and_reload()

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -30,8 +30,7 @@
 import logging
 log = logging.getLogger(__name__)
 
-STATEMENTS = "__galaxy_statements__"  # this is the name of the property in a Datatype class where new metadata spec element Statements are stored
-
+STATEMENTS = "__galaxy_statements__" #this is the name of the property in a Datatype class where new metadata spec element Statements are stored
 
 class Statement( object ):
     """
@@ -44,17 +43,14 @@
         self.target = target
 
     def __call__( self, *args, **kwargs ):
-        # get the locals dictionary of the frame object one down in the call stack (i.e. the Datatype class calling MetadataElement)
-        class_locals = sys._getframe( 1 ).f_locals
-        # get and set '__galaxy_statments__' to an empty list if not in locals dict
-        statements = class_locals.setdefault( STATEMENTS, [] )
-        # add Statement containing info to populate a MetadataElementSpec
-        statements.append( ( self, args, kwargs ) )
+        class_locals = sys._getframe( 1 ).f_locals #get the locals dictionary of the frame object one down in the call stack (i.e. the Datatype class calling MetadataElement)
+        statements = class_locals.setdefault( STATEMENTS, [] ) #get and set '__galaxy_statments__' to an empty list if not in locals dict
+        statements.append( ( self, args, kwargs ) ) #add Statement containing info to populate a MetadataElementSpec
 
     @classmethod
     def process( cls, element ):
         for statement, args, kwargs in getattr( element, STATEMENTS, [] ):
-            statement.target( element, *args, **kwargs )  # statement.target is MetadataElementSpec, element is a Datatype class
+            statement.target( element, *args, **kwargs ) #statement.target is MetadataElementSpec, element is a Datatype class
 
 
 class MetadataCollection( object ):
@@ -66,7 +62,7 @@
     """
     def __init__(self, parent ):
         self.parent = parent
-        # initialize dict if needed
+        #initialize dict if needed
         if self.parent._metadata is None:
             self.parent._metadata = {}
 
@@ -76,10 +72,7 @@
         return None
 
     def set_parent( self, parent ):
-        # use weakref to prevent a circular reference interfering with garbage
-        # collection: hda/lda (parent) <--> MetadataCollection (self) ; needs to be
-        # hashable, so cannot use proxy.
-        self.__dict__["_parent"] = weakref.ref( parent )
+        self.__dict__["_parent"] = weakref.ref( parent ) # use weakref to prevent a circular reference interfering with garbage collection: hda/lda (parent) <--> MetadataCollection (self) ; needs to be hashable, so cannot use proxy.
     parent = property( get_parent, set_parent )
 
     @property
@@ -151,7 +144,7 @@
             elif isinstance( json_dict, dict ):
                 JSONified_dict = json_dict
             else:
-                raise ValueError( "json_dict must be either a dictionary or a string, got %s." % ( type( json_dict ) ) )
+                raise ValueError( "json_dict must be either a dictionary or a string, got %s."  % ( type( json_dict ) ) )
         else:
             raise ValueError( "You must provide either a filename or a json_dict" )
         for name, spec in self.spec.items():
@@ -163,12 +156,12 @@
                     from_ext_kwds[ 'path_rewriter' ] = path_rewriter
                 dataset._metadata[ name ] = param.from_external_value( external_value, dataset, **from_ext_kwds )
             elif name in dataset._metadata:
-                # if the metadata value is not found in our externally set metadata but it has a value in the 'old'
-                # metadata associated with our dataset, we'll delete it from our dataset's metadata dict
+                #if the metadata value is not found in our externally set metadata but it has a value in the 'old'
+                #metadata associated with our dataset, we'll delete it from our dataset's metadata dict
                 del dataset._metadata[ name ]
 
     def to_JSON_dict( self, filename=None ):
-        # galaxy.model.customtypes.json_encoder.encode()
+        #galaxy.model.customtypes.json_encoder.encode()
         meta_dict = {}
         dataset_meta_dict = self.parent._metadata
         for name, spec in self.spec.items():
@@ -179,9 +172,7 @@
         json.dump( meta_dict, open( filename, 'wb+' ) )
 
     def __getstate__( self ):
-        # cannot pickle a weakref item (self._parent), when
-        # data._metadata_collection is None, it will be recreated on demand
-        return None
+        return None #cannot pickle a weakref item (self._parent), when data._metadata_collection is None, it will be recreated on demand
 
 
 class MetadataSpecCollection( odict ):
@@ -191,8 +182,8 @@
     list.  append() is also implemented for simplicity and does not
     "append".
     """
-    def __init__( self, dict=None ):
-        odict.__init__( self, dict=None )
+    def __init__( self, dict = None ):
+        odict.__init__( self, dict = None )
 
     def append( self, item ):
         self[item.name] = item
@@ -233,8 +224,7 @@
             return value
         if self.spec.get("optional"):
             checked = False
-            if value:
-                checked = "true"
+            if value: checked = "true"
             checkbox = form_builder.CheckboxField( "is_" + self.spec.name, checked=checked )
             return checkbox.get_html() + self.get_html_field( value=value, context=context, other_values=other_values, **kwd ).get_html()
         else:
@@ -246,11 +236,11 @@
     def to_safe_string( self, value ):
         return sanitize_lists_to_string( self.to_string( value ) )
 
-    def make_copy( self, value, target_context=None, source_context=None ):
+    def make_copy( self, value, target_context = None, source_context = None ):
         return copy.deepcopy( value )
 
     @classmethod
-    def marshal( cls, value ):
+    def marshal ( cls, value ):
         """
         This method should/can be overridden to convert the incoming
         value to whatever type it is supposed to be.
@@ -295,9 +285,9 @@
     Defines a metadata element and adds it to the metadata_spec (which
     is a MetadataSpecCollection) of datatype.
     """
-    def __init__( self, datatype, name=None, desc=None,
-                  param=MetadataParameter, default=None, no_value=None,
-                  visible=True, set_in_upload=False, **kwargs ):
+    def __init__( self, datatype,
+                  name=None, desc=None, param=MetadataParameter, default=None, no_value = None,
+                  visible=True, set_in_upload = False, **kwargs ):
         self.name = name
         self.desc = desc or name
         self.default = default
@@ -327,7 +317,7 @@
         return self.param.unwrap( value )
 
     def __str__( self ):
-        # TODO??: assuming param is the class of this MetadataElementSpec - add the plain class name for that
+        #TODO??: assuming param is the class of this MetadataElementSpec - add the plain class name for that
         spec_dict = dict( param_class=self.param.__class__.__name__ )
         spec_dict.update( self.__dict__ )
         return ( "{name} ({param_class}): {desc}, defaults to '{default}'".format( **spec_dict ) )
@@ -341,7 +331,6 @@
 MetadataParameter sub-classes.
 """
 
