Merge galaxy/galaxy-central default branch.

lib/galaxy/exceptions/__init__.py

@@ -60,6 +60,10 @@ class MalformedId( MessageException ):
     status_code = 400
     err_code = error_codes.MALFORMED_ID
 
+class UnknownContentsType( MessageException ):
+    status_code = 400
+    err_code = error_codes.UNKNOWN_CONTENTS_TYPE
+
 class RequestParameterMissingException( MessageException ):
     status_code = 400
     err_code = error_codes.USER_REQUEST_MISSING_PARAMETER

lib/galaxy/exceptions/error_codes.json

@@ -49,6 +49,11 @@
     "code": 400009,
     "message": "The id of the resource is malformed."
     },
+   {
+    "name": "UNKNOWN_CONTENTS_TYPE",
+    "code": 400010,
+    "message": "The request contains unknown type of contents."
+    },
    {
     "name": "USER_NO_API_KEY",
     "code": 403001,

lib/galaxy/model/tool_shed_install/__init__.py

@@ -4,6 +4,7 @@ from galaxy.model.item_attrs import Dictifiable
 from galaxy.util.bunch import Bunch
 from galaxy.util import asbool
 from tool_shed.util import common_util
+from urlparse import urljoin
 
 log = logging.getLogger( __name__ )
 
@@ -73,6 +74,12 @@ class ToolShedRepository( object ):
     def can_reinstall_or_activate( self ):
         return self.deleted
 
+    def get_sharable_url( self, app ):
+        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed )
+        if tool_shed_url:
+            return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) )
+        return tool_shed_url
+
     def get_shed_config_filename( self ):
         shed_config_filename = None
         if self.metadata:

lib/galaxy/tools/errors.py

@@ -28,7 +28,9 @@ ${message}
 -----------------------------------------------------------------------------
 job id: ${job_id}
 tool id: ${job_tool_id}
+tool version: ${tool_version}
 job pid or drm id: ${job_runner_external_id}
+job tool version: ${job_tool_version}
 -----------------------------------------------------------------------------
 job command line:
 ${job_command_line}
@@ -86,7 +88,9 @@ class ErrorReporter( object ):
                               history_item_name=hda.get_display_name(),
                               history_view_link=history_view_link,
                               job_id=job.id,
+                              tool_version=job.tool_version,
                               job_tool_id=job.tool_id,
+                              job_tool_version=hda.tool_version,
                               job_runner_external_id=job.job_runner_external_id,
                               job_command_line=job.command_line,
                               job_stderr=util.unicodify( job.stderr ),

lib/galaxy/tools/parameters/basic.py

@@ -979,7 +979,7 @@ class SelectToolParameter( ToolParameter ):
                 if option[2]:
                     # Found selected option.
                     value = option[1]
-            d[ 'value' ] = options
+            d[ 'value' ] = value
 
         return d
 

lib/galaxy/util/biostar.py

@@ -86,7 +86,14 @@ def populate_tag_payload( payload=None, tool=None ):
 def populate_tool_payload( payload=None, tool=None ):
     payload = populate_tag_payload( payload=payload, tool=tool )
     payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name )
-    payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id )
+    tool_url = None
+    if tool.tool_shed_repository:
+        tool_url = tool.tool_shed_repository.get_sharable_url( tool.app )
+        if tool_url:
+            tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url )
+    if not tool_url:
+        tool_url = ''
+    payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url )
     return payload
 
 def determine_cookie_domain( galaxy_hostname, biostar_hostname ):

lib/galaxy/webapps/galaxy/api/folder_contents.py

@@ -1,10 +1,15 @@
 """
-API operations on the contents of a folder.
+API operations on the contents of a library folder.
 """
-import logging
 from galaxy import web
+from galaxy import exceptions
+from galaxy.web import _future_expose_api as expose_api
+from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
+from sqlalchemy.orm.exc import MultipleResultsFound
+from sqlalchemy.orm.exc import NoResultFound
 from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems
 
+import logging
 log = logging.getLogger( __name__ )
 
 class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ):
@@ -12,7 +17,111 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary
     Class controls retrieval, creation and updating of folder contents.
     """
 
-    def load_folder_contents( self, trans, folder ):
+    @expose_api_anonymous
+    def index( self, trans, folder_id, **kwd ):
+        """
+        GET /api/folders/{encoded_folder_id}/contents
+        Displays a collection (list) of a folder's contents (files and folders).
+        Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it.
+        Full path is provided in response as a separate object providing data for breadcrumb path building.
+        """
+
+        if ( len( folder_id ) == 17 and folder_id.startswith( 'F' ) ):
+            try:
+                decoded_folder_id = trans.security.decode_id( folder_id[ 1: ] )
+            except TypeError:
+                raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) )
+        else:
+            raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) )
+
+        try:
+            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one()
+        except MultipleResultsFound:
+            raise exceptions.InconsistentDatabase( 'Multiple folders with same id found.' )
+        except NoResultFound:
+            raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
+        except Exception:
+            raise exceptions.InternalServerError( 'Error loading from the database.' )
+
+        current_user_roles = trans.get_current_user_roles()
+        can_add_library_item = trans.user_is_admin() or trans.app.security_agent.can_add_library_item( current_user_roles, folder )
+
+        if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ):
+            if folder.parent_id == None:
+                try:
+                    library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one()
+                except Exception:
+                    raise exceptions.InternalServerError( 'Error loading from the database.' )
+                if trans.app.security_agent.library_is_public( library, contents=False ):
+                    pass
+                else:
+                    if trans.user:
+                        log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) )
+                    else:
+                        log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) )
+                    raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) 
+            else:
+                if trans.user:
+                    log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) )
+                else:
+                    log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) )
+                raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
+        
+        def build_path( folder ):
+            """
+            Search the path upwards recursively and load the whole route of names and ids for breadcrumb building purposes.
+            """
+            path_to_root = []
+            # We are almost in root
+            if folder.parent_id is None:
+                path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) )
+            else:
+            # We add the current folder and traverse up one folder.
+                path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) )
+                upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id )
+                path_to_root.extend( build_path( upper_folder ) )
+            return path_to_root
+            
+        # Return the reversed path so it starts with the library node.
+        full_path = build_path( folder )[::-1]
+
+        folder_contents = []
+        time_updated = ''
+        time_created = ''
+        # Go through every accessible item in the folder and include its meta-data.
+        for content_item in self._load_folder_contents( trans, folder ):
+            if trans.app.security_agent.can_access_library_item( current_user_roles, content_item, trans.user ):
+                return_item = {}
+                encoded_id = trans.security.encode_id( content_item.id )
+                time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" )
+                time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" )
+
+                # For folder return also hierarchy values
+                if content_item.api_type == 'folder':
+                    encoded_id = 'F' + encoded_id
+                    return_item.update ( dict ( item_count = content_item.item_count ) )
+
+                if content_item.api_type == 'file':
+                    library_dataset_dict = content_item.to_dict()
+                    library_dataset_dict['data_type']
+                    library_dataset_dict['file_size']
+                    library_dataset_dict['date_uploaded']
+                    return_item.update ( dict ( data_type = library_dataset_dict['data_type'],
+                                                file_size = library_dataset_dict['file_size'],
+                                                date_uploaded = library_dataset_dict['date_uploaded'] ) )
+
+                # For every item return also the default meta-data
+                return_item.update( dict( id = encoded_id,
+                                   type = content_item.api_type,
+                                   name = content_item.name,
+                                   time_updated = time_updated,
+                                   time_created = time_created
+                                    ) )
+                folder_contents.append( return_item )
+
+        return { 'metadata' : { 'full_path' : full_path, 'can_add_library_item': can_add_library_item }, 'folder_contents' : folder_contents }
+
+    def _load_folder_contents( self, trans, folder ):
         """
         Loads all contents of the folder (folders and data sets) but only in the first level.
         """
@@ -33,101 +142,12 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary
                 content_items.append( dataset )
         return content_items
 
-    @web.expose_api
-    def index( self, trans, folder_id, **kwd ):
-        """
-        GET /api/folders/{encoded_folder_id}/contents
-        Displays a collection (list) of a folder's contents (files and folders).
-        Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it.
-        Full path is provided as a separate object in response providing data for breadcrumb path building.
-        """
-        folder_container = []
-        current_user_roles = trans.get_current_user_roles()
-
-        if ( folder_id.startswith( 'F' ) ):
-            try:
-                decoded_folder_id = trans.security.decode_id( folder_id[1:] )
-            except TypeError:
-                trans.response.status = 400
-                return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id )
-
-        try:
-            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id )
-        except:
-            folder = None
-            log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id )
-
-        # We didn't find the folder or user does not have an access to it.
-        if not folder:
-            trans.response.status = 400
-            return "Invalid folder id ( %s ) specified." % str( folder_id )
-        
-        if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ):
-            log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) )
-            trans.response.status = 400
-            return "Invalid folder id ( %s ) specified." % str( folder_id )
-        
-        def build_path( folder ):
-            """
-            Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes.
-            """
-            path_to_root = []
-            # We are almost in root
-            if folder.parent_id is None:
-                path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) )
-            else:
-            # We add the current folder and traverse up one folder.
-                path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) )
-                upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id )
-                path_to_root.extend( build_path( upper_folder ) )
-            return path_to_root
-            
-        # Return the reversed path so it starts with the library node.
-        full_path = build_path( folder )[::-1]
-        folder_container.append( dict( full_path = full_path ) )
-        
-        folder_contents = []
-        time_updated = ''
-        time_created = ''
-        # Go through every item in the folder and include its meta-data.
-        for content_item in self.load_folder_contents( trans, folder ):
-            return_item = {}
-            encoded_id = trans.security.encode_id( content_item.id )
-            time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" )
-            time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" )
-            
-            # For folder return also hierarchy values
-            if content_item.api_type == 'folder':
-                encoded_id = 'F' + encoded_id
-                return_item.update ( dict ( item_count = content_item.item_count ) )
-
-            if content_item.api_type == 'file':
-                library_dataset_dict = content_item.to_dict()
-                library_dataset_dict['data_type']
-                library_dataset_dict['file_size']
-                library_dataset_dict['date_uploaded']
-                return_item.update ( dict ( data_type = library_dataset_dict['data_type'],
-                                            file_size = library_dataset_dict['file_size'],
-                                            date_uploaded = library_dataset_dict['date_uploaded'] ) )
-
-            # For every item return also the default meta-data
-            return_item.update( dict( id = encoded_id,
-                               type = content_item.api_type,
-                               name = content_item.name,
-                               time_updated = time_updated,
-                               time_created = time_created
-                                ) )
-            folder_contents.append( return_item )
-        # Put the data in the container
-        folder_container.append( dict( folder_contents = folder_contents ) )
-        return folder_container
-
     @web.expose_api
     def show( self, trans, id, library_id, **kwd ):
         """
         GET /api/folders/{encoded_folder_id}/
         """
-        pass
+        raise exceptions.NotImplemented( 'Showing the library folder content is not implemented.' )
 
     @web.expose_api
     def create( self, trans, library_id, payload, **kwd ):
@@ -136,11 +156,11 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary
         Creates a new folder. This should be superseded by the
         LibraryController.
         """
-        pass
+        raise exceptions.NotImplemented( 'Creating the library folder content is not implemented.' )
 
     @web.expose_api
     def update( self, trans, id,  library_id, payload, **kwd ):
         """
         PUT /api/folders/{encoded_folder_id}/contents
         """
-        pass
+        raise exceptions.NotImplemented( 'Updating the library folder content is not implemented.' )

lib/galaxy/webapps/galaxy/api/folders.py

@@ -1,14 +1,17 @@
 """
-API operations on folders
+API operations on library folders
 """
-import logging, os, string, shutil, urllib, re, socket, traceback
+import os, string, shutil, urllib, re, socket, traceback
 from galaxy import datatypes, jobs, web, security
+from galaxy.web import _future_expose_api as expose_api
+from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
 from galaxy.web.base.controller import BaseAPIController,UsesLibraryMixin,UsesLibraryMixinItems
 from galaxy.util.sanitize_html import sanitize_html
 
 from cgi import escape, FieldStorage
 from paste.httpexceptions import HTTPBadRequest
 
+import logging
 log = logging.getLogger( __name__ )
 
 class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ):
@@ -18,9 +21,9 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
         """
         GET /api/folders/
         This would normally display a list of folders. However, that would
-        be across multiple libraries, so it's not implemented yet.
+        be across multiple libraries, so it's not implemented.
         """
-        pass
+        raise exceptions.NotImplemented( 'Listing all accessible library folders is not implemented.' )
 
     @web.expose_api
     def show( self, trans, id, **kwd ):

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -188,8 +188,7 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio
         hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
         return hda_dict
 
-    #TODO: allow anon users to copy hdas, ldas
-    @expose_api
+    @expose_api_anonymous
     def create( self, trans, history_id, payload, **kwd ):
         """
         create( self, trans, history_id, payload, **kwd )
@@ -434,10 +433,7 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio
         return validated_payload
 
     def __handle_unknown_contents_type( self, trans, contents_type ):
-        # TODO: raise a message exception instead of setting status and returning dict.
-        trans.response.status = 400
-        return { 'error': 'Unknown contents type %s' % type }
-
+        raise exceptions.UnknownContentsType('Unknown contents type: %s' % type)
 
 class HDAManager( object ):
 

lib/galaxy/webapps/galaxy/api/lda_datasets.py

@@ -12,9 +12,13 @@ import tempfile
 import urllib
 import urllib2
 import zipfile
-from paste.httpexceptions import HTTPBadRequest
-from galaxy import util, web
-from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound
+from galaxy import exceptions
+from galaxy.web import _future_expose_api as expose_api
+from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
+# from paste.httpexceptions import HTTPBadRequest
+from galaxy import util
+from galaxy import web
+# from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound
 from galaxy.security import Action
 from galaxy.util.streamball import StreamBall
 from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin
@@ -24,7 +28,7 @@ log = logging.getLogger( __name__ )
 
 class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
 
-    @web.expose_api
+    @expose_api_anonymous
     def show( self, trans, id, **kwd ):
         """
         show( self, trans, id, **kwd )
@@ -41,19 +45,20 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
         try:
             dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True )
         except Exception, e:
-            trans.response.status = 500
-            return str( e )
-        try:
-            rval = dataset.to_dict()
-        except Exception, e:
-            rval = "Error in dataset API at listing contents: " + str( e )
-            log.error( rval + ": %s" % str(e), exc_info=True )
-            trans.response.status = 500
-            return "Error in dataset API at listing contents: " + str( e )
+            raise exceptions.ObjectNotFound( 'Requested dataset was not found.' )
+            # trans.response.status = 500
+            # return str( e )
+        # try:
+        rval = dataset.to_dict()
+        # except Exception, e:
+        #     rval = "Error in dataset API at listing contents: " + str( e )
+        #     log.error( rval + ": %s" % str(e), exc_info=True )
+        #     trans.response.status = 500
+        #     return "Error in dataset API at listing contents: " + str( e )
 
         rval['id'] = trans.security.encode_id(rval['id']);
         rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']);
-        rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id'])
+        rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id'])
         return rval
 
     @web.expose

lib/galaxy/webapps/galaxy/api/libraries.py

@@ -7,7 +7,7 @@ from galaxy import exceptions
 from galaxy.web import _future_expose_api as expose_api
 from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
 from galaxy.model.orm import and_, not_, or_
-from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy.web.base.controller import BaseAPIController
 
 import logging
 log = logging.getLogger( __name__ )
@@ -61,7 +61,6 @@ class LibrariesController( BaseAPIController ):
             if trans.app.security_agent.library_is_public( library, contents=False ):
                 item[ 'public' ] = True
             current_user_roles = trans.get_current_user_roles()
-            # can_user_add = trans.app.security_agent.can_add_library_item( current_user_roles, library.root_folder )
             if not trans.user_is_admin():
                 item['can_user_add'] = trans.app.security_agent.can_add_library_item( current_user_roles, library )
                 item['can_user_modify'] = trans.app.security_agent.can_modify_library_item( current_user_roles, library )
@@ -98,7 +97,7 @@ class LibrariesController( BaseAPIController ):
         deleted = util.string_as_bool( deleted )
         try:
             decoded_library_id = trans.security.decode_id( library_id )
-        except Exception:
+        except TypeError:
             raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id )
         try:
             library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id )
@@ -144,7 +143,14 @@ class LibrariesController( BaseAPIController ):
         library.root_folder = root_folder
         trans.sa_session.add_all( ( library, root_folder ) )
         trans.sa_session.flush()
-        return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )
+
+        item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )
+        item['can_user_add'] = True
+        item['can_user_modify'] = True
+        item['can_user_manage'] = True
+        if trans.app.security_agent.library_is_public( library, contents=False ):
+            item[ 'public' ] = True
+        return item
 
     @expose_api
     def update( self, trans, id, **kwd ):

lib/galaxy/webapps/galaxy/api/library_contents.py

@@ -17,8 +17,7 @@ import logging
 log = logging.getLogger( __name__ )
 
 
-class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems,
-                                 UsesHistoryDatasetAssociationMixin ):
+class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ):
 
     @expose_api
     def index( self, trans, library_id, **kwd ):

lib/galaxy/webapps/galaxy/buildapp.py

@@ -284,7 +284,7 @@ def app_factory( global_conf, **kwargs ):
     # ====================
 
     # Handle displaying tool help images and README file images contained in repositories installed from the tool shed.
-    webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file',
+    webapp.add_route( '/admin_toolshed/static/images/:repository_id/{image_file:.+?}',
                       controller='admin_toolshed',
                       action='display_image_in_repository',
                       repository_id=None,

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -16,6 +16,7 @@ from tool_shed.util import common_install_util
 from tool_shed.util import data_manager_util
 from tool_shed.util import datatype_util
 from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
 from tool_shed.util import metadata_util
 from tool_shed.util import readme_util
 from tool_shed.util import repository_dependency_util
@@ -1851,7 +1852,7 @@ class AdminToolshed( AdminGalaxy ):
                         repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) )
                     else:
                         repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) )
-                    repo = hg.repository( suc.get_configured_ui(), path=repo_files_dir )
+                    repo = hg.repository( hg_util.get_configured_ui(), path=repo_files_dir )
                     repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
                     repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev )
                     suc.update_repository( repo, latest_ctx_rev )

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -13,6 +13,7 @@ import tool_shed.repository_types.util as rt_util
 import tool_shed.util.shed_util_common as suc
 from tool_shed.galaxy_install import repository_util
 from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
 from tool_shed.util import import_util
 from tool_shed.util import metadata_util
 from tool_shed.util import repository_maintenance_util
@@ -49,7 +50,7 @@ class RepositoriesController( BaseAPIController ):
                 log.debug( error_message )
                 return []
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
             ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True )
             return ordered_installable_revisions
         else:
@@ -133,7 +134,7 @@ class RepositoriesController( BaseAPIController ):
                 # The changeset_revision column in the repository_metadata table has been updated with a new
                 # value value, so find the changeset_revision to which we need to update.
                 repo_dir = repository.repo_path( trans.app )
-                repo = hg.repository( suc.get_configured_ui(), repo_dir )
+                repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
                 new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
                 repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
                                                                                          encoded_repository_id,

lib/galaxy/webapps/tool_shed/api/repository_revisions.py

@@ -6,6 +6,7 @@ from galaxy import util
 from galaxy.model.orm import and_, not_, select
 from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest
 from tool_shed.util import export_util
+from tool_shed.util import hg_util
 import tool_shed.util.shed_util_common as suc
 
 from galaxy import eggs
@@ -168,7 +169,7 @@ class RepositoryRevisionsController( BaseAPIController ):
                     # The changeset_revision column in the repository_metadata table has been updated with a new
                     # value value, so find the changeset_revision to which we need to update.
                     repo_dir = repository_dependency.repo_path( trans.app )
-                    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+                    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
                     new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency,
                                                                                            repo,
                                                                                            changeset_revision )

lib/galaxy/webapps/tool_shed/controllers/repository.py

@@ -19,6 +19,7 @@ from tool_shed.util import common_util
 from tool_shed.util import container_util
 from tool_shed.util import encoding_util
 from tool_shed.util import export_util
+from tool_shed.util import hg_util
 from tool_shed.util import import_util
 from tool_shed.util import metadata_util
 from tool_shed.util import readme_util
@@ -719,7 +720,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         status = kwd.get( 'status', 'done' )
         commit_message = kwd.get( 'commit_message', 'Deleted selected files' )
         repository = suc.get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         # Update repository files for browsing.
         suc.update_repository( repo )
         changeset_revision = repository.tip( trans.app )
@@ -891,9 +892,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         changeset_revision = kwd.get( 'changeset_revision', None )
         repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         # Default to the current changeset revision.
-        update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+        update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
         latest_changeset_revision = changeset_revision
         from_update_manager = kwd.get( 'from_update_manager', False )
         if from_update_manager:
@@ -937,10 +938,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                 update_to_changeset_hash = None
                 for changeset in repo.changelog:
                     changeset_hash = str( repo.changectx( changeset ) )
-                    ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
+                    ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash )
                     if update_to_changeset_hash:
                         if changeset_hash == repository.tip( trans.app ):
-                            update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
+                            update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash )
                             latest_changeset_revision = changeset_hash
                             break
                         else:
@@ -949,7 +950,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                                                      changeset_hash )
                             if repository_metadata:
                                 # We found a RepositoryMetadata record.
-                                update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
+                                update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash )
                                 latest_changeset_revision = changeset_hash
                                 break
                             else:
@@ -1213,7 +1214,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         else:
             containers_dict = None
             export_repository_dependencies_check_box = None
-        revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True )
+        revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True )
         return trans.fill_template( "/webapps/tool_shed/repository/export_repository.mako",
                                     changeset_revision=changeset_revision,
                                     containers_dict=containers_dict,
@@ -1466,9 +1467,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ]
         includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ]
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         # Default to the received changeset revision and ctx_rev.
-        update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+        update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
         ctx_rev = str( update_to_ctx.rev() )
         latest_changeset_revision = changeset_revision
         update_dict = dict( changeset_revision=changeset_revision,
@@ -1497,7 +1498,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                     has_repository_dependencies = False
                     has_repository_dependencies_only_if_compiling_contained_td = False
                     changeset_hash = str( repo.changectx( changeset ) )
-                    ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
+                    ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash )
                     if update_to_changeset_hash:
                         update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
                                                                                                            trans.security.encode_id( repository.id ),
@@ -1515,10 +1516,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                             # We found a RepositoryMetadata record.
                             if changeset_hash == repository.tip( trans.app ):
                                 # The current ctx is the repository tip, so use it.
-                                update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
+                                update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash )
                                 latest_changeset_revision = changeset_hash
                             else:
-                                update_to_ctx = suc.get_changectx_for_changeset( repo, update_to_changeset_hash )
+                                update_to_ctx = hg_util.get_changectx_for_changeset( repo, update_to_changeset_hash )
                                 latest_changeset_revision = update_to_changeset_hash
                             break
                     elif not update_to_changeset_hash and changeset_hash == changeset_revision:
@@ -1544,8 +1545,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         changeset_revision = kwd[ 'changeset_revision' ]
         repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
-        ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
+        ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
         if ctx:
             return str( ctx.rev() )
         return ''
@@ -1560,8 +1561,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     def get_file_from_changeset_revision( self, repo_files_dir, changeset_revision, file_name, dir ):
         """Return file_name from the received changeset_revision of the repository manifest."""
         stripped_file_name = suc.strip_path( file_name )
-        repo = hg.repository( suc.get_configured_ui(), repo_files_dir )
-        ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir )
+        ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
         named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir )
         return named_tmp_file
 
