commit/galaxy-central: 4 new changesets

13 Aug 2012

4 new commits in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/d960803cbacc/
changeset:   d960803cbacc
user:        jmchilton
date:        2012-08-09 22:15:23
summary:     JJ's initial work on extending the API to allow operations on groups.
affected #:  5 files

diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -544,7 +544,10 @@
         else:
             return False
 
-class Group( object ):
+class Group( object, APIItem  ):
+    api_collection_visible_keys = ( 'id', 'name' )
+    api_element_visible_keys = ( 'id', 'name' )
+
     def __init__( self, name = None ):
         self.name = name
         self.deleted = False


diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/api/group_roles.py
--- /dev/null
+++ b/lib/galaxy/web/api/group_roles.py
@@ -0,0 +1,124 @@
+"""
+API operations on Group objects.
+"""
+import logging
+from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy import web
+
+log = logging.getLogger( __name__ )
+
+class GroupRolesAPIController( BaseAPIController ):
+
+    @web.expose_api
+    @web.require_admin
+    def index( self, trans, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/roles
+        Displays a collection (list) of groups.
+        """
+        decoded_group_id = trans.security.decode_id( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        rval = []
+        try:
+            for gra in group.roles:
+                role = gra.role
+                encoded_id = trans.security.encode_id( role.id )
+                rval.append( dict( id = encoded_id,
+                                   name = role.name,
+                                   url = url_for( 'group_role', group_id=group_id, id=encoded_id, ) ) )
+        except Exception, e:
+            rval = "Error in group API at listing roles"
+            log.error( rval + ": %s" % str(e) )
+            trans.response.status = 500
+        return rval
+
+    @web.expose_api
+    @web.require_admin
+    def show( self, trans, id, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/roles/{encoded_role_id}
+        Displays information about a group role.
+        """
+        role_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_role_id =  trans.security.decode_id( role_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id )
+            for gra in group.roles:
+                if gra.role == role:
+                    item = dict( id = role_id,
+                                   name = role.name,
+                                   url = url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This
+            if not item:
+                item = "role %s not in group %s" % (role.name,group.name)
+        except Exception, e:
+            item = "Error in group_role API group %s role %s" % (group.name, role.name)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def update( self, trans, id, group_id, **kwd ):
+        """
+        PUT /api/groups/{encoded_group_id}/roles/{encoded_role_id}
+        Adds a role to a group
+        """
+        role_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_role_id =  trans.security.decode_id( role_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id )
+            for gra in group.roles:
+                if gra.role == role:
+                    item = dict( id = role_id,
+                                   name = role.name,
+                                   url = url_for( 'group_role', group_id=group_id, id=role_id) ) 
+            if not item:
+                gra = trans.app.model.GroupRoleAssociation( group, role )
+                # Add GroupRoleAssociation
+                trans.sa_session.add( gra )
+                trans.sa_session.flush()
+                item = dict( id = role_id,
+                             name = role.name,
+                             url = url_for( 'group_role', group_id=group_id, id=role_id) ) 
+        except Exception, e:
+            item = "Error in group_role API Adding role %s to group %s" % (role.name,group.name)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def delete( self, trans, id, group_id, **kwd ):
+        """
+        DELETE /api/groups/{encoded_group_id}/roles/{encoded_role_id}
+        Removes a role from a group
+        """
+        role_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_role_id =  trans.security.decode_id( role_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id )
+            for gra in group.roles:
+                if gra.role == role:
+                    trans.sa_session.delete( gra )
+                    trans.sa_session.flush()
+                    item = dict( id = role_id,
+                                 name = role.name,
+                                 url = url_for( 'group_role', group_id=group_id, id=role_id) ) 
+            if not item:
+                item = "role %s not in group %s" % (role.name,group.name)
+        except Exception, e:
+            item = "Error in group_role API Removing role %s from group %s" % (role.name,group.name)
+            log.error(item + ": %s" % str(e))
+        return item


diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/api/group_users.py
--- /dev/null
+++ b/lib/galaxy/web/api/group_users.py
@@ -0,0 +1,124 @@
+"""
+API operations on Group objects.
+"""
+import logging
+from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy import web
+
+log = logging.getLogger( __name__ )
+
+class GroupUsersAPIController( BaseAPIController ):
+
+    @web.expose_api
+    @web.require_admin
+    def index( self, trans, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/users
+        Displays a collection (list) of groups.
+        """
+        decoded_group_id = trans.security.decode_id( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        rval = []
+        try:
+            for uga in group.users:
+                user = uga.user
+                encoded_id = trans.security.encode_id( user.id )
+                rval.append( dict( id = encoded_id,
+                                   email = user.email,
+                                   url = url_for( 'group_user', group_id=group_id, id=encoded_id, ) ) )
+        except Exception, e:
+            rval = "Error in group API at listing users"
+            log.error( rval + ": %s" % str(e) )
+            trans.response.status = 500
+        return rval
+
+    @web.expose_api
+    @web.require_admin
+    def show( self, trans, id, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/users/{encoded_user_id}
+        Displays information about a group user.
+        """
+        user_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_user_id =  trans.security.decode_id( user_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
+            for uga in group.users:
+                if uga.user == user:
+                    item = dict( id = user_id,
+                                   email = user.email,
+                                   url = url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This
+            if not item:
+                item = "user %s not in group %s" % (user.email,group.name)
+        except Exception, e:
+            item = "Error in group_user API group %s user %s" % (group.name, user.email)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def update( self, trans, id, group_id, **kwd ):
+        """
+        PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
+        Adds a user to a group
+        """
+        user_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_user_id =  trans.security.decode_id( user_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
+            for uga in group.users:
+                if uga.user == user:
+                    item = dict( id = user_id,
+                                   email = user.email,
+                                   url = url_for( 'group_user', group_id=group_id, id=user_id) ) 
+            if not item:
+                uga = trans.app.model.UserGroupAssociation( user, group )
+                # Add UserGroupAssociations
+                trans.sa_session.add( uga )
+                trans.sa_session.flush()
+                item = dict( id = user_id,
+                             email = user.email,
+                             url = url_for( 'group_user', group_id=group_id, id=user_id) ) 
+        except Exception, e:
+            item = "Error in group_user API Adding user %s to group %s" % (user.email,group.name)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def delete( self, trans, id, group_id, **kwd ):
+        """
+        DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id}
+        Removes a user from a group
+        """
+        user_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_user_id =  trans.security.decode_id( user_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
+            for uga in group.users:
+                if uga.user == user:
+                    trans.sa_session.delete( uga )
+                    trans.sa_session.flush()
+                    item = dict( id = user_id,
+                                 email = user.email,
+                                 url = url_for( 'group_user', group_id=group_id, id=user_id) ) 
+            if not item:
+                item = "user %s not in group %s" % (user.email,group.name)
+        except Exception, e:
+            item = "Error in group_user API Removing user %s from group %s" % (user.email,group.name)
+            log.error(item + ": %s" % str(e))
+        return item


diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/api/groups.py
--- /dev/null
+++ b/lib/galaxy/web/api/groups.py
@@ -0,0 +1,128 @@
+"""
+API operations on Group objects.
+"""
+import logging
+from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy import web
+
+
+log = logging.getLogger( __name__ )
+
+
+class GroupAPIController( BaseAPIController ):
+
+    @web.expose_api
+    @web.require_admin
+    def index( self, trans, **kwd ):
+        """
+        GET /api/groups
+        Displays a collection (list) of groups.
+        """
+        rval = []
+        for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted == False ):
+            if trans.user_is_admin():
+                item = group.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+                encoded_id = trans.security.encode_id( group.id )
+                item['url'] = url_for( 'group', id=encoded_id )
+                rval.append( item )
+        return rval
+
+    @web.expose_api
+    def create( self, trans, payload, **kwd ):
+        """
+        POST /api/groups
+        Creates a new group.
+        """
+        log.info("groups payload%s\n" % (payload)) 
+        if not trans.user_is_admin():
+            trans.response.status = 403
+            return "You are not authorized to create a new group."
+        name = payload.get( 'name', None )
+        if not name:
+            trans.response.status = 400
+            return "Enter a valid name"
+        if trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first():
+            trans.response.status = 400
+            return "A group with that name already exists"
+
+        group = trans.app.model.Group( name=name )
+        trans.sa_session.add( group )
+        user_ids = payload.get( 'user_ids', [] )
+        for i in user_ids:
+          log.info("user_id: %s\n" % (i )) 
+          log.info("%s %s\n" % (i, trans.security.decode_id( i ) )) 
+        users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ]
+        role_ids = payload.get( 'role_ids', [] )
+        roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ]
+        trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users )
+        """
+        # Create the UserGroupAssociations
+        for user in users:
+            trans.app.security_agent.associate_user_group( user, group )
+        # Create the GroupRoleAssociations
+        for role in roles:
+            trans.app.security_agent.associate_group_role( group, role )
+        """
+        trans.sa_session.flush()
+        encoded_id = trans.security.encode_id( group.id )
+        item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+        item['url'] = url_for( 'group', id=encoded_id )
+        return [ item ]
+
+    @web.expose_api
+    @web.require_admin
+    def show( self, trans, id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}
+        Displays information about a group.
+        """
+        group_id = id
+        try:
+            decoded_group_id = trans.security.decode_id( group_id )
+        except TypeError:
+            trans.response.status = 400
+            return "Malformed group id ( %s ) specified, unable to decode." % str( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+        item['url'] = url_for( 'group', id=group_id )
+        item['users_url'] = url_for( 'group_users', group_id=group_id )
+        item['roles_url'] = url_for( 'group_roles', group_id=group_id )
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def update( self, trans, id, payload, **kwd ):
+        """
+        PUT /api/groups/{encoded_group_id}
+        Modifies a group.
+        """
+        group_id = id
+        try:
+            decoded_group_id = trans.security.decode_id( group_id )
+        except TypeError:
+            trans.response.status = 400
+            return "Malformed group id ( %s ) specified, unable to decode." % str( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        name = payload.get( 'name', None )
+        if name:
+          group.name = name
+          trans.sa_session.add(group)
+        user_ids = payload.get( 'user_ids', [] )
+        users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ]
+        role_ids = payload.get( 'role_ids', [] )
+        roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ]
+        trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users,delete_existing_assocs=False )
+        trans.sa_session.flush()
+


diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/buildapp.py
--- a/lib/galaxy/web/buildapp.py
+++ b/lib/galaxy/web/buildapp.py
@@ -122,6 +122,18 @@
                                 'permissions',
                                 path_prefix='/api/libraries/:library_id',
                                 parent_resources=dict( member_name='library', collection_name='libraries' ) )      
+    webapp.api_mapper.resource( 'user',
+                                'users',
+                                controller='group_users',
+                                name_prefix='group_',
+                                path_prefix='/api/groups/:group_id',
+                                parent_resources=dict( member_name='group', collection_name='groups' ) )
+    webapp.api_mapper.resource( 'role',
+                                'roles',
+                                controller='group_roles',
+                                name_prefix='group_',
+                                path_prefix='/api/groups/:group_id',
+                                parent_resources=dict( member_name='group', collection_name='groups' ) )
     webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' )
     webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' )
@@ -129,6 +141,7 @@
     webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' )
     webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' )
     webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' )
+    webapp.api_mapper.resource( 'group', 'groups', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' )
     webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' )



https://bitbucket.org/galaxy/galaxy-central/changeset/761c58466d97/
changeset:   761c58466d97
user:        jmchilton
date:        2012-08-09 22:18:00
summary:     Merge.
affected #:  19 files

diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 buildbot_setup.sh
--- a/buildbot_setup.sh
+++ b/buildbot_setup.sh
@@ -68,8 +68,13 @@
 datatypes_conf.xml.sample
 universe_wsgi.ini.sample
 tool_data_table_conf.xml.sample
+migrated_tools_conf.xml.sample
+tool-data/shared/ensembl/builds.txt.sample
+tool-data/shared/igv/igv_build_sites.txt.sample
+tool-data/shared/ncbi/builds.txt.sample
+tool-data/shared/rviewer/rviewer_build_sites.txt.sample
 tool-data/shared/ucsc/builds.txt.sample
-migrated_tools_conf.xml.sample
+tool-data/shared/ucsc/publicbuilds.txt.sample
 "
 
 DIRS="


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 contrib/multiproccess.sh
--- a/contrib/multiproccess.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/bash
-
-# copy this script to the top level galaxy directory and modify the following
-# for your environment
-
-web_server_names=(web{0..2}) # server names: web0 web1 web2
-runner_server_names=(runner0) # server name: runner0
-
-web_config='universe_wsgi.webapp.ini'
-runner_config='universe_wsgi.runner.ini'
-
-# actually do the requested action
-
-if [ -z "$1" ]; then
-    echo "usage: multiprocess.sh <--daemon|--stop-daemon>"
-    exit 1
-fi
-
-for server_name in ${web_server_names[@]}; do
-    echo "[$server_name]"
-    python ./scripts/paster.py serve $web_config --server-name=$server_name --pid-file=$server_name.pid --log-file=$server_name.log $@
-done
-for server_name in ${runner_server_names[@]}; do
-    echo "[$server_name]"
-    python ./scripts/paster.py serve $runner_config --server-name=$server_name --pid-file=$server_name.pid --log-file=$server_name.log $@
-done


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/tool_shed/install_manager.py
--- a/lib/galaxy/tool_shed/install_manager.py
+++ b/lib/galaxy/tool_shed/install_manager.py
@@ -2,7 +2,7 @@
 Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml).
 All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed.
 """
-import urllib2
+import urllib2, tempfile
 from galaxy.tools import ToolSection
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
@@ -132,7 +132,7 @@
                 tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections )
                 for k, v in tool_panel_dict_for_tool_config.items():
                     tool_panel_dict_for_display[ k ] = v
-        metadata_dict = generate_metadata_using_disk_files( self.toolbox, relative_install_dir, repository_clone_url )
+        metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( self.app, relative_install_dir, repository_clone_url )
         tool_shed_repository.metadata = metadata_dict
         self.app.sa_session.add( tool_shed_repository )
         self.app.sa_session.flush()
@@ -142,7 +142,7 @@
         else:
             tool_dependencies = None
         if 'tools' in metadata_dict:
-            work_dir = make_tmp_directory()
+            work_dir = tempfile.mkdtemp()
             repository_tools_tups = get_repository_tools_tups( self.app, metadata_dict )
             if repository_tools_tups:
                 sample_files = metadata_dict.get( 'sample_files', [] )
@@ -195,7 +195,7 @@
                 tool_shed_repository.includes_datatypes = True
             self.app.sa_session.add( tool_shed_repository )
             self.app.sa_session.flush()
-            work_dir = make_tmp_directory()
+            work_dir = tempfile.mkdtemp()
             datatypes_config = get_config_from_repository( self.app,
                                                            'datatypes_conf.xml',
                                                            tool_shed_repository,


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -4,6 +4,7 @@
 import pkg_resources
 
 pkg_resources.require( "simplejson" )
+pkg_resources.require( "Mako" )
 
 import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback
 import simplejson
@@ -2344,7 +2345,7 @@
             command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip()
         except Exception, e:
             # Modify exception message to be more clear
-            #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ) )
+            #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ), )
             raise
         if self.interpreter:
             # TODO: path munging for cluster/dataset server relocatability
@@ -2441,7 +2442,7 @@
             if code:
                 return code( *args, **kwargs )
         except Exception, e:
-            e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ) )
+            e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ), )
             raise
     def exec_before_job( self, app, inp_data, out_data, param_dict={} ):
         pass