-
 class SelectParameter( MetadataParameter ):
     def __init__( self, spec ):
         MetadataParameter.__init__( self, spec )
@@ -389,24 +378,18 @@
         return MetadataParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd )
 
     def wrap( self, value, session ):
-        # do we really need this (wasteful)? - yes because we are not sure that
-        # all existing selects have been stored previously as lists. Also this
-        # will handle the case where defaults/no_values are specified and are
-        # single non-list values.
-        value = self.marshal( value )
+        value = self.marshal( value ) #do we really need this (wasteful)? - yes because we are not sure that all existing selects have been stored previously as lists. Also this will handle the case where defaults/no_values are specified and are single non-list values.
         if self.multiple:
             return value
         elif value:
-            return value[0]  # single select, only return the first value
+            return value[0] #single select, only return the first value
         return None
 
     @classmethod
     def marshal( cls, value ):
         # Store select as list, even if single item
-        if value is None:
-            return []
-        if not isinstance( value, list ):
-            return [value]
+        if value is None: return []
+        if not isinstance( value, list ): return [value]
         return value
 
 
@@ -499,7 +482,7 @@
 class DictParameter( MetadataParameter ):
 
     def to_string( self, value ):
-        return json.dumps( value )
+        return  json.dumps( value )
 
     def to_safe_string( self, value ):
         # We do not sanitize json dicts
@@ -560,7 +543,7 @@
     def make_copy( self, value, target_context, source_context ):
         value = self.wrap( value, object_session( target_context.parent ) )
         if value:
-            new_value = galaxy.model.MetadataFile( dataset=target_context.parent, name=self.spec.name )
+            new_value = galaxy.model.MetadataFile( dataset = target_context.parent, name = self.spec.name )
             object_session( target_context.parent ).add( new_value )
             object_session( target_context.parent ).flush()
             shutil.copy( value.file_name, new_value.file_name )
@@ -582,18 +565,14 @@
         if isinstance( value, MetadataTempFile ):
             mf = parent.metadata.get( self.spec.name, None)
             if mf is None:
-                mf = self.new_file( dataset=parent, **value.kwds )
+                mf = self.new_file( dataset = parent, **value.kwds )
             # Ensure the metadata file gets updated with content
             file_name = value.file_name
             if path_rewriter:
                 # Job may have run with a different (non-local) tmp/working
                 # directory. Correct.
                 file_name = path_rewriter( file_name )
-            parent.dataset.object_store.update_from_file( mf,
-                                                          file_name=file_name,
-                                                          extra_dir='_metadata_files',
-                                                          extra_dir_at_root=True,
-                                                          alt_name=os.path.basename(mf.file_name) )
+            parent.dataset.object_store.update_from_file( mf, file_name=file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) )
             os.unlink( file_name )
             value = mf.id
         return value
@@ -608,22 +587,22 @@
             value = MetadataTempFile.to_JSON( value )
         return value
 
-    def new_file( self, dataset=None, **kwds ):
+    def new_file( self, dataset = None, **kwds ):
         if object_session( dataset ):
-            mf = galaxy.model.MetadataFile( name=self.spec.name, dataset=dataset, **kwds )
+            mf = galaxy.model.MetadataFile( name = self.spec.name, dataset = dataset, **kwds )
             object_session( dataset ).add( mf )
-            object_session( dataset ).flush()  # flush to assign id
+            object_session( dataset ).flush() #flush to assign id
             return mf
         else:
-            # we need to make a tmp file that is accessable to the head node,
-            # we will be copying its contents into the MetadataFile objects filename after restoring from JSON
-            # we do not include 'dataset' in the kwds passed, as from_JSON_value() will handle this for us
+            #we need to make a tmp file that is accessable to the head node,
+            #we will be copying its contents into the MetadataFile objects filename after restoring from JSON
+            #we do not include 'dataset' in the kwds passed, as from_JSON_value() will handle this for us
             return MetadataTempFile( **kwds )
 
 
-# This class is used when a database file connection is not available
+#This class is used when a database file connection is not available
 class MetadataTempFile( object ):
-    tmp_dir = 'database/tmp'  # this should be overwritten as necessary in calling scripts
+    tmp_dir = 'database/tmp' #this should be overwritten as necessary in calling scripts
 
     def __init__( self, **kwds ):
         self.kwds = kwds
@@ -632,19 +611,17 @@
     @property
     def file_name( self ):
         if self._filename is None:
-            # we need to create a tmp file, accessable across all nodes/heads, save the name, and return it
-            self._filename = abspath( tempfile.NamedTemporaryFile( dir=self.tmp_dir, prefix="metadata_temp_file_" ).name )
-            open( self._filename, 'wb+' )  # create an empty file, so it can't be reused using tempfile
+            #we need to create a tmp file, accessable across all nodes/heads, save the name, and return it
+            self._filename = abspath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name )
+            open( self._filename, 'wb+' ) #create an empty file, so it can't be reused using tempfile
         return self._filename
 
     def to_JSON( self ):
-        return { '__class__': self.__class__.__name__,
-                 'filename': self.file_name,
-                 'kwds': self.kwds }
+        return { '__class__':self.__class__.__name__, 'filename':self.file_name, 'kwds':self.kwds }
 
     @classmethod
     def from_JSON( cls, json_dict ):
-        # need to ensure our keywords are not unicode
+        #need to ensure our keywords are not unicode
         rval = cls( **stringify_dictionary_keys( json_dict['kwds'] ) )
         rval._filename = json_dict['filename']
         return rval
@@ -666,16 +643,10 @@
             log.debug( 'Failed to cleanup MetadataTempFile temp files from %s: %s' % ( filename, e ) )
 
 
+#Class with methods allowing set_meta() to be called externally to the Galaxy head
 class JobExternalOutputMetadataWrapper( object ):
-    """
-    Class with methods allowing set_meta() to be called externally to the
-    Galaxy head.
-    This class allows access to external metadata filenames for all outputs
-    associated with a job.
-    We will use JSON as the medium of exchange of information, except for the
-    DatasetInstance object which will use pickle (in the future this could be
-    JSONified as well)
-    """
+    #this class allows access to external metadata filenames for all outputs associated with a job
+    #We will use JSON as the medium of exchange of information, except for the DatasetInstance object which will use pickle (in the future this could be JSONified as well)
 
     def __init__( self, job ):
         self.job_id = job.id
@@ -683,12 +654,12 @@
     def get_output_filenames_by_dataset( self, dataset, sa_session ):
         if isinstance( dataset, galaxy.model.HistoryDatasetAssociation ):
             return sa_session.query( galaxy.model.JobExternalOutputMetadata ) \
-                             .filter_by( job_id=self.job_id, history_dataset_association_id=dataset.id ) \
-                             .first()  # there should only be one or None
+                             .filter_by( job_id = self.job_id, history_dataset_association_id = dataset.id ) \
+                             .first() #there should only be one or None
         elif isinstance( dataset, galaxy.model.LibraryDatasetDatasetAssociation ):
             return sa_session.query( galaxy.model.JobExternalOutputMetadata ) \
-                             .filter_by( job_id=self.job_id, library_dataset_dataset_association_id=dataset.id ) \
-                             .first()  # there should only be one or None
+                             .filter_by( job_id = self.job_id, library_dataset_dataset_association_id = dataset.id ) \
+                             .first() #there should only be one or None
         return None
 
     def get_dataset_metadata_key( self, dataset ):
@@ -696,12 +667,8 @@
         # need to make different keys for them, since ids can overlap
         return "%s_%d" % ( dataset.__class__.__name__, dataset.id )
 