@@ -1604,7 +1605,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                            trans.model.Repository.table.c.user_id == user.id ) ):
             repository = repository_metadata.repository
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
             latest_downloadable_changeset_revsion = suc.get_latest_downloadable_changeset_revision( trans, repository, repo )
             if repository_metadata.changeset_revision == latest_downloadable_changeset_revsion:
                 # We'll display only the test run for the latest installable revision in the rss feed.
@@ -1672,7 +1673,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         if repository_name is not None and repository_owner is not None:
             repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
             if repository:
-                repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+                repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
                 return suc.get_latest_downloadable_changeset_revision( trans, repository, repo )
         return suc.INITIAL_CHANGELOG_HASH
 
@@ -1855,7 +1856,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         changeset_revision = kwd[ 'changeset_revision' ]
         repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         tool_version_dicts = []
         for changeset in repo.changelog:
             current_changeset_revision = str( repo.changectx( changeset ) )
@@ -1880,7 +1881,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         repository_id = trans.security.encode_id( repository.id )
         repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if not repository_metadata:
             # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository
@@ -1889,7 +1890,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                                repo,
                                                                                after_changeset_revision=changeset_revision )
             repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
-        ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+        ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
         repo_info_dict = repository_util.create_repo_info_dict( trans=trans,
                                                                 repository_clone_url=repository_clone_url,
                                                                 changeset_revision=changeset_revision,
@@ -2165,7 +2166,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         repository = suc.get_repository_in_tool_shed( trans, id )
         repository_type = kwd.get( 'repository_type', str( repository.type ) )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         repo_name = kwd.get( 'repo_name', repository.name )
         changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
         description = kwd.get( 'description', repository.description )
@@ -2317,7 +2318,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                                             selected_value=changeset_revision,
                                                                                             add_id_to_name=False,
                                                                                             downloadable=False )
-        revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False )
+        revision_label = hg_util.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False )
         repository_metadata = None
         metadata = None
         is_malicious = False
@@ -2326,7 +2327,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         if changeset_revision != suc.INITIAL_CHANGELOG_HASH:
             repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
             if repository_metadata:
-                revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False )
+                revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False )
                 metadata = repository_metadata.metadata
                 is_malicious = repository_metadata.malicious
             else:
@@ -2337,7 +2338,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                 if previous_changeset_revision != suc.INITIAL_CHANGELOG_HASH:
                     repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision )
                     if repository_metadata:
-                        revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision, include_date=False )
+                        revision_label = hg_util.get_revision_label( trans, repository, previous_changeset_revision, include_date=False )
                         metadata = repository_metadata.metadata
                         is_malicious = repository_metadata.malicious
                         changeset_revision = previous_changeset_revision
@@ -2443,7 +2444,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                 # There is no repository_metadata defined for the changeset_revision, so see if it was defined
                 # in a previous changeset in the changelog.
                 repo_dir = repository.repo_path( trans.app )
-                repo = hg.repository( suc.get_configured_ui(), repo_dir )
+                repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
                 previous_changeset_revision = \
                     suc.get_previous_metadata_changeset_revision( repository,
                                                                   repo,
@@ -2520,7 +2521,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         changeset_revision = kwd.get( 'changeset_revision', None )
         repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         # Get the next installable changeset_revision beyond the received changeset_revision.
         changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
         if changeset_revision:
@@ -2540,7 +2541,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
         repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata:
@@ -2577,7 +2578,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
             repository_metadata_id = None
             metadata = None
             repository_dependencies = None
-        revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True )
+        revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True )
         changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans,
                                                                                             repository,
                                                                                             selected_value=changeset_revision,
@@ -2607,7 +2608,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         changeset_revision = kwd.get( 'changeset_revision', None )
         repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         # Get the lower bound changeset revision.
         lower_bound_changeset_revision = suc.get_previous_metadata_changeset_revision( repository, repo, changeset_revision, downloadable=True )
         # Build the list of changeset revision hashes.
@@ -2633,7 +2634,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                               status='error' ) )
         repository = suc.get_repository_in_tool_shed( trans, id )
         changeset_revision = repository.tip( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         if repository.user == trans.user:
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='browse_repositories',
@@ -2651,7 +2652,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                                               changeset_revision,
                                                                                               metadata_only=True )
         repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository )
-        revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True )
+        revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True )
         return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako',
                                     repository=repository,
                                     metadata=metadata,
@@ -2702,7 +2703,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         commit_message = kwd.get( 'commit_message', 'Deleted selected files' )
         repository = suc.get_repository_in_tool_shed( trans, id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' )
         if kwd.get( 'select_files_to_delete_button', False ):
             if selected_files_to_delete:
@@ -2742,7 +2743,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                 # Update the repository files for browsing.
                 suc.update_repository( repo )
                 # Get the new repository tip.
-                repo = hg.repository( suc.get_configured_ui(), repo_dir )
+                repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
                 if tip == repository.tip( trans.app ):
                     message += 'No changes to repository.  '
                     kwd[ 'message' ] = message
@@ -2931,7 +2932,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
             if not repository_metadata:
                 # Get updates to the received changeset_revision if any exist.
                 repo_dir = repository.repo_path( trans.app )
-                repo = hg.repository( suc.get_configured_ui(), repo_dir )
+                repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
                 upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
                 if upper_bound_changeset_revision:
                     changeset_revision = upper_bound_changeset_revision
@@ -2971,7 +2972,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                                      trans.security.encode_id( repository.id ),
                                                                                      changeset_revision )
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
             tool_shed_status_dict = {}
             # Handle repository deprecation.
             tool_shed_status_dict[ 'repository_deprecated' ] = str( repository.deprecated )
@@ -3063,7 +3064,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         message = kwd.get( 'message', ''  )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         changesets = []
         for changeset in repo.changelog:
             ctx = repo.changectx( changeset )
@@ -3074,7 +3075,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
             change_dict = { 'ctx' : ctx,
                             'rev' : str( ctx.rev() ),
                             'date' : date,
-                            'display_date' : suc.get_readable_ctx_date( ctx ),
+                            'display_date' : hg_util.get_readable_ctx_date( ctx ),
                             'description' : ctx.description(),
                             'files' : ctx.files(),
                             'user' : ctx.user(),
@@ -3098,8 +3099,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         message = kwd.get( 'message', ''  )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-        ctx = suc.get_changectx_for_changeset( repo, ctx_str )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
+        ctx = hg_util.get_changectx_for_changeset( repo, ctx_str )
         if ctx is None:
             message = "Repository does not include changeset revision '%s'." % str( ctx_str )
             status = 'error'
@@ -3129,7 +3130,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True )
         # For rendering the prev button.
         if ctx_parent:
-            ctx_parent_date = suc.get_readable_ctx_date( ctx_parent )
+            ctx_parent_date = hg_util.get_readable_ctx_date( ctx_parent )
             ctx_parent_rev = ctx_parent.rev()
             if ctx_parent_rev < 0:
                  prev = None
@@ -3138,7 +3139,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         else:
            prev = None
         if ctx_child:
-            ctx_child_date = suc.get_readable_ctx_date( ctx_child )
+            ctx_child_date = hg_util.get_readable_ctx_date( ctx_child )
             ctx_child_rev = ctx_child.rev()
             next = "<b>%s:%s</b> <i>(%s)</i>" % ( ctx_child_rev, ctx_child, ctx_child_date )
         else:
@@ -3187,7 +3188,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         message = kwd.get( 'message', ''  )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model )
         changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
         display_reviews = kwd.get( 'display_reviews', False )
@@ -3221,7 +3222,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                                             selected_value=changeset_revision,
                                                                                             add_id_to_name=False,
                                                                                             downloadable=False )
-        revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False )
+        revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False )
         repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
         if repository_metadata:
             metadata = repository_metadata.metadata
@@ -3277,13 +3278,13 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
         repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_files_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_files_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir )
         tool_metadata_dict = {}
         tool_lineage = []
         tool = None
         guid = None
         original_tool_data_path = trans.app.config.tool_data_path
-        revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False )
+        revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False )
         repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata:
             repository_metadata_id = trans.security.encode_id( repository_metadata.id )

lib/galaxy/webapps/tool_shed/controllers/repository_review.py

@@ -7,6 +7,7 @@ from galaxy.model.orm import and_
 from galaxy.webapps.tool_shed.util import ratings_util
 from tool_shed.util.container_util import STRSEP
 import tool_shed.util.shed_util_common as suc
+from tool_shed.util import hg_util
 from tool_shed.util import review_util
 from galaxy.util.odict import odict
 import tool_shed.grids.repository_review_grids as repository_review_grids
@@ -72,8 +73,8 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
         status = kwd.get( 'status', 'done' )
         review = review_util.get_review( trans, kwd[ 'id' ] )
         repository = review.repository
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-        rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
+        rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
         return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako',
                                     repository=repository,
                                     changeset_revision_label=changeset_revision_label,
@@ -232,7 +233,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
         for component in review_util.get_components( trans ):
             components_dict[ component.name ] = dict( component=component, component_review=None )
         repository = review.repository
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         for component_review in review.component_reviews:
             if component_review and component_review.component:
                 component_name = component_review.component.name
@@ -337,7 +338,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
                                                                                  name='revision_approved',
                                                                                  selected_value=selected_value,
                                                                                  for_component=False )
-        rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
+        rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
         return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako',
                                     repository=repository,
                                     review=review,
@@ -470,7 +471,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
         if repository_id:
             repository = suc.get_repository_in_tool_shed( trans, repository_id )
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
             metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
             reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
             reviews_dict = odict()
@@ -478,7 +479,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
                 ctx = repo.changectx( changeset )
                 changeset_revision = str( ctx )
                 if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes:
-                    rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
+                    rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
                     if changeset_revision in reviewed_revision_hashes:
                         # Find the review for this changeset_revision
                         repository_reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision )
@@ -517,9 +518,9 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
         changeset_revision = kwd.get( 'changeset_revision', None )
         repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
-        rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
+        rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
         reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision )
         return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako',
                                     repository=repository,
@@ -582,9 +583,9 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] )
         changeset_revision = kwd.get( 'changeset_revision', None )
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         previous_reviews_dict = review_util.get_previous_repository_reviews( trans, repository, changeset_revision )
-        rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
+        rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
         return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako',
                                     repository=repository,
                                     changeset_revision=changeset_revision,

lib/galaxy/webapps/tool_shed/controllers/upload.py

@@ -11,6 +11,7 @@ from galaxy.datatypes import checkers
 import tool_shed.repository_types.util as rt_util
 import tool_shed.util.shed_util_common as suc
 from tool_shed.util import commit_util
+from tool_shed.util import hg_util
 from tool_shed.util import metadata_util
 from tool_shed.util import repository_dependency_util
 from tool_shed.util import tool_dependency_util
@@ -39,7 +40,7 @@ class UploadController( BaseUIController ):
         repository_id = kwd.get( 'repository_id', '' )
         repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) )
         remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) )
         uploaded_file = None
@@ -63,7 +64,7 @@ class UploadController( BaseUIController ):
                 repo_url = 'http%s' % url[ len( 'hg' ): ]
                 repo_url = repo_url.encode( 'ascii', 'replace' )
                 try:
-                    commands.clone( suc.get_configured_ui(), repo_url, uploaded_directory )
+                    commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory )
                 except Exception, e:
                     message = 'Error uploading via mercurial clone: %s' % suc.to_html_string( str( e ) )
                     status = 'error'
@@ -323,7 +324,7 @@ class UploadController( BaseUIController ):
     def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar,
                           commit_message, new_repo_alert ):
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         undesirable_dirs_removed = 0
         undesirable_files_removed = 0
         if upload_point is not None:
@@ -387,7 +388,7 @@ class UploadController( BaseUIController ):
     def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ):
         # Upload a tar archive of files.
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         undesirable_dirs_removed = 0
         undesirable_files_removed = 0
         ok, message = commit_util.check_archive( repository, tar )

lib/tool_shed/galaxy_install/repository_util.py

@@ -15,6 +15,7 @@ from tool_shed.util import container_util
 from tool_shed.util import data_manager_util
 from tool_shed.util import datatype_util
 from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
 from tool_shed.util import repository_dependency_util
 from tool_shed.util import metadata_util
 from tool_shed.util import tool_dependency_util
@@ -186,7 +187,7 @@ def get_repair_dict( trans, repository ):
 def get_repo_info_dict( trans, repository_id, changeset_revision ):
     repository = suc.get_repository_in_tool_shed( trans, repository_id )
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
     repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
                                                                              repository_id,
@@ -225,7 +226,7 @@ def get_repo_info_dict( trans, repository_id, changeset_revision ):
         has_repository_dependencies_only_if_compiling_contained_td = False
         includes_tool_dependencies = False
         includes_tools_for_display_in_tool_panel = False
-    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+    ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
     repo_info_dict = create_repo_info_dict( trans=trans,
                                             repository_clone_url=repository_clone_url,
                                             changeset_revision=changeset_revision,
@@ -574,7 +575,7 @@ def install_tool_shed_repository( trans, tool_shed_repository, repo_info_dict, t
             current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None )
             current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None )
             if current_ctx_rev != ctx_rev:
-                repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) )
+                repo = hg.repository( hg_util.get_configured_ui(), path=os.path.abspath( install_dir ) )
                 pull_repository( repo, repository_clone_url, current_changeset_revision )
                 suc.update_repository( repo, ctx_rev=current_ctx_rev )
         handle_repository_contents( trans,
@@ -804,7 +805,7 @@ def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, r
 
 def pull_repository( repo, repository_clone_url, ctx_rev ):
     """Pull changes from a remote repository to a local one."""
-    commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] )
+    commands.pull( hg_util.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] )
 
 def repair_tool_shed_repository( trans, repository, repo_info_dict ):
 

lib/tool_shed/grids/admin_grids.py

@@ -5,6 +5,7 @@ from galaxy.web.framework.helpers import time_ago
 from galaxy.webapps.tool_shed import model
 from galaxy.model.orm import and_
 import tool_shed.util.shed_util_common as suc
+from tool_shed.util import hg_util
 from tool_shed.grids.repository_grids import CategoryGrid
 from tool_shed.grids.repository_grids import RepositoryGrid
 
@@ -425,9 +426,11 @@ class RepositoryMetadataGrid( grids.Grid ):
 
         def get_value( self, trans, grid, repository_metadata ):
             repository = repository_metadata.repository
-            repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-            ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
-            return suc.get_revision_label( trans, repository, repository_metadata.changeset_revision, include_date=True )
+            return hg_util.get_revision_label( trans,
+                                               repository,
+                                               repository_metadata.changeset_revision,
+                                               include_date=True,
+                                               include_hash=True )
 
 
     class ToolsColumn( grids.TextColumn ):

lib/tool_shed/grids/repository_grids.py

@@ -6,6 +6,7 @@ from galaxy.model.orm import and_
 from galaxy.model.orm import or_
 from galaxy.util import json
 from galaxy.util import listify
+from tool_shed.util import hg_util
 import tool_shed.util.shed_util_common as suc
 import tool_shed.grids.util as grids_util
 import tool_shed.repository_types.util as rt_util
@@ -116,7 +117,7 @@ class RepositoryGrid( grids.Grid ):
         def get_value( self, trans, grid, repository ):
             """Display the current repository heads."""
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
             heads = suc.get_repository_heads( repo )
             multiple_heads = len( heads ) > 1
             if multiple_heads:
@@ -124,7 +125,7 @@ class RepositoryGrid( grids.Grid ):
             else:
                 heads_str = ''
             for ctx in heads:
-                heads_str += '%s<br/>' % suc.get_revision_label_from_ctx( ctx, include_date=True )
+                heads_str += '%s<br/>' % hg_util.get_revision_label_from_ctx( ctx, include_date=True )
             heads_str.rstrip( '<br/>' )
             if multiple_heads:
                 heads_str += '</font>'
@@ -1338,7 +1339,7 @@ class RepositoryMetadataGrid( grids.Grid ):
         def get_value( self, trans, grid, repository_metadata ):
             repository = repository_metadata.repository
             changeset_revision = repository_metadata.changeset_revision
-            changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True )
+            changeset_revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True )
             return changeset_revision_label
 
 
@@ -1482,7 +1483,7 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
                                                                                                                                           changeset_revision )
                                 if not required_repository_metadata:
                                     repo_dir = required_repository.repo_path( trans.app )
-                                    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+                                    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
                                     updated_changeset_revision = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset_revision )
                                     required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans,
                                                                                                                                               required_repository_id,
@@ -2029,7 +2030,7 @@ def get_latest_downloadable_repository_metadata( trans, repository ):
      tool_dependency_definition.
     """
     encoded_repository_id = trans.security.encode_id( repository.id )
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     tip_ctx = str( repo.changectx( repo.changelog.tip() ) )
     repository_metadata = None
     try:
@@ -2077,7 +2078,7 @@ def get_latest_repository_metadata( trans, repository ):
      tool_dependency_definition.
     """
     encoded_repository_id = trans.security.encode_id( repository.id )
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     tip_ctx = str( repo.changectx( repo.changelog.tip() ) )
     try:
         repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx )

lib/tool_shed/grids/repository_review_grids.py

@@ -6,6 +6,7 @@ from galaxy.model.orm import and_
 from galaxy.model.orm import or_
 from tool_shed.grids.repository_grids import RepositoryGrid
 import tool_shed.util.shed_util_common as suc
+from tool_shed.util import hg_util
 from tool_shed.util import metadata_util
 
 from galaxy import eggs
@@ -66,10 +67,10 @@ class RepositoriesWithReviewsGrid( RepositoryGrid ):
             # Restrict to revisions that have been reviewed.
             if repository.reviews:
                 rval = ''
-                repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+                repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
                 for review in repository.reviews:
                     changeset_revision = review.changeset_revision
-                    rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
+                    rev, label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
                     rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
                         ( trans.security.encode_id( repository.id ), changeset_revision, label )
                 return rval
@@ -85,9 +86,11 @@ class RepositoriesWithReviewsGrid( RepositoryGrid ):
                 rval = ''
                 for repository_metadata in repository_metadata_revisions:
                     rev, label, changeset_revision = \
-                        metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans,
-                                                                                                 repository_metadata,
-                                                                                                 repository=repository )
+                        hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans,
+                                                                                           repository_metadata,
+                                                                                           repository=repository,
+                                                                                           include_date=True,
+                                                                                           include_hash=False )
                     rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
                         ( trans.security.encode_id( repository.id ), changeset_revision, label )
                 return rval
@@ -308,7 +311,11 @@ class RepositoryReviewsByUserGrid( grids.Grid ):
                 rval += 'edit_review'
             else:
                 rval +='browse_review'
-            revision_label = suc.get_revision_label( trans, review.repository, review.changeset_revision, include_date=True )
+            revision_label = hg_util.get_revision_label( trans,
+                                                         review.repository,
+                                                         review.changeset_revision,
+                                                         include_date=True,
+                                                         include_hash=False )
             rval += '?id=%s">%s</a>' % ( encoded_review_id, revision_label )
             return rval
 

lib/tool_shed/grids/util.py

@@ -1,7 +1,7 @@
 import logging
 import os
 import tool_shed.util.shed_util_common as suc
-import tool_shed.util.metadata_util as metadata_util
+from tool_shed.util import hg_util
 from galaxy.web.form_builder import SelectField
 from galaxy.util.bunch import Bunch
 
@@ -96,9 +96,11 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non
         repository_metadata_revisions = repository.metadata_revisions
     for repository_metadata in repository_metadata_revisions:
         rev, label, changeset_revision = \
-            metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans,
-                                                                                     repository_metadata,
-                                                                                     repository=repository )
+            hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans,
+                                                                               repository_metadata,
+                                                                               repository=repository,
+                                                                               include_date=True,
+                                                                               include_hash=False )
         changeset_tups.append( ( rev, label, changeset_revision ) )
         refresh_on_change_values.append( changeset_revision )
     # Sort options by the revision label.  Even though the downloadable_revisions query sorts by update_time,

lib/tool_shed/scripts/check_repositories_for_functional_tests.py

@@ -14,6 +14,7 @@ eggs.require( 'mercurial' )
 
 import ConfigParser
 import galaxy.webapps.tool_shed.config as tool_shed_config
+from tool_shed.util import hg_util
 import tool_shed.util.shed_util_common as suc
 import logging
 import shutil
@@ -109,7 +110,7 @@ def check_and_update_repository_metadata( app, info_only=False, verbosity=1 ):
         if tool_dicts is not None:
             # Clone the repository up to the changeset revision we're checking.
             repo_dir = repository.repo_path( app )
-            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
             work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cafr"  )
             cloned_ok, error_message = suc.clone_repository( repo_dir, work_dir, changeset_revision )
             if cloned_ok:
@@ -368,7 +369,7 @@ def should_set_do_not_test_flag( app, repository, changeset_revision, testable_r
     """
     if not testable_revision:
         repo_dir = repository.repo_path( app )
-        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
         changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True )
         if len( changeset_revisions ) > 1:
             latest_downloadable_revision = changeset_revisions[ -1 ]

lib/tool_shed/util/commit_util.py

@@ -12,6 +12,7 @@ from galaxy.util import json
 from galaxy.util.odict import odict
 from galaxy.web import url_for
 import tool_shed.util.shed_util_common as suc
+from tool_shed.util import hg_util
 from tool_shed.util import tool_util
 from tool_shed.util import xml_util
 import tool_shed.repository_types.util as rt_util
@@ -156,7 +157,7 @@ def handle_complex_repository_dependency_elem( trans, elem, sub_elem_index, sub_
 def handle_directory_changes( trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert,
                               commit_message, undesirable_dirs_removed, undesirable_files_removed ):
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     content_alert_str = ''
     files_to_remove = []
     filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ]
@@ -342,7 +343,7 @@ def handle_repository_dependency_elem( trans, elem, unpopulate=False ):
         repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
         if repository:
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
             lastest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo )
             if lastest_installable_changeset_revision != suc.INITIAL_CHANGELOG_HASH:
                 elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision

lib/tool_shed/util/export_util.py

@@ -14,6 +14,7 @@ from tool_shed.util import commit_util
 from tool_shed.util import common_install_util
 from tool_shed.util import common_util
 from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
 from tool_shed.util import repository_dependency_util
 from tool_shed.util import xml_util
 