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -3,6 +3,7 @@
 from datetime import date, datetime, timedelta
 from time import strftime, gmtime
 from galaxy import util
+from galaxy.tools import parameters
 from galaxy.datatypes.checkers import *
 from galaxy.util.json import *
 from galaxy.tools.search import ToolBoxSearch
@@ -247,6 +248,52 @@
         except:
             pass
     return converter_path, display_path
+def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ):
+    """
+    Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make 
+    sure the files exist.
+    """
+    invalid_files_and_errors_tups = []
+    correction_msg = ''
+    for input_param in tool.input_params:
+        if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic:
+            # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist.
+            options = input_param.dynamic_options or input_param.options
+            if options:
+                if options.tool_data_table or options.missing_tool_data_table_name:
+                    # Make sure the repository contains a tool_data_table_conf.xml.sample file.
+                    sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir )
+                    if sample_tool_data_table_conf:
+                        error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf )
+                        if error:
+                            invalid_files_and_errors_tups.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) )
+                        else:
+                            options.missing_tool_data_table_name = None
+                    else:
+                        correction_msg = "This file requires an entry in the tool_data_table_conf.xml file.  Upload a file named tool_data_table_conf.xml.sample "
+                        correction_msg += "to the repository that includes the required entry to correct this error.<br/>"
+                        invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) )
+                if options.index_file or options.missing_index_file:
+                    # Make sure the repository contains the required xxx.loc.sample file.
+                    index_file = options.index_file or options.missing_index_file
+                    index_file_name = strip_path( index_file )
+                    sample_found = False
+                    for sample_file in sample_files:
+                        sample_file_name = strip_path( sample_file )
+                        if sample_file_name == '%s.sample' % index_file_name:
+                            options.index_file = index_file_name
+                            options.missing_index_file = None
+                            if options.tool_data_table:
+                                options.tool_data_table.missing_index_file = None
+                            sample_found = True
+                            break
+                    if not sample_found:
+                        correction_msg = "This file refers to a file named <b>%s</b>.  " % str( index_file )
+                        correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name )
+                        invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) )
+    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
+    reset_tool_data_tables( app )
+    return invalid_files_and_errors_tups
 def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ):
     # Persist the current in-memory list of config_elems to a file named by the value of config_filename.  
     fd, filename = tempfile.mkstemp()
@@ -383,7 +430,7 @@
 def create_tool_dependency_objects( app, tool_shed_repository, current_changeset_revision, set_status=True ):
     # Create or update a ToolDependency for each entry in tool_dependencies_config.  This method is called when installing a new tool_shed_repository.
     tool_dependency_objects = []
-    work_dir = make_tmp_directory()
+    work_dir = tempfile.mkdtemp()
     # Get the tool_dependencies.xml file from the repository.
     tool_dependencies_config = get_config_from_repository( app,
                                                            'tool_dependencies.xml',
@@ -501,6 +548,76 @@
             if not can_generate_dependency_metadata:
                 break
     return can_generate_dependency_metadata
+def generate_metadata_for_changeset_revision( app, repository_files_dir, repository_clone_url ):
+    """
+    Generate metadata for a repository using it's files on disk.  To generate metadata for changeset revisions older than the repository tip,
+    the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's
+    disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be a temporary directory containing a clone).
+    """
+    metadata_dict = {}
+    invalid_file_tups = []
+    invalid_tool_configs = []
+    tool_dependencies_config = None
+    datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir )
+    if datatypes_config:
+        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
+    sample_files = get_sample_files_from_disk( repository_files_dir )
+    if sample_files:
+        metadata_dict[ 'sample_files' ] = sample_files
+    # Find all tool configs and exported workflows.
+    for root, dirs, files in os.walk( repository_files_dir ):
+        if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+            if '.hg' in dirs:
+                dirs.remove( '.hg' )
+            for name in files:
+                # Find all tool configs.
+                if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ):
+                    full_path = os.path.abspath( os.path.join( root, name ) )
+                    if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ]
+                             or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ):
+                        try:
+                            # Make sure we're looking at a tool config and not a display application config or something else.
+                            element_tree = util.parse_xml( full_path )
+                            element_tree_root = element_tree.getroot()
+                            is_tool = element_tree_root.tag == 'tool'
+                        except Exception, e:
+                            print "Error parsing %s", full_path, ", exception: ", str( e )
+                            is_tool = False
+                        if is_tool:
+                            try:
+                                tool = app.toolbox.load_tool( full_path )
+                            except Exception, e:
+                                tool = None
+                                invalid_tool_configs.append( name )
+                            if tool is not None:
+                                invalid_files_and_errors_tups = check_tool_input_params( app, repository_files_dir, name, tool, sample_files )
+                                can_set_metadata = True
+                                for tup in invalid_files_and_errors_tups:
+                                    if name in tup:
+                                        can_set_metadata = False
+                                        invalid_tool_configs.append( name )
+                                        break
+                                if can_set_metadata:
+                                    metadata_dict = generate_tool_metadata( os.path.join( root, name ), tool, repository_clone_url, metadata_dict )
+                                else:
+                                    invalid_file_tups.extend( invalid_files_and_errors_tups )
+                # Find all exported workflows
+                elif name.endswith( '.ga' ):
+                    relative_path = os.path.join( root, name )
+                    fp = open( relative_path, 'rb' )
+                    workflow_text = fp.read()
+                    fp.close()
+                    exported_workflow_dict = from_json_string( workflow_text )
+                    if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                        metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
+    if 'tools' in metadata_dict:
+        # This step must be done after metadata for tools has been defined.
+        tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', repository_files_dir )
+        if tool_dependencies_config:
+            metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict )
+    if invalid_tool_configs:
+        metadata_dict [ 'invalid_tools' ] = invalid_tool_configs
+    return metadata_dict, invalid_file_tups
 def generate_package_dependency_metadata( elem, tool_dependencies_dict ):
     """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set."""
     requirements_dict = {}
@@ -517,58 +634,6 @@
     if requirements_dict:
         tool_dependencies_dict[ dependency_key ] = requirements_dict
     return tool_dependencies_dict
-def generate_metadata_using_disk_files( toolbox, relative_install_dir, repository_clone_url ):
-    """Generate metadata using only the repository files on disk - files are not retrieved from the repository manifest."""
-    metadata_dict = {}
-    tool_dependencies_config = None
-    datatypes_config = get_config_from_disk( 'datatypes_conf.xml', relative_install_dir )
-    if datatypes_config:
-        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
-    sample_files = get_sample_files_from_disk( relative_install_dir )
-    if sample_files:
-        metadata_dict[ 'sample_files' ] = sample_files
-    # Find all tool configs and exported workflows.
-    for root, dirs, files in os.walk( relative_install_dir ):
-        if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
-            if '.hg' in dirs:
-                dirs.remove( '.hg' )
-            for name in files:
-                # Find all tool configs.
-                if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ):
-                    full_path = os.path.abspath( os.path.join( root, name ) )
-                    if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ]
-                             or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ):
-                        try:
-                            # Make sure we're looking at a tool config and not a display application config or something else.
-                            element_tree = util.parse_xml( full_path )
-                            element_tree_root = element_tree.getroot()
-                            is_tool = element_tree_root.tag == 'tool'
-                        except Exception, e:
-                            log.debug( "Error parsing %s, exception: %s" % ( full_path, str( e ) ) )
-                            is_tool = False
-                        if is_tool:
-                            try:
-                                tool = toolbox.load_tool( full_path )
-                            except Exception, e:
-                                tool = None
-                            if tool is not None:
-                                tool_config = os.path.join( root, name )
-                                metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict )
-                # Find all exported workflows
-                elif name.endswith( '.ga' ):
-                    relative_path = os.path.join( root, name )
-                    fp = open( relative_path, 'rb' )
-                    workflow_text = fp.read()
-                    fp.close()
-                    exported_workflow_dict = from_json_string( workflow_text )
-                    if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                        metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
-    if 'tools' in metadata_dict:
-        # This step must be done after metadata for tools has been defined.
-        tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir )
-        if tool_dependencies_config:
-            metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict )
-    return metadata_dict
 def generate_tool_guid( repository_clone_url, tool ):
     """
     Generate a guid for the installed tool.  It is critical that this guid matches the guid for
@@ -1266,7 +1331,7 @@
 def load_installed_datatypes( app, repository, relative_install_dir, deactivate=False ):
     # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later.
     metadata = repository.metadata
-    work_dir = make_tmp_directory()
+    work_dir = tempfile.mkdtemp()
     repository_dict = None
     datatypes_config = get_config_from_repository( app,
                                                    'datatypes_conf.xml',
@@ -1293,17 +1358,6 @@
 def load_installed_display_applications( app, installed_repository_dict, deactivate=False ):
     # Load or deactivate proprietary datatype display applications
     app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate )
-def make_tmp_directory():
-    tmp_dir = os.getenv( 'TMPDIR', '' )
-    if tmp_dir:
-        tmp_dir = tmp_dir.strip()
-    else:
-        home_dir = os.getenv( 'HOME' )
-        tmp_dir = os.path.join( home_dir, 'tmp' )
-    work_dir = os.path.join( tmp_dir, 'work_tmp' )
-    if not os.path.exists( work_dir ):
-        os.makedirs( work_dir )
-    return work_dir
 def open_repository_files_folder( trans, folder_path ):
     try:
         files_list = get_repository_files( trans, folder_path )


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -1,4 +1,4 @@
-import urllib2
+import urllib2, tempfile
 from galaxy.web.controllers.admin import *
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
@@ -522,7 +522,7 @@
         # Get the tool_shed_repository from one of the tool_dependencies.
         message = ''
         tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
-        work_dir = make_tmp_directory()
+        work_dir = tempfile.mkdtemp()
         # Get the tool_dependencies.xml file from the repository.
         tool_dependencies_config = get_config_from_repository( trans.app,
                                                                'tool_dependencies.xml',
@@ -654,7 +654,7 @@
                     message += "from the installed repository's <b>Repository Actions</b> menu.  "
                     status = 'error'
             if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata:
-                work_dir = make_tmp_directory()
+                work_dir = tempfile.mkdtemp()
                 # Install tool dependencies.
                 update_tool_shed_repository_status( trans.app,
                                                     tool_shed_repository,
@@ -684,7 +684,7 @@
         Generate the metadata for the installed tool shed repository, among other things.  This method is called from Galaxy (never the tool shed)
         when an admin is installing a new repository or reinstalling an uninstalled repository.
         """
-        metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url )
+        metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url )
         tool_shed_repository.metadata = metadata_dict
         trans.sa_session.add( tool_shed_repository )
         trans.sa_session.flush()
@@ -695,7 +695,7 @@
             repository_tools_tups = get_repository_tools_tups( trans.app, metadata_dict )
             if repository_tools_tups:
                 # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                work_dir = make_tmp_directory()
+                work_dir = tempfile.mkdtemp()
                 repository_tools_tups = handle_missing_data_table_entry( trans.app,
                                                                          tool_shed_repository,
                                                                          tool_shed_repository.changeset_revision,
@@ -726,7 +726,7 @@
                 tool_shed_repository.includes_datatypes = True
             trans.sa_session.add( tool_shed_repository )
             trans.sa_session.flush()
-            work_dir = make_tmp_directory()
+            work_dir = tempfile.mkdtemp()
             datatypes_config = get_config_from_repository( trans.app,
                                                            'datatypes_conf.xml',
                                                            tool_shed_repository,
@@ -779,7 +779,7 @@
             message = "The repository information has been updated."
         elif params.get( 'set_metadata_button', False ):
             repository_clone_url = generate_clone_url( trans, repository )
-            metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url )
+            metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url )
             if metadata_dict:
                 repository.metadata = metadata_dict
                 trans.sa_session.add( repository )
@@ -1479,7 +1479,7 @@
                     update_repository( repo, latest_ctx_rev )
                     # Update the repository metadata.
                     tool_shed = clean_tool_shed_url( tool_shed_url )
-                    metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url )
+                    metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url )
                     repository.metadata = metadata_dict
                     # Update the repository changeset_revision in the database.
                     repository.changeset_revision = latest_changeset_revision