-    def setup_external_metadata( self, datasets, sa_session, exec_dir=None,
-                                 tmp_dir=None, dataset_files_path=None,
-                                 output_fnames=None, config_root=None,
-                                 config_file=None, datatypes_config=None,
-                                 job_metadata=None, compute_tmp_dir=None,
-                                 include_command=True, kwds=None ):
+    def setup_external_metadata( self, datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None,
+                                 output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, kwds=None ):
         kwds = kwds or {}
         if tmp_dir is None:
             tmp_dir = MetadataTempFile.tmp_dir
@@ -715,13 +682,13 @@
                 compute_path = os.path.join(compute_tmp_dir, path_relative)
             return compute_path
 
-        # fill in metadata_files_dict and return the command with args required to set metadata
+        #fill in metadata_files_dict and return the command with args required to set metadata
         def __metadata_files_list_to_cmd_line( metadata_files ):
             def __get_filename_override():
                 if output_fnames:
                     for dataset_path in output_fnames:
-                        if dataset_path.real_path == metadata_files.dataset.file_name:
-                            return dataset_path.false_path or dataset_path.real_path
+                        if dataset_path.false_path and dataset_path.real_path == metadata_files.dataset.file_name:
+                            return dataset_path.false_path
                 return ""
             line = "%s,%s,%s,%s,%s,%s" % (
                 metadata_path_on_compute(metadata_files.filename_in),
@@ -746,44 +713,43 @@
         metadata_files_list = []
         for dataset in datasets:
             key = self.get_dataset_metadata_key( dataset )
-            # future note:
-            # wonkiness in job execution causes build command line to be called more than once
-            # when setting metadata externally, via 'auto-detect' button in edit attributes, etc.,
-            # we don't want to overwrite (losing the ability to cleanup) our existing dataset keys and files,
-            # so we will only populate the dictionary once
+            #future note:
+            #wonkiness in job execution causes build command line to be called more than once
+            #when setting metadata externally, via 'auto-detect' button in edit attributes, etc.,
+            #we don't want to overwrite (losing the ability to cleanup) our existing dataset keys and files,
+            #so we will only populate the dictionary once
             metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )
             if not metadata_files:
-                metadata_files = galaxy.model.JobExternalOutputMetadata( dataset=dataset)
+                metadata_files = galaxy.model.JobExternalOutputMetadata( dataset = dataset)
                 metadata_files.job_id = self.job_id
-                # we are using tempfile to create unique filenames, tempfile always returns an absolute path
-                # we will use pathnames relative to the galaxy root, to accommodate instances where the galaxy root
-                # is located differently, i.e. on a cluster node with a different filesystem structure
+                #we are using tempfile to create unique filenames, tempfile always returns an absolute path
+                #we will use pathnames relative to the galaxy root, to accommodate instances where the galaxy root
+                #is located differently, i.e. on a cluster node with a different filesystem structure
 
-                # file to store existing dataset
-                metadata_files.filename_in = abspath( tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="metadata_in_%s_" % key ).name )
+                #file to store existing dataset
+                metadata_files.filename_in = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_in_%s_" % key ).name )
 
-                # FIXME: HACK
-                # sqlalchemy introduced 'expire_on_commit' flag for sessionmaker at version 0.5x
-                # This may be causing the dataset attribute of the dataset_association object to no-longer be loaded into memory when needed for pickling.
-                # For now, we'll simply 'touch' dataset_association.dataset to force it back into memory.
-                dataset.dataset  # force dataset_association.dataset to be loaded before pickling
-                # A better fix could be setting 'expire_on_commit=False' on the session, or modifying where commits occur, or ?
+                #FIXME: HACK
+                #sqlalchemy introduced 'expire_on_commit' flag for sessionmaker at version 0.5x
+                #This may be causing the dataset attribute of the dataset_association object to no-longer be loaded into memory when needed for pickling.
+                #For now, we'll simply 'touch' dataset_association.dataset to force it back into memory.
+                dataset.dataset #force dataset_association.dataset to be loaded before pickling
+                #A better fix could be setting 'expire_on_commit=False' on the session, or modifying where commits occur, or ?
 
                 cPickle.dump( dataset, open( metadata_files.filename_in, 'wb+' ) )
-                # file to store metadata results of set_meta()
-                metadata_files.filename_out = abspath( tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="metadata_out_%s_" % key ).name )
-                open( metadata_files.filename_out, 'wb+' )  # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
-                # file to store a 'return code' indicating the results of the set_meta() call
-                # results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure )
-                metadata_files.filename_results_code = abspath( tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="metadata_results_%s_" % key ).name )
-                # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
-                json.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) )
-                # file to store kwds passed to set_meta()
-                metadata_files.filename_kwds = abspath( tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="metadata_kwds_%s_" % key ).name )
+                #file to store metadata results of set_meta()
+                metadata_files.filename_out = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_out_%s_" % key ).name )
+                open( metadata_files.filename_out, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
+                #file to store a 'return code' indicating the results of the set_meta() call
+                #results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure )
+                metadata_files.filename_results_code = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name )
+                json.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
+                #file to store kwds passed to set_meta()
+                metadata_files.filename_kwds = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name )
                 json.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True )
-                # existing metadata file parameters need to be overridden with cluster-writable file locations
-                metadata_files.filename_override_metadata = abspath( tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="metadata_override_%s_" % key ).name )
-                open( metadata_files.filename_override_metadata, 'wb+' )  # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
+                #existing metadata file parameters need to be overridden with cluster-writable file locations
+                metadata_files.filename_override_metadata = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name )
+                open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
                 override_metadata = []
                 for meta_key, spec_value in dataset.metadata.spec.iteritems():
                     if isinstance( spec_value.param, FileParameter ) and dataset.metadata.get( meta_key, None ) is not None:
@@ -791,27 +757,17 @@
                         shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name )
                         override_metadata.append( ( meta_key, metadata_temp.to_JSON() ) )
                 json.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) )
-                # add to session and flush
+                #add to session and flush
                 sa_session.add( metadata_files )
                 sa_session.flush()
             metadata_files_list.append( metadata_files )
-        args = "%s %s %s" % ( datatypes_config,
-                              job_metadata,
-                              " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
-        if include_command:
-            # return command required to build
-            fd, fp = tempfile.mkstemp( suffix='.py', dir=tmp_dir, prefix="set_metadata_" )
-            metadata_script_file = abspath( fp )
-            os.fdopen( fd, 'w' ).write( 'from galaxy.metadata.set_metadata import set_metadata; set_metadata()' )
-            return "python %s %s" % ( metadata_script_file, args )
-        else:
-            # return args to galaxy.metadata.set_metadata required to build
-            return args
+        #return command required to build
+        return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, compute_tmp_dir or tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
 