@@ -37,7 +38,7 @@ class ExportedRepositoryRegistry( object ):
 
 def archive_repository_revision( trans, ui, repository, archive_dir, changeset_revision ):
     '''Create an un-versioned archive of a repository.'''
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     options_dict = suc.get_mercurial_default_options_dict( 'archive' )
     options_dict[ 'rev' ] = changeset_revision
     error_message = ''
@@ -233,8 +234,8 @@ def get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision
                                                                                        key_rd_dicts_to_be_processed=None,
                                                                                        all_repository_dependencies=None,
                                                                                        handled_key_rd_dicts=None )
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
+    ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
     repo_info_dict = {}
     # Cast unicode to string.
     repo_info_dict[ str( repository.name ) ] = ( str( repository.description ),

lib/tool_shed/util/hg_util.py

@@ -0,0 +1,108 @@
+import logging
+from datetime import datetime
+from time import gmtime
+from time import strftime
+
+from galaxy import eggs
+eggs.require( 'mercurial' )
+
+from mercurial import cmdutil
+from mercurial import commands
+from mercurial import hg
+from mercurial import ui
+
+def get_changectx_for_changeset( repo, changeset_revision, **kwd ):
+    """Retrieve a specified changectx from a repository."""
+    for changeset in repo.changelog:
+        ctx = repo.changectx( changeset )
+        if str( ctx ) == changeset_revision:
+            return ctx
+    return None
+
+def get_configured_ui():
+    """Configure any desired ui settings."""
+    _ui = ui.ui()
+    # The following will suppress all messages.  This is
+    # the same as adding the following setting to the repo
+    # hgrc file' [ui] section:
+    # quiet = True
+    _ui.setconfig( 'ui', 'quiet', True )
+    return _ui
+    
+def get_readable_ctx_date( ctx ):
+    """Convert the date of the changeset (the received ctx) to a human-readable date."""
+    t, tz = ctx.date()
+    date = datetime( *gmtime( float( t ) - tz )[ :6 ] )
+    ctx_date = date.strftime( "%Y-%m-%d" )
+    return ctx_date
+
+def get_revision_label( trans, repository, changeset_revision, include_date=True, include_hash=True ):
+    """
+    Return a string consisting of the human read-able changeset rev and the changeset revision string
+    which includes the revision date if the receive include_date is True.
+    """
+    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    if ctx:
+        return get_revision_label_from_ctx( ctx, include_date=include_date, include_hash=include_hash )
+    else:
+        if include_hash:
+            return "-1:%s" % changeset_revision
+        else:
+            return "-1"
+
+def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None,
+                                                               include_date=True, include_hash=True ):
+    if repository is None:
+        repository = repository_metadata.repository
+    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    changeset_revision = repository_metadata.changeset_revision
+    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    if ctx:
+        rev = '%04d' % ctx.rev()
+        if include_date:
+            changeset_revision_date = get_readable_ctx_date( ctx )
+            if include_hash:
+                label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date )
+            else:
+                label = "%s (%s)" % ( str( ctx.rev() ), changeset_revision_date )
+        else:
+            if include_hash:
+                label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
+            else:
+                label = "%s" % str( ctx.rev() )
+    else:
+        rev = '-1'
+        if include_hash:
+            label = "-1:%s" % changeset_revision
+        else:
+            label = "-1"
+    return rev, label, changeset_revision
+
+def get_revision_label_from_ctx( ctx, include_date=True, include_hash=True ):
+    if include_date:
+        if include_hash:
+            return '%s:%s <i><font color="#666666">(%s)</font></i>' % \
+                ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) )
+        else:
+            return '%s <i><font color="#666666">(%s)</font></i>' % \
+                ( str( ctx.rev() ), str( get_readable_ctx_date( ctx ) ) )
+    else:
+        if include_hash:
+            return '%s:%s' % ( str( ctx.rev() ), str( ctx ) )
+        else:
+            return '%s' % str( ctx.rev() )
+
+def get_rev_label_from_changeset_revision( repo, changeset_revision, include_date=True, include_hash=True ):
+    """
+    Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash
+    which includes the revision date if the receive include_date is True.
+    """
+    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    if ctx:
+        rev = '%04d' % ctx.rev()
+        label = get_revision_label_from_ctx( ctx, include_date=include_date )
+    else:
+        rev = '-1'
+        label = "-1:%s" % changeset_revision
+    return rev, label

lib/tool_shed/util/import_util.py

@@ -8,6 +8,7 @@ from galaxy import util
 from galaxy.datatypes import checkers
 from tool_shed.util import commit_util
 from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
 from tool_shed.util import metadata_util
 from tool_shed.util import xml_util
 import tool_shed.util.shed_util_common as suc
@@ -212,7 +213,7 @@ def import_repository_archive( trans, repository, repository_archive_dict ):
     archive_file_path = os.path.join( file_path, archive_file_name )
     archive = tarfile.open( archive_file_path, 'r:*' )
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     undesirable_dirs_removed = 0
     undesirable_files_removed = 0
     ok, error_message = commit_util.check_archive( repository, archive )

lib/tool_shed/util/metadata_util.py

@@ -15,6 +15,7 @@ from tool_shed.repository_types.metadata import TipOnly
 from tool_shed.util import common_util
 from tool_shed.util import common_install_util
 from tool_shed.util import container_util
+from tool_shed.util import hg_util
 from tool_shed.util import readme_util
 from tool_shed.util import tool_dependency_util
 from tool_shed.util import tool_util
@@ -347,7 +348,7 @@ def create_or_update_repository_metadata( trans, id, repository, changeset_revis
         # changeset revision in the received repository's changelog (up to the received changeset revision) to see if it is contained in the
         # skip_tool_test table.  If it is, but is not associated with a repository_metadata record, reset that skip_tool_test record to the
         # newly created repository_metadata record.
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         for changeset in repo.changelog:
             changeset_hash = str( repo.changectx( changeset ) )
             skip_tool_test = suc.get_skip_tool_test_by_changeset_revision( trans, changeset_hash )
@@ -1048,7 +1049,7 @@ def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_
 def get_latest_repository_metadata( trans, decoded_repository_id, downloadable=False ):
     """Get last metadata defined for a specified repository from the database."""
     repository = trans.sa_session.query( trans.model.Repository ).get( decoded_repository_id )
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     if downloadable:
         changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo )
     else:
@@ -1121,21 +1122,6 @@ def get_repository_metadata_revisions_for_review( repository, reviewed=True ):
                 repository_metadata_revisions.append( metadata_revision )
     return repository_metadata_revisions
 
-def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ):
-    if repository is None:
-        repository = repository_metadata.repository
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-    changeset_revision = repository_metadata.changeset_revision
-    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
-    if ctx:
-        changeset_revision_date = suc.get_readable_ctx_date( ctx )
-        rev = '%04d' % ctx.rev()
-        label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date )
-    else:
-        rev = '-1'
-        label = "-1:%s" % changeset_revision
-    return rev, label, changeset_revision
-
 def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None,
                                 resetting_all_metadata_on_repository=False ):
     if resetting_all_metadata_on_repository:
@@ -1294,7 +1280,7 @@ def handle_repository_elem( app, repository_elem, only_if_compiling_contained_td
                 log.debug( error_message )
                 is_valid = False
                 return repository_dependency_tup, is_valid, error_message
-            repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) )
+            repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( app ) )
             # The received changeset_revision may be None since defining it in the dependency definition is optional.
             # If this is the case, the default will be to set it's value to the repository dependency tip revision.
             # This probably occurs only when handling circular dependency definitions.
@@ -1360,7 +1346,7 @@ def is_level_one_certified( trans, repository ):
     """
     if repository.deleted:
         return ( None, False )
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     # Get the latest installable changeset revision since that is all that is currently configured for testing.
     latest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo )
     if latest_installable_changeset_revision not in [ None, suc.INITIAL_CHANGELOG_HASH ]:
@@ -1797,7 +1783,7 @@ def reset_all_metadata_on_repository_in_tool_shed( trans, id ):
     repository = suc.get_repository_in_tool_shed( trans, id )
     log.debug( "Resetting all metadata on repository: %s" % repository.name )
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
     # The list of changeset_revisions refers to repository_metadata records that have been created or updated.  When the following loop
     # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list.
@@ -1978,7 +1964,7 @@ def set_repository_metadata( trans, repository, content_alert_str='', **kwd ):
     encoded_id = trans.security.encode_id( repository.id )
     repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
                                                                                  repository=repository,
                                                                                  changeset_revision=repository.tip( trans.app ),

lib/tool_shed/util/readme_util.py

@@ -9,6 +9,7 @@ from galaxy.util import rst_to_html
 from galaxy.util import unicodify
 import tool_shed.util.shed_util_common as suc
 from tool_shed.util import common_util
+from tool_shed.util import hg_util
 
 eggs.require( 'mercurial' )
 
@@ -25,7 +26,7 @@ def build_readme_files_dict( trans, repository, changeset_revision, metadata, to
     if trans.webapp.name == 'galaxy':
         can_use_disk_files = True
     else:
-        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
         latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo )
         can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
     readme_files_dict = {}
@@ -74,7 +75,7 @@ def build_readme_files_dict( trans, repository, changeset_revision, metadata, to
                         readme_files_dict[ readme_file_name ] = text_of_reasonable_length
                 else:
                     # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest.
-                    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+                    ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
                     if ctx:
                         fctx = suc.get_file_context_from_ctx( ctx, readme_file_name )
                         if fctx and fctx not in [ 'DELETED' ]:

lib/tool_shed/util/repository_dependency_util.py

@@ -9,6 +9,7 @@ from tool_shed.util import common_util
 from tool_shed.util import common_install_util
 from tool_shed.util import container_util
 from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
 from tool_shed.util import metadata_util
 from tool_shed.util import tool_util
 
@@ -532,7 +533,7 @@ def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_d
                 else:
                     # The repository changeset_revision is no longer installable, so see if there's been an update.
                     repo_dir = repository.repo_path( trans.app )
-                    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+                    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
                     changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision )
                     repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans,
                                                                                                                      trans.security.encode_id( repository.id ),

lib/tool_shed/util/repository_maintenance_util.py

@@ -3,6 +3,7 @@ import logging
 import os
 import re
 import tool_shed.util.shed_util_common as suc
+from tool_shed.util import hg_util
 from tool_shed.util import import_util
 from galaxy import util
 from galaxy.web.form_builder import build_select_field
@@ -47,7 +48,7 @@ def create_hgrc_file( trans, repository ):
     # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api.  The hg
     # purge extension purges all files and directories not being tracked by mercurial in the current repository.  It'll remove unknown files
     # and empty directories.  This is not currently used because it is not supported in the mercurial API.
-    repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), path=repository.repo_path( trans.app ) )
     fp = repo.opener( 'hgrc', 'wb' )
     fp.write( '[paths]\n' )
     fp.write( 'default = .\n' )
@@ -83,7 +84,7 @@ def create_repository( trans, name, type, description, long_description, user_id
     if not os.path.exists( repository_path ):
         os.makedirs( repository_path )
     # Create the local repository.
-    repo = hg.repository( suc.get_configured_ui(), repository_path, create=True )
+    repo = hg.repository( hg_util.get_configured_ui(), repository_path, create=True )
     # Add an entry in the hgweb.config file for the local repository.
     lhs = "repos/%s/%s" % ( repository.user.username, repository.name )
     trans.app.hgweb_config_manager.add_entry( lhs, repository_path )

lib/tool_shed/util/review_util.py

@@ -3,6 +3,7 @@ import os
 from galaxy import eggs
 from galaxy.model.orm import and_
 from galaxy.util.odict import odict
+from tool_shed.util import hg_util
 import tool_shed.util.shed_util_common as suc
 
 eggs.require( 'mercurial' )
@@ -58,13 +59,13 @@ def get_components( trans ):
 
 def get_previous_repository_reviews( trans, repository, changeset_revision ):
     """Return an ordered dictionary of repository reviews up to and including the received changeset revision."""
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
     previous_reviews_dict = odict()
     for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ):
         previous_changeset_revision = str( repo.changectx( changeset ) )
         if previous_changeset_revision in reviewed_revision_hashes:
-            previous_rev, previous_changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, previous_changeset_revision )
+            previous_rev, previous_changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, previous_changeset_revision )
             revision_reviews = get_reviews_by_repository_id_changeset_revision( trans,
                                                                                 trans.security.encode_id( repository.id ),
                                                                                 previous_changeset_revision )
@@ -93,7 +94,7 @@ def get_reviews_by_repository_id_changeset_revision( trans, repository_id, chang
 
 def has_previous_repository_reviews( trans, repository, changeset_revision ):
     """Determine if a repository has a changeset revision review prior to the received changeset revision."""
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
     for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ):
         previous_changeset_revision = str( repo.changectx( changeset ) )

lib/tool_shed/util/shed_util_common.py

@@ -4,9 +4,6 @@ import re
 import shutil
 import string
 import tempfile
-from datetime import datetime
-from time import gmtime
-from time import strftime
 from galaxy import util
 from galaxy.util import asbool
 from galaxy.util import json
@@ -19,6 +16,7 @@ from galaxy.model.orm import or_
 import sqlalchemy.orm.exc
 from tool_shed.util import common_util
 from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
 from tool_shed.util import xml_util
 import tool_shed.repository_types.util as rt_util
 from xml.etree import ElementTree as XmlET
@@ -143,7 +141,7 @@ def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
 
 def changeset_is_valid( app, repository, changeset_revision ):
     """Make sure a changeset hash is valid for a specified repository."""
-    repo = hg.repository( get_configured_ui(), repository.repo_path( app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( app ) )
     for changeset in repo.changelog:
         changeset_hash = str( repo.changectx( changeset ) )
         if changeset_revision == changeset_hash:
@@ -167,7 +165,7 @@ def check_or_update_tool_shed_status_for_installed_repository( trans, repository
 def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ):
     """Clone the repository up to the specified changeset_revision.  No subsequent revisions will be present in the cloned repository."""
     try:
-        commands.clone( get_configured_ui(),
+        commands.clone( hg_util.get_configured_ui(),
                         str( repository_clone_url ),
                         dest=str( repository_file_dir ),
                         pull=True,
@@ -469,14 +467,6 @@ def get_category_by_name( trans, name ):
     except sqlalchemy.orm.exc.NoResultFound:
         return None
 
-def get_changectx_for_changeset( repo, changeset_revision, **kwd ):
-    """Retrieve a specified changectx from a repository."""
-    for changeset in repo.changelog:
-        ctx = repo.changectx( changeset )
-        if str( ctx ) == changeset_revision:
-            return ctx
-    return None
-
 def get_config( config_file, repo, ctx, dir ):
     """Return the latest version of config_filename from the repository manifest."""
     config_file = strip_path( config_file )
@@ -496,16 +486,6 @@ def get_config_from_disk( config_file, relative_install_dir ):
                     return os.path.abspath( os.path.join( root, name ) )
     return None
 
-def get_configured_ui():
-    """Configure any desired ui settings."""
-    _ui = ui.ui()
-    # The following will suppress all messages.  This is
-    # the same as adding the following setting to the repo
-    # hgrc file' [ui] section:
-    # quiet = True
-    _ui.setconfig( 'ui', 'quiet', True )
-    return _ui
-
 def get_ctx_rev( app, tool_shed_url, name, owner, changeset_revision ):
     """
     Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the
@@ -539,7 +519,7 @@ def get_current_repository_metadata_for_changeset_revision( trans, repository, c
     if repository_metadata:
         return repository_metadata
     # The installable changeset_revision may have been changed because it was "moved ahead" in the repository changelog.
-    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) )
     updated_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision=changeset_revision )
     if updated_changeset_revision:
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, updated_changeset_revision )
@@ -590,7 +570,7 @@ def get_dependent_downloadable_revisions( trans, repository_metadata ):
                                         # record, so updates must be necessary.
                                         defined_repository = get_repository_by_name_and_owner( trans.app, name, owner )
                                         defined_repo_dir = defined_repository.repo_path( trans.app )
-                                        defined_repo = hg.repository( get_configured_ui(), defined_repo_dir )
+                                        defined_repo = hg.repository( hg_util.get_configured_ui(), defined_repo_dir )
                                         updated_changeset_revision = \
                                             get_next_downloadable_changeset_revision( defined_repository,
                                                                                       defined_repo,
@@ -799,7 +779,7 @@ def get_ordered_metadata_changeset_revisions( repository, repo, downloadable=Tru
     changeset_tups = []
     for repository_metadata in metadata_revisions:
         changeset_revision = repository_metadata.changeset_revision
-        ctx = get_changectx_for_changeset( repo, changeset_revision )
+        ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
         if ctx:
             rev = '%04d' % ctx.rev()
         else:
@@ -913,13 +893,6 @@ def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, or
             return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
                                    .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False )
 
-def get_readable_ctx_date( ctx ):
-    """Convert the date of the changeset (the received ctx) to a human-readable date."""
-    t, tz = ctx.date()
-    date = datetime( *gmtime( float( t ) - tz )[ :6 ] )
-    ctx_date = date.strftime( "%Y-%m-%d" )
-    return ctx_date
-
 def get_repo_info_tuple_contents( repo_info_tuple ):
     """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced."""
     if len( repo_info_tuple ) == 6:
@@ -1211,38 +1184,6 @@ def get_reversed_changelog_changesets( repo ):
         reversed_changelog.insert( 0, changeset )
     return reversed_changelog
 
-def get_revision_label( trans, repository, changeset_revision, include_date=True ):
-    """
-    Return a string consisting of the human read-able changeset rev and the changeset revision string
-    which includes the revision date if the receive include_date is True.
-    """
-    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
-    ctx = get_changectx_for_changeset( repo, changeset_revision )
-    if ctx:
-        return get_revision_label_from_ctx( ctx, include_date=include_date )
-    else:
-        return "-1:%s" % changeset_revision
-
-def get_revision_label_from_ctx( ctx, include_date=True ):
-    if include_date:
-        return '%s:%s <i><font color="#666666">(%s)</font></i>' % \
-            ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) )
-    return '%s:%s' % ( str( ctx.rev() ), str( ctx ) )
-
-def get_rev_label_from_changeset_revision( repo, changeset_revision, include_date=True ):
-    """
-    Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash
-    which includes the revision date if the receive include_date is True.
-    """
-    ctx = get_changectx_for_changeset( repo, changeset_revision )
-    if ctx:
-        rev = '%04d' % ctx.rev()
-        label = get_revision_label_from_ctx( ctx, include_date=include_date )
-    else:
-        rev = '-1'
-        label = "-1:%s" % changeset_revision
-    return rev, label
-
 def get_shed_tool_conf_dict( app, shed_tool_conf ):
     """Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict associated with the file."""
     for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ):
@@ -1434,7 +1375,7 @@ def get_updated_changeset_revisions( trans, name, owner, changeset_revision ):
     """
     repository = get_repository_by_name_and_owner( trans.app, name, owner )
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     # Get the upper bound changeset revision.
     upper_bound_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
     # Build the list of changeset revision hashes defining each available update up to, but excluding, upper_bound_changeset_revision.
@@ -1487,7 +1428,7 @@ def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert
        that was included in the change set.
     """
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     sharable_link = generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None )
     smtp_server = trans.app.config.smtp_server
     if smtp_server and ( new_repo_alert or repository.email_alerts ):
@@ -1510,7 +1451,7 @@ def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert
             template = new_repo_email_alert_template
         else:
             template = email_alert_template
-        display_date = get_readable_ctx_date( ctx )
+        display_date = hg_util.get_readable_ctx_date( ctx )
         admin_body = string.Template( template ).safe_substitute( host=trans.request.host,
                                                                   sharable_link=sharable_link,
                                                                   repository_name=repository.name,
@@ -1859,7 +1800,7 @@ def update_repository( repo, ctx_rev=None ):
     # I = ignored
     # It would be nice if we could use mercurial's purge extension to remove untracked files.  The problem is that
     # purging is not supported by the mercurial API.
-    commands.update( get_configured_ui(), repo, rev=ctx_rev )
+    commands.update( hg_util.get_configured_ui(), repo, rev=ctx_rev )
 
 def update_tool_shed_repository_status( app, tool_shed_repository, status, error_message=None ):
     """Update the status of a tool shed repository in the process of being installed into Galaxy."""

lib/tool_shed/util/tool_util.py

@@ -15,6 +15,7 @@ from galaxy.util.expressions import ExpressionContext
 from galaxy.web.form_builder import SelectField
 from galaxy.tools.actions.upload import UploadToolAction
 from tool_shed.util import common_util
+from tool_shed.util import hg_util
 from tool_shed.util import xml_util
 import tool_shed.util.shed_util_common as suc
 from xml.etree import ElementTree as XmlET
@@ -538,7 +539,7 @@ def get_version_lineage_for_tool( trans, repository_id, repository_metadata, gui
     """
     repository = suc.get_repository_by_id( trans, repository_id )
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_dir )
     # Initialize the tool lineage
     version_lineage = [ guid ]
     # Get all ancestor guids of the received guid.
@@ -637,7 +638,7 @@ def handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, reposito
 def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, repository_id, changeset_revision, tool_config_filename, work_dir ):
     tool = None
     message = ''
-    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+    ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
     # We're not currently doing anything with the returned list of deleted_sample_files here.  It is intended to help handle sample files that are in
     # the manifest, but have been deleted from disk.
     sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir )
@@ -866,7 +867,7 @@ def load_tool_from_changeset_revision( trans, repository_id, changeset_revision,
     original_tool_data_path = trans.app.config.tool_data_path
     repository = suc.get_repository_in_tool_shed( trans, repository_id )
     repo_files_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_files_dir )
+    repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir )
     message = ''
     tool = None
     can_use_disk_file = False