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/web/controllers/data_admin.py
--- a/lib/galaxy/web/controllers/data_admin.py
+++ b/lib/galaxy/web/controllers/data_admin.py
@@ -30,25 +30,28 @@
     @web.expose
     @web.require_admin
     def manage_data( self, trans, **kwd ):
-        genomes = dict()
         if trans.app.config.get_bool( 'enable_beta_job_managers', False ) == False:
-            return trans.fill_template( '/admin/data_admin/betajob.mako' )
-        for line in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data:
-            defstate = dict( state='Generate', style=self.jobstyles[ 'new' ] )
-            indexers = dict( bowtie_indexes=defstate, bowtie2_indexes=defstate, bwa_indexes=defstate, perm_base_indexes=defstate, srma_indexes=defstate, sam_fa_indexes=defstate )
-            dbkey = line[0]
-            name = line[2]
-            indexers[ 'name' ] = name
-            indexers[ 'fapath' ] = line[3]
-            genomes[ dbkey ] = indexers
-        for table in [ 'bowtie_indexes', 'bowtie2_indexes', 'bwa_indexes', 'srma_indexes' ]:
-            for line in trans.app.tool_data_tables.data_tables[ table ].data:
-                dbkey = line[0]
-                genomes[ dbkey ][ table ] = dict( state='Generated', style=self.jobstyles[ 'done' ] )
-        for line in trans.app.tool_data_tables.data_tables[ 'sam_fa_indexes' ].data:
-            genomes[ line[1] ][ 'sam_fa_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] )
-        for line in trans.app.tool_data_tables.data_tables[ 'perm_base_indexes' ].data:
-            genomes[ line[1].split(':')[0] ][ 'perm_base_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] )
+            return trans.fill_template( '/admin/data_admin/generic_error.mako', message='This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.' )
+        if 'all_fasta' not in trans.app.tool_data_tables.data_tables:
+            return trans.fill_template( '/admin/data_admin/generic_error.mako', message='The local data manager requires that an all_fasta entry exists in your tool_data_table_conf.xml.' )
+        indextable = {}
+        dbkeys = []
+        labels = { 'bowtie_indexes': 'Bowtie', 'bowtie2_indexes': 'Bowtie 2', 'bwa_indexes': 'BWA', 'srma_indexes': 'Picard', 'sam_fa_indexes': 'SAM', 'perm_base_indexes': 'PerM' }
+        tablenames = { 'Bowtie': 'bowtie_indexes', 'Bowtie 2': 'bowtie2_indexes', 'BWA': 'bwa_indexes', 'Picard': 'srma_indexes', 'SAM': 'sam_fa_indexes', 'PerM': 'perm_base_indexes' }
+        indexfuncs = dict( bowtie_indexes='bowtie', bowtie2_indexes='bowtie2', bwa_indexes='bwa', srma_indexes='picard', sam_fa_indexes='sam', perm_base_indexes='perm' )
+        for genome in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data:
+            dbkey = genome[0]
+            dbkeys.append( dbkey )
+            indextable[ dbkey ] = dict( indexes=dict(), name=genome[2], path=genome[3] )
+        for genome in indextable:
+            for label in labels:
+                indextable[ genome ][ 'indexes' ][ label ] = 'Generate'
+                if label not in trans.app.tool_data_tables.data_tables:
+                    indextable[ genome ][ 'indexes' ][ label ] = 'Disabled'
+                else:
+                    for row in trans.app.tool_data_tables.data_tables[ label ].data:
+                        if genome in row or row[0].startswith( genome ):
+                            indextable[ genome ][ 'indexes' ][ label ] = 'Generated'
         jobgrid = []
         sa_session = trans.app.model.context.current
         jobs = sa_session.query( model.GenomeIndexToolData ).order_by( model.GenomeIndexToolData.created_time.desc() ).filter_by( user_id=trans.get_user().id ).group_by( model.GenomeIndexToolData.deferred ).limit( 20 ).all()
@@ -65,7 +68,8 @@
                 jobtype = 'index'
             indexers = ', '.join( params['indexes'] )
             jobgrid.append( dict( jobtype=jobtype, indexers=indexers, rowclass=state, deferred=job.deferred.id, state=state, intname=job.deferred.params[ 'intname' ], dbkey=job.deferred.params[ 'dbkey' ] ) )
-        return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, genomes=genomes )
+        styles = dict( Generate=self.jobstyles['new'], Generated=self.jobstyles['ok'], Disabled=self.jobstyles['error'] )
+        return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, indextable=indextable, labels=labels, dbkeys=dbkeys, styles=styles, indexfuncs=indexfuncs )
     
     @web.expose
     @web.require_admin


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -655,7 +655,7 @@
             'name':  module.get_name(),
             'tool_id': module.get_tool_id(),
             'tool_state': module.get_state(),
-            'tooltip': module.get_tooltip(),
+            'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
             'data_inputs': module.get_data_inputs(),
             'data_outputs': module.get_data_outputs(),
             'form_html': module.get_config_form(),
@@ -732,7 +732,7 @@
                 'tool_id': module.get_tool_id(),
                 'name': module.get_name(),
                 'tool_state': module.get_state(),
-                'tooltip': module.get_tooltip(),
+                'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
                 'tool_errors': module.get_errors(),
                 'data_inputs': module.get_data_inputs(),
                 'data_outputs': module.get_data_outputs(),


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -1,15 +1,13 @@
-import os, string, socket, logging, simplejson, binascii
+import os, string, socket, logging, simplejson, binascii, tempfile
 from time import strftime
 from datetime import *
 from galaxy.datatypes.checkers import *
 from galaxy.tools import *
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.hash_util import *
-from galaxy.util.shed_util import clone_repository, copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata
-from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_config_from_disk, get_configured_ui
-from galaxy.util.shed_util import get_named_tmpfile_from_ctx, get_sample_files_from_disk, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH
-from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path, to_html_escaped
-from galaxy.util.shed_util import to_html_str, update_repository
+from galaxy.util.shed_util import clone_repository, generate_metadata_for_changeset_revision, get_changectx_for_changeset, get_config_from_disk
+from galaxy.util.shed_util import get_configured_ui, get_named_tmpfile_from_ctx, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH
+from galaxy.util.shed_util import reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path
 from galaxy.web.base.controller import *
 from galaxy.webapps.community import model
 from galaxy.model.orm import *
@@ -107,11 +105,8 @@
             trans.sa_session.flush()
         return item_rating
 