     def external_metadata_set_successfully( self, dataset, sa_session ):
         metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )
         if not metadata_files:
-            return False  # this file doesn't exist
+            return False # this file doesn't exist
         rval, rstring = json.load( open( metadata_files.filename_results_code ) )
         if not rval:
             log.debug( 'setting metadata externally failed for %s %s: %s' % ( dataset.__class__.__name__, dataset.id, rstring ) )
@@ -820,15 +776,11 @@
     def cleanup_external_metadata( self, sa_session ):
         log.debug( 'Cleaning up external metadata files' )
         for metadata_files in sa_session.query( galaxy.model.Job ).get( self.job_id ).external_output_metadata:
-            # we need to confirm that any MetadataTempFile files were removed, if not we need to remove them
-            # can occur if the job was stopped before completion, but a MetadataTempFile is used in the set_meta
+            #we need to confirm that any MetadataTempFile files were removed, if not we need to remove them
+            #can occur if the job was stopped before completion, but a MetadataTempFile is used in the set_meta
             MetadataTempFile.cleanup_from_JSON_dict_filename( metadata_files.filename_out )
             dataset_key = self.get_dataset_metadata_key( metadata_files.dataset )
-            for key, fname in [ ( 'filename_in', metadata_files.filename_in ),
-                                ( 'filename_out', metadata_files.filename_out ),
-                                ( 'filename_results_code', metadata_files.filename_results_code ),
-                                ( 'filename_kwds', metadata_files.filename_kwds ),
-                                ( 'filename_override_metadata', metadata_files.filename_override_metadata ) ]:
+            for key, fname in [ ( 'filename_in', metadata_files.filename_in ), ( 'filename_out', metadata_files.filename_out ), ( 'filename_results_code', metadata_files.filename_results_code ), ( 'filename_kwds', metadata_files.filename_kwds ), ( 'filename_override_metadata', metadata_files.filename_override_metadata ) ]:
                 try:
                     os.remove( fname )
                 except Exception, e:

diff -r da996e89dbfb8249deeeafd30489a62970f8af7d -r 708cab19708d8158044eb5b1048740734cb2bc2a lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -482,6 +482,14 @@
             data.init_meta( copy_from=data )
         return data
 
+    def old_change_datatype( self, data, ext ):
+        """Creates and returns a new datatype based on an existing data and an extension"""
+        newdata = factory( ext )( id=data.id )
+        for key, value in data.__dict__.items():
+            setattr( newdata, key, value )
+        newdata.ext = ext
+        return newdata
+
     def load_datatype_converters( self, toolbox, installed_repository_dict=None, deactivate=False ):
         """
         If deactivate is False, add datatype converters from self.converters or self.proprietary_converters
@@ -645,15 +653,12 @@
                   <requirement type="package">samtools</requirement></requirements><action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
-              <command>python $set_metadata $__SET_EXTERNAL_METADATA_COMMAND_LINE__</command>
+              <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command><inputs><param format="data" name="input1" type="data" label="File to set metadata on."/><param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/><param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/></inputs>
-              <configfiles>
-                <configfile name="set_metadata">from galaxy.metadata.set_metadata import set_metadata; set_metadata()</configfile>
-              </configfiles></tool>
             """
         tmp_name = tempfile.NamedTemporaryFile()

This diff is so big that we needed to truncate the remainder.

https://bitbucket.org/galaxy/galaxy-central/commits/6395e7035143/
Changeset:   6395e7035143
User:        natefoo
Date:        2015-03-17 02:50:21+00:00
Summary:     Merge v15.03.1 to default
Affected #:  27 files

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -23,3 +23,6 @@
 782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06
 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13
 5cdf5dc395f16f47e88a5567775dcd21b4906f08 latest_2015.01.13
+738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03
+9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1
+9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 latest_15.03

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 client/galaxy/scripts/mvc/history/history-model.js
--- a/client/galaxy/scripts/mvc/history/history-model.js
+++ b/client/galaxy/scripts/mvc/history/history-model.js
@@ -208,7 +208,7 @@
     /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */
     purge : function( options ){
         if( this.get( 'purged' ) ){ return jQuery.when(); }
-        return this.save( { purged: true }, options );
+        return this.save( { deleted: true, purged: true }, options );
     },
     /** save this history, _Mark_ing it as undeleted */
     undelete : function( options ){

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -667,11 +667,20 @@
         # need to make different keys for them, since ids can overlap
         return "%s_%d" % ( dataset.__class__.__name__, dataset.id )
 
-    def setup_external_metadata( self, datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None,
-                                 output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, kwds=None ):
+    def setup_external_metadata( self, datasets, sa_session, exec_dir=None,
+                                 tmp_dir=None, dataset_files_path=None,
+                                 output_fnames=None, config_root=None,
+                                 config_file=None, datatypes_config=None,
+                                 job_metadata=None, compute_tmp_dir=None,
+                                 include_command=True, kwds=None ):
         kwds = kwds or {}
         if tmp_dir is None:
             tmp_dir = MetadataTempFile.tmp_dir
+        else:
+            MetadataTempFile.tmp_dir = tmp_dir
+
+        if not os.path.exists(tmp_dir):
+            os.makedirs(tmp_dir)
 
         # path is calculated for Galaxy, may be different on compute - rewrite
         # for the compute server.
@@ -687,8 +696,8 @@
             def __get_filename_override():
                 if output_fnames:
                     for dataset_path in output_fnames:
-                        if dataset_path.false_path and dataset_path.real_path == metadata_files.dataset.file_name:
-                            return dataset_path.false_path
+                        if dataset_path.real_path == metadata_files.dataset.file_name:
+                            return dataset_path.false_path or dataset_path.real_path
                 return ""
             line = "%s,%s,%s,%s,%s,%s" % (
                 metadata_path_on_compute(metadata_files.filename_in),
@@ -761,8 +770,18 @@
                 sa_session.add( metadata_files )
                 sa_session.flush()
             metadata_files_list.append( metadata_files )
-        #return command required to build
-        return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, compute_tmp_dir or tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
+        args = "%s %s %s" % ( datatypes_config,
+                              job_metadata,
+                              " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
+        if include_command:
+            #return command required to build
+            fd, fp = tempfile.mkstemp( suffix='.py', dir = tmp_dir, prefix = "set_metadata_" )
+            metadata_script_file = abspath( fp )
+            os.fdopen( fd, 'w' ).write( 'from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()' )
+            return "python %s %s" % ( metadata_path_on_compute(metadata_script_file), args )
+        else:
+            # return args to galaxy_ext.metadata.set_metadata required to build
+            return args
 
     def external_metadata_set_successfully( self, dataset, sa_session ):
         metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -653,12 +653,15 @@
                   <requirement type="package">samtools</requirement></requirements><action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
-              <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command>
+              <command>python $set_metadata $__SET_EXTERNAL_METADATA_COMMAND_LINE__</command><inputs><param format="data" name="input1" type="data" label="File to set metadata on."/><param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/><param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/></inputs>
+              <configfiles>
+                <configfile name="set_metadata">from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()</configfile>
+              </configfiles></tool>
             """
         tmp_name = tempfile.NamedTemporaryFile()