scripts/migrate_tools/0010_tools.xml

@@ -3,17 +3,17 @@
     <repository owner="devteam" name="analyze_covariates" changeset_revision="738bc749f9a3" description="Analyze Covariates">
         <tool id="gatk_analyze_covariates" version="0.0.5" file="gatk/analyze_covariates.xml" />
     </repository>
-    <repository owner="devteam" name="basecoverage" changeset_revision="1e6a9e97fa41" description="Base Coverage of all intervals">
-        <tool id="gops_basecoverage_1" version="0.0.1" file="new_operations/basecoverage.xml" />
+    <repository owner="devteam" name="basecoverage" changeset_revision="642849141ae9" description="Base Coverage of all intervals">
+        <tool id="gops_basecoverage_1" version="1.0.0" file="new_operations/basecoverage.xml" />
     </repository>
-    <repository owner="devteam" name="best_regression_subsets" changeset_revision="e769cde223a5" description="Perform Best-subsets Regression">
-        <tool id="BestSubsetsRegression1" version="0.0.1" file="regVariation/best_regression_subsets.xml" />
+    <repository owner="devteam" name="best_regression_subsets" changeset_revision="4f33ec73e445" description="Perform Best-subsets Regression">
+        <tool id="BestSubsetsRegression1" version="1.0.0" file="regVariation/best_regression_subsets.xml" />
     </repository>
-    <repository owner="devteam" name="cluster" changeset_revision="d5677eecbad4" description="Cluster">
-        <tool id="gops_cluster_1" version="0.0.1" file="new_operations/cluster.xml" />
+    <repository owner="devteam" name="cluster" changeset_revision="9fcc3a1c3d26" description="Cluster">
+        <tool id="gops_cluster_1" version="1.0.0" file="new_operations/cluster.xml" />
     </repository>
-    <repository owner="devteam" name="complement" changeset_revision="d958d5a0d1e8" description="Complement intervals of a dataset">
-        <tool id="gops_complement_1" version="0.0.1" file="new_operations/complement.xml" />
+    <repository owner="devteam" name="complement" changeset_revision="67c4ed724bfd" description="Complement intervals of a dataset">
+        <tool id="gops_complement_1" version="1.0.0" file="new_operations/complement.xml" />
     </repository>
     <repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values">
         <tool id="compute_q_values" version="1.0.1" file="regVariation/compute_q_values.xml" />
@@ -24,8 +24,8 @@
     <repository owner="devteam" name="count_covariates" changeset_revision="14e304b70425" description="Count Covariates on BAM files">
         <tool id="gatk_count_covariates" version="0.0.5" file="gatk/count_covariates.xml" />
     </repository>
-    <repository owner="devteam" name="coverage" changeset_revision="1e864693a1c0" description="Coverage of a set of intervals on second set of intervals">
-        <tool id="gops_coverage_1" version="0.0.1" file="new_operations/coverage.xml" />
+    <repository owner="devteam" name="coverage" changeset_revision="16b62a897aac" description="Coverage of a set of intervals on second set of intervals">
+        <tool id="gops_coverage_1" version="1.0.0" file="new_operations/coverage.xml" />
     </repository>
     <repository owner="devteam" name="depth_of_coverage" changeset_revision="c3f08370fc82" description="Depth of Coverage on BAM files">
         <tool id="gatk_depth_of_coverage" version="0.0.2" file="gatk/depth_of_coverage.xml" />
@@ -36,23 +36,23 @@
     <repository owner="devteam" name="flanking_features" changeset_revision="90100b587723" description="Fetch closest non-overlapping feature for every interval">
         <tool id="flanking_features_1" version="4.0.1" file="new_operations/flanking_features.xml" />
     </repository>
-    <repository owner="devteam" name="get_flanks" changeset_revision="a72f0decd7b3" description="Get flanks - returns flanking region/s for every gene">
-        <tool id="get_flanks1" version="0.0.1" file="new_operations/get_flanks.xml" />
+    <repository owner="devteam" name="get_flanks" changeset_revision="c3b1781c6fd1" description="Get flanks - returns flanking region/s for every gene">
+        <tool id="get_flanks1" version="1.0.0" file="new_operations/get_flanks.xml" />
     </repository>
     <repository owner="devteam" name="getindelrates_3way" changeset_revision="d427e5acb9ee" description="Estimate Indel Rates for 3-way alignments">
         <tool id="indelRates_3way" version="1.0.0" file="regVariation/getIndelRates_3way.xml" />
     </repository>
-    <repository owner="devteam" name="getindels_2way" changeset_revision="91655316fcf0" description="Fetch Indels from pairwise alignments">
-        <tool id="getIndels_2way" version="0.0.1" file="regVariation/getIndels_2way.xml" />
+    <repository owner="devteam" name="getindels_2way" changeset_revision="f1dc6f5fce6e" description="Fetch Indels from pairwise alignments">
+        <tool id="getIndels_2way" version="1.0.0" file="regVariation/getIndels_2way.xml" />
     </repository>
     <repository owner="devteam" name="indel_realigner" changeset_revision="bb0beda6cf83" description="Indel Realigner - perform local realignment">
         <tool id="gatk_indel_realigner" version="0.0.6" file="gatk/indel_realigner.xml" />
     </repository>
-    <repository owner="devteam" name="intersect" changeset_revision="5b3c6135a982" description="Intersect the intervals of two datasets">
-        <tool id="gops_intersect_1" version="0.0.1" file="new_operations/intersect.xml" />
+    <repository owner="devteam" name="intersect" changeset_revision="81ad85f731b9" description="Intersect the intervals of two datasets">
+        <tool id="gops_intersect_1" version="1.0.0" file="new_operations/intersect.xml" />
     </repository>
-    <repository owner="devteam" name="join" changeset_revision="e56b47dce68a" description="Join the intervals of two datasets side-by-side">
-        <tool id="gops_join_1" version="0.0.1" file="new_operations/join.xml" />
+    <repository owner="devteam" name="join" changeset_revision="11a49f94d086" description="Join the intervals of two datasets side-by-side">
+        <tool id="gops_join_1" version="1.0.0" file="new_operations/join.xml" />
     </repository>
     <repository owner="devteam" name="linear_regression" changeset_revision="cf431604ec3e" description="Perform Linear Regression">
         <tool id="LinearRegression1" version="1.0.1" file="regVariation/linear_regression.xml" />
@@ -63,11 +63,11 @@
     <repository owner="devteam" name="maf_cpg_filter" changeset_revision="7f2a12cb047d" description="Mask CpG/non-CpG sites from MAF file">
         <tool id="cpgFilter" version="1.0.0" file="regVariation/maf_cpg_filter.xml" />
     </repository>
-    <repository owner="devteam" name="merge" changeset_revision="b488a1fa07f6" description="Merge the overlapping intervals of a dataset">
-        <tool id="gops_merge_1" version="0.0.1" file="new_operations/merge.xml" />
+    <repository owner="devteam" name="merge" changeset_revision="55e88307811d" description="Merge the overlapping intervals of a dataset">
+        <tool id="gops_merge_1" version="1.0.0" file="new_operations/merge.xml" />
     </repository>
-    <repository owner="devteam" name="microsats_alignment_level" changeset_revision="d4368a5a3fc7" description="Extract Orthologous Microsatellites from pair-wise alignments">
-        <tool id="microsats_align1" version="0.0.1" file="regVariation/microsats_alignment_level.xml" />
+    <repository owner="devteam" name="microsats_alignment_level" changeset_revision="7852385470f3" description="Extract Orthologous Microsatellites from pair-wise alignments">
+        <tool id="microsats_align1" version="1.0.0" file="regVariation/microsats_alignment_level.xml" />
     </repository>
     <repository owner="devteam" name="microsats_mutability" changeset_revision="4aa1ee5d8510" description="Estimate microsatellite mutability by specified attributes">
         <tool id="microsats_mutability1" version="1.1.0" file="regVariation/microsats_mutability.xml" />
@@ -93,8 +93,8 @@
     <repository owner="devteam" name="substitutions" changeset_revision="c54f5d0bbb58" description="Fetch substitutions from pairwise alignments">
         <tool id="substitutions1" version="1.0.0" file="regVariation/substitutions.xml" />
     </repository>
-    <repository owner="devteam" name="subtract" changeset_revision="5bc2dacbe729" description="Subtract the intervals of two datasets">
-        <tool id="gops_subtract_1" version="0.0.1" file="new_operations/subtract.xml" />
+    <repository owner="devteam" name="subtract" changeset_revision="7bf44b9d7a8b" description="Subtract the intervals of two datasets">
+        <tool id="gops_subtract_1" version="1.0.0" file="new_operations/subtract.xml" />
     </repository>
     <repository owner="devteam" name="subtract_query" changeset_revision="5f6ebef89722" description="Subtract Whole Dataset from another dataset">
         <tool id="subtract_query1" version="0.1" file="new_operations/subtract_query.xml" />
@@ -135,7 +135,7 @@
     <repository owner="devteam" name="weightedaverage" changeset_revision="90611e86a998" description="Assign weighted-average of the values of features overlapping an interval">
         <tool id="wtavg" version="1.0.0" file="regVariation/WeightedAverage.xml" />
     </repository>
-    <repository owner="devteam" name="windowsplitter" changeset_revision="e5490ea33640" description="Make windows">
-        <tool id="winSplitter" version="0.0.1" file="regVariation/windowSplitter.xml" />
+    <repository owner="devteam" name="windowsplitter" changeset_revision="75abda2290cc" description="Make windows">
+        <tool id="winSplitter" version="1.0.0" file="regVariation/windowSplitter.xml" />
     </repository>
 </toolshed>

static/scripts/galaxy.library.js

@@ -2,28 +2,30 @@
 // === MAIN GALAXY LIBRARY MODULE ====
 // MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
 
-// global variables
-var library_router  = null;
-
 // dependencies
 define([
-    "galaxy.masthead", 
+    "galaxy.masthead",
     "utils/utils",
     "libs/toastr",
     "mvc/base-mvc",
     "mvc/library/library-model",
     "mvc/library/library-folderlist-view",
     "mvc/library/library-librarylist-view",
-    "mvc/library/library-librarytoolbar-view"], 
-function(mod_masthead, 
-         mod_utils, 
+    "mvc/library/library-librarytoolbar-view",
+    "mvc/library/library-foldertoolbar-view"
+    ],
+function(mod_masthead,
+         mod_utils,
          mod_toastr,
          mod_baseMVC,
          mod_library_model,
          mod_folderlist_view,
          mod_librarylist_view,
-         mod_librarytoolbar_view) {
+         mod_librarytoolbar_view,
+         mod_foldertoolbar_view
+         ) {
 
+// ============================================================================
 //ROUTER
 var LibraryRouter = Backbone.Router.extend({
     routes: {
@@ -44,12 +46,14 @@ var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({
     }
 });
 
-// galaxy library wrapper View
+// ============================================================================
+// Main controller of Galaxy Library
 var GalaxyLibrary = Backbone.View.extend({
-    toolbarView: null,
+    libraryToolbarView: null,
     libraryListView: null,
     library_router: null,
-    folderContentView: null,
+    folderToolbarView: null,
+    folderListView: null,
     initialize : function(){
         Galaxy.libraries = this;
 
@@ -59,25 +63,26 @@ var GalaxyLibrary = Backbone.View.extend({
 
         this.library_router.on('route:libraries', function() {
           // initialize and render the toolbar first
-          Galaxy.libraries.toolbarView = new mod_librarytoolbar_view.ToolbarView();
+          Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
           // initialize and render libraries second
           Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
         });
 
         this.library_router.on('route:folder_content', function(id) {
-          // render folder contents
-          if (!Galaxy.libraries.folderContentView) {Galaxy.libraries.folderContentView = new mod_folderlist_view.FolderContentView();}
-          Galaxy.libraries.folderContentView.render({id: id});
+            // TODO place caching here, sessionstorage/localstorage?
+            Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id});
+            Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id});
         });
 
        this.library_router.on('route:download', function(folder_id, format) {
-          if ($('#center').find(':checked').length === 0) { 
+          if ($('#center').find(':checked').length === 0) {
+            mod_toastr.info('You have to select some datasets to download')
             // this happens rarely when there is a server/data error and client gets an actual response instead of an attachment
             // we don't know what was selected so we can't download again, we redirect to the folder provided
             Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true});
           } else {
             // send download stream
-            Galaxy.libraries.folderContentView.download(folder_id, format);
+            Galaxy.libraries.folderToolbarView.download(folder_id, format);
             Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true});
           }
         });
@@ -86,7 +91,6 @@ var GalaxyLibrary = Backbone.View.extend({
     }
 });
 
-// return
 return {
     GalaxyApp: GalaxyLibrary
 };

static/scripts/galaxy.workflow_editor.canvas.js

@@ -172,101 +172,98 @@ function Node( element ) {
 }
 $.extend( Node.prototype, {
     new_input_terminal : function( input ) {
-        var t = $("<div class='terminal input-terminal'></div>");
+        var t = $("<div class='terminal input-terminal'></div>")[ 0 ];
         this.enable_input_terminal( t, input.name, input.extensions, input.multiple );
         return t;
     },
-    enable_input_terminal : function( elements, name, types, multiple ) {
+    enable_input_terminal : function( element, name, types, multiple ) {
         var node = this;
-        $(elements).each( function() {
-            var terminal = this.terminal = new InputTerminal( this, types, multiple );
-            terminal.node = node;
-            terminal.name = name;
-            $(this).bind( "dropinit", function( e, d ) {
-                // Accept a dragable if it is an output terminal and has a
-                // compatible type
-                return $(d.drag).hasClass( "output-terminal" ) && terminal.can_accept( d.drag.terminal );
-            }).bind( "dropstart", function( e, d  ) {
-                if (d.proxy.terminal) { 
-                    d.proxy.terminal.connectors[0].inner_color = "#BBFFBB";
-                }
-            }).bind( "dropend", function ( e, d ) {
-                if (d.proxy.terminal) { 
-                    d.proxy.terminal.connectors[0].inner_color = "#FFFFFF";
-                }
-            }).bind( "drop", function( e, d ) {
-                ( new Connector( d.drag.terminal, terminal ) ).redraw();
-            }).bind( "hover", function() {
-                // If connected, create a popup to allow disconnection
-                if ( terminal.connectors.length > 0 ) {
-                    // Create callout
-                    var t = $("<div class='callout'></div>")
-                        .css( { display: 'none' } )
-                        .appendTo( "body" )
-                        .append(
-                            $("<div class='button'></div>").append(
-                                $("<div/>").addClass("fa-icon-button fa fa-times").click( function() {
-                                    $.each( terminal.connectors, function( _, x ) {
-                                        if (x) {
-                                            x.destroy();
-                                        }
-                                    });
-                                    t.remove();
-                                })))
-                        .bind( "mouseleave", function() {
-                            $(this).remove();
-                        });
-                    // Position it and show
-                    t.css({
-                            top: $(this).offset().top - 2,
-                            left: $(this).offset().left - t.width(),
-                            'padding-right': $(this).width()
-                        }).show();
-                }
-            });
-            node.input_terminals[name] = terminal;
+
+        var terminal = element.terminal = new InputTerminal( element, types, multiple );
+        terminal.node = node;
+        terminal.name = name;
+        $(element).bind( "dropinit", function( e, d ) {
+            // Accept a dragable if it is an output terminal and has a
+            // compatible type
+            return $(d.drag).hasClass( "output-terminal" ) && terminal.can_accept( d.drag.terminal );
+        }).bind( "dropstart", function( e, d  ) {
+            if (d.proxy.terminal) { 
+                d.proxy.terminal.connectors[0].inner_color = "#BBFFBB";
+            }
+        }).bind( "dropend", function ( e, d ) {
+            if (d.proxy.terminal) { 
+                d.proxy.terminal.connectors[0].inner_color = "#FFFFFF";
+            }
+        }).bind( "drop", function( e, d ) {
+            ( new Connector( d.drag.terminal, terminal ) ).redraw();
+        }).bind( "hover", function() {
+            // If connected, create a popup to allow disconnection
+            if ( terminal.connectors.length > 0 ) {
+                // Create callout
+                var t = $("<div class='callout'></div>")
+                    .css( { display: 'none' } )
+                    .appendTo( "body" )
+                    .append(
+                        $("<div class='button'></div>").append(
+                            $("<div/>").addClass("fa-icon-button fa fa-times").click( function() {
+                                $.each( terminal.connectors, function( _, x ) {
+                                    if (x) {
+                                        x.destroy();
+                                    }
+                                });
+                                t.remove();
+                            })))
+                    .bind( "mouseleave", function() {
+                        $(this).remove();
+                    });
+                // Position it and show
+                t.css({
+                        top: $(element).offset().top - 2,
+                        left: $(element).offset().left - t.width(),
+                        'padding-right': $(element).width()
+                    }).show();
+            }
         });
+        node.input_terminals[name] = terminal;
     },
-    enable_output_terminal : function( elements, name, type ) {
+    enable_output_terminal : function( element, name, type ) {
         var node = this;
-        $(elements).each( function() {
-            var terminal_element = this;
-            var terminal = this.terminal = new OutputTerminal( this, type );
-            terminal.node = node;
-            terminal.name = name;
-            $(this).bind( "dragstart", function( e, d ) { 
-                $( d.available ).addClass( "input-terminal-active" );
-                // Save PJAs in the case of change datatype actions.
-                workflow.check_changes_in_active_form(); 
-                // Drag proxy div
-                var h = $( '<div class="drag-terminal" style="position: absolute;"></div>' )
-                    .appendTo( "#canvas-container" ).get(0);
-                // Terminal and connection to display noodle while dragging
-                h.terminal = new OutputTerminal( h );
-                var c = new Connector();
-                c.dragging = true;
-                c.connect( this.terminal, h.terminal );
-                return h;
-            }).bind( "drag", function ( e, d ) {
-                var onmove = function() {
-                    var po = $(d.proxy).offsetParent().offset(),
-                        x = d.offsetX - po.left,
-                        y = d.offsetY - po.top;
-                    $(d.proxy).css( { left: x, top: y } );
-                    d.proxy.terminal.redraw();
-                    // FIXME: global
-                    canvas_manager.update_viewport_overlay();
-                };
-                onmove();
-                $("#canvas-container").get(0).scroll_panel.test( e, onmove );
-            }).bind( "dragend", function ( e, d ) {
-                d.proxy.terminal.connectors[0].destroy();
-                $(d.proxy).remove();
-                $( d.available ).removeClass( "input-terminal-active" );
-                $("#canvas-container").get(0).scroll_panel.stop();
-            });
-            node.output_terminals[name] = terminal;
+        var terminal_element = element;
+        var terminal = element.terminal = new OutputTerminal( element, type );
+        terminal.node = node;
+        terminal.name = name;
+        $(element).bind( "dragstart", function( e, d ) { 
+            $( d.available ).addClass( "input-terminal-active" );
+            // Save PJAs in the case of change datatype actions.
+            workflow.check_changes_in_active_form(); 
+            // Drag proxy div
+            var h = $( '<div class="drag-terminal" style="position: absolute;"></div>' )
+                .appendTo( "#canvas-container" ).get(0);
+            // Terminal and connection to display noodle while dragging
+            h.terminal = new OutputTerminal( h );
+            var c = new Connector();
+            c.dragging = true;
+            c.connect( element.terminal, h.terminal );
+            return h;
+        }).bind( "drag", function ( e, d ) {
+            var onmove = function() {
+                var po = $(d.proxy).offsetParent().offset(),
+                    x = d.offsetX - po.left,
+                    y = d.offsetY - po.top;
+                $(d.proxy).css( { left: x, top: y } );
+                d.proxy.terminal.redraw();
+                // FIXME: global
+                canvas_manager.update_viewport_overlay();
+            };
+            onmove();
+            $("#canvas-container").get(0).scroll_panel.test( e, onmove );
+        }).bind( "dragend", function ( e, d ) {
+            d.proxy.terminal.connectors[0].destroy();
+            $(d.proxy).remove();
+            $( d.available ).removeClass( "input-terminal-active" );
+            $("#canvas-container").get(0).scroll_panel.stop();
         });
+        node.output_terminals[name] = terminal;
     },
     redraw : function () {
         $.each( this.input_terminals, function( _, t ) {
@@ -342,7 +339,7 @@ $.extend( Node.prototype, {
         }
         $.each( data.data_outputs, function( i, output ) {
             var t = $( "<div class='terminal output-terminal'></div>" );
-            node.enable_output_terminal( t, output.name, output.extensions );
+            node.enable_output_terminal( t[ 0 ], output.name, output.extensions );
             var label = output.name;
             if ( output.extensions.indexOf( 'input' ) < 0 ) {
                 label = label + " (" + output.extensions.join(", ") + ")";
@@ -422,7 +419,6 @@ $.extend( Node.prototype, {
         // Update input rows
         var old_body = el.find( "div.inputs" );
         var new_body = $("<div class='inputs'></div>");
-        var old = old_body.find( "div.input-data-row");
         $.each( data.data_inputs, function( i, input ) {
             var t = node.new_input_terminal( input );
             // If already connected save old connection
@@ -430,8 +426,8 @@ $.extend( Node.prototype, {
                 $(this).find( ".input-terminal" ).each( function() {
                     var c = this.terminal.connectors[0];
                     if ( c ) {
-                        t[0].terminal.connectors[0] = c;
-                        c.handle2 = t[0].terminal;
+                        t.terminal.connectors[0] = c;
+                        c.handle2 = t.terminal;
                     }
                 });
                 $(this).remove();
@@ -893,6 +889,18 @@ function prebuild_node( type, title_text, tool_id ) {
     return node;
 }
 
+function add_node( type, title_text, tool_id ) {
+    // Abstraction for use by galaxy.workflow.js to hide
+    // some editor details from workflow code and reduce duplication
+    // between add_node_for_tool and add_node_for_module.
+    var node = prebuild_node( type, title_text, tool_id );
+    workflow.add_node( node );
+    workflow.fit_canvas_to_nodes();
+    canvas_manager.draw_overview();
+    workflow.activate_node( node );    
+    return node;
+}
+
 
 var ext_to_type = null;
 var type_to_type = null;

static/scripts/galaxy.workflows.js

@@ -320,11 +320,7 @@ function scroll_to_nodes() {
 
 // Add a new step to the workflow by tool id
 function add_node_for_tool( id, title ) {
-    var node = prebuild_node( 'tool', title, id );
-    workflow.add_node( node );
-    workflow.fit_canvas_to_nodes();
-    canvas_manager.draw_overview();
-    workflow.activate_node( node );
+    node = add_node( 'tool', title, id );
     $.ajax( {
         url: get_new_module_info_url,
         data: { type: "tool", tool_id: id, "_": "true" },
@@ -344,11 +340,7 @@ function add_node_for_tool( id, title ) {
 }
 
 function add_node_for_module( type, title ) {
-    node = prebuild_node( type, title );
-    workflow.add_node( node );
-    workflow.fit_canvas_to_nodes();
-    canvas_manager.draw_overview();
-    workflow.activate_node( node );
+    node = add_node( type, title );
     $.ajax( {
         url: get_new_module_info_url,
         data: { type: type, "_": "true" },

static/scripts/mvc/library/library-folderlist-view.js

@@ -1,458 +1,126 @@
 // dependencies
 define([
-    "galaxy.masthead", 
+    "galaxy.masthead",
     "utils/utils",
     "libs/toastr",
-    "mvc/library/library-model"], 
-function(mod_masthead, 
-         mod_utils, 
+    "mvc/library/library-model",
+    "mvc/library/library-folderrow-view"],
+function(mod_masthead,
+         mod_utils,
          mod_toastr,
-         mod_library_model) {
+         mod_library_model,
+         mod_library_folderrow_view) {
 
-  //main view for folder browsing
-var FolderContentView = Backbone.View.extend({
-    // main element definition
-    el : '#center',
-    // progress percentage
-    progress: 0,
-    // progress rate per one item
-    progressStep: 1,
-    // last selected history in modal for UX
-    lastSelectedHistory: '',
-    // self modal
-    modal : null,
-    // loaded folders
-    folders : null,
+var FolderListView = Backbone.View.extend({
+  // main element definition
+  el : '#folder_items_element',
+  // progress percentage
+  progress: 0,
+  // progress rate per one item
+  progressStep: 1,
+  // self modal
+  modal : null,
 