-## ---- Utility methods -------------------------------------------------------
-
 def add_repository_metadata_tool_versions( trans, id, changeset_revisions ):
-    # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' }
-    # pairs for each tool in each changeset revision.
+    # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision.
     for index, changeset_revision in enumerate( changeset_revisions ):
         tool_versions_dict = {}
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
@@ -120,57 +115,24 @@
             if metadata:
                 tool_dicts = metadata.get( 'tools', [] )
                 if index == 0:
-                    # The first changset_revision is a special case because it will have no ancestor
-                    # changeset_revisions in which to match tools.  The parent tool id for tools in
-                    # the first changeset_revision will be the "old_id" in the tool config.
+                    # The first changset_revision is a special case because it will have no ancestor changeset_revisions in which to match tools.
+                    # The parent tool id for tools in the first changeset_revision will be the "old_id" in the tool config.
                     for tool_dict in tool_dicts:
                         tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ]
                 else:
                     for tool_dict in tool_dicts:
                         # We have at least 2 changeset revisions to compare tool guids and tool ids.
-                        parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] )
+                        parent_id = get_parent_id( trans,
+                                                   id,
+                                                   tool_dict[ 'id' ],
+                                                   tool_dict[ 'version' ],
+                                                   tool_dict[ 'guid' ],
+                                                   changeset_revisions[ 0:index ] )
                         tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id
                 if tool_versions_dict:
                     repository_metadata.tool_versions = tool_versions_dict
                     trans.sa_session.add( repository_metadata )
                     trans.sa_session.flush()
-def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ):
-    """Build a SelectField whose options are the changeset_rev strings of all downloadable revisions of the received repository."""
-    repo = hg.repository( get_configured_ui(), repository.repo_path )
-    options = []
-    changeset_tups = []
-    refresh_on_change_values = []
-    for repository_metadata in repository.downloadable_revisions:
-        changeset_revision = repository_metadata.changeset_revision
-        ctx = get_changectx_for_changeset( repo, changeset_revision )
-        if ctx:
-            rev = '%04d' % ctx.rev()
-            label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
-        else:
-            rev = '-1'
-            label = "-1:%s" % changeset_revision
-        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,
-    # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time.
-    for changeset_tup in sorted( changeset_tups ):
-        # Display the latest revision first.
-        options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) )
-    if add_id_to_name:
-        name = 'changeset_revision_%d' % repository.id
-    else:
-        name = 'changeset_revision'
-    select_field = SelectField( name=name,
-                                refresh_on_change=True,
-                                refresh_on_change_values=refresh_on_change_values )
-    for option_tup in options:
-        selected = selected_value and option_tup[1] == selected_value
-        select_field.add_option( option_tup[0], option_tup[1], selected=selected )
-    return select_field
-def changeset_is_downloadable( metadata_dict ):
-    # A RepositoryMetadata record will be created if metadata_dict includes only invalid stuff like 'invalid_tools', but in this case
-    # it won't be downloadable.
-    return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict
 def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
     """Check the malicious flag in repository metadata for a specified change set"""
     repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
@@ -188,60 +150,12 @@
             if user_email in admin_users:
                 return True
     return False
-def check_tool_input_params( trans, repo_dir, tool_config, tool, sample_files, invalid_files ):
-    """
-    Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make 
-    sure the files exist.
-    """
-    can_set_metadata = True
-    correction_msg = ''
-    for input_param in tool.input_params:
-        if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic:
-            # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist.
-            options = input_param.dynamic_options or input_param.options
-            if options:
-                if options.tool_data_table or options.missing_tool_data_table_name:
-                    # Make sure the repository contains a tool_data_table_conf.xml.sample file.
-                    sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir )
-                    if sample_tool_data_table_conf:
-                        error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_tool_data_table_conf )
-                        if error:
-                            can_set_metadata = False
-                            invalid_files.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) )
-                        else:
-                            options.missing_tool_data_table_name = None
-                    else:
-                        can_set_metadata = False
-                        correction_msg = "This file requires an entry in the tool_data_table_conf.xml file.  Upload a file named tool_data_table_conf.xml.sample "
-                        correction_msg += "to the repository that includes the required entry to correct this error.<br/>"
-                        invalid_files.append( ( tool_config, correction_msg ) )
-                if options.index_file or options.missing_index_file:
-                    # Make sure the repository contains the required xxx.loc.sample file.
-                    index_file = options.index_file or options.missing_index_file
-                    index_file_name = strip_path( index_file )
-                    sample_found = False
-                    for sample_file in sample_files:
-                        sample_file_name = strip_path( sample_file )
-                        if sample_file_name == '%s.sample' % index_file_name:
-                            options.index_file = index_file_name
-                            options.missing_index_file = None
-                            if options.tool_data_table:
-                                options.tool_data_table.missing_index_file = None
-                            sample_found = True
-                            break
-                    if not sample_found:
-                        can_set_metadata = False
-                        correction_msg = "This file refers to a file named <b>%s</b>.  " % str( index_file )
-                        correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name )
-                        invalid_files.append( ( tool_config, correction_msg ) )
-    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-    reset_tool_data_tables( trans.app )
-    return can_set_metadata, invalid_files
 def clean_repository_metadata( trans, id, changeset_revisions ):
     # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions.
     # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older
     # records, so we'll order by update_time descending and delete records that have the same changeset_revision we come across later..
-    changeset_revisions_checked = [] 
+    changeset_revisions_checked = []
+    cleaned_changeset_revisions = []
     for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \
                                                .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \
                                                .order_by( trans.model.RepositoryMetadata.table.c.changeset_revision,
@@ -251,6 +165,9 @@
         if can_delete:
             trans.sa_session.delete( repository_metadata )
             trans.sa_session.flush()
+        else:
+            cleaned_changeset_revisions.append( changeset_revision )
+    return cleaned_changeset_revisions
 def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ):
     # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict.  This changeset_revision is an ancestor of
     # current_changeset_revision which is associated with current_metadata_dict.  A new repository_metadata record will be created only
@@ -369,14 +286,19 @@
             return file_path
     return None
 def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ):
+    downloadable = is_downloadable( metadata_dict )
     repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
     if repository_metadata:
         repository_metadata.metadata = metadata_dict
+        repository_metadata.downloadable = downloadable
     else:
-        repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
-    repository_metadata.downloadable = changeset_is_downloadable( metadata_dict )
+        repository_metadata = trans.model.RepositoryMetadata( repository_id=repository.id,
+                                                              changeset_revision=changeset_revision,
+                                                              metadata=metadata_dict,
+                                                              downloadable=downloadable )
     trans.sa_session.add( repository_metadata )
     trans.sa_session.flush()
+    return repository_metadata
 def generate_clone_url( trans, repository_id ):
     """Generate the URL for cloning a repository."""
     repository = get_repository( trans, repository_id )
@@ -387,69 +309,6 @@
         return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name )
     else:
         return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name )
-def generate_metadata_for_changeset_revision( trans, repository_files_dir, repository_clone_url ):
-    """
-    Generate metadata for a repository using it's files on disk.  To generate metadata for changeset revisions older than the repository tip,
-    the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's
-    disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be a temporary directory containing a clone).
-    """
-    metadata_dict = {}
-    invalid_files = []
-    invalid_tool_configs = []
-    tool_dependencies_config = None
-    datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir )
-    if datatypes_config:
-        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
-    sample_files = get_sample_files_from_disk( repository_files_dir )
-    if sample_files:
-        metadata_dict[ 'sample_files' ] = sample_files
-    # Find all tool configs and exported workflows.
-    for root, dirs, files in os.walk( repository_files_dir ):
-        if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
-            if '.hg' in dirs:
-                dirs.remove( '.hg' )
-            for name in files:
-                # Find all tool configs.
-                if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ):
-                    full_path = os.path.abspath( os.path.join( root, name ) )
-                    if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ]
-                             or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ):
-                        try:
-                            # Make sure we're looking at a tool config and not a display application config or something else.
-                            element_tree = util.parse_xml( full_path )
-                            element_tree_root = element_tree.getroot()
-                            is_tool = element_tree_root.tag == 'tool'
-                        except Exception, e:
-                            print "Error parsing %s", full_path, ", exception: ", str( e )
-                            is_tool = False
-                        if is_tool:
-                            try:
-                                tool = trans.app.toolbox.load_tool( full_path )
-                                tool_config = os.path.join( root, name )
-                            except Exception, e:
-                                tool = None
-                                invalid_tool_configs.append( name )
-                            if tool is not None:
-                                can_set_metadata, invalid_files = check_tool_input_params( trans, repository_files_dir, tool_config, tool, sample_files, invalid_files )
-                                if can_set_metadata:
-                                    metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict )
-                # Find all exported workflows
-                elif name.endswith( '.ga' ):
-                    relative_path = os.path.join( root, name )
-                    fp = open( relative_path, 'rb' )
-                    workflow_text = fp.read()
-                    fp.close()
-                    exported_workflow_dict = from_json_string( workflow_text )
-                    if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                        metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
-    if 'tools' in metadata_dict:
-        # This step must be done after metadata for tools has been defined.
-        tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', repository_files_dir )
-        if tool_dependencies_config:
-            metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict )
-    if invalid_tool_configs:
-        metadata_dict [ 'invalid_tools' ] = invalid_tool_configs
-    return metadata_dict, invalid_files
 def generate_tool_guid( trans, repository, tool ):
     """
     Generate a guid for the received tool.  The form of the guid is    
@@ -588,10 +447,23 @@
                              .first()
 def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ):
     """Get metadata for a specified repository change set from the database"""
-    return trans.sa_session.query( trans.model.RepositoryMetadata ) \
-                           .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ),
-                                          trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \
-                           .first()
+    # Make sure there are no duplicate records, and return the single unique record for the changeset_revision.  Duplicate records were somehow
+    # creatd in the past.  This may or may not be resolved, so when it is confirmed that the cause of duplicate records has been corrected, tweak 
+    # this method accordingly.
+    all_metadata_records = trans.sa_session.query( trans.model.RepositoryMetadata ) \
+                                           .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ),
+                                                          trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \
+                                           .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \
+                                           .all()
+    if len( all_metadata_records ) > 1:
+        # Delete all recrds older than the last one updated.
+        for repository_metadata in all_metadata_records[ 1: ]:
+            trans.sa_session.delete( repository_metadata )
+            trans.sa_session.flush()
+        return all_metadata_records[ 0 ]
+    elif all_metadata_records:
+        return all_metadata_records[ 0 ]
+    return None
 def get_repository_metadata_by_id( trans, id ):
     """Get repository metadata from the database"""
     return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) )
@@ -700,6 +572,8 @@
                     util.send_mail( frm, to, subject, body, trans.app.config )
             except Exception, e:
                 log.exception( "An error occurred sending a tool shed repository update alert by email." )
+def is_downloadable( metadata_dict ):
+    return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict
 def load_tool( trans, config_file ):
     """Load a single tool from the file named by `config_file` and return an instance of `Tool`."""
     # Parse XML configuration file and get the root element
@@ -762,7 +636,7 @@
     ctx = get_changectx_for_changeset( repo, changeset_revision )
     tool = None
     message = ''
-    work_dir = make_tmp_directory()
+    work_dir = tempfile.mkdtemp()
     sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir )
     if sample_files:
         trans.app.config.tool_data_path = work_dir
@@ -913,7 +787,7 @@
         print "Cloning repository revision: ", str( ctx.rev() )
         clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) )
         print "Generating metadata for changset revision: ", str( ctx.rev() )
-        current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, work_dir, repository_clone_url )
+        current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, work_dir, repository_clone_url )
         if current_metadata_dict:
             if not metadata_changeset_revision and not metadata_dict:
                 # We're at the first change set in the change log.
@@ -935,7 +809,7 @@
                 elif comparison == 'not equal and not subset':
                     metadata_changeset_revision = ancestor_changeset_revision
                     metadata_dict = ancestor_metadata_dict
-                    create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict )
+                    repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict )
                     changeset_revisions.append( metadata_changeset_revision )
                     ancestor_changeset_revision = current_changeset_revision
                     ancestor_metadata_dict = current_metadata_dict
@@ -947,7 +821,7 @@
                 metadata_changeset_revision = current_changeset_revision
                 metadata_dict = current_metadata_dict
                 # We're at the end of the change log.
-                create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict )
+                repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict )
                 changeset_revisions.append( metadata_changeset_revision )
                 ancestor_changeset_revision = None
                 ancestor_metadata_dict = None
@@ -958,7 +832,7 @@
             metadata_dict = ancestor_metadata_dict
             if not ctx.children():
                 # We're at the end of the change log.
-                create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict )
+                repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict )
                 changeset_revisions.append( metadata_changeset_revision )
                 ancestor_changeset_revision = None
                 ancestor_metadata_dict = None
@@ -968,8 +842,9 @@
             except:
                 pass
     # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions.
-    clean_repository_metadata( trans, id, changeset_revisions )
-    add_repository_metadata_tool_versions( trans, id, changeset_revisions )
+    cleaned_changeset_revisions = clean_repository_metadata( trans, id, changeset_revisions )
+    # Set tool version information for all downloadable changeset revisions.
+    add_repository_metadata_tool_versions( trans, id, cleaned_changeset_revisions )
 def set_repository_metadata( trans, repository, content_alert_str='', **kwd ):
     """
     Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset
@@ -980,46 +855,60 @@
     repository_clone_url = generate_clone_url( trans, trans.security.encode_id( repository.id ) )
     repo_dir = repository.repo_path
     repo = hg.repository( get_configured_ui(), repo_dir )
-    metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repo_dir, repository_clone_url )
+    metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url )
     if metadata_dict:
+        downloadable = is_downloadable( metadata_dict )
+        repository_metadata = None
         if new_tool_metadata_required( trans, repository, metadata_dict ) or new_workflow_metadata_required( trans, repository, metadata_dict ):
             # Create a new repository_metadata table row.
-            repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict )
-            trans.sa_session.add( repository_metadata )
-            try:
-                trans.sa_session.flush()
-                # If this is the first record stored for this repository, see if we need to send any email alerts.
-                if len( repository.downloadable_revisions ) == 1:
-                    handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
-            except TypeError, e:
-                message = "Unable to save metadata for this repository, exception: %s" % str( e )
-                status = 'error'
+            repository_metadata = create_or_update_repository_metadata( trans,
+                                                                        trans.security.encode_id( repository.id ),
+                                                                        repository,
+                                                                        repository.tip,
+                                                                        metadata_dict )
+            # If this is the first record stored for this repository, see if we need to send any email alerts.
+            if len( repository.downloadable_revisions ) == 1:
+                handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
         else:
             repository_metadata = get_latest_repository_metadata( trans, repository.id )
             if repository_metadata:
+                downloadable = is_downloadable( metadata_dict )
                 # Update the last saved repository_metadata table row.
                 repository_metadata.changeset_revision = repository.tip
                 repository_metadata.metadata = metadata_dict
-                repository_metadata.downloadable = changeset_is_downloadable( metadata_dict )
+                repository_metadata.downloadable = downloadable
                 trans.sa_session.add( repository_metadata )
                 trans.sa_session.flush()
             else:
                 # There are no tools in the repository, and we're setting metadata on the repository tip.
-                repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict )
-                trans.sa_session.add( repository_metadata )
-                trans.sa_session.flush()
-    elif len( repo ) == 1 and not invalid_files:
+                repository_metadata = create_or_update_repository_metadata( trans,
+                                                                            trans.security.encode_id( repository.id ),
+                                                                            repository,
+                                                                            repository.tip,
+                                                                            metadata_dict )
+        if 'tools' in metadata_dict and repository_metadata and status != 'error':
+            # Set tool versions on the new downloadable change set.  The order of the list of changesets is critical, so we use the repo's changelog.
+            downloadable_changeset_revisions = [ rm.changeset_revision for rm in repository.downloadable_revisions ]
+            changeset_revisions = []
+            for changeset in repo.changelog:
+                changeset_revision = str( repo.changectx( changeset ) )
+                if changeset_revision in downloadable_changeset_revisions:
+                    changeset_revisions.append( changeset_revision )
+            # Now append the latest changeset_revision we just updated above.
+            changeset_revisions.append( repository_metadata.changeset_revision )
+            add_repository_metadata_tool_versions( trans, trans.security.encode_id( repository.id ), changeset_revisions )
+    elif len( repo ) == 1 and not invalid_file_tups:
         message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip )
         message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
         status = "error"
-    if invalid_files:
+    if invalid_file_tups:
         if metadata_dict:
             message += "Metadata was defined for some items in revision '%s'.  " % str( repository.tip )
             message += "Correct the following problems if necessary and reset metadata.<br/>"
         else:
             message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip )
             message += "installed into a local Galaxy instance.  Correct the following problems and reset metadata.<br/>"
-        for itc_tup in invalid_files:
+        for itc_tup in invalid_file_tups:
             tool_file, exception_msg = itc_tup
             if exception_msg.find( 'No such file or directory' ) >= 0:
                 exception_items = exception_msg.split()