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -831,8 +831,7 @@
 
         self.command_line, self.extra_filenames = tool_evaluator.build()
         # FIXME: for now, tools get Galaxy's lib dir in their path
-        if self.command_line and self.command_line.startswith( 'python' ):
-            self.galaxy_lib_dir = os.path.abspath( "lib" )  # cwd = galaxy root
+        self.galaxy_lib_dir = os.path.abspath( "lib" )  # cwd = galaxy root
         # Shell fragment to inject dependencies
         self.dependency_shell_commands = self.tool.build_dependency_shell_commands()
         # We need command_line persisted to the db in order for Galaxy to re-queue the job

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/jobs/actions/post.py
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -156,7 +156,7 @@
             #      "replace" option so you can replace a portion of the name,
             #      support multiple #{name} in one rename action...
 
-            if new_name.find("#{") > -1:
+            while new_name.find("#{") > -1:
                 to_be_replaced = ""
                 #  This assumes a single instance of #{variable} will exist
                 start_pos = new_name.find("#{") + 2

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/jobs/command_factory.py
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -145,7 +145,7 @@
     metadata_command = metadata_command.strip()
     if metadata_command:
         commands_builder.capture_return_code()
-        commands_builder.append_command("cd %s; %s" % (exec_dir, metadata_command))
+        commands_builder.append_command(metadata_command)
 
 
 def __copy_if_exists_command(work_dir_output):

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -680,6 +680,9 @@
         except Empty:
             pass
         for job, error_msg in jobs_to_check:
+            if job.state != job.states.DELETED_NEW and job.finished:
+                log.debug('Job %s already finished, not deleting or stopping', job.id)
+                continue
             final_state = job.states.DELETED
             if error_msg is not None:
                 final_state = job.states.ERROR

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/managers/hdas.py
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -156,11 +156,12 @@
         self.dataset_manager.error_unless_dataset_purge_allowed( trans, hda )
         super( HDAManager, self ).purge( trans, hda, flush=flush )
 
-        # signal to stop the creating job?
         if hda.creating_job_associations:
             job = hda.creating_job_associations[0].job
-            job.mark_deleted( self.app.config.track_jobs_in_database )
-            self.app.job_manager.job_stop_queue.put( job.id )
+            if not job.finished:
+                # signal to stop the creating job
+                job.mark_deleted( self.app.config.track_jobs_in_database )
+                self.app.job_manager.job_stop_queue.put( job.id )
 
         # more importantly, purge dataset as well
         if hda.dataset.user_can_purge:

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/metadata
--- /dev/null
+++ b/lib/galaxy/metadata
@@ -0,0 +1,1 @@
+../galaxy_ext/metadata
\ No newline at end of file

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -517,6 +517,9 @@
         """
         Mark this job as deleted, and mark any output datasets as discarded.
         """
+        if self.finished:
+            # Do not modify the state/outputs of jobs that are already terminal
+            return
         if track_jobs_in_database:
             self.state = Job.states.DELETED_NEW
         else:

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/objectstore/__init__.py
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -392,39 +392,39 @@
         super(NestedObjectStore, self).shutdown()
 
     def exists(self, obj, **kwargs):
-        return self.__call_method('exists', obj, False, False, **kwargs)
+        return self._call_method('exists', obj, False, False, **kwargs)
 
     def file_ready(self, obj, **kwargs):
-        return self.__call_method('file_ready', obj, False, False, **kwargs)
+        return self._call_method('file_ready', obj, False, False, **kwargs)
 
     def create(self, obj, **kwargs):
         random.choice(self.backends.values()).create(obj, **kwargs)
 
     def empty(self, obj, **kwargs):
-        return self.__call_method('empty', obj, True, False, **kwargs)
+        return self._call_method('empty', obj, True, False, **kwargs)
 
     def size(self, obj, **kwargs):
-        return self.__call_method('size', obj, 0, False, **kwargs)
+        return self._call_method('size', obj, 0, False, **kwargs)
 
     def delete(self, obj, **kwargs):
-        return self.__call_method('delete', obj, False, False, **kwargs)
+        return self._call_method('delete', obj, False, False, **kwargs)
 
     def get_data(self, obj, **kwargs):
-        return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('get_data', obj, ObjectNotFound, True, **kwargs)
 
     def get_filename(self, obj, **kwargs):
-        return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
 
     def update_from_file(self, obj, **kwargs):
         if kwargs.get('create', False):
             self.create(obj, **kwargs)
             kwargs['create'] = False
-        return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
 
     def get_object_url(self, obj, **kwargs):
-        return self.__call_method('get_object_url', obj, None, False, **kwargs)
+        return self._call_method('get_object_url', obj, None, False, **kwargs)
 
-    def __call_method(self, method, obj, default, default_is_exception, **kwargs):
+    def _call_method(self, method, obj, default, default_is_exception, **kwargs):
         """
         Check all children object stores for the first one with the dataset
         """
@@ -432,7 +432,7 @@
             if store.exists(obj, **kwargs):
                 return store.__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
-            raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s'
+            raise default( 'objectstore, _call_method failed: %s on %s, kwargs: %s'
                 % ( method, str( obj ), str( kwargs ) ) )
         else:
             return default
@@ -535,12 +535,12 @@
                 log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id))
             self.backends[obj.object_store_id].create(obj, **kwargs)
 
-    def __call_method(self, method, obj, default, default_is_exception, **kwargs):
+    def _call_method(self, method, obj, default, default_is_exception, **kwargs):
         object_store_id = self.__get_store_id_for(obj, **kwargs)
         if object_store_id is not None:
             return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
-            raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s'
+            raise default( 'objectstore, _call_method failed: %s on %s, kwargs: %s'
                 % ( method, str( obj ), str( kwargs ) ) )
         else:
             return default