+  folderContainer: null,
+
+  // event binding
+  events: {
+    'click #select-all-checkboxes' : 'selectAll',
+    'click .dataset_row' : 'selectClickedRow'
+  },
     // initialize
-    initialize : function(){
-        this.folders = [];
+    initialize : function(options){
+        var that = this;
+        this.options = _.defaults(this.options || {}, options);
         this.queue = jQuery.Deferred();
         this.queue.resolve();
-    },
-
-// MMMMMMMMMMMMMMMMMM
-// === TEMPLATES ====
-// MMMMMMMMMMMMMMMMMM
-
-    // main template for folder browsing
-    templateFolder : function (){
-        var tmpl_array = [];
-
-        // CONTAINER
-        tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');
-        tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-folders" target="_blank">Trello</a>.</h3>');
-
-        // TOOLBAR
-        tmpl_array.push('<div id="library_folder_toolbar" >');
-        tmpl_array.push('   <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span> <span class="fa fa-folder-close"></span> folder</button>');
-        tmpl_array.push('   <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>');
-        tmpl_array.push('   <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');
-        tmpl_array.push('       <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
-        tmpl_array.push('       <span class="fa fa-download"></span> download <span class="caret"></span>');
-        tmpl_array.push('       </button>');
-        tmpl_array.push('       <ul class="dropdown-menu" role="menu">');
-        tmpl_array.push('          <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');
-        tmpl_array.push('          <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');
-        tmpl_array.push('          <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');
-        tmpl_array.push('       </ul>');
-        tmpl_array.push('   </div>');
-
-        tmpl_array.push('</div>');
-
-        // BREADCRUMBS
-        tmpl_array.push('<ol class="breadcrumb">');
-        tmpl_array.push('   <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
-        tmpl_array.push('   <% _.each(path, function(path_item) { %>');
-        tmpl_array.push('   <% if (path_item[0] != id) { %>');
-        tmpl_array.push('   <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ');
-        tmpl_array.push(    '<% } else { %>');
-        tmpl_array.push('   <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
-        tmpl_array.push('   <% } %>');
-        tmpl_array.push('   <% }); %>');
-        tmpl_array.push('</ol>');
-
-
-        // FOLDER CONTENT
-        tmpl_array.push('<table id="folder_table" class="grid table table-condensed">');
-        tmpl_array.push('   <thead>');
-        tmpl_array.push('       <th class="button_heading"></th>');
-        tmpl_array.push('       <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
-        tmpl_array.push('       <th>name</th>');
-        tmpl_array.push('       <th>data type</th>');
-        tmpl_array.push('       <th>size</th>');
-        tmpl_array.push('       <th>date (UTC)</th>');
-        tmpl_array.push('   </thead>');
-        tmpl_array.push('   <tbody>');
-        tmpl_array.push('       <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
-        tmpl_array.push('       <td></td>');
-        tmpl_array.push('       <td></td>');
-        tmpl_array.push('       <td></td>');
-        tmpl_array.push('       <td></td>');
-        tmpl_array.push('       <td></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <% _.each(items, function(content_item) { %>');
-        tmpl_array.push('           <% if (content_item.get("type") === "folder") { %>'); // folder
-        tmpl_array.push('               <tr class="folder_row light" id="<%- content_item.id %>">');
-        tmpl_array.push('                   <td>');
-        tmpl_array.push('                       <span title="Folder" class="fa fa-folder-o"></span>');
-        tmpl_array.push('                   </td>');
-        tmpl_array.push('                   <td></td>');
-        tmpl_array.push('                   <td>');
-        tmpl_array.push('                       <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');
-        tmpl_array.push('                       <% if (content_item.get("item_count") === 0) { %>'); // empty folder
-        tmpl_array.push('                           <span class="muted">(empty folder)</span>');
-        tmpl_array.push('                       <% } %>');
-        tmpl_array.push('                   </td>');
-        tmpl_array.push('                   <td>folder</td>');
-        tmpl_array.push('                   <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size
-        tmpl_array.push('                   <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
-        tmpl_array.push('               </tr>');
-        tmpl_array.push('           <% } else {  %>');
-        tmpl_array.push('               <tr class="dataset_row light" id="<%- content_item.id %>">');
-        tmpl_array.push('                   <td>');
-        tmpl_array.push('                       <span title="Dataset" class="fa fa-file-o"></span>');
-        tmpl_array.push('                   </td>');
-        tmpl_array.push('                   <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');
-        tmpl_array.push('                   <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset
-        tmpl_array.push('                   <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type
-        tmpl_array.push('                   <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size
-        tmpl_array.push('                   <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
-        tmpl_array.push('               </tr>');
-        tmpl_array.push('               <% } %>  ');
-        tmpl_array.push('       <% }); %>');
-        tmpl_array.push('       ');
-        tmpl_array.push('   </tbody>');
-        tmpl_array.push('</table>');
-
-        tmpl_array.push('</div>');
-        return tmpl_array.join('');
-    },
-    templateDatasetModal : function(){
-        var tmpl_array = [];
-
-        tmpl_array.push('<div class="modal_table">');
-        tmpl_array.push('   <table class="grid table table-striped table-condensed">');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
-        tmpl_array.push('           <td><%= _.escape(item.get("name")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row">Data type</th>');
-        tmpl_array.push('           <td><%= _.escape(item.get("data_type")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row">Genome build</th>');
-        tmpl_array.push('           <td><%= _.escape(item.get("genome_build")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('           <th scope="row">Size</th>');
-        tmpl_array.push('           <td><%= _.escape(size) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row">Date uploaded (UTC)</th>');
-        tmpl_array.push('           <td><%= _.escape(item.get("date_uploaded")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row">Uploaded by</th>');
-        tmpl_array.push('           <td><%= _.escape(item.get("uploaded_by")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('           <tr scope="row">');
-        tmpl_array.push('           <th scope="row">Data Lines</th>');
-        tmpl_array.push('           <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <th scope="row">Comment Lines</th>');
-        tmpl_array.push('           <% if (item.get("metadata_comment_lines") === "") { %>');
-        tmpl_array.push('               <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');
-        tmpl_array.push('           <% } else { %>');
-        tmpl_array.push('               <td scope="row">unknown</td>');
-        tmpl_array.push('           <% } %>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row">Number of Columns</th>');
-        tmpl_array.push('           <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row">Column Types</th>');
-        tmpl_array.push('           <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('       <tr>');
-        tmpl_array.push('           <th scope="row">Miscellaneous information</th>');
-        tmpl_array.push('           <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');
-        tmpl_array.push('       </tr>');
-        tmpl_array.push('   </table>');
-        tmpl_array.push('   <pre class="peek">');
-        tmpl_array.push('   </pre>');
-        tmpl_array.push('</div>');
-
-        return tmpl_array.join('');
-    },
-
-    templateHistorySelectInModal : function(){
-        var tmpl_array = [];
-
-        tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');
-        tmpl_array.push('Select history: ');
-        tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');
-        tmpl_array.push('   <% _.each(histories, function(history) { %>'); //history select box
-        tmpl_array.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
-        tmpl_array.push('   <% }); %>');
-        tmpl_array.push('</select>');
-        tmpl_array.push('</span>');
-
-        return tmpl_array.join('');
-        },
-
-    templateBulkImportInModal : function(){
-        var tmpl_array = [];
-
-        tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');
-        tmpl_array.push('Select history: ');
-        tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');
-        tmpl_array.push('   <% _.each(histories, function(history) { %>'); //history select box
-        tmpl_array.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
-        tmpl_array.push('   <% }); %>');
-        tmpl_array.push('</select>');
-        tmpl_array.push('</span>');
-
-        return tmpl_array.join('');
-        },
-
-      templateProgressBar : function (){
-        var tmpl_array = [];
-
-        tmpl_array.push('<div class="import_text">');
-        tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>');
-        tmpl_array.push('</div>');
-        tmpl_array.push('<div class="progress">');
-        tmpl_array.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
-        tmpl_array.push('       <span class="completion_span">0% Complete</span>');
-        tmpl_array.push('   </div>');
-        tmpl_array.push('</div>');
-        tmpl_array.push('');
-
-        return tmpl_array.join('');
-      },
-
-    templateNewFolderInModal: function(){
-        tmpl_array = [];
-
-        tmpl_array.push('<div id="new_folder_modal">');
-        tmpl_array.push('<form>');
-        tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');
-        tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');
-        tmpl_array.push('</form>');
-        tmpl_array.push('</div>');
-
-        return tmpl_array.join('');
-    },
-
-// MMMMMMMMMMMMMMM
-// === EVENTS ====
-// MMMMMMMMMMMMMMM
-
-      // event binding
-      events: {
-            'click #select-all-checkboxes' : 'selectAll',
-            'click #toolbtn_bulk_import' : 'modalBulkImport',
-            'click #toolbtn_dl' : 'bulkDownload',
-            'click #toolbtn_create_folder' : 'createFolderFromModal',
-            'click .library-dataset' : 'showDatasetDetails',
-            'click .dataset_row' : 'selectClickedRow'
-        },
-
-// MMMMMMMMMMMMMMMMMM
-// === FUNCTIONS ====
-// MMMMMMMMMMMMMMMMMM
-
-      //render the folder view
-      render: function (options) {
-        //hack to show scrollbars
-        $("#center").css('overflow','auto');
-
-        view = this;
-        var that = this;
-
-        var folderContainer = new mod_library_model.FolderContainer({id: options.id});
-        folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents';
-
-        folderContainer.fetch({
-          success: function (container) {
-
-            // prepare nice size strings
-              for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) {
-                  var model = folderContainer.attributes.folder.models[i]
-                  if (model.get('type') === 'file'){
-                    model.set('readable_size', that.size_to_string(model.get('file_size')))
-                  }
-              };
-
-              // find the upper id
-              var path = folderContainer.full_path;
-              var upper_folder_id;
-              if (path.length === 1){ // library is above us
-                upper_folder_id = 0;
-              } else {
-                upper_folder_id = path[path.length-2][0];
-              }
-
-              var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id });
-              // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id });
-              that.$el.html(template);
 
+        this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id});
+        this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents';
+        this.folderContainer.fetch({
+            success: function (folderContainer) {
+                that.render();
             },
-              error: function(){
-                mod_toastr.error('An error occured :(');
-              }
-          })
-        },
+            error: function(){
+              mod_toastr.error('An error occured :(');
+            }
+        });
+    },
+
+    render: function (options) {
+      this.options = _.defaults(this.options || {}, options);
+      var template = this.templateFolder();
+      var contains_file = false;
+
+      // TODO move to server
+      // prepare nice size strings
+      for (var i = 0; i < this.folderContainer.attributes.folder.models.length; i++) {
+        var model = this.folderContainer.attributes.folder.models[i];
+        if (model.get('type') === 'file'){
+          contains_file = true;
+          model.set('readable_size', this.size_to_string(model.get('file_size')));
+        }
+      }
+
+      // TODO move to server
+      // find the upper id in the full path
+      var path = this.folderContainer.attributes.metadata.full_path;
+      var upper_folder_id;
+      if (path.length === 1){ // the library is above us
+        upper_folder_id = 0;
+      } else {
+        upper_folder_id = path[path.length-2][0];
+      }
+
+      this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, items: this.folderContainer.attributes.folder.models, id: this.options.id, upper_folder_id: upper_folder_id }));
+
+      if (this.folderContainer.attributes.folder.models.length > 0){
+        this.renderRows();
+      }
+      if (this.folderContainer.attributes.metadata.can_add_library_item === true){
+        Galaxy.libraries.folderToolbarView.configureElements({ can_add_library_item: this.folderContainer.attributes.metadata.can_add_library_item, contains_file: contains_file });
+      }
+
+      // initialize the library tooltips
+      $("#center [data-toggle]").tooltip();
+      //hack to show scrollbars
+      $("#center").css('overflow','auto');
+    },
+
+    renderRows: function(){
+      for (var i = 0; i < this.folderContainer.attributes.folder.models.length; i++) {
+        var folder_item = this.folderContainer.attributes.folder.models[i];
+        var rowView = new mod_library_folderrow_view.FolderRowView(folder_item);
+        this.$el.find('#folder_list_body').append(rowView.el);
+      }
+    },
 
       // convert size to nice string
-      size_to_string : function (size)
-      {
-            // identify unit
-            var unit = "";
-            if (size >= 100000000000)   { size = size / 100000000000; unit = "TB"; } else
-            if (size >= 100000000)      { size = size / 100000000; unit = "GB"; } else
-            if (size >= 100000)         { size = size / 100000; unit = "MB"; } else
-            if (size >= 100)            { size = size / 100; unit = "KB"; } else
-            { size = size * 10; unit = "b"; }
-            // return formatted string
-            return (Math.round(size) / 10) + unit;
-        },
-
-      //show modal with current dataset info
-      showDatasetDetails : function(event){
-        // prevent default
-        event.preventDefault();
-
-        //TODO check whether we already have the data
-
-        //load the ID of the row
-        var id = $(event.target).parent().parent().parent().attr('id');
-        if (typeof id === 'undefined'){
-            id = $(event.target).parent().attr('id');
-        }        
-        if (typeof id === 'undefined'){
-            id = $(event.target).parent().parent().attr('id')
-        }
-
-        //create new item
-        var item = new mod_library_model.Item();
-        var histories = new mod_library_model.GalaxyHistories();
-        item.id = id;
-        var self = this;
-
-        //fetch the dataset info
-        item.fetch({
-          success: function (item) {
-        // TODO can render here already
-                //fetch user histories for import purposes
-                histories.fetch({
-                    success: function (histories){
-                        self.renderModalAfterFetch(item, histories)
-                    },
-                      error: function(){
-                        mod_toastr.error('An error occured during fetching histories:(');
-                        self.renderModalAfterFetch(item)
-                    }
-                });
-            },
-              error: function(){
-                mod_toastr.error('An error occured during loading dataset details :(');
-              }
-        });
-    },
-
-      // show the current dataset in a modal
-      renderModalAfterFetch : function(item, histories){
-        var size = this.size_to_string(item.get('file_size'));
-        var template = _.template(this.templateDatasetModal(), { item : item, size : size });
-            // make modal
-            var self = this;
-            this.modal = Galaxy.modal;
-            this.modal.show({
-                closing_events  : true,
-                title           : 'Dataset Details',
-                body            : template,
-                buttons         : {
-                    'Import'    : function() { self.importCurrentIntoHistory() },
-                    'Download'  : function() { self.downloadCurrent() },
-                    'Close'     : function() { self.modal.hide() }
-                }
-            });
-            
-            $(".peek").html('Peek:' + item.get("peek"));
-
-            // show the import-into-history footer only if the request for histories succeeded
-            if (typeof history.models !== undefined){
-                var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models});
-                $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl);
-                // preset last selected history if we know it
-                if (self.lastSelectedHistory.length > 0) {
-                    $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory);
-                }
-            }
-        },
-
-        // download dataset shown currently in modal
-        downloadCurrent : function(){
-            //disable the buttons
-            this.modal.disableButton('Import');
-            this.modal.disableButton('Download');
-
-            var library_dataset_id = [];
-            library_dataset_id.push($('#id_row').attr('data-id'));
-            var url = '/api/libraries/datasets/download/uncompressed';
-            var data = {'ldda_ids' : library_dataset_id};
-
-            // we assume the view is existent
-            folderContentView.processDownload(url, data);
-            this.modal.enableButton('Import');
-            this.modal.enableButton('Download');
-        },
-
-        // import dataset shown currently in modal into selected history
-        importCurrentIntoHistory : function(){
-            //disable the buttons
-            this.modal.disableButton('Import');
-            this.modal.disableButton('Download');
-
-            var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val();
-            this.lastSelectedHistory = history_id; //save selected history for further use
-
-            var library_dataset_id = $('#id_row').attr('data-id');
-            var historyItem = new mod_library_model.HistoryItem();
-            var self = this;
-            historyItem.url = historyItem.urlRoot + history_id + '/contents';
-
-            // save the dataset into selected history
-            historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){
-                mod_toastr.success('Dataset imported');
-                //enable the buttons
-                self.modal.enableButton('Import');
-                self.modal.enableButton('Download');
-            }, error : function(){
-                mod_toastr.error('An error occured! Dataset not imported. Please try again.')
-                //enable the buttons
-                self.modal.enableButton('Import');
-                self.modal.enableButton('Download');
-            }
-        });
-        },
+      size_to_string : function (size){
+        // identify unit
+        var unit = "";
+        if (size >= 100000000000)   { size = size / 100000000000; unit = "TB"; } else
+        if (size >= 100000000)      { size = size / 100000000; unit = "GB"; } else
+        if (size >= 100000)         { size = size / 100000; unit = "MB"; } else
+        if (size >= 100)            { size = size / 100; unit = "KB"; } else
+        { size = size * 10; unit = "b"; }
+        // return formatted string
+        return (Math.round(size) / 10) + unit;
+      },
 
         // select all datasets
         selectAll : function (event) {
              var selected = event.target.checked;
              that = this;
              // Iterate each checkbox
-             $(':checkbox').each(function () { 
-                this.checked = selected; 
+             $(':checkbox').each(function() {
+                this.checked = selected;
                 $row = $(this.parentElement.parentElement);
                 // Change color of selected/unselected
                 (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row);
             });
              // Show the tools in menu
-             this.checkTools();
+             // this.checkTools();
          },
 
          // Check checkbox on row itself or row checkbox click
@@ -485,7 +153,7 @@ var FolderContentView = Backbone.View.extend({
                         this.makeWhiteRow($row);
                     }
                 }
-                this.checkTools();
+                // this.checkTools();
         },
 
         makeDarkRow: function($row){
@@ -507,207 +175,56 @@ var FolderContentView = Backbone.View.extend({
             $row.find('span').removeClass('fa-file');
         },
 
-        // show toolbar in case something is selected
-        checkTools : function(){
-            var checkedValues = $('#folder_table').find(':checked');
-            if(checkedValues.length > 0){
-                $('#toolbtn_bulk_import').show();
-                $('#toolbtn_dl').show();
-            } else {
-                $('#toolbtn_bulk_import').hide();
-                $('#toolbtn_dl').hide();
-            }
-        },
+// MMMMMMMMMMMMMMMMMM
+// === TEMPLATES ====
+// MMMMMMMMMMMMMMMMMM
 
-        // show bulk import modal
-        modalBulkImport : function(){
-            var self = this;
-            // fetch histories
-            var histories = new mod_library_model.GalaxyHistories();
-            histories.fetch({
-                    success: function (histories){
-                        // make modal
-                        var history_modal_tmpl =  _.template(self.templateBulkImportInModal(), {histories : histories.models});
-                        self.modal = Galaxy.modal;
-                        self.modal.show({
-                            closing_events  : true,
-                            title           : 'Import into History',
-                            body            : history_modal_tmpl,
-                            buttons         : {
-                                'Import'    : function() {self.importAllIntoHistory()},
-                                'Close'     : function() {self.modal.hide();}
-                            }
-                        });
-                    },
-                    error: function(){
-                      mod_toastr.error('An error occured :(');
-                    }
-                });
-        },
+    // main template for folder browsing
+    templateFolder : function (){
+        var tmpl_array = [];
 
-        // import all selected datasets into history
-        importAllIntoHistory : function (){
-            //disable the button to prevent multiple submission
-            this.modal.disableButton('Import');
+        // BREADCRUMBS
+        tmpl_array.push('<ol class="breadcrumb">');
+        tmpl_array.push('   <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
+        tmpl_array.push('   <% _.each(path, function(path_item) { %>');
+        tmpl_array.push('   <% if (path_item[0] != id) { %>');
+        tmpl_array.push('   <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ');
+        tmpl_array.push(    '<% } else { %>');
+        tmpl_array.push('   <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
+        tmpl_array.push('   <% } %>');
+        tmpl_array.push('   <% }); %>');
+        tmpl_array.push('</ol>');
 
-            var history_id = $("select[name=dataset_import_bulk] option:selected").val();
-            var history_name = $("select[name=dataset_import_bulk] option:selected").text();
+        // FOLDER CONTENT
+        tmpl_array.push('<table id="folder_table" class="grid table table-condensed">');
+        tmpl_array.push('   <thead>');
+        tmpl_array.push('       <th class="button_heading"></th>');
+        tmpl_array.push('       <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
+        tmpl_array.push('       <th>name</th>');
+        tmpl_array.push('       <th>data type</th>');
+        tmpl_array.push('       <th>size</th>');
+        tmpl_array.push('       <th>date (UTC)</th>');
+        tmpl_array.push('   </thead>');
+        tmpl_array.push('   <tbody id="folder_list_body">');
+        tmpl_array.push('       <tr>');
+        tmpl_array.push('           <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('       </tr>');
 
-            var dataset_ids = [];
-            $('#folder_table').find(':checked').each(function(){
-                if (this.parentElement.parentElement.id != '') {
-                    dataset_ids.push(this.parentElement.parentElement.id);
-                }
-            });
-            var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name });
-            $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl);
+        tmpl_array.push('   </tbody>');
+        tmpl_array.push('</table>');
 
-            // init the progress bar
-            var progressStep = 100 / dataset_ids.length;
-            this.initProgress(progressStep);
-
-            // prepare the dataset objects to be imported
-            var datasets_to_import = [];
-            for (var i = dataset_ids.length - 1; i >= 0; i--) {
-                library_dataset_id = dataset_ids[i];
-                var historyItem = new mod_library_model.HistoryItem();
-                var self = this;
-                historyItem.url = historyItem.urlRoot + history_id + '/contents';
-                historyItem.content = library_dataset_id;
-                historyItem.source = 'library';
-                datasets_to_import.push(historyItem);
-            };
-
-            // call the recursive function to call ajax one after each other (request FIFO queue)
-            this.chainCall(datasets_to_import);
-        },
-
-        chainCall: function(history_item_set){
-            var self = this;
-            var popped_item = history_item_set.pop();
-            if (typeof popped_item === "undefined") {
-                mod_toastr.success('All datasets imported');
-                this.modal.hide();
-                return
-            }
-                var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){
-                        self.updateProgress();
-                        // responses.push(a1);
-                        self.chainCall(history_item_set);
-                    });
-        },
-
-        initProgress: function(progressStep){
-            this.progress = 0;
-            this.progressStep = progressStep;
-        },
-        updateProgress: function(){
-            this.progress += this.progressStep;
-            $('.progress-bar-import').width(Math.round(this.progress) + '%');
-            txt_representation = Math.round(this.progress) + '% Complete';
-            $('.completion_span').text(txt_representation);
-        },
-
-
-
-      // download selected datasets
-      download : function(folder_id, format){
-        var dataset_ids = [];
-            $('#folder_table').find(':checked').each(function(){
-                if (this.parentElement.parentElement.id != '') {
-                    dataset_ids.push(this.parentElement.parentElement.id);
-                }
-            });
-
-        var url = '/api/libraries/datasets/download/' + format;
-        var data = {'ldda_ids' : dataset_ids};
-        this.processDownload(url, data, 'get');
-      },
-
-      // create hidden form and submit through POST to initialize download
-      processDownload: function(url, data, method){
-        //url and data options required
-        if( url && data ){
-                //data can be string of parameters or array/object
-                data = typeof data == 'string' ? data : $.param(data);
-                //split params into form inputs
-                var inputs = '';
-                $.each(data.split('&'), function(){
-                        var pair = this.split('=');
-                        inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
-                });
-                //send request
-                $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
-                .appendTo('body').submit().remove();
-                
-                mod_toastr.info('Your download will begin soon');
-        };
-      },
-
-      // shows modal for creating folder
-      createFolderFromModal: function(){
-        event.preventDefault();
-        event.stopPropagation();
-
-        // create modal
-        var self = this;
-        this.modal = Galaxy.modal;
-        this.modal.show({
-            closing_events  : true,
-            title           : 'Create New Folder',
-            body            : this.templateNewFolderInModal(),
-            buttons         : {
-                'Create'    : function() {self.create_new_folder_event()},
-                'Close'     : function() {self.modal.hide(); self.modal = null;}
-            }
-        });
-      },
-
-    // create the new folder from modal
-    create_new_folder_event: function(){
-        var folderDetails = this.serialize_new_folder();
-        if (this.validate_new_folder(folderDetails)){
-            var folder = new mod_library_model.FolderAsModel();
-
-            url_items = Backbone.history.fragment.split('/');
-            current_folder_id = url_items[url_items.length-1];
-            folder.url = folder.urlRoot + '/' + current_folder_id ;
-
-            var self = this;
-            folder.save(folderDetails, {
-              success: function (folder) {
-                self.modal.hide();
-                mod_toastr.success('Folder created');
-                self.render({id: current_folder_id});
-              },
-              error: function(){
-                mod_toastr.error('An error occured :(');
-              }
-            });
-        } else {
-            mod_toastr.error('Folder\'s name is missing');
-        }
-        return false;
-    },
-
-    // serialize data from the form
-    serialize_new_folder : function(){
-        return {
-            name: $("input[name='Name']").val(),
-            description: $("input[name='Description']").val()
-        };
-    },
-
-    // validate new library info
-    validate_new_folder: function(folderDetails){
-        return folderDetails.name !== '';
+        return _.template(tmpl_array.join(''));
     }
 
     });
 
-// return
 return {
-    FolderContentView: FolderContentView
+    FolderListView: FolderListView
 };
 