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -9,8 +9,8 @@
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.model.orm import *
-from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, make_tmp_directory, NOT_TOOL_CONFIGS
-from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, strip_path
+from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, NOT_TOOL_CONFIGS
+from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, strip_path, to_html_escaped, update_repository
 from galaxy.tool_shed.encoding_util import *
 from common import *
 
@@ -113,7 +113,7 @@
             grids.GridColumn.__init__( self, col_name )
         def get_value( self, trans, grid, repository ):
             """Display a SelectField whose options are the changeset_revision strings of all downloadable_revisions of this repository."""
-            select_field = build_changeset_revision_select_field( trans, repository )
+            select_field = build_changeset_revision_select_field( trans, repository, downloadable_only=False )
             if len( select_field.options ) > 1:
                 return select_field.get_html()
             return repository.revision
@@ -268,7 +268,7 @@
             grids.GridColumn.__init__( self, col_name )
         def get_value( self, trans, grid, repository ):
             """Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository."""
-            select_field = build_changeset_revision_select_field( trans, repository )
+            select_field = build_changeset_revision_select_field( trans, repository, downloadable_only=True )
             if len( select_field.options ) > 1:
                 return select_field.get_html()
             return repository.revision
@@ -1346,19 +1346,14 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'error' )
         webapp = get_webapp( trans, **kwd )
+        repository_clone_url = generate_clone_url( trans, repository_id )
         repository = get_repository( trans, repository_id )
         repo_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_dir )
         ctx = get_changectx_for_changeset( repo, changeset_revision )
         invalid_message = ''
-        metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans,
-                                                                                                       repo,
-                                                                                                       repository_id,
-                                                                                                       ctx,
-                                                                                                       changeset_revision,
-                                                                                                       repo_dir,
-                                                                                                       updating_tip=changeset_revision==repository.tip )
-        for invalid_file_tup in invalid_files:
+        metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url )
+        for invalid_file_tup in invalid_file_tups:
             invalid_tool_config, invalid_msg = invalid_file_tup
             invalid_tool_config_name = strip_path( invalid_tool_config )
             if tool_config == invalid_tool_config_name:
@@ -1554,7 +1549,8 @@
         changeset_revision_select_field = build_changeset_revision_select_field( trans,
                                                                                  repository,
                                                                                  selected_value=changeset_revision,
-                                                                                 add_id_to_name=False )
+                                                                                 add_id_to_name=False,
+                                                                                 downloadable_only=False )
         revision_label = get_revision_label( trans, repository, changeset_revision )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
         if repository_metadata:
@@ -1657,7 +1653,8 @@
         changeset_revision_select_field = build_changeset_revision_select_field( trans,
                                                                                  repository,
                                                                                  selected_value=changeset_revision,
-                                                                                 add_id_to_name=False )
+                                                                                 add_id_to_name=False,
+                                                                                 downloadable_only=False )
         return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako',
                                     repository=repository,
                                     repository_metadata_id=repository_metadata_id,
@@ -2128,7 +2125,8 @@
         changeset_revision_select_field = build_changeset_revision_select_field( trans,
                                                                                  repository,
                                                                                  selected_value=changeset_revision,
-                                                                                 add_id_to_name=False )
+                                                                                 add_id_to_name=False,
+                                                                                 downloadable_only=False )
         revision_label = get_revision_label( trans, repository, changeset_revision )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
         if repository_metadata:
@@ -2185,7 +2183,8 @@
         changeset_revision_select_field = build_changeset_revision_select_field( trans,
                                                                                  repository,
                                                                                  selected_value=changeset_revision,
-                                                                                 add_id_to_name=False )
+                                                                                 add_id_to_name=False,
+                                                                                 downloadable_only=False )
         return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako",
                                     repository=repository,
                                     tool=tool,
@@ -2197,3 +2196,42 @@
                                     webapp=webapp,
                                     message=message,
                                     status=status )
+
+# ----- Utility methods -----
+def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, downloadable_only=False ):
+    """Build a SelectField whose options are the changeset_rev strings of all downloadable revisions of the received repository."""
+    repo = hg.repository( get_configured_ui(), repository.repo_path )
+    options = []
+    changeset_tups = []
+    refresh_on_change_values = []
+    if downloadable_only:
+        repository_metadata_revisions = repository.downloadable_revisions
+    else:
+        repository_metadata_revisions = repository.metadata_revisions
+    for repository_metadata in repository_metadata_revisions:
+        changeset_revision = repository_metadata.changeset_revision
+        ctx = get_changectx_for_changeset( repo, changeset_revision )
+        if ctx:
+            rev = '%04d' % ctx.rev()
+            label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
+        else:
+            rev = '-1'
+            label = "-1:%s" % changeset_revision
+        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,
+    # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time.
+    for changeset_tup in sorted( changeset_tups ):
+        # Display the latest revision first.
+        options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) )
+    if add_id_to_name:
+        name = 'changeset_revision_%d' % repository.id
+    else:
+        name = 'changeset_revision'
+    select_field = SelectField( name=name,
+                                refresh_on_change=True,
+                                refresh_on_change_values=refresh_on_change_values )
+    for option_tup in options:
+        selected = selected_value and option_tup[1] == selected_value
+        select_field.add_option( option_tup[0], option_tup[1], selected=selected )
+    return select_field


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/webapps/community/model/__init__.py
--- a/lib/galaxy/webapps/community/model/__init__.py
+++ b/lib/galaxy/webapps/community/model/__init__.py
@@ -166,12 +166,13 @@
         fp.close()
 
 class RepositoryMetadata( object ):
-    def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False ):
+    def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False ):
         self.repository_id = repository_id
         self.changeset_revision = changeset_revision
         self.metadata = metadata or dict()
         self.tool_versions = tool_versions or dict()
         self.malicious = malicious
+        self.downloadable = downloadable
     
 class ItemRatingAssociation( object ):
     def __init__( self, id=None, user=None, item=None, rating=0, comment='' ):


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -49,7 +49,7 @@
         return self.name
     def get_tool_id( self ):
         return None
-    def get_tooltip( self ):
+    def get_tooltip( self, static_path='' ):
         return None
     