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2587,11 +2587,9 @@
         hda_source_dict = {} # Mapping from HDA in history to source HDAs.
         for hda in history.datasets:
             source_hda = hda.copied_from_history_dataset_association
-            while source_hda:#should this check library datasets as well?
-                #FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
-                #but is still less than perfect when eg individual datasets are copied between histories
-                if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
-                    hda_source_dict[ source_hda ] = hda
+            while source_hda:
+                if source_hda.dataset.id not in hda_source_dict or source_hda.hid == hda.hid:
+                    hda_source_dict[ source_hda.dataset.id ] = hda
                 source_hda = source_hda.copied_from_history_dataset_association
 
         # Ditto for dataset collections.
@@ -2599,8 +2597,8 @@
         for hdca in history.dataset_collections:
             source_hdca = hdca.copied_from_history_dataset_collection_association
             while source_hdca:
-                if source_hdca not in hdca_source_dict or source_hdca.hid == hdca.hid:
-                    hdca_source_dict[ source_hdca ] = hdca
+                if source_hdca.collection.id not in hdca_source_dict or source_hdca.hid == hdca.hid:
+                    hdca_source_dict[ source_hdca.collection.id ] = hdca
                 source_hdca = source_hdca.copied_from_history_dataset_collection_association
 
         # Unpack unvalidated values to strings, they'll be validated when the
@@ -2619,17 +2617,21 @@
                 if isinstance(value,list):
                     values = []
                     for val in value:
-                        if is_hashable( val ):
-                            if val in history.datasets:
+                        if isinstance(val, trans.app.model.HistoryDatasetAssociation):
+                            if val.dataset.id in hda_source_dict:
+                                values.append( hda_source_dict[ val.dataset.id ] )
+                            else:
                                 values.append( val )
-                            elif val in hda_source_dict:
-                                values.append( hda_source_dict[ val ])
                     return values
-                if is_hashable( value ) and value not in history.datasets and value in hda_source_dict:
-                    return hda_source_dict[ value ]
+                if isinstance(value, trans.app.model.HistoryDatasetAssociation):
+                    if value.dataset.id in hda_source_dict:
+                        return hda_source_dict[ value.dataset.id ]
+                if isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation):
+                    if value.collection.id in hdca_source_dict:
+                        return hdca_source_dict[ value.collection.id ]
             elif isinstance( input, DataCollectionToolParameter ):
-                if is_hashable( value ) and value not in history.dataset_collections and value in hdca_source_dict:
-                    return hdca_source_dict[ value ]
+                if value.collection.id in hdca_source_dict:
+                    return hdca_source_dict[ value.collection.id ]
         visit_input_values( tool_inputs, params, rerun_callback )
 
     def _compare_tool_version( self, trans, job ):

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/tools/actions/metadata.py
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -1,11 +1,15 @@
+import logging
+
 from __init__ import ToolAction
 from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
 from galaxy.util.odict import odict
 from galaxy.util.json import dumps
+from galaxy.jobs.datasets import DatasetPath
 
-import logging
+
 log = logging.getLogger( __name__ )
 
+
 class SetMetadataToolAction( ToolAction ):
     """Tool action used for setting external metadata on an existing dataset"""
 
@@ -65,17 +69,21 @@
         #add parameters to job_parameter table
         # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)?
         incoming[ '__ORIGINAL_DATASET_STATE__' ] = dataset.state
+        input_paths = [DatasetPath( dataset.id, real_path=dataset.file_name, mutable=False )]
+        app.object_store.create(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
+        job_working_dir = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
         external_metadata_wrapper = JobExternalOutputMetadataWrapper( job )
         cmd_line = external_metadata_wrapper.setup_external_metadata( dataset,
                                                                       sa_session,
                                                                       exec_dir = None,
-                                                                      tmp_dir = app.config.new_file_path,
+                                                                      tmp_dir = job_working_dir,
                                                                       dataset_files_path = app.model.Dataset.file_path,
-                                                                      output_fnames = None,
+                                                                      output_fnames = input_paths,
                                                                       config_root = app.config.root,
                                                                       config_file = app.config.config_file,
                                                                       datatypes_config = app.datatypes_registry.integrated_datatypes_configs,
                                                                       job_metadata = None,
+                                                                      include_command = False,
                                                                       kwds = { 'overwrite' : overwrite } )
         incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line
         for name, value in tool.params_to_strings( incoming, app ).iteritems():

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/tools/imp_exp/__init__.py
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -17,12 +17,15 @@
         <tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history"><type class="ExportHistoryTool" module="galaxy.tools"/><action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/>
-          <command>$__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command>
+          <command>python $export_history $__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command><inputs><param name="__HISTORY_TO_EXPORT__" type="hidden"/><param name="compress" type="boolean"/><param name="__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__" type="hidden"/></inputs>
+          <configfiles>
+            <configfile name="export_history">from galaxy.tools.imp_exp.export_history import main; main()</configfile>
+          </configfiles><outputs><data format="gzip" name="output_file"/></outputs>
@@ -530,11 +533,9 @@
         options = ""
         if jeha.compressed:
             options = "-G"
-        return "python %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ),
-                                           "lib/galaxy/tools/imp_exp/export_history.py" ),
-                                           options, history_attrs_filename,
-                                           datasets_attrs_filename,
-                                           jobs_attrs_filename )
+        return "%s %s %s %s" % ( options, history_attrs_filename,
+                                 datasets_attrs_filename,
+                                 jobs_attrs_filename )
 
     def cleanup_after_job( self, db_session ):
         """ Remove temporary directory and attribute files generated during setup for this job. """

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/tools/imp_exp/export_history.py
--- a/lib/galaxy/tools/imp_exp/export_history.py
+++ b/lib/galaxy/tools/imp_exp/export_history.py
@@ -70,7 +70,7 @@
     except Exception, e:
         return 'Error creating history archive: %s' % str( e ), sys.stderr
 
-if __name__ == "__main__":
+def main():
     # Parse command line.
     parser = optparse.OptionParser()
     parser.add_option( '-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.' )
@@ -81,3 +81,6 @@
     # Create archive.
     status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip )
     print status
+
+if __name__ == "__main__":
+    main()

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/version.py
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,1 +1,3 @@
 VERSION_MAJOR = "15.03"
+VERSION_MINOR = "1"
+VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/webapps/galaxy/api/users.py
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -105,7 +105,7 @@
         POST /api/users
         Creates a new Galaxy user.
         """
-        if not trans.app.config.allow_user_creation:
+        if not trans.app.config.allow_user_creation and not trans.user_is_admin():
             raise exceptions.ConfigDoesNotAllowException( 'User creation is not allowed in this Galaxy instance' )
         if trans.app.config.use_remote_user and trans.user_is_admin():
             user = trans.get_or_create_remote_user( remote_user_email=payload['remote_user_email'] )