 });

static/scripts/mvc/library/library-folderrow-view.js

@@ -0,0 +1,310 @@
+// dependencies
+define([
+    "galaxy.masthead",
+    "utils/utils",
+    "libs/toastr",
+    "mvc/library/library-model"],
+function(mod_masthead,
+         mod_utils,
+         mod_toastr,
+         mod_library_model) {
+
+// galaxy library row view
+var FolderRowView = Backbone.View.extend({
+  // last selected history in modal for UX
+  lastSelectedHistory: '',
+
+  events: {
+    'click .library-dataset' : 'showDatasetDetails'
+  },
+
+  options: {
+    type: null
+  },
+
+  initialize : function(folder_item){
+    this.render(folder_item);
+  },
+
+  render: function(folder_item){
+    // if (typeof folder_item === 'undefined'){
+      // folder_item = Galaxy.libraries.libraryFolderView.collection.get(this.$el.data('id'));
+    // }
+    var template = null;
+    if (folder_item.get('type') === 'folder'){
+      this.options.type = 'folder';
+      template = this.templateRowFolder();
+    } else {
+      this.options.type = 'file';
+      template = this.templateRowFile();
+    }
+    this.setElement(template({content_item:folder_item}));
+    this.$el.show();
+    return this;
+  },
+
+  //show modal with current dataset info
+  showDatasetDetails : function(event){
+    // prevent default
+    event.preventDefault();
+
+    var id = this.id;
+
+    //create new item
+    var item = new mod_library_model.Item();
+    var histories = new mod_library_model.GalaxyHistories();
+    item.id = id;
+    var self = this;
+
+    //fetch the dataset info
+    item.fetch({
+      success: function (item) {
+    // TODO can start rendering here already
+            //fetch user histories for import purposes
+            histories.fetch({
+                success: function (histories){
+                    self.renderModalAfterFetch(item, histories);
+                },
+                  error: function(){
+                    mod_toastr.error('An error occured during fetching histories:(');
+                    self.renderModalAfterFetch(item);
+                }
+            });
+        },
+          error: function(){
+            mod_toastr.error('An error occured during loading dataset details :(');
+          }
+    });
+},
+
+  // show the current dataset in a modal
+  renderModalAfterFetch : function(item, histories){
+    var size = this.size_to_string(item.get('file_size'));
+    var template = _.template(this.templateDatasetModal(), { item : item, size : size });
+        // make modal
+        var self = this;
+        this.modal = Galaxy.modal;
+        this.modal.show({
+            closing_events  : true,
+            title           : 'Dataset Details',
+            body            : template,
+            buttons         : {
+                'Import'    : function() { self.importCurrentIntoHistory(); },
+                'Download'  : function() { self.downloadCurrent(); },
+                'Close'     : function() { self.modal.hide(); }
+            }
+        });
+        
+        $(".peek").html(item.get("peek"));
+
+        // show the import-into-history footer only if the request for histories succeeded
+        if (typeof history.models !== undefined){
+            var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models});
+            $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl);
+            // preset last selected history if we know it
+            if (self.lastSelectedHistory.length > 0) {
+                $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory);
+            }
+        }
+    },
+
+    // TODO this is dup func, unify
+    // convert size to nice string
+    size_to_string : function (size){
+      // identify unit
+      var unit = "";
+      if (size >= 100000000000)   { size = size / 100000000000; unit = "TB"; } else
+      if (size >= 100000000)      { size = size / 100000000; unit = "GB"; } else
+      if (size >= 100000)         { size = size / 100000; unit = "MB"; } else
+      if (size >= 100)            { size = size / 100; unit = "KB"; } else
+      { size = size * 10; unit = "b"; }
+      // return formatted string
+      return (Math.round(size) / 10) + unit;
+    },
+
+    // download dataset shown currently in modal
+    downloadCurrent : function(){
+        //disable the buttons
+        this.modal.disableButton('Import');
+        this.modal.disableButton('Download');
+
+        var library_dataset_id = [];
+        library_dataset_id.push($('#id_row').attr('data-id'));
+        var url = '/api/libraries/datasets/download/uncompressed';
+        var data = {'ldda_ids' : library_dataset_id};
+
+        this.processDownload(url, data);
+        this.modal.enableButton('Import');
+        this.modal.enableButton('Download');
+    },
+
+  // TODO this is dup func, unify
+  // create hidden form and submit through POST to initialize download
+  processDownload: function(url, data, method){
+    //url and data options required
+    if( url && data ){
+      //data can be string of parameters or array/object
+      data = typeof data == 'string' ? data : $.param(data);
+      //split params into form inputs
+      var inputs = '';
+      $.each(data.split('&'), function(){
+        var pair = this.split('=');
+        inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
+      });
+      //send request
+      $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
+      .appendTo('body').submit().remove();
+      
+      mod_toastr.info('Your download will begin soon');
+    }
+  },
+
+    // import dataset shown currently in modal into selected history
+    importCurrentIntoHistory : function(){
+        //disable the buttons
+        this.modal.disableButton('Import');
+        this.modal.disableButton('Download');
+
+        var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val();
+        this.lastSelectedHistory = history_id; //save selected history for further use
+
+        var library_dataset_id = $('#id_row').attr('data-id');
+        var historyItem = new mod_library_model.HistoryItem();
+        var self = this;
+        historyItem.url = historyItem.urlRoot + history_id + '/contents';
+
+        // save the dataset into selected history
+        historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){
+            mod_toastr.success('Dataset imported');
+            //enable the buttons
+            self.modal.enableButton('Import');
+            self.modal.enableButton('Download');
+        }, error : function(){
+            mod_toastr.error('An error occured! Dataset not imported. Please try again.');
+            //enable the buttons
+            self.modal.enableButton('Import');
+            self.modal.enableButton('Download');
+        }
+    });
+    },
+
+  templateRowFolder: function() {
+    tmpl_array = [];
+
+    tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');
+    tmpl_array.push('  <td>');
+    tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>');
+    tmpl_array.push('  </td>');
+    tmpl_array.push('  <td></td>');
+    tmpl_array.push('  <td>');
+    tmpl_array.push('    <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');
+    tmpl_array.push('    <% if (content_item.get("item_count") === 0) { %>'); // empty folder
+    tmpl_array.push('      <span>(empty folder)</span>');
+    tmpl_array.push('    <% } %>');
+    tmpl_array.push('  </td>');
+    tmpl_array.push('  <td>folder</td>');
+    tmpl_array.push('  <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size
+    tmpl_array.push('  <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
+    tmpl_array.push('</tr>');
+
+    return _.template(tmpl_array.join(''));
+  },
+
+  templateRowFile: function(){
+    tmpl_array = [];
+
+    tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');
+    tmpl_array.push('  <td>');
+    tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>');
+    tmpl_array.push('  </td>');
+    tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');
+    tmpl_array.push('  <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset
+    tmpl_array.push('  <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type
+    tmpl_array.push('  <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size
+    tmpl_array.push('  <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
+    tmpl_array.push('</tr>');
+
+    return _.template(tmpl_array.join(''));
+  },
+
+templateDatasetModal : function(){
+  var tmpl_array = [];
+
+  tmpl_array.push('<div class="modal_table">');
+  tmpl_array.push('   <table class="grid table table-striped table-condensed">');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
+  tmpl_array.push('           <td><%= _.escape(item.get("name")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row">Data type</th>');
+  tmpl_array.push('           <td><%= _.escape(item.get("data_type")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row">Genome build</th>');
+  tmpl_array.push('           <td><%= _.escape(item.get("genome_build")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('           <th scope="row">Size</th>');
+  tmpl_array.push('           <td><%= _.escape(size) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row">Date uploaded (UTC)</th>');
+  tmpl_array.push('           <td><%= _.escape(item.get("date_uploaded")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row">Uploaded by</th>');
+  tmpl_array.push('           <td><%= _.escape(item.get("uploaded_by")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('           <tr scope="row">');
+  tmpl_array.push('           <th scope="row">Data Lines</th>');
+  tmpl_array.push('           <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <th scope="row">Comment Lines</th>');
+  tmpl_array.push('           <% if (item.get("metadata_comment_lines") === "") { %>');
+  tmpl_array.push('               <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');
+  tmpl_array.push('           <% } else { %>');
+  tmpl_array.push('               <td scope="row">unknown</td>');
+  tmpl_array.push('           <% } %>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row">Number of Columns</th>');
+  tmpl_array.push('           <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row">Column Types</th>');
+  tmpl_array.push('           <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('       <tr>');
+  tmpl_array.push('           <th scope="row">Miscellaneous information</th>');
+  tmpl_array.push('           <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');
+  tmpl_array.push('       </tr>');
+  tmpl_array.push('   </table>');
+  tmpl_array.push('   <pre class="peek">');
+  tmpl_array.push('   </pre>');
+  tmpl_array.push('</div>');
+
+  return tmpl_array.join('');
+},
+
+templateHistorySelectInModal : function(){
+  var tmpl_array = [];
+
+  tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');
+  tmpl_array.push('Select history: ');
+  tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');
+  tmpl_array.push('   <% _.each(histories, function(history) { %>'); //history select box
+  tmpl_array.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
+  tmpl_array.push('   <% }); %>');
+  tmpl_array.push('</select>');
+  tmpl_array.push('</span>');
+
+    return tmpl_array.join('');
+}
+   
+});
+
+return {
+    FolderRowView: FolderRowView
+};
+
+});

static/scripts/mvc/library/library-foldertoolbar-view.js

@@ -0,0 +1,320 @@
+// dependencies
+define([
+    "galaxy.masthead",
+    "utils/utils",
+    "libs/toastr",
+    "mvc/library/library-model"],
+function(mod_masthead,
+         mod_utils,
+         mod_toastr,
+         mod_library_model) {
+
+var FolderToolbarView = Backbone.View.extend({
+  el: '#center',
+
+  events: {
+    'click #toolbtn_create_folder'  : 'createFolderFromModal',
+    'click #toolbtn_bulk_import'    : 'modalBulkImport'
+  },
+
+  defaults: {
+    'can_add_library_item'  : false,
+    'contains_file'         : false
+  },
+
+  modal : null,
+
+  initialize: function(options){
+    this.options = _.defaults(options || {}, this.defaults);
+    this.render();
+  },
+
+  render: function(options){
+    this.options = _.extend(this.options, options);
+    var toolbar_template = this.templateToolBar();
+    var is_admin = Galaxy.currUser.isAdmin();
+    this.$el.html(toolbar_template({id: this.options.id, admin_user: is_admin}));
+  },
+
+  configureElements: function(options){
+    this.options = _.extend(this.options, options);
+    if (this.options.can_add_library_item === true){
+      $('#toolbtn_create_folder').show();
+      $('#toolbtn_upload_files').show();
+    }
+    if (this.options.contains_file === true){
+      $('#toolbtn_bulk_import').show();
+      $('#toolbtn_dl').show();
+    }
+    this.$el.find('[data-toggle]').tooltip();
+  },
+
+  // shows modal for creating folder
+  createFolderFromModal: function(){
+    event.preventDefault();
+    event.stopPropagation();
+
+    // create modal
+    var self = this;
+    var template = this.templateNewFolderInModal();
+    this.modal = Galaxy.modal;
+    this.modal.show({
+        closing_events  : true,
+        title           : 'Create New Folder',
+        body            : template(),
+        buttons         : {
+            'Create'    : function() {self.create_new_folder_event();},
+            'Close'     : function() {self.modal.hide(); self.modal = null;}
+        }
+    });
+  },
+
+  // create the new folder from modal
+  create_new_folder_event: function(){
+      var folderDetails = this.serialize_new_folder();
+      if (this.validate_new_folder(folderDetails)){
+          var folder = new mod_library_model.FolderAsModel();
+          url_items = Backbone.history.fragment.split('/');
+          current_folder_id = url_items[url_items.length-1];
+          folder.url = folder.urlRoot + '/' + current_folder_id ;
+
+          var self = this;
+          folder.save(folderDetails, {
+            success: function (folder) {
+              self.modal.hide();
+              mod_toastr.success('Folder created');
+              Galaxy.libraries.folderListView.render({id: current_folder_id});
+            },
+            error: function(){
+              mod_toastr.error('An error occured :(');
+            }
+          });
+      } else {
+          mod_toastr.error('Folder\'s name is missing');
+      }
+      return false;
+  },
+
+  // serialize data from the modal
+  serialize_new_folder : function(){
+      return {
+          name: $("input[name='Name']").val(),
+          description: $("input[name='Description']").val()
+      };
+  },
+
+  // validate new folder info
+  validate_new_folder: function(folderDetails){
+      return folderDetails.name !== '';
+  },
+
+
+  // show bulk import modal
+  modalBulkImport : function(){
+      var checkedValues = $('#folder_table').find(':checked');
+      if(checkedValues.length === 0){
+          mod_toastr.info('You have to select some datasets first');
+      } else {
+          var self = this;
+          // fetch histories
+          var template = this.templateBulkImportInModal();
+          var histories = new mod_library_model.GalaxyHistories();
+          histories.fetch({
+                  success: function (histories){
+                      // make modal
+                      // var history_modal_tmpl =  template({histories : histories.models});
+                      self.modal = Galaxy.modal;
+                      self.modal.show({
+                          closing_events  : true,
+                          title           : 'Import into History',
+                          body            : template({histories : histories.models}),
+                          buttons         : {
+                              'Import'    : function() {self.importAllIntoHistory();},
+                              'Close'     : function() {self.modal.hide();}
+                          }
+                      });
+                  },
+                  error: function(){
+                    mod_toastr.error('An error occured :(');
+                  }
+              });
+      }
+  },
+
+  // import all selected datasets into history
+  importAllIntoHistory : function (){
+      //disable the button to prevent multiple submission
+      this.modal.disableButton('Import');
+
+      var history_id = $("select[name=dataset_import_bulk] option:selected").val();
+      var history_name = $("select[name=dataset_import_bulk] option:selected").text();
+
+      var dataset_ids = [];
+      $('#folder_table').find(':checked').each(function(){
+          if (this.parentElement.parentElement.id !== '') {
+              dataset_ids.push(this.parentElement.parentElement.id);
+          }
+      });
+      var progress_bar_tmpl = this.templateProgressBar();
+      $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl({ history_name : history_name }));
+
+      // init the progress bar
+      var progressStep = 100 / dataset_ids.length;
+      this.initProgress(progressStep);
+
+      // prepare the dataset objects to be imported
+      var datasets_to_import = [];
+      for (var i = dataset_ids.length - 1; i >= 0; i--) {
+          library_dataset_id = dataset_ids[i];
+          var historyItem = new mod_library_model.HistoryItem();
+          var self = this;
+          historyItem.url = historyItem.urlRoot + history_id + '/contents';
+          historyItem.content = library_dataset_id;
+          historyItem.source = 'library';
+          datasets_to_import.push(historyItem);
+      }
+      // call the recursive function to call ajax one after each other (request FIFO queue)
+      this.chainCall(datasets_to_import);
+  },
+
+  chainCall: function(history_item_set){
+    var self = this;
+    var popped_item = history_item_set.pop();
+    if (typeof popped_item === "undefined") {
+        mod_toastr.success('All datasets imported');
+        this.modal.hide();
+        return;
+    }
+        var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){
+                self.updateProgress();
+                self.chainCall(history_item_set);
+            });
+  },
+
+  initProgress: function(progressStep){
+      this.progress = 0;
+      this.progressStep = progressStep;
+  },
+
+  updateProgress: function(){
+      this.progress += this.progressStep;
+      $('.progress-bar-import').width(Math.round(this.progress) + '%');
+      txt_representation = Math.round(this.progress) + '% Complete';
+      $('.completion_span').text(txt_representation);
+  },
+
+  // download selected datasets
+  download : function(folder_id, format){
+    var dataset_ids = [];
+        $('#folder_table').find(':checked').each(function(){
+            if (this.parentElement.parentElement.id !== '') {
+                dataset_ids.push(this.parentElement.parentElement.id);
+            }
+        });
+
+    var url = '/api/libraries/datasets/download/' + format;
+    var data = {'ldda_ids' : dataset_ids};
+    this.processDownload(url, data, 'get');
+  },
+
+  // create hidden form and submit through POST to initialize download
+  processDownload: function(url, data, method){
+    //url and data options required
+    if( url && data ){
+            //data can be string of parameters or array/object
+            data = typeof data == 'string' ? data : $.param(data);
+            //split params into form inputs
+            var inputs = '';
+            $.each(data.split('&'), function(){
+                    var pair = this.split('=');
+                    inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
+            });
+            //send request
+            $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
+            .appendTo('body').submit().remove();
+            
+            mod_toastr.info('Your download will begin soon');
+    }
+  },
+
+  templateToolBar: function(){
+    tmpl_array = [];
+
+    // CONTAINER
+    tmpl_array.push('<div class="library_style_container">');
+    tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-folders" target="_blank">Trello</a>.</h3>');
+    // TOOLBAR
+    tmpl_array.push('<div id="library_folder_toolbar" >');
+    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span> <span class="fa fa-folder-close"></span> folder</button>');
+    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Upload Files to Current Folder" id="toolbtn_upload_files" class="primary-button" type="button" style="display:none;"><span class="fa fa-upload"></span> upload</button>');
+    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to history</button>');
+    tmpl_array.push('   <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display:none; ">');
+    tmpl_array.push('       <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
+    tmpl_array.push('       <span class="fa fa-download"></span> download <span class="caret"></span>');
+    tmpl_array.push('       </button>');
+    tmpl_array.push('       <ul class="dropdown-menu" role="menu">');
+    tmpl_array.push('          <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');
+    tmpl_array.push('          <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');
+    tmpl_array.push('          <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');
+    tmpl_array.push('       </ul>');
+    tmpl_array.push('   </div>');
+    tmpl_array.push('   </div>');
+    tmpl_array.push('   <div id="folder_items_element">');
+    // library items will append here
+    tmpl_array.push('   </div>');
+    tmpl_array.push('</div>');
+
+    return _.template(tmpl_array.join(''));
+  },
+
+  templateNewFolderInModal: function(){
+    tmpl_array = [];
+
+    tmpl_array.push('<div id="new_folder_modal">');
+    tmpl_array.push('<form>');
+    tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');
+    tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');
+    tmpl_array.push('</form>');
+    tmpl_array.push('</div>');
+
+    return _.template(tmpl_array.join(''));
+  },
+
+
+  templateBulkImportInModal : function(){
+    var tmpl_array = [];
+
+    tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');
+    tmpl_array.push('Select history: ');
+    tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');
+    tmpl_array.push('   <% _.each(histories, function(history) { %>'); //history select box
+    tmpl_array.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
+    tmpl_array.push('   <% }); %>');
+    tmpl_array.push('</select>');
+    tmpl_array.push('</span>');
+
+    return _.template(tmpl_array.join(''));
+  },
+
+  templateProgressBar : function (){
+    var tmpl_array = [];
+
+    tmpl_array.push('<div class="import_text">');
+    tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>');
+    tmpl_array.push('</div>');
+    tmpl_array.push('<div class="progress">');
+    tmpl_array.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
+    tmpl_array.push('       <span class="completion_span">0% Complete</span>');
+    tmpl_array.push('   </div>');
+    tmpl_array.push('</div>');
+    tmpl_array.push('');
+
+    return _.template(tmpl_array.join(''));
+  }
+});
+
+return {
+    FolderToolbarView: FolderToolbarView
+};
+
+});

static/scripts/mvc/library/library-librarylist-view.js

@@ -1,14 +1,14 @@
 // dependencies
 define([
     "galaxy.masthead",
-    "mvc/base-mvc", 
+    "mvc/base-mvc",
     "utils/utils",
     "libs/toastr",
     "mvc/library/library-model",
-    "mvc/library/library-libraryrow-view"], 
+    "mvc/library/library-libraryrow-view"],
 function(mod_masthead,
-         mod_baseMVC, 
-         mod_utils, 
+         mod_baseMVC,
+         mod_utils,
          mod_toastr,
          mod_library_model,
          mod_library_libraryrow_view) {
@@ -29,7 +29,8 @@ var LibraryListView = Backbone.View.extend({
     rowViews: {},
 
     // initialize
-    initialize : function(){
+    initialize : function(options){
+        this.options = _.defaults(this.options || {}, options);
         var viewContext = this;
 
         this.rowViews = {};
@@ -43,7 +44,7 @@ var LibraryListView = Backbone.View.extend({
           error: function(model, response){
             mod_toastr.error('An error occured. Please try again.');
           }
-        })
+        });
     },
 
     /** Renders the libraries table either from the object's own collection, 
@@ -52,9 +53,8 @@ var LibraryListView = Backbone.View.extend({
     render: function (options) {
         var template = this.templateLibraryList();
         var libraries_to_render = null;
-        var include_deleted = true;
         var include_deleted = Galaxy.libraries.preferences.get('with_deleted');
-        var models = null
+        var models = null;
         if (typeof options !== 'undefined'){
             include_deleted = typeof options.with_deleted !== 'undefined' ? options.with_deleted : false;
             models = typeof options.models !== 'undefined' ? options.models : null;
@@ -64,7 +64,7 @@ var LibraryListView = Backbone.View.extend({
             if (include_deleted){ // show all the libraries
               libraries_to_render = this.collection.models;
             } else{ // show only undeleted libraries
-              libraries_to_render = this.collection.where({deleted: false});;
+              libraries_to_render = this.collection.where({deleted: false});
             }
         } else if (models !== null){
             libraries_to_render = models;
@@ -74,7 +74,9 @@ var LibraryListView = Backbone.View.extend({
 
         this.$el.html(template({length: libraries_to_render.length, order: Galaxy.libraries.preferences.get('sort_order') }));
 
-        this.renderRows(libraries_to_render);
+        if (libraries_to_render.length > 0){
+            this.renderRows(libraries_to_render);
+        }
         // initialize the library tooltips
         $("#center [data-toggle]").tooltip();
         // modification of upper DOM element to show scrollbars due to the #center element inheritance
@@ -92,9 +94,9 @@ var LibraryListView = Backbone.View.extend({
             var rowView = new mod_library_libraryrow_view.LibraryRowView(library);
             this.$el.find('#library_list_body').append(rowView.el);
             // save new rowView to cache
-            this.rowViews[library.get('id')] = rowView; 
+            this.rowViews[library.get('id')] = rowView;
           }
-        };
+        }
     },
 
     sort_clicked : function(){
@@ -115,17 +117,17 @@ var LibraryListView = Backbone.View.extend({
             if (order === 'asc'){
                 // this.collection.sort_order = 'asc';
                 this.collection.comparator = function(libraryA, libraryB){
-                      if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return 1; // after
-                      if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return -1; // before
+                      if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) {return 1;} // after
+                      if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) {return -1;} // before
                       return 0; // equal
-                }
+                };
             } else if (order === 'desc'){
                 // this.collection.sort_order = 'desc';
                 this.collection.comparator = function(libraryA, libraryB){
-                      if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return -1; // before
-                      if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return 1; // after
+                      if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) {return -1;} // before
+                      if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) {return 1;} // after
                       return 0; // equal
-                }
+                };
             }
             this.collection.sort();
         }
@@ -140,7 +142,7 @@ var LibraryListView = Backbone.View.extend({
 
         tmpl_array.push('<div class="library_container table-responsive">');
         tmpl_array.push('<% if(length === 0) { %>');
-        tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");
+        tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');
         tmpl_array.push('<% } else{ %>');
         tmpl_array.push('<table class="grid table table-condensed">');
         tmpl_array.push('   <thead>');
@@ -175,7 +177,7 @@ var LibraryListView = Backbone.View.extend({
 
     redirectToHome: function(){
         window.location = '../';
-    },    
+    },
     redirectToLogin: function(){
         window.location = '/user/login';
     },
@@ -193,7 +195,7 @@ var LibraryListView = Backbone.View.extend({
             title           : 'Create New Library',
             body            : this.templateNewLibraryInModal(),
             buttons         : {
-                'Create'    : function() {self.create_new_library_event()},
+                'Create'    : function() {self.create_new_library_event();},
                 'Close'     : function() {self.modal.hide();}
             }
         });
@@ -245,7 +247,6 @@ var LibraryListView = Backbone.View.extend({
     }
 });
 
-// return
 return {
     LibraryListView: LibraryListView
 };

static/scripts/mvc/library/library-libraryrow-view.js

@@ -1,11 +1,11 @@
 // dependencies
 define([
-    "galaxy.masthead", 
+    "galaxy.masthead",
     "utils/utils",
     "libs/toastr",
-    "mvc/library/library-model"], 
-function(mod_masthead, 
-         mod_utils, 
+    "mvc/library/library-model"],
+function(mod_masthead,
+         mod_utils,
          mod_toastr,
          mod_library_model) {
 
@@ -39,7 +39,7 @@ var LibraryRowView = Backbone.View.extend({
 
   render: function(library){
     if (typeof library === 'undefined'){
-      var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data('id'));
+      library = Galaxy.libraries.libraryListView.collection.get(this.$el.data('id'));
     }
     this.prepareButtons(library);
     var tmpl = this.templateRow();
@@ -51,7 +51,7 @@ var LibraryRowView = Backbone.View.extend({
   repaint: function(library){
     /* need to hide manually because of the element removal in setElement 
     invoked in render() */
-    $(".tooltip").hide(); 
+    $(".tooltip").hide();
     /* we need to store the old element to be able to replace it with 
     new one */
     var old_element = this.$el;
@@ -83,13 +83,13 @@ var LibraryRowView = Backbone.View.extend({
         vis_config.undelete_library_btn = false;
         if (library.get('can_user_add') === true){
           vis_config.upload_library_btn = true;
-        }    
+        }
         if (library.get('can_user_modify') === true){
           vis_config.edit_library_btn = true;
-        }    
+        }
         if (library.get('can_user_manage') === true){
           vis_config.permission_library_btn = true;
-        }    
+        }
       }
     } else if (this.edit_mode === true){
       vis_config.upload_library_btn = false;
@@ -136,7 +136,7 @@ var LibraryRowView = Backbone.View.extend({
             is_changed = true;
         } else{
             mod_toastr.warning('Library name has to be at least 3 characters long');
-            return
+            return;
         }
     }
 