     ## ---- Configuration time -----------------------------------------------
@@ -258,8 +258,8 @@
         return self.state.encode( self.tool, self.trans.app, secure=secure )
     def get_errors( self ):
         return self.errors
-    def get_tooltip( self ):
-        return self.tool.help
+    def get_tooltip( self, static_path='' ):
+        return self.tool.help.render( static_path=static_path )
     def get_data_inputs( self ):
         data_inputs = []
         def callback( input, value, prefixed_name, prefixed_label ):


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/admin/data_admin/betajob.mako
--- a/templates/admin/data_admin/betajob.mako
+++ /dev/null
@@ -1,35 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/library/common/common.mako" import="common_javascripts" />
-
-<%!
-    def inherit(context):
-        if context.get('use_panels'):
-            return '/webapps/galaxy/base_panels.mako'
-        else:
-            return '/base.mako'
-%>
-<%inherit file="${inherit(context)}"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.message_box_visible=False
-    self.active_view="user"
-    self.overlay_visible=False
-    self.has_accessible_datasets = False
-%>
-</%def>
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "autocomplete_tagging" )}
-</%def>
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-</%def>
-##
-## Override methods from base.mako and base_panels.mako
-##
-<p class="panel-error-message">This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.</p>
\ No newline at end of file


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/admin/data_admin/generic_error.mako
--- /dev/null
+++ b/templates/admin/data_admin/generic_error.mako
@@ -0,0 +1,35 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/library/common/common.mako" import="common_javascripts" />
+
+<%!
+    def inherit(context):
+        if context.get('use_panels'):
+            return '/webapps/galaxy/base_panels.mako'
+        else:
+            return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.message_box_visible=False
+    self.active_view="user"
+    self.overlay_visible=False
+    self.has_accessible_datasets = False
+%>
+</%def>
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "autocomplete_tagging" )}
+</%def>
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+</%def>
+##
+## Override methods from base.mako and base_panels.mako
+##
+<p class="panel-error-message">${message}</p>
\ No newline at end of file


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/admin/data_admin/local_data.mako
--- a/templates/admin/data_admin/local_data.mako
+++ b/templates/admin/data_admin/local_data.mako
@@ -44,6 +44,7 @@
     td, th { padding-left: 10px; padding-right: 10px; }
     td.state-color-new { text-decoration: underline; }
     td.panel-done-message { background-image: none; padding: 0px 10px 0px 10px; }
+    td.panel-error-message { background-image: none; padding: 0px 10px 0px 10px; }
 </style><div class="toolForm">
     %if message:
@@ -52,19 +53,23 @@
     <div class="toolFormTitle">Currently tracked builds <a class="action-button" href="${h.url_for( controller='data_admin', action='add_genome' )}">Add new</a></div><div class="toolFormBody"><h2>Locally cached data:</h2>
-        <h3>NOTE: Indexers queued here will not be reflected in the table until Galaxy is restarted.</h3>
+        <h3>NOTE: Indexes generated here will not be reflected in the table until Galaxy is restarted.</h3><table id="locfiles">
-            <tr><th>Database ID</th><th>Name</th><th>Bowtie</th><th>Bowtie 2</th><th>BWA</th><th>Sam</th><th>Picard</th><th>PerM</th></tr>
-            %for dbkey in sorted(genomes.keys()):
+            <tr>
+                <th>DB Key</th>
+                <th>Name</th>
+                %for label in labels:
+                    <th>${labels[label]}</th>
+                %endfor
+            </tr>
+            %for dbkey in sorted(dbkeys):
                 <tr><td>${dbkey}</td>
-                    <td>${genomes[dbkey]['name']}</td>
-                    <td id="${dbkey}-bowtie" class="indexcell ${genomes[dbkey]['bowtie_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie_indexes']['state']}</td>
-                    <td id="${dbkey}-bowtie2" class="indexcell ${genomes[dbkey]['bowtie2_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie2" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie2_indexes']['state']}</td>
-                    <td id="${dbkey}-bwa" class="indexcell ${genomes[dbkey]['bwa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bwa" data-dbkey="${dbkey}">${genomes[dbkey]['bwa_indexes']['state']}</td>
-                    <td id="${dbkey}-sam" class="indexcell ${genomes[dbkey]['sam_fa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="sam" data-dbkey="${dbkey}">${genomes[dbkey]['sam_fa_indexes']['state']}</td>
-                    <td id="${dbkey}-picard" class="indexcell ${genomes[dbkey]['srma_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="picard" data-dbkey="${dbkey}">${genomes[dbkey]['srma_indexes']['state']}</td>
-                    <td id="${dbkey}-perm" class="indexcell ${genomes[dbkey]['perm_base_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="perm" data-dbkey="${dbkey}">${genomes[dbkey]['perm_base_indexes']['state']}</td>
+                    <td>${indextable[dbkey]['name']}</td>
+                    %for label in labels:
+                        <td id="${dbkey}-${indexfuncs[label]}" class="indexcell ${styles[indextable[dbkey]['indexes'][label]]}" data-fapath="${indextable[dbkey]['path']}" data-longname="${indextable[dbkey]['name']}" data-index="${indexfuncs[label]}" data-dbkey="${dbkey}">${indextable[dbkey]['indexes'][label]}</td>
+                    %endfor
+
                 </tr>
             %endfor
         </table>
@@ -124,6 +129,7 @@
             jsondata["name"] = $('#job-' + jobid).attr('data-name');
             jsondata["dbkey"] = $('#job-' + jobid).attr('data-dbkey');
             jsondata["indexes"] = $('#job-' + jobid).attr('data-indexes');
+            tdid = jq(jsondata["dbkey"] + '-' + jsondata["indexes"]);
             newhtml = makeNewHTML(jsondata);
             $('#job-' + jobid).replaceWith(newhtml);
             if ($.inArray(jsondata["status"], finalstates) == -1) {
@@ -133,7 +139,7 @@
                 });
             }
             if (jsondata["status"] == 'done' || jsondata["status"] == 'ok') {
-                elem = $('#' + jsondata["dbkey"] + '-' + jsondata["indexes"]);
+                elem = $(tdid);
                 elem.html('Generated');
                 elem.attr('class', 'indexcell panel-done-message');
             }
@@ -156,5 +162,8 @@
             }
         });
     });
-
+    
+    function jq(id) { 
+        return '#' + id.replace(/(:|\.)/g,'\\$1');
+    }
 </script>
\ No newline at end of file


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako
--- a/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako
+++ b/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako
@@ -43,14 +43,17 @@
     ${render_msg( message, status )}
 %endif
 
+<div class="warningmessage">
+    Resetting metadata may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk.
+    Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not be helpful.  Watch 
+    the tool shed paster log to pass the time if necessary.
+</div>
+
 <div class="toolForm"><div class="toolFormTitle">Reset all metadata on each selected repository</div><form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}" method="post" ><div class="form-row">
-                Check each repository for which you want to reset metadata.  Repository names are followed by owners in parentheses.  Resetting metadata
-                may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk.
-                Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not
-                be helpful.  Watch the tool shed paster log to pass the time if necessary.
+                Check each repository for which you want to reset metadata.  Repository names are followed by owners in parentheses.
             </div><div style="clear: both"></div><div class="form-row">


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/webapps/community/repository/tool_form.mako
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -186,12 +186,15 @@
                 <div class="toolHelp"><div class="toolHelpBody"><%
+                            tool_help = tool.help
+                            # Help is Mako template, so render using current static path.
+                            tool_help = tool_help.render( static_path=h.url_for( '/static' ) )
                             # Convert to unicode to display non-ascii characters.
-                            if type( tool.help ) is not unicode:
-                                tool.help = unicode( tool.help, 'utf-8')
+                            if type( tool_help ) is not unicode:
+                                tool_help = unicode( tool_help, 'utf-8')
                         %>
-                        ${tool.help}
-                    </div>        
+                        ${tool_help}
+                    </div></div>
             %endif
         %else:


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 test/functional/test_library_templates.py
--- a/test/functional/test_library_templates.py
+++ b/test/functional/test_library_templates.py
@@ -398,7 +398,7 @@
                                      folder_id=self.security.encode_id( folder3.id ),
                                      upload_option='import_from_history',
                                      hda_ids=self.security.encode_id( hda.id ),
-                                     strings_displayed=[ '<input type="hidden" name="%s" value="Option1"/>' % select_field_name ] )
+                                     strings_displayed=[ '<select name="%s" last_selected_value="Option1">' % select_field_name ] )
         ldda = get_latest_ldda_by_name( filename )
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',


diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 tools/new_operations/operation_filter.py
--- a/tools/new_operations/operation_filter.py
+++ b/tools/new_operations/operation_filter.py
@@ -3,6 +3,9 @@
 from galaxy import eggs
 from galaxy import jobs
 from galaxy.tools.parameters import DataToolParameter
+
+from galaxy.jobs.handler import JOB_ERROR
+
 # Older py compatibility
 try:
     set()
@@ -63,8 +66,8 @@
                 raise Exception( stderr )
 
         except Exception, exc:
-            data.blurb = jobs.JOB_ERROR
-            data.state = jobs.JOB_ERROR
+            data.blurb = JOB_ERROR
+            data.state = JOB_ERROR
 
 ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
 ##     pass



https://bitbucket.org/galaxy/galaxy-central/changeset/713ee9f0ae6a/
changeset:   713ee9f0ae6a
user:        dannon
date:        2012-08-13 19:22:51
summary:     Merge pull request.
affected #:  5 files

diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -544,7 +544,10 @@
         else:
             return False
 