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/webapps/galaxy/controllers/history.py
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -359,6 +359,15 @@
                     history.purged = True
                     self.sa_session.add( history )
                     self.sa_session.flush()
+                for hda in history.datasets:
+                    # Not all datasets have jobs associated with them (e.g., datasets imported from libraries).
+                    if hda.creating_job_associations:
+                        # HDA has associated job, so try marking it deleted.
+                        job = hda.creating_job_associations[0].job
+                        if job.history_id == history.id and not job.finished:
+                            # No need to check other outputs since the job's parent history is this history
+                            job.mark_deleted( trans.app.config.track_jobs_in_database )
+                            trans.app.job_manager.job_stop_queue.put( job.id )
         trans.sa_session.flush()
         if n_deleted:
             part = "Deleted %d %s" % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) )
@@ -1125,7 +1134,7 @@
             if hda.creating_job_associations:
                 # HDA has associated job, so try marking it deleted.
                 job = hda.creating_job_associations[0].job
-                if job.history_id == history.id and job.state in [ trans.app.model.Job.states.QUEUED, trans.app.model.Job.states.RUNNING, trans.app.model.Job.states.NEW ]:
+                if job.history_id == history.id and not job.finished:
                     # No need to check other outputs since the job's parent history is this history
                     job.mark_deleted( trans.app.config.track_jobs_in_database )
                     trans.app.job_manager.job_stop_queue.put( job.id )
@@ -1224,33 +1233,28 @@
             # Use current history.
             history = trans.history
             id = trans.security.encode_id( history.id )
-
         if not history:
             return trans.show_error_message( "This history does not exist or you cannot export this history." )
-
-        #
         # If history has already been exported and it has not changed since export, stream it.
-        #
         jeha = history.latest_export
         if jeha and jeha.up_to_date:
             if jeha.ready:
                 if preview:
                     url = url_for( controller='history', action="export_archive", id=id, qualified=True )
-                    return trans.show_message( "History Ready: '%(n)s'. Use this link to download \
-                                                the archive or import it to another Galaxy server: \
-                                                <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) )
+                    return trans.show_message( "History Ready: '%(n)s'. Use this link to download "
+                                               "the archive or import it to another Galaxy server: "
+                                               "<a href='%(u)s'>%(u)s</a>" % ( { 'n': history.name, 'u': url } ) )
                 else:
                     return self.serve_ready_history_export( trans, jeha )
             elif jeha.preparing:
-                return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" \
-                        % ( { 'n' : history.name, 's' : url_for( controller='history', action="export_archive", id=id, qualified=True ) } ) )
-
+                return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>"
+                                           % ( { 'n': history.name, 's': url_for( controller='history', action="export_archive", id=id, qualified=True ) } ) )
         self.queue_history_export( trans, history, gzip=gzip, include_hidden=include_hidden, include_deleted=include_deleted )
         url = url_for( controller='history', action="export_archive", id=id, qualified=True )
-        return trans.show_message( "Exporting History '%(n)s'. Use this link to download \
-                                    the archive or import it to another Galaxy server: \
-                                    <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) )
-        #TODO: used in this file and index.mako
+        return trans.show_message( "Exporting History '%(n)s'. You will need to <a href='%(share)s'>make this history 'accessible'</a> in order to import this to another galaxy sever. <br/>"
+                                   "Use this link to download the archive or import it to another Galaxy server: "
+                                   "<a href='%(u)s'>%(u)s</a>" % ( { 'share': url_for(controller='history', action='sharing'), 'n': history.name, 'u': url } ) )
+        # TODO: used in this file and index.mako
 
     @web.expose
     @web.json

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1,6 +1,7 @@
 import base64
 import httplib
 import json
+import logging
 import os
 import sgmllib
 import urllib2
@@ -41,6 +42,8 @@
 from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING
 from markupsafe import escape
 
+log = logging.getLogger( __name__ )
+
 
 class StoredWorkflowListGrid( grids.Grid ):
 
@@ -895,8 +898,9 @@
                     data = json.loads( workflow_data )
                 except Exception, e:
                     data = None
-                    message = "The data content does not appear to be a Galaxy workflow.<br/>Exception: %s" % str( e )
+                    message = "The data content does not appear to be a Galaxy workflow."
                     status = 'error'
+                    log.exception("Error importing workflow.")
                 if data:
                     # Create workflow if possible.  If a required tool is not available in the local
                     # Galaxy instance, the tool information will be available in the step_dict.

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy_ext/__init__.py
--- /dev/null
+++ b/lib/galaxy_ext/__init__.py
@@ -0,0 +1,4 @@
+""" Package for things which are loaded from outside Galaxy and which we can be
+sure will not conflict with the `galaxy` namespace, which may be provided by
+other packages (e.g. galaxy_ops in the toolshed).
+"""

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy_ext/metadata/__init__.py
--- /dev/null
+++ b/lib/galaxy_ext/metadata/__init__.py
@@ -0,0 +1,2 @@
+""" Work with Galaxy metadata
+"""