@@ -183,7 +183,7 @@ var LibraryRowView = Backbone.View.extend({
         Galaxy.libraries.libraryListView.collection.add(library);
         row_view.edit_mode = false;
         if (Galaxy.libraries.preferences.get('with_deleted') === false){
-          $(".tooltip").hide(); 
+          $('.tooltip').hide();
           row_view.$el.remove();
         } else if (Galaxy.libraries.preferences.get('with_deleted') === true){
           row_view.repaint(library);
@@ -247,12 +247,11 @@ var LibraryRowView = Backbone.View.extend({
     tmpl_array.push('               </td>');
     tmpl_array.push('           </tr>');
 
-    return _.template(tmpl_array.join('')); 
+    return _.template(tmpl_array.join(''));
   }
    
 });
 
-  // return
 return {
     LibraryRowView: LibraryRowView
 };

static/scripts/mvc/library/library-librarytoolbar-view.js

@@ -1,18 +1,18 @@
 // dependencies
 define([
-    "galaxy.masthead", 
+    "galaxy.masthead",
     "utils/utils",
     "libs/toastr",
-    "mvc/library/library-model"], 
-function(mod_masthead, 
-         mod_utils, 
+    "mvc/library/library-model"],
+function(mod_masthead,
+         mod_utils,
          mod_toastr,
          mod_library_model) {
 
-var ToolbarView = Backbone.View.extend({
+var LibraryToolbarView = Backbone.View.extend({
   el: '#center',
 
-  events: {        
+  events: {
     'click #create_new_library_btn' : 'delegate_modal',
     'click #include_deleted_chk'    : 'check_include_deleted'
   },
@@ -23,14 +23,16 @@ var ToolbarView = Backbone.View.extend({
 
   render: function(){
     var toolbar_template = this.templateToolBar();
-    this.$el.html(toolbar_template({admin_user: Galaxy.currUser.isAdmin(), anon_user: Galaxy.currUser.isAnonymous()}))
+    var is_admin = Galaxy.currUser.isAdmin();
+    var is_anonym = Galaxy.currUser.isAnonymous();
+    this.$el.html(toolbar_template({admin_user: is_admin, anon_user: is_anonym}));
     if (Galaxy.currUser.isAdmin() === true){
       this.$el.find('#include_deleted_chk')[0].checked = Galaxy.libraries.preferences.get('with_deleted');
     }
   },
 
   delegate_modal: function(event){
-    // probably should refactor to have this functionality in this view, not in the library view
+    // probably should refactor to have this functionality in this view, not in the library list view
     Galaxy.libraries.libraryListView.show_library_modal(event);
   },
 
@@ -48,7 +50,7 @@ var ToolbarView = Backbone.View.extend({
   templateToolBar: function(){
     tmpl_array = [];
 
-    tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');
+    tmpl_array.push('<div class="library_style_container">');
     // TOOLBAR
     tmpl_array.push('  <div id="toolbar_form" margin-top:0.5em; ">');
     tmpl_array.push('       <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-folders" target="_blank">Trello</a>.</h3>');
@@ -60,16 +62,16 @@ var ToolbarView = Backbone.View.extend({
     tmpl_array.push('   <% } %>');
     tmpl_array.push('  </div>');
     tmpl_array.push('  <div id="libraries_element">');
+    // table with libraries will append here
     tmpl_array.push('  </div>');
     tmpl_array.push('</div>');
 
     return _.template(tmpl_array.join(''));
   }
-})
+});
 
-// return
 return {
-    ToolbarView: ToolbarView
+    LibraryToolbarView: LibraryToolbarView
 };
 
 });

static/scripts/mvc/library/library-model.js

@@ -66,16 +66,14 @@ define([], function() {
     var FolderContainer = Backbone.Model.extend({
         defaults : {
             folder : new Folder(),
-            full_path : "unknown",
             urlRoot : "/api/folders/",
             id : "unknown"
         },
     parse : function(obj) {
-      this.full_path = obj[0].full_path;
-          // response is not a simple array, it contains metadata
-          // this will update the inner collection
-          this.get("folder").reset(obj[1].folder_contents);
-          return obj;
+      // response is not a simple array, it contains metadata
+      // this will update the inner collection
+      this.get("folder").reset(obj.folder_contents);
+      return obj;
       }
     });
 

static/scripts/mvc/tools.js

@@ -42,7 +42,7 @@ var ToolParameter = Backbone.Model.extend({
         num_samples: 5
     },
 
-    initialize: function() {
+    initialize: function(options) {
         this.attributes.html = unescape(this.attributes.html);
     },
 
@@ -124,6 +124,8 @@ var Tool = Backbone.Model.extend({
         outputs: []
     },
 
+    urlRoot: galaxy_config.root + 'api/tools',
+
     initialize: function(options) {
 
         // Set parameters.
@@ -133,7 +135,16 @@ var Tool = Backbone.Model.extend({
         })));
     },
 
-    urlRoot: galaxy_config.root + 'api/tools',
+    /**
+     *
+     */
+    toJSON: function() {
+        var rval = Backbone.Model.prototype.toJSON.call(this);
+
+        // Convert inputs to JSON manually.
+        rval.inputs = this.get('inputs').map(function(i) { return i.toJSON(); });
+        return rval;
+    },
 
     /**
      * Removes inputs of a particular type; this is useful because not all inputs can be handled by

static/scripts/packed/galaxy.library.js

@@ -1 +1 @@
-var library_router=null;define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view"],function(e,c,g,j,h,a,f,d){var k=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var i=j.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({toolbarView:null,libraryListView:null,library_router:null,folderContentView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new i({id:"global-lib-prefs"});this.library_router=new k();this.library_router.on("route:libraries",function(){Galaxy.libraries.toolbarView=new d.ToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(l){if(!Galaxy.libraries.folderContentView){Galaxy.libraries.folderContentView=new a.FolderContentView()}Galaxy.libraries.folderContentView.render({id:l})});this.library_router.on("route:download",function(l,m){if($("#center").find(":checked").length===0){Galaxy.libraries.library_router.navigate("folders/"+l,{trigger:true,replace:true})}else{Galaxy.libraries.folderContentView.download(l,m);Galaxy.libraries.library_router.navigate("folders/"+l,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}});
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#center").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}});

static/scripts/packed/mvc/library/library-librarytoolbar-view.js

@@ -1 +1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,d,e,c){var b=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();this.$el.html(f({admin_user:Galaxy.currUser.isAdmin(),anon_user:Galaxy.currUser.isAnonymous()}));if(Galaxy.currUser.isAdmin()===true){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(f){Galaxy.libraries.libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');tmpl_array.push('  <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push('       <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-folders" target="_blank">Trello</a>.</h3>');tmpl_array.push("   <% if(admin_user === true) { %>");tmpl_array.push('       <div id="library_toolbar">');tmpl_array.push('           <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"> <span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push('           <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push("       </div>");tmpl_array.push("   <% } %>");tmpl_array.push("  </div>");tmpl_array.push('  <div id="libraries_element">');tmpl_array.push("  </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});return{ToolbarView:b}});
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,c,d,b){var e=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var h=this.templateToolBar();var g=Galaxy.currUser.isAdmin();var f=Galaxy.currUser.isAnonymous();this.$el.html(h({admin_user:g,anon_user:f}));if(Galaxy.currUser.isAdmin()===true){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(f){Galaxy.libraries.libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('  <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push('       <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-folders" target="_blank">Trello</a>.</h3>');tmpl_array.push("   <% if(admin_user === true) { %>");tmpl_array.push('       <div id="library_toolbar">');tmpl_array.push('           <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"> <span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push('           <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push("       </div>");tmpl_array.push("   <% } %>");tmpl_array.push("  </div>");tmpl_array.push('  <div id="libraries_element">');tmpl_array.push("  </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});return{LibraryToolbarView:e}});

static/scripts/packed/mvc/library/library-model.js

@@ -1 +1 @@
-define([],function(){var e=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(k){var j=true;if((!show_delete)&&(this.get("deleted"))){j=false}return j}});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var h=Backbone.Collection.extend({url:"/api/libraries",model:e,sort_key:"name",sort_order:null,initialize:function(j){j=j||{}},getVisible:function(k,l){l=l||[];var j=new h(this.filter(function(m){return m.isVisible(k)}));return j}});var f=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:f});var d=Backbone.Model.extend({defaults:{folder:new c(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(j){this.full_path=j[0].full_path;this.get("folder").reset(j[1].folder_contents);return j}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var g=Backbone.Model.extend({url:"/api/histories/"});var i=Backbone.Collection.extend({url:"/api/histories",model:g});return{Library:e,FolderAsModel:a,Libraries:h,Item:f,Folder:c,FolderContainer:d,HistoryItem:b,GalaxyHistory:g,GalaxyHistories:i}});
+define([],function(){var e=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(k){var j=true;if((!show_delete)&&(this.get("deleted"))){j=false}return j}});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var h=Backbone.Collection.extend({url:"/api/libraries",model:e,sort_key:"name",sort_order:null,initialize:function(j){j=j||{}},getVisible:function(k,l){l=l||[];var j=new h(this.filter(function(m){return m.isVisible(k)}));return j}});var f=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:f});var d=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(j){this.get("folder").reset(j.folder_contents);return j}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var g=Backbone.Model.extend({url:"/api/histories/"});var i=Backbone.Collection.extend({url:"/api/histories",model:g});return{Library:e,FolderAsModel:a,Libraries:h,Item:f,Folder:c,FolderContainer:d,HistoryItem:b,GalaxyHistory:g,GalaxyHistories:i}});

static/scripts/utils/config.js

@@ -304,6 +304,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
 });
 
 return {
+    ConfigSetting: ConfigSetting,
     ConfigSettingCollection: ConfigSettingCollection,
     ConfigSettingCollectionView: ConfigSettingCollectionView
 };

static/scripts/utils/metrics-logger.js

@@ -0,0 +1,386 @@
+define([
+], function(){
+/*global window, jQuery, console */
+/*=============================================================================
+TODO:
+    broken pipe due to onunload post in webkit, safari
+        need to use persistence
+
+=============================================================================*/
+/** @class MetricsLogger
+ *
+ *  Object to cache, output, and post log/metric messages to the server.
+ *  Meant to be attached to the Galaxy object.
+ *
+ *  Log from objects by either attaching logger directly:
+ *      panel.logger.metric( 'user dataset deletion', panel.user.id, hda.toJSON() )
+ *  or using the LoggableMixin or addLogging function:
+ *      MyBackboneModel.extend( LoggableMixin ).extend({ ... })
+ *      addLogging( MyBackboneModel, 'my-backbone-model' )
+ *
+ *  Log from templates by calling directly from Galaxy object:
+ *      Galaxy.logger.metric( 'template loaded', { ownedByUser : true });
+ *
+ *  If you attempt to log an un-serializable object (circular reference, window, etc.),
+ *  that entry will not be cached (or sent). If you set consoleLevel and consoleLogger
+ *  appropriately, a warning will be shown when this happens:
+ *      > panel.metric( 'something weird with window', { window : window })
+ *      !'Metrics logger could not stringify logArguments: ...'
+ */
+function MetricsLogger( options ){
+    options = options || {};
+    var self = this;
+
+    //TODO: this might be used if we store the logs in browser storage
+    ///**  */
+    //self.userId = options.userId || null;
+
+    /** the (optional) console to emit logs to */
+    self.consoleLogger = options.consoleLogger || null;
+
+    self._init( options );
+    return self;
+}
+
+//----------------------------------------------------------------------------- defaults and constants
+// see: python std lib, logging
+MetricsLogger.ALL  =  0;
+MetricsLogger.DEBUG = 10;
+MetricsLogger.INFO  = 20;
+MetricsLogger.WARN  = 30;
+MetricsLogger.ERROR = 40;
+// metrics levels here?
+//MetricsLogger.MinorEvent  = 45;
+//MetricsLogger.MajorEvent  = 50;
+MetricsLogger.METRIC = 50;
+MetricsLogger.NONE = 100;
+
+/** default options - override these through the constructor */
+MetricsLogger.defaultOptions = {
+    /** if an incoming message has a level >= this, it will be cached - can also be a string (e.g. 'debug') */
+    logLevel            : MetricsLogger.INFO,
+    /** if an incoming message has a level >= this, it will be output to the console */
+    consoleLevel        : MetricsLogger.NONE,
+    /** the default 'namespace' or label associated with an incoming message (if none is passed) */
+    defaultNamespace    : 'Galaxy',
+    /** the prefix attached to client-side logs to distinguish them in the metrics db */
+    clientPrefix        : 'client.',
+
+    /** the maximum number of messages the cache should hold; if exceeded older messages are removed first */
+    maxCacheSize        : 3000,
+    /** the number of messages accumulate before posting to the server; should be <= maxCacheSize */
+    postSize            : 1000,
+    /** T/F whether to add a timestamp to incoming cached messages */
+    addTime             : true,
+
+    /** the relative url to post messages to */
+    postUrl             : '/api/metrics',
+
+    /** post when the page is unloaded? */// needs to be true if using the LoggingCache (for now)
+    postOnUnload        : true,
+
+    /** an (optional) function that should return an object; used to send additional data with the metrics */
+    getPingData         : undefined,
+    /** an (optional) function that will handle the servers response after successfully posting messages */
+    onServerResponse    : undefined
+};
+
+//----------------------------------------------------------------------------- set up
+/** initialize the logger with options, set up instance vars and cache, and add onpageunload to window */
+MetricsLogger.prototype._init = function _init( options ){
+    var self = this;
+    self.options = {};
+    for( var k in MetricsLogger.defaultOptions ){
+        if( MetricsLogger.defaultOptions.hasOwnProperty( k ) ){
+            self.options[ k ] = ( options.hasOwnProperty( k ) )?( options[ k ] ):( MetricsLogger.defaultOptions[ k ] );
+        }
+    }
+    self.options.logLevel = self._parseLevel( self.options.logLevel );
+    self.options.consoleLevel = self._parseLevel( self.options.consoleLevel );
+    //self._emitToConsole( 'debug', 'MetricsLogger', 'MetricsLogger.options:', self.options );
+
+    self._sending = false;
+    self._postSize = self.options.postSize;
+    self._initCache();
+
+    // post the entire cache on unload (since LoggingCache isn't persistent ATM)
+    if( self.options.postOnUnload ){
+        self.onpageunload = function onpageunload( ev ){
+            ev.preventDefault();
+            self._postCache({ count: self.cache.length() });
+        };
+        window.addEventListener( 'unload', self.onpageunload );
+    }
+
+    return self;
+};
+
+/** initialize the cache */
+MetricsLogger.prototype._initCache = function _initCache(){
+    this.cache = new LoggingCache({ maxSize : this.options.maxCacheSize });
+
+};
+
+/** return the numeric log level if level in 'none, debug, log, info, warn, error' */
+MetricsLogger.prototype._parseLevel = function _parseLevel( level ){
+    var type = typeof level;
+    if( type === 'number' ){ return level; }
+    var upper = level.toUpperCase();
+    if( type === 'string' && MetricsLogger.hasOwnProperty( upper ) ){
+        return MetricsLogger[ upper ];
+    }
+    throw new Error( 'Unknown log level: ' + level );
+};
+
+
+//----------------------------------------------------------------------------- main entry point
+/** record a log/message's arguments to the cache and/or the console based on level and namespace */
+MetricsLogger.prototype.emit = function emit( level, namespace, logArguments ){
+    //this._emitToConsole( 'debug', 'MetricsLogger', [ 'emit:', level, namespace, logArguments ]);
+    var self = this;
+    namespace = namespace || self.options.defaultNamespace;
+    if( !level || !logArguments ){
+        return self;
+    }
+    // add to cache if proper level
+//TODO: respect do not track?
+    //if( !navigator.doNotTrack && level >= self.options.logLevel ){
+    level = self._parseLevel( level );
+    if( level >= self.options.logLevel ){
+        self._addToCache( level, namespace, logArguments );
+    }
+    // also emit to consoleLogger if proper level for that
+    if( self.consoleLogger && level >= self.options.consoleLevel ){
+        self._emitToConsole( level, namespace, logArguments );
+    }
+    return self;
+};
+
+//----------------------------------------------------------------------------- cache
+/** add a message to the cache and if messages.length is high enough post them to the server */
+MetricsLogger.prototype._addToCache = function _addToCache( level, namespace, logArguments ){
+    this._emitToConsole( 'debug', 'MetricsLogger',
+        [ '_addToCache:', arguments, this.options.addTime, this.cache.length() ]);
+    //this._emitToConsole( 'debug', 'MetricsLogger', [ '\t logArguments:', logArguments ]);
+    var self = this;
+    // try add to the cache and if we've got _postSize number of entries, attempt to post them to the server
+    try {
+        var newLength = self.cache.add( self._buildEntry( level, namespace, logArguments ) );
+        if( newLength >= self._postSize ){
+            self._postCache();
+        }
+    // discard entry if an error occurs, but warn if level set to do so
+    } catch( err ){
+        if( self.options.consoleLevel <= MetricsLogger.WARN ){
+            console.warn( 'Metrics logger could not stringify logArguments:', namespace, logArguments );
+            console.error( err );
+        }
+    }
+    return self;
+};
+
+/** build a log cache entry object from the given level, namespace, and arguments (optionally adding timestamp */
+MetricsLogger.prototype._buildEntry = function _buildEntry( level, namespace, logArguments ){
+    this._emitToConsole( 'debug', 'MetricsLogger', [ '_buildEntry:', arguments ]);
+    var entry = {
+            level       : level,
+            namespace   : this.options.clientPrefix + namespace,
+            args        : logArguments
+        };
+    if( this.options.addTime ){
+        entry.time = new Date().toISOString();
+    }
+    return entry;
+};
+
+/** post _postSize messages from the cache to the server, removing them if successful
+ *      if the post fails, wait until maxCacheSize is accumulated instead and try again then
+ *      in addition to the messages from the cache ('metrics'), any info from getPingData (if set) will be sent
+ *      onServerResponse will be called (if set) with any response from the server
+ */
+MetricsLogger.prototype._postCache = function _postCache( options ){
+    options = options || {};
+    this._emitToConsole( 'info', 'MetricsLogger', [ '_postCache', options, this._postSize ]);
+//TODO: remove jq dependence
+
+    // short circuit if we're already sending
+    if( !this.options.postUrl || this._sending ){
+        return jQuery.when({});
+    }
+
+    var self = this,
+        postSize = options.count || self._postSize,
+        // do not splice - remove after *successful* post
+        entries = self.cache.get( postSize ),
+        entriesLength = entries.length,
+        // use the optional getPingData to add any extra info we may want to send
+        postData = ( typeof self.options.getPingData === 'function' )?( self.options.getPingData() ):( {} );
+    //console.debug( postSize, entriesLength );
+
+    // add the metrics and send
+    postData.metrics = self._preprocessCache( entries );
+    self._sending = true;
+    return jQuery.post( self.options.postUrl, postData )
+        .always( function(){
+            self._sending = false;
+        })
+        .fail( function(){
+            // if we failed the previous time, set the next post target to the max num of entries
+            self._postSize = self.options.maxCacheSize;
+        })
+        .done( function( response ){
+            if( typeof self.options.onServerResponse === 'function' ){
+                self.options.onServerResponse( response );
+            }
+            // only remove if post successful
+            self.cache.remove( entriesLength );
+            console.debug( 'removed entries:', entriesLength, 'size now:', self.cache.length() );
+            // if we succeeded, reset the post target to the normal num of entries
+            self._postSize = self.options.postSize;
+        });
+    // return the xhr promise
+};
+
+/** Preprocess a number of cache entries for sending to the server (stringification) */
+MetricsLogger.prototype._preprocessCache = function _preprocessCache( entries ){
+    return [ '[', ( entries.join( ',\n' ) ), ']' ].join( '\n' );
+    //return [ '[', ( entries.join( ',' ) ), ']' ].join( '' );
+};
+
+
+//----------------------------------------------------------------------------- console
+/** output message to console based on level and consoleLogger type */
+MetricsLogger.prototype._emitToConsole = function _emitToConsole( level, namespace, logArguments ){
+    //console.debug( '_emitToConsole:', level, namespace, logArguments );
+    var self = this;
+    if( !self.consoleLogger ){ return self; }
+
+    var args = Array.prototype.slice.call( logArguments, 0 );
+    args.unshift( namespace );
+//TODO: script location and/or source maps?
+//TODO: branch on navigator.userAgent == AIIEEE - it only has log
+    if(        level >= MetricsLogger.METRIC && typeof( self.consoleLogger.info ) === 'function' ){
+        return self.consoleLogger.info.apply( self.consoleLogger, args );
+
+    } else if( level >= MetricsLogger.ERROR && typeof( self.consoleLogger.error ) === 'function' ){
+        return self.consoleLogger.error.apply( self.consoleLogger, args );
+    } else if( level >= MetricsLogger.WARN && typeof( self.consoleLogger.warn ) === 'function' ){
+        self.consoleLogger.warn.apply( self.consoleLogger, args );
+    } else if( level >= MetricsLogger.INFO && typeof( self.consoleLogger.info ) === 'function' ){
+        self.consoleLogger.info.apply( self.consoleLogger, args );
+    } else if( level >= MetricsLogger.DEBUG && typeof( self.consoleLogger.debug ) === 'function' ){
+        self.consoleLogger.debug.apply( self.consoleLogger, args );
+    } else if( typeof( self.consoleLogger.log ) === 'function' ){
+        self.consoleLogger.log.apply( self.consoleLogger, args );
+    }
+    return self;
+};
+
+//----------------------------------------------------------------------------- shortcuts
+// generic functions when logging from non-namespaced object (e.g. templates)
+/** debug to default namespace */
+MetricsLogger.prototype.debug = function debug(){
+    this.emit( MetricsLogger.DEBUG, this.options.defaultNamespace, arguments );
+};
+
+/** log to default namespace */
+MetricsLogger.prototype.log = function log(){
+    this.emit( 1, this.options.defaultNamespace, arguments );
+};
+
+/** info to default namespace */
+MetricsLogger.prototype.info = function info(){
+    this.emit( MetricsLogger.INFO, this.options.defaultNamespace, arguments );
+};
+
+/** warn to default namespace */
+MetricsLogger.prototype.warn = function warn(){
+    this.emit( MetricsLogger.WARN, this.options.defaultNamespace, arguments );
+};
+
+/** error to default namespace */
+MetricsLogger.prototype.error = function error(){
+    this.emit( MetricsLogger.ERROR, this.options.defaultNamespace, arguments );
+};
+
+/** metric to default namespace */
+MetricsLogger.prototype.metric = function metric(){
+    this.emit( MetricsLogger.METRIC, this.options.defaultNamespace, arguments );
+};
+
+
+//=============================================================================
+/** @class LoggingCache
+ *  Simple implementation of cache wrapping an array.
+ *
+ *  Formats an entry before it's cached and only keeps options.maxSize number
+ *  of entries. Older entries are deleted first.
+ */
+function LoggingCache( options ){
+    var self = this;
+    self._cache = [];
+    return self._init( options || {} );
+}
+
+/** default options */
+LoggingCache.defaultOptions = {
+    /** maximum number of entries to keep before discarding oldest */
+    maxSize     : 5000
+};
+
+/** initialize with options */
+LoggingCache.prototype._init = function _init( options ){
+    this.maxSize = options.maxSize || LoggingCache.defaultOptions.maxSize;
+    return this;
+};
+
+/** add an entry to the cache, removing the oldest beforehand if size >= maxSize */
+LoggingCache.prototype.add = function add( entry ){
+    var self = this,
+        overage = ( self.length() + 1 ) - self.maxSize;
+    if( overage > 0 ){
+        self.remove( overage );
+    }
+    self._cache.push( self._preprocessEntry( entry ) );
+    return self.length();
+};
+
+/** process the entry before caching */
+LoggingCache.prototype._preprocessEntry = function _preprocessEntry( entry ){
+    return JSON.stringify( entry );
+};
+
+/** return the length --- oh, getters where are you? */
+LoggingCache.prototype.length = function length(){
+    return this._cache.length;
+};
+
+/** get count number of entries starting with the oldest */
+LoggingCache.prototype.get = function get( count ){
+    return this._cache.slice( 0, count );
+};
+
+/** remove count number of entries starting with the oldest */
+LoggingCache.prototype.remove = function remove( count ){
+    return this._cache.splice( 0, count );
+};
+
+/** stringify count number of entries (but do not remove) */
+LoggingCache.prototype.stringify = function stringify( count ){
+    return [ '[', ( this.get( count ).join( ',\n' ) ), ']' ].join( '\n' );
+};
+
+/** outputs entire cache to console */
+LoggingCache.prototype.print = function print(){
+    // popup? (really, carl? a popup?) - easier to copy/paste
+    this._cache.forEach( function( entry ){
+        console.log( entry );
+    });
+};
+
+
+//=============================================================================
+    return {
+        MetricsLogger  : MetricsLogger
+    };
+});

static/scripts/viz/sweepster.js

@@ -3,8 +3,8 @@
  * genomic visualization.
  */
 
-define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], 
-       function(_, d3, util, visualization, tracks, tools, data) {
+define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data", "utils/config"], 
+       function(_, d3, util, visualization, tracks, tools, data, config) {
 
 /**
  * A collection of tool input settings. Object is useful for keeping a list of settings 
@@ -257,7 +257,7 @@ var SweepsterTrack = Backbone.Model.extend({
     },
     
     initialize: function(options) {
-        this.set('regions', new visualization.GenomeRegionCollection(options.regions));
+        this.set('regions', options.regions);
         if (options.track) {
             // FIXME: find a better way to deal with needed URLs:
             var track_config = _.extend({
@@ -310,12 +310,12 @@ var SweepsterVisualization = visualization.Visualization.extend({
         this.set('dataset', new data.Dataset(options.dataset));
         this.set('tool', new tools.Tool(options.tool));
         this.set('regions', new visualization.GenomeRegionCollection(options.regions));
-        this.set('tracks', new SweepsterTrackCollection(options.tracks));
+        this.set('tracks', new TrackCollection(options.tracks));
 
         var tool_with_samplable_inputs = this.get('tool');
         this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);
         // Remove complex parameters for now.
-        tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional' ] );
+        tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional', 'text' ] );
         
         this.set('parameter_tree', new ToolParameterTree({ 
             tool: tool_with_samplable_inputs,
@@ -430,7 +430,7 @@ var SweepsterTrackView = Backbone.View.extend({
                     var canvas = self.canvas_manager.new_canvas();
                     canvas.width = self.TILE_LEN;
                     canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width);
-                    track.draw_tile(tile_data, canvas.getContext('2d'), mode, resolution, region, w_scale);
+                    track.draw_tile(tile_data, canvas.getContext('2d'), mode, region, w_scale);
                     $(tile_containers[index]).empty().append(canvas);
                 });
             });
@@ -680,8 +680,18 @@ var SweepsterVisualizationView = Backbone.View.extend({
         });
 
         // Set block, reverse strand block colors; these colors will be used for all tracks.
-        this.block_color = util.get_random_color();
-        this.reverse_strand_color = util.get_random_color( [ this.block_color, "#ffffff" ] );
+        this.config = config.ConfigSettingCollection.from_models_and_saved_values( 
+            [
+                { key: 'name', label: 'Name', type: 'text', default_value: '' },
+                { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" },
+                { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" },
+                { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" },
+                { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" },
+                { key: 'n_color', label: 'N Color', type: 'color', default_value: "#AAAAAA" },
+                { key: 'block_color', label: 'Block color', type: 'color' },
+                { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' },
+            ], {}
+        );
     },
     
     render: function() {
@@ -792,6 +802,11 @@ var SweepsterVisualizationView = Backbone.View.extend({
         $("#right .unified-panel-header-inner").append(menu.$el);
     },
 
+    get_base_color: function(base) {
+        return this.config.get_value(base.toLowerCase() + '_color') || 
+               this.config.get_value('n_color');
+    },
+
     run_tool_on_dataset: function(settings) {
         var tool = this.model.get('tool'),
             tool_name = tool.get('name'),
@@ -904,14 +919,12 @@ var SweepsterVisualizationView = Backbone.View.extend({
                             // the tool parameters and parameter tree.
                             track_config.tool = null;
 
+                            track_config.prefs = self.config.to_key_value_dict();
+
                             // Create and add track for output dataset.
                             var track_obj = tracks.object_from_template(track_config, self, null);
                             track_obj.init_for_tool_data();
                             
-                            // Set track block colors.
-                            track_obj.prefs.block_color = self.block_color;
-                            track_obj.prefs.reverse_strand_color = self.reverse_strand_color;
-
                             pm_track.set('track', track_obj);
                         });
                     }, index * 10000);

static/scripts/viz/trackster/tracks.js

@@ -2243,7 +2243,7 @@ extend(Track.prototype, Drawable.prototype, {
             on_click_fn: function(track) {
                 var template =
                     '<strong>Tool</strong>: <%= track.tool.get("name") %><br/>' +
-                    '<strong>Dataset</strong>: <%= track.config.get("name") %><br/>' +
+                    '<strong>Dataset</strong>: <%= track.config.get_value("name") %><br/>' +
                     '<strong>Region(s)</strong>: <select name="regions">' +
                     '<option value="cur">current viewing area</option>' +
                     '<option value="bookmarks">bookmarks</option>' +

static/style/blue/base.css

@@ -1299,6 +1299,7 @@ td.right-center{vertical-align:middle !important;text-align:right}
 .library_table td{border-top:1px solid #5f6990 !important}
 .library_table th{border-bottom:2px solid #5f6990 !important}
 .library_table a{color:#0A143D}.library_table a:hover{color:maroon}
+.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important}
 tr.light td{background-color:white;color:black}
 tr.light:hover td{background-color:#f5e8cc}
 tr.dark td{background-color:#d6b161;color:white}

static/style/blue/library.css

@@ -10,6 +10,7 @@ td.right-center{vertical-align:middle !important;text-align:right}
 .library_table td{border-top:1px solid #5f6990 !important}
 .library_table th{border-bottom:2px solid #5f6990 !important}
 .library_table a{color:#0A143D}.library_table a:hover{color:maroon}
+.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important}
 tr.light td{background-color:white;color:black}
 tr.light:hover td{background-color:#f5e8cc}
 tr.dark td{background-color:#d6b161;color:white}

static/style/src/less/library.less

@@ -49,6 +49,12 @@ td.right-center{
         }
     }
 }
+.library_style_container{
+    width: 95%; 
+    margin: auto; 
+    margin-top:2em; 
+    overflow: auto !important; 
+}
 
 tr.light td
 {

templates/webapps/galaxy/tool_form.mako

@@ -378,3 +378,10 @@
         </div>
     </div>
 %endif
+%if tool.tool_shed_repository:
+    <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %>
+    %if tool_url:
+        <br/>
+        ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) }
+    %endif
+%endif

templates/webapps/tool_shed/common/common.mako

@@ -107,7 +107,7 @@
 <%def name="render_multiple_heads_message( heads )">
     <div class="warningmessage">
         <%
-            from tool_shed.util.shed_util_common import get_revision_label_from_ctx
+            from tool_shed.util.hg_util import get_revision_label_from_ctx
             heads_str = ''
             for ctx in heads:
                 heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True )

templates/webapps/tool_shed/repository/view_changeset.mako

@@ -49,7 +49,7 @@ ${render_tool_shed_repository_actions( repository=repository )}
 %endif
 <div class="toolForm">
     <%
-        from tool_shed.util.shed_util_common import get_readable_ctx_date
+        from tool_shed.util.hg_util import get_readable_ctx_date
         changeset_revision_date = get_readable_ctx_date( ctx )
         if can_download:
             title_str = 'Changeset <b>%s:%s</b> <i>(%s)</i>' % ( ctx.rev(), ctx, changeset_revision_date )

test/qunit/tests/workflow_editor_tests.html

@@ -0,0 +1,10 @@
+<!doctype html>
+<!-- Minimal outline test page for a requirejs+qunit testing setup,
+     test environment is bootstrapped in test-common.js -->
+<html>
+  <head>
+    <script data-main="../test-common" src="../scripts/libs/require.js"></script>
+  </head>
+  <body>
+  </body>
+</html>

test/qunit/tests/workflow_editor_tests.js

@@ -0,0 +1,379 @@
+/* global define, QUnit, module, test, ok, equal, deepEqual, notEqual */
+/* global Workflow, CanvasManager, InputTerminal, Connector, add_node */
+define([
+    "galaxy.workflow_editor.canvas",
+    "jquery",
+    "sinon-qunit"
+], function(
+    workflowEditor,
+    $,
+    sinon
+){
+    "use strict";
+
+    // globals cosumed by workflow editor
+    window.show_form_for_tool = sinon.spy();
+    window.workflow = null;
+    window.canvas_manager = null;
+
+    // Stub used over stubbing issubtype for unit testing datatype comparisons.
+    var issubtypeStub = null;
+
+    QUnit.moduleStart(function() {
+        if( issubtypeStub === null) {
+            issubtypeStub = sinon.stub( window, "issubtype" );
+        }
+    });
+    QUnit.moduleDone(function() {
+        if( issubtypeStub !== null) {
+            issubtypeStub.restore();
+            issubtypeStub = null;
+        }
+    });
+
+    var with_canvas_container = function( f ) {
+        var canvas_container = $("<div id='canvas-container'>");
+        $("body").append( canvas_container );
+        f( canvas_container );
+        canvas_container.remove();
+    };
+
+    var with_workflow_global = function( f ) {
+        var overview = $( "<div id='overview'><canvas id='overview-canvas'></canvas><div id='overview-viewport'></div></div>" );
+        var canvas_viewport = $( "<div id='canvas-viewport'><div id='canvas-container'></div></div>" );
+
+        $("body").append( overview, canvas_viewport );
+        window.canvas_manager = new CanvasManager( canvas_viewport, overview );
+        with_canvas_container( function( canvas_container ) {
+            window.workflow = new Workflow( canvas_container );
+            f( window.workflow );
+            window.workflow = null;
+        } );
+        window.canvas_manager = null;
+        overview.remove();
+        canvas_viewport.remove();
+    };
+
+    module( "Input terminal model test", {
+        setup: function() {
+            this.node = {  };
+            this.element = $( "<div>" );
+            this.input_terminal = new InputTerminal( this.element, [ "txt" ] );
+            this.input_terminal.node = this.node;
+        },
+        test_connector: function( attr ) {
+            var connector = attr || {};
+            this.input_terminal.connectors.push( connector );
+            return connector;
+        },
+        with_test_connector: function( attr, f ) {
+            this.test_connector( attr );
+            f();
+            this.reset_connectors();
+        },
+        reset_connectors: function( ) {
+            this.input_terminal.connectors = [];
+        },
+        test_accept: function( other ) {
+            other = other || { node: {}, datatypes: [ "txt" ] };
+            return this.input_terminal.can_accept( other );
+        }
+    } );
+
+    test( "test connect", function() {
+        this.node.changed = sinon.spy();
+
+        var connector = {};
+        this.input_terminal.connect( connector );
+
+        // Assert node changed called
+        ok( this.node.changed.called );
+        // Assert connectors updated
+        ok( this.input_terminal.connectors[ 0 ] === connector );
+    } );
+
+    test( "test disconnect", function() {
+        this.node.changed = sinon.spy();
+
+        var connector = this.test_connector( {} );
+        this.input_terminal.disconnect( connector );
+
+        // Assert node changed called
+        ok( this.node.changed.called );
+        // Assert connectors updated
+        equal( this.input_terminal.connectors.length, 0 );
+    } );
+
+    test( "test redraw", function() {
+        var connector = this.test_connector( { redraw: sinon.spy() } );
+        this.input_terminal.redraw();
+        // Assert connectors were redrawn
+        ok( connector.redraw.called );
+    } );
+
+    test( "test destroy", function() {
+        var connector = this.test_connector( { destroy: sinon.spy() } );
+
+        this.input_terminal.destroy();
+        // Assert connectors were redrawn
+        ok( connector.destroy.called );
+    } );
+
+    test( "can accept correct datatype", function() {
+        issubtypeStub.returns(true);
+        ok( this.test_accept() ) ;
+    } );
+
+    test( "cannot accept incorrect datatypes", function() {
+        issubtypeStub.returns(false);
+        ok( ! this.test_accept() );
+    } );
+
+    test( "can accept inputs", function() {
+        issubtypeStub.returns(false);
+        // Other is data input module - always accept (currently - could be
+        // more intelligent by looking at what else input is connected to.
+        var other = { node: {}, datatypes: [ "input" ] };
+        ok( this.test_accept( other ) );
+    } );
+
+    test( "cannot accept when already connected", function() {
+        issubtypeStub.returns(true);
+        var self = this;
+        // If other is subtype but already connected, cannot accept
+        this.with_test_connector( {}, function() {
+            ok( ! self.test_accept() );
+        } );
+    } );
+
+    module( "Connector test", {
+
+    } );
+
+    test( "connects only if both valid handles", function() {
+        var input = { connect: sinon.spy() };
+        var output = { connect: sinon.spy() };
+        new Connector( input, null );
+        new Connector( null, output );
+        // Not attempts to connect...
+        ok( ! input.connect.called );
+        ok( ! output.connect.called );
+
+        new Connector( input, output );
+        ok( input.connect.called );
+        ok( output.connect.called );
+    });
+
+    test( "default attributes", function() {
+        var input = { connect: sinon.spy() };
+        var output = { connect: sinon.spy() };
+        var connector = new Connector( input, output );
+
+        equal( connector.dragging, false );
+        equal( connector.canvas, null );
+        equal( connector.inner_color, "#FFFFFF" );
+        equal( connector.outer_color, "#D8B365" );
+    } );
+
+    test( "destroy", function() {
+        var input = { connect: sinon.spy(), disconnect: sinon.spy() };
+        var output = { connect: sinon.spy(), disconnect: sinon.spy() };
+        var connector = new Connector( input, output );
+
+        connector.destroy();
+        ok( input.disconnect.called );
+        ok( output.disconnect.called );
+    } );
+
+    test( "initial redraw", function() {
+        with_canvas_container( function( canvas_container ) {
+            var input = { connect: sinon.spy(), element: $("<div>") };
+            var output = { connect: sinon.spy(), element: $("<div>") };
+            var connector = new Connector( input, output );
+
+            connector.redraw();
+            // Ensure canvas gets set
+            ok( connector.canvas );
+            // Ensure it gest added to canvas container
+            equal( canvas_container.children()[ 0 ], connector.canvas );
+        } );
+    } );
+
+    module( "Node unit test", {
+        setup: function() {
+            this.input_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
+            this.output_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
+            this.element = $("<div><div class='toolFormBody'></div></div>");
+            this.node = new Node( this.element );
+            this.node.input_terminals.i1 = this.input_terminal;
+            this.node.output_terminals.o1 = this.output_terminal;
+        },
+        $: function( selector ) {
+            return $( this.node.element.find( selector ) );
+        },
+        expect_workflow_node_changed: function( f ) {
+            var node = this.node;
+            with_workflow_global( function( workflow ) {
+                var node_changed_spy = sinon.spy( workflow, "node_changed" );
+                f();
+                ok( node_changed_spy.calledWith( node ) );
+            } );
+        },
+        init_field_data_simple: function() {
+            var data = {
+                data_inputs: [ {name: "input1", extensions: [ "data" ] } ],
+                data_outputs: [ {name: "output1", extensions: [ "data" ] } ],
+            };
+            this.node.init_field_data( data );
+        },
+        update_field_data_with_new_input: function() {
+            var new_data = {
+                data_inputs: [
+                    { name: "input1", extensions: [ "data" ] },
+                    { name: "extra_0|input1", extensions: [ "data" ] },
+                ],
+                data_outputs: [ {name: "output1", extensions: [ "data" ] } ],
+                post_job_actions: "{}"
+            };
+            this.node.update_field_data( new_data );
+        }
+    } );
+
+    test( "make active", function() {
+        ok( ! this.element.hasClass( "toolForm-active" ) );
+        this.node.make_active();
+        ok( this.element.hasClass( "toolForm-active" ) );
+    } );
+
+    test( "destroy", function() {
+        var test = this;
+        with_workflow_global( function( workflow ) {
+            var remove_node_spy = sinon.spy( workflow, "remove_node" );
+            test.node.destroy();
+            ok( test.input_terminal.destroy.called );
+            ok( test.output_terminal.destroy.called );
+            ok( remove_node_spy.calledWith( test.node ) );
+        } );
+    } );
+
+    test( "error", function() {
+        // Test body of toolFormBody div updated and workflow notified of change.
+        var test = this;
+        this.expect_workflow_node_changed( function() {
+            test.node.error( "TOOL ERROR" );
+            equal( $( test.$(".toolFormBody").children()[ 0 ] ).html(), "TOOL ERROR" );
+        } );
+    } );
+
+    test( "init_field_data properties", function() {
+        var node = this.node;
+        this.expect_workflow_node_changed( function( ) {
+            var data = {
+                data_inputs: [],
+                data_outputs: [],
+                type: "tool",
+                name: "cat1",
+                form_html: "<form>",
+                tool_state: "ok",
+                tool_errors: false,
+                tooltip: "tool tooltip",
+                annotation: "tool annotation",
+                workflow_outputs: [ "out1" ],
+            };
+            node.init_field_data( data );
+            equal( node.type, "tool" );
+            equal( node.name, "cat1" );
+            equal( node.form_html, "<form>" );
+            equal( node.tool_state, "ok" );
+            equal( node.tooltip, "tool tooltip" );
+            equal( node.annotation, "tool annotation" );
+            deepEqual( node.post_job_actions, {} );
+            deepEqual( node.workflow_outputs, [ "out1" ] );
+        } );
+    } );
+
+    test( "init_field_data data", function() {
+        var test = this;
+        this.expect_workflow_node_changed( function( ) {
+            // pre-init not tool form body...
+            equal( test.$( ".output-terminal" ).length, 0 );
+            equal( test.$( ".input-terminal" ).length, 0 );
+            equal( test.$( ".rule" ).length, 0 );
+
+            test.init_field_data_simple();
+
+            // After init tool form should have three "rows"/divs - , inputs div, one output, and rule...
+            equal( test.$( ".output-terminal" ).length, 1 );
+            equal( test.$( ".input-terminal" ).length, 1 );
+            equal( test.$( ".rule" ).length, 1 );
+
+            equal( test.$( ".toolFormBody" ).children().length, 3 );
+        } );
+    } );
+
+    test( "update_field_data updated data inputs and outputs", function() {
+        var test = this;
+        this.expect_workflow_node_changed( function( ) {
+            // Call init with one input and output.
+            test.init_field_data_simple();
+
+            test.update_field_data_with_new_input();
+
+            // Now there are 2 inputs...
+            equal( test.$( ".input-terminal" ).length, 2 );
+            equal( test.$( ".output-terminal" ).length, 1 );
+            equal( test.$( ".rule" ).length, 1 );
+        } );
+    } );
+
+    test( "update_field_data preserves connectors", function() {
+        var test = this;
+        var node = this.node;
+        this.expect_workflow_node_changed( function( ) {
+            // Call init with one input and output.
+            test.init_field_data_simple();
+
+            var connector = new Connector();
+            var old_input_terminal = node.input_terminals.input1;
+            old_input_terminal.connectors.push( connector );
+
+            test.update_field_data_with_new_input();
+            
+            var new_input_terminal = node.input_terminals.input1;
+            equal( old_input_terminal, old_input_terminal );
+            notEqual( old_input_terminal, new_input_terminal );
+            equal( connector, new_input_terminal.connectors[ 0 ] );
+        } );
+    } );
+
+    test( "update_field_data destroys old terminals", function() {
+        var test = this;
+        var node = this.node;
+        this.expect_workflow_node_changed( function( ) {
+            var data = {
+                data_inputs: [ { name: "input1", extensions: [ "data" ] },
+                               { name: "willDisappear", extensions: [ "data" ] } ],
+                data_outputs: [ {name: "output1", extensions: [ "data" ] } ],
+            };
+            node.init_field_data( data );
+
+            var old_input_terminal = node.input_terminals.willDisappear;
+            var destroy_spy = sinon.spy( old_input_terminal, "destroy" );
+            // Update
+            test.update_field_data_with_new_input();
+
+            ok( destroy_spy.called );
+        } );
+    } );
+
+    module( "add_node" );
+
+    test( "node added to workflow", function() {
+        with_workflow_global( function( workflow ) {
+            var add_node_spy = sinon.spy( workflow, "add_node" );
+            var node = add_node( "tool", "Cat Files", "cat1" );
+            ok( add_node_spy.calledWith( node ) );
+        } );
+    } );
+
+});

test/tool_shed/base/twilltestcase.py

@@ -1418,10 +1418,10 @@ class ShedTwillTestCase( TwillTestCase ):
     def verify_repository_reviews( self, repository, reviewer=None, strings_displayed=[], strings_not_displayed=[] ):
         changeset_revision = self.get_repository_tip( repository )
         # Verify that the currently logged in user has a repository review for the specified repository, reviewer, and changeset revision.
-        strings_displayed=[ repository.name, reviewer.username, changeset_revision ]
+        strings_displayed=[ repository.name, reviewer.username ]
         self.display_reviewed_repositories_owned_by_user( strings_displayed=strings_displayed )
         # Verify that the reviewer has reviewed the specified repository's changeset revision.
-        strings_displayed=[ repository.name, repository.description, changeset_revision ]
+        strings_displayed=[ repository.name, repository.description ]
         self.display_repository_reviews_by_user( reviewer, strings_displayed=strings_displayed )
         # Load the review and check for the components passed in strings_displayed.
         review = test_db_util.get_repository_review_by_user_id_changeset_revision( reviewer.id, repository.id, changeset_revision )

test/tool_shed/functional/test_0420_citable_urls_for_repositories.py

@@ -104,7 +104,6 @@ class TestRepositoryCitableURLs( ShedTwillTestCase ):
         strings_displayed = [ '/repository/browse_repositories', encoded_user_id, 'operation=repositories_by_user' ]
         strings_displayed.append( encoded_user_id )
         strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420' ]
-        strings_displayed_in_iframe.append( self.get_repository_tip( repository ) )
         self.load_citable_url( username='user1', 
                                repository_name=None, 
                                changeset_revision=None, 
@@ -208,7 +207,6 @@ class TestRepositoryCitableURLs( ShedTwillTestCase ):
         strings_displayed.extend( [ 'list+of+repositories+owned', 'does+not+include+one+named', '%21%21invalid%21%21', 'status=error' ] )
         strings_displayed_in_iframe = [ 'user1', 'filtering_0420' ]
         strings_displayed_in_iframe.append( 'Repositories Owned by user1' )
-        strings_displayed_in_iframe.append( tip_revision )
         self.load_citable_url( username='user1', 
                                repository_name='!!invalid!!', 
                                changeset_revision=None,