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 lib/galaxy_ext/metadata/set_metadata.py
--- /dev/null
+++ b/lib/galaxy_ext/metadata/set_metadata.py
@@ -0,0 +1,125 @@
+"""
+Execute an external process to set_meta() on a provided list of pickled datasets.
+
+This was formerly scripts/set_metadata.py and expects these arguments:
+
+    %prog datatypes_conf.xml job_metadata_file metadata_in,metadata_kwds,metadata_out,metadata_results_code,output_filename_override,metadata_override...
+
+Galaxy should be importable on sys.path and output_filename_override should be
+set to the path of the dataset on which metadata is being set
+(output_filename_override could previously be left empty and the path would be
+constructed automatically).
+"""
+
+import logging
+logging.basicConfig()
+log = logging.getLogger( __name__ )
+
+import cPickle
+import json
+import os
+import sys
+
+# ensure supported version
+assert sys.version_info[:2] >= ( 2, 6 ) and sys.version_info[:2] <= ( 2, 7 ), 'Python version must be 2.6 or 2.7, this is: %s' % sys.version
+
+# insert *this* galaxy before all others on sys.path
+new_path = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
+sys.path.insert( 0, new_path )
+
+from galaxy import eggs
+import pkg_resources
+import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
+galaxy.model.Job()  # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
+from galaxy.util import stringify_dictionary_keys
+from sqlalchemy.orm import clear_mappers
+
+
+def set_meta_with_tool_provided( dataset_instance, file_dict, set_meta_kwds ):
+    # This method is somewhat odd, in that we set the metadata attributes from tool,
+    # then call set_meta, then set metadata attributes from tool again.
+    # This is intentional due to interplay of overwrite kwd, the fact that some metadata
+    # parameters may rely on the values of others, and that we are accepting the
+    # values provided by the tool as Truth. 
+    for metadata_name, metadata_value in file_dict.get( 'metadata', {} ).iteritems():
+        setattr( dataset_instance.metadata, metadata_name, metadata_value )
+    dataset_instance.datatype.set_meta( dataset_instance, **set_meta_kwds )
+    for metadata_name, metadata_value in file_dict.get( 'metadata', {} ).iteritems():
+        setattr( dataset_instance.metadata, metadata_name, metadata_value )
+
+def set_metadata():
+    # locate galaxy_root for loading datatypes
+    galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir))
+    galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tool_job_working_directory = os.path.abspath(os.getcwd())
+
+    # Set up datatypes registry
+    datatypes_config = sys.argv.pop( 1 )
+    datatypes_registry = galaxy.datatypes.registry.Registry()
+    datatypes_registry.load_datatypes( root_dir=galaxy_root, config=datatypes_config )
+    galaxy.model.set_datatypes_registry( datatypes_registry )
+
+    job_metadata = sys.argv.pop( 1 )
+    existing_job_metadata_dict = {}
+    new_job_metadata_dict = {}
+    if job_metadata != "None" and os.path.exists( job_metadata ):
+        for line in open( job_metadata, 'r' ):
+            try:
+                line = stringify_dictionary_keys( json.loads( line ) )
+                if line['type'] == 'dataset':
+                    existing_job_metadata_dict[ line['dataset_id'] ] = line
+                elif line['type'] == 'new_primary_dataset':
+                    new_job_metadata_dict[ line[ 'filename' ] ] = line
+            except:
+                continue
+
+    for filenames in sys.argv[1:]:
+        fields = filenames.split( ',' )
+        filename_in = fields.pop( 0 )
+        filename_kwds = fields.pop( 0 )
+        filename_out = fields.pop( 0 )
+        filename_results_code = fields.pop( 0 )
+        dataset_filename_override = fields.pop( 0 )
+        # Need to be careful with the way that these parameters are populated from the filename splitting,
+        # because if a job is running when the server is updated, any existing external metadata command-lines
+        #will not have info about the newly added override_metadata file
+        if fields:
+            override_metadata = fields.pop( 0 )
+        else:
+            override_metadata = None
+        set_meta_kwds = stringify_dictionary_keys( json.load( open( filename_kwds ) ) )  # load kwds; need to ensure our keywords are not unicode
+        try:
+            dataset = cPickle.load( open( filename_in ) )  # load DatasetInstance
+            dataset.dataset.external_filename = dataset_filename_override
+            files_path = os.path.abspath(os.path.join( tool_job_working_directory, "dataset_%s_files" % (dataset.dataset.id) ))
+            dataset.dataset.external_extra_files_path = files_path
+            if dataset.dataset.id in existing_job_metadata_dict:
+                dataset.extension = existing_job_metadata_dict[ dataset.dataset.id ].get( 'ext', dataset.extension )
+            # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
+            if override_metadata:
+                override_metadata = json.load( open( override_metadata ) )
+                for metadata_name, metadata_file_override in override_metadata:
+                    if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
+                        metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
+                    setattr( dataset.metadata, metadata_name, metadata_file_override )
+            file_dict = existing_job_metadata_dict.get( dataset.dataset.id, {} )
+            set_meta_with_tool_provided( dataset, file_dict, set_meta_kwds )
+            dataset.metadata.to_JSON_dict( filename_out )  # write out results of set_meta
+            json.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) )  # setting metadata has succeeded
+        except Exception, e:
+            json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) )  # setting metadata has failed somehow
+
+    for i, ( filename, file_dict ) in enumerate( new_job_metadata_dict.iteritems(), start=1 ):
+        new_dataset = galaxy.model.Dataset( id=-i, external_filename=os.path.join( tool_job_working_directory, file_dict[ 'filename' ] ) )
+        extra_files = file_dict.get( 'extra_files', None )
+        if extra_files is not None:
+            new_dataset._extra_files_path = os.path.join( tool_job_working_directory, extra_files )
+        new_dataset.state = new_dataset.states.OK
+        new_dataset_instance = galaxy.model.HistoryDatasetAssociation( id=-i, dataset=new_dataset, extension=file_dict.get( 'ext', 'data' ) )
+        set_meta_with_tool_provided( new_dataset_instance, file_dict, set_meta_kwds )
+        file_dict[ 'metadata' ] = json.loads( new_dataset_instance.metadata.to_JSON_dict() ) #storing metadata in external form, need to turn back into dict, then later jsonify
+    if existing_job_metadata_dict or new_job_metadata_dict:
+        with open( job_metadata, 'wb' ) as job_metadata_fh:
+            for value in existing_job_metadata_dict.values() + new_job_metadata_dict.values():
+                job_metadata_fh.write( "%s\n" % ( json.dumps( value ) ) )
+
+    clear_mappers()

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 static/scripts/mvc/history/history-model.js
--- a/static/scripts/mvc/history/history-model.js
+++ b/static/scripts/mvc/history/history-model.js
@@ -208,7 +208,7 @@
     /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */
     purge : function( options ){
         if( this.get( 'purged' ) ){ return jQuery.when(); }
-        return this.save( { purged: true }, options );
+        return this.save( { deleted: true, purged: true }, options );
     },
     /** save this history, _Mark_ing it as undeleted */
     undelete : function( options ){

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 static/scripts/packed/mvc/history/history-model.js
--- a/static/scripts/packed/mvc/history/history-model.js
+++ b/static/scripts/packed/mvc/history/history-model.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}});
\ No newline at end of file
+define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}});
\ No newline at end of file

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 templates/webapps/galaxy/workflow/run.mako
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -513,7 +513,7 @@
     <div class="metadataFormTitle">Workflow Parameters</div><div class="metadataFormBody">
     %for parm in wf_parms:
-        <div class='form-row'><label style='width:100px;'>${parm}<input style="border:2px solid ${wf_parms[parm]};border-left-width:8px;" type="text" class='wf_parm_input ptag_${parm}' name="wf_parm|${parm}" value=""/></label></div>
+        <div class='form-row'><label>${parm}<br/><input size=40 style="border:2px solid ${wf_parms[parm]};border-left-width:8px;" type="text" class='wf_parm_input ptag_${parm}' name="wf_parm|${parm}" value=""/></label></div>
     %endfor
     </div></div>

diff -r 708cab19708d8158044eb5b1048740734cb2bc2a -r 6395e70351435911f7ab75863c1b48b54e20a919 test/unit/jobs/test_command_factory.py
--- a/test/unit/jobs/test_command_factory.py
+++ b/test/unit/jobs/test_command_factory.py
@@ -72,7 +72,7 @@
         self.include_metadata = True
         self.include_work_dir_outputs = False
         self.job_wrapper.metadata_line = TEST_METADATA_LINE
-        expected_command = '%s; return_code=$?; cd %s; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, getcwd(), TEST_METADATA_LINE)
+        expected_command = '%s; return_code=$?; %s; sh -c "exit $return_code"' % (MOCK_COMMAND_LINE, TEST_METADATA_LINE)
         self.__assert_command_is( expected_command )
 
     def test_empty_metadata(self):

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[galaxy-commits] commit/galaxy-central: 5 new changesets

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