-class Group( object ):
+class Group( object, APIItem  ):
+    api_collection_visible_keys = ( 'id', 'name' )
+    api_element_visible_keys = ( 'id', 'name' )
+
     def __init__( self, name = None ):
         self.name = name
         self.deleted = False


diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/api/group_roles.py
--- /dev/null
+++ b/lib/galaxy/web/api/group_roles.py
@@ -0,0 +1,124 @@
+"""
+API operations on Group objects.
+"""
+import logging
+from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy import web
+
+log = logging.getLogger( __name__ )
+
+class GroupRolesAPIController( BaseAPIController ):
+
+    @web.expose_api
+    @web.require_admin
+    def index( self, trans, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/roles
+        Displays a collection (list) of groups.
+        """
+        decoded_group_id = trans.security.decode_id( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        rval = []
+        try:
+            for gra in group.roles:
+                role = gra.role
+                encoded_id = trans.security.encode_id( role.id )
+                rval.append( dict( id = encoded_id,
+                                   name = role.name,
+                                   url = url_for( 'group_role', group_id=group_id, id=encoded_id, ) ) )
+        except Exception, e:
+            rval = "Error in group API at listing roles"
+            log.error( rval + ": %s" % str(e) )
+            trans.response.status = 500
+        return rval
+
+    @web.expose_api
+    @web.require_admin
+    def show( self, trans, id, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/roles/{encoded_role_id}
+        Displays information about a group role.
+        """
+        role_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_role_id =  trans.security.decode_id( role_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id )
+            for gra in group.roles:
+                if gra.role == role:
+                    item = dict( id = role_id,
+                                   name = role.name,
+                                   url = url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This
+            if not item:
+                item = "role %s not in group %s" % (role.name,group.name)
+        except Exception, e:
+            item = "Error in group_role API group %s role %s" % (group.name, role.name)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def update( self, trans, id, group_id, **kwd ):
+        """
+        PUT /api/groups/{encoded_group_id}/roles/{encoded_role_id}
+        Adds a role to a group
+        """
+        role_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_role_id =  trans.security.decode_id( role_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id )
+            for gra in group.roles:
+                if gra.role == role:
+                    item = dict( id = role_id,
+                                   name = role.name,
+                                   url = url_for( 'group_role', group_id=group_id, id=role_id) ) 
+            if not item:
+                gra = trans.app.model.GroupRoleAssociation( group, role )
+                # Add GroupRoleAssociation
+                trans.sa_session.add( gra )
+                trans.sa_session.flush()
+                item = dict( id = role_id,
+                             name = role.name,
+                             url = url_for( 'group_role', group_id=group_id, id=role_id) ) 
+        except Exception, e:
+            item = "Error in group_role API Adding role %s to group %s" % (role.name,group.name)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def delete( self, trans, id, group_id, **kwd ):
+        """
+        DELETE /api/groups/{encoded_group_id}/roles/{encoded_role_id}
+        Removes a role from a group
+        """
+        role_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_role_id =  trans.security.decode_id( role_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id )
+            for gra in group.roles:
+                if gra.role == role:
+                    trans.sa_session.delete( gra )
+                    trans.sa_session.flush()
+                    item = dict( id = role_id,
+                                 name = role.name,
+                                 url = url_for( 'group_role', group_id=group_id, id=role_id) ) 
+            if not item:
+                item = "role %s not in group %s" % (role.name,group.name)
+        except Exception, e:
+            item = "Error in group_role API Removing role %s from group %s" % (role.name,group.name)
+            log.error(item + ": %s" % str(e))
+        return item


diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/api/group_users.py
--- /dev/null
+++ b/lib/galaxy/web/api/group_users.py
@@ -0,0 +1,124 @@
+"""
+API operations on Group objects.
+"""
+import logging
+from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy import web
+
+log = logging.getLogger( __name__ )
+
+class GroupUsersAPIController( BaseAPIController ):
+
+    @web.expose_api
+    @web.require_admin
+    def index( self, trans, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/users
+        Displays a collection (list) of groups.
+        """
+        decoded_group_id = trans.security.decode_id( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        rval = []
+        try:
+            for uga in group.users:
+                user = uga.user
+                encoded_id = trans.security.encode_id( user.id )
+                rval.append( dict( id = encoded_id,
+                                   email = user.email,
+                                   url = url_for( 'group_user', group_id=group_id, id=encoded_id, ) ) )
+        except Exception, e:
+            rval = "Error in group API at listing users"
+            log.error( rval + ": %s" % str(e) )
+            trans.response.status = 500
+        return rval
+
+    @web.expose_api
+    @web.require_admin
+    def show( self, trans, id, group_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}/users/{encoded_user_id}
+        Displays information about a group user.
+        """
+        user_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_user_id =  trans.security.decode_id( user_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
+            for uga in group.users:
+                if uga.user == user:
+                    item = dict( id = user_id,
+                                   email = user.email,
+                                   url = url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This
+            if not item:
+                item = "user %s not in group %s" % (user.email,group.name)
+        except Exception, e:
+            item = "Error in group_user API group %s user %s" % (group.name, user.email)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def update( self, trans, id, group_id, **kwd ):
+        """
+        PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
+        Adds a user to a group
+        """
+        user_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_user_id =  trans.security.decode_id( user_id )
+        item = None
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
+            for uga in group.users:
+                if uga.user == user:
+                    item = dict( id = user_id,
+                                   email = user.email,
+                                   url = url_for( 'group_user', group_id=group_id, id=user_id) ) 
+            if not item:
+                uga = trans.app.model.UserGroupAssociation( user, group )
+                # Add UserGroupAssociations
+                trans.sa_session.add( uga )
+                trans.sa_session.flush()
+                item = dict( id = user_id,
+                             email = user.email,
+                             url = url_for( 'group_user', group_id=group_id, id=user_id) ) 
+        except Exception, e:
+            item = "Error in group_user API Adding user %s to group %s" % (user.email,group.name)
+            log.error(item + ": %s" % str(e))
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def delete( self, trans, id, group_id, **kwd ):
+        """
+        DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id}
+        Removes a user from a group
+        """
+        user_id = id
+        decoded_group_id = trans.security.decode_id( group_id )
+        decoded_user_id =  trans.security.decode_id( user_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+            user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id )
+            for uga in group.users:
+                if uga.user == user:
+                    trans.sa_session.delete( uga )
+                    trans.sa_session.flush()
+                    item = dict( id = user_id,
+                                 email = user.email,
+                                 url = url_for( 'group_user', group_id=group_id, id=user_id) ) 
+            if not item:
+                item = "user %s not in group %s" % (user.email,group.name)
+        except Exception, e:
+            item = "Error in group_user API Removing user %s from group %s" % (user.email,group.name)
+            log.error(item + ": %s" % str(e))
+        return item


diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/api/groups.py
--- /dev/null
+++ b/lib/galaxy/web/api/groups.py
@@ -0,0 +1,128 @@
+"""
+API operations on Group objects.
+"""
+import logging
+from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy import web
+
+
+log = logging.getLogger( __name__ )
+
+
+class GroupAPIController( BaseAPIController ):
+
+    @web.expose_api
+    @web.require_admin
+    def index( self, trans, **kwd ):
+        """
+        GET /api/groups
+        Displays a collection (list) of groups.
+        """
+        rval = []
+        for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted == False ):
+            if trans.user_is_admin():
+                item = group.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+                encoded_id = trans.security.encode_id( group.id )
+                item['url'] = url_for( 'group', id=encoded_id )
+                rval.append( item )
+        return rval
+
+    @web.expose_api
+    def create( self, trans, payload, **kwd ):
+        """
+        POST /api/groups
+        Creates a new group.
+        """
+        log.info("groups payload%s\n" % (payload)) 
+        if not trans.user_is_admin():
+            trans.response.status = 403
+            return "You are not authorized to create a new group."
+        name = payload.get( 'name', None )
+        if not name:
+            trans.response.status = 400
+            return "Enter a valid name"
+        if trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first():
+            trans.response.status = 400
+            return "A group with that name already exists"
+
+        group = trans.app.model.Group( name=name )
+        trans.sa_session.add( group )
+        user_ids = payload.get( 'user_ids', [] )
+        for i in user_ids:
+          log.info("user_id: %s\n" % (i )) 
+          log.info("%s %s\n" % (i, trans.security.decode_id( i ) )) 
+        users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ]
+        role_ids = payload.get( 'role_ids', [] )
+        roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ]
+        trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users )
+        """
+        # Create the UserGroupAssociations
+        for user in users:
+            trans.app.security_agent.associate_user_group( user, group )
+        # Create the GroupRoleAssociations
+        for role in roles:
+            trans.app.security_agent.associate_group_role( group, role )
+        """
+        trans.sa_session.flush()
+        encoded_id = trans.security.encode_id( group.id )
+        item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+        item['url'] = url_for( 'group', id=encoded_id )
+        return [ item ]
+
+    @web.expose_api
+    @web.require_admin
+    def show( self, trans, id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}
+        Displays information about a group.
+        """
+        group_id = id
+        try:
+            decoded_group_id = trans.security.decode_id( group_id )
+        except TypeError:
+            trans.response.status = 400
+            return "Malformed group id ( %s ) specified, unable to decode." % str( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+        item['url'] = url_for( 'group', id=group_id )
+        item['users_url'] = url_for( 'group_users', group_id=group_id )
+        item['roles_url'] = url_for( 'group_roles', group_id=group_id )
+        return item
+
+    @web.expose_api
+    @web.require_admin
+    def update( self, trans, id, payload, **kwd ):
+        """
+        PUT /api/groups/{encoded_group_id}
+        Modifies a group.
+        """
+        group_id = id
+        try:
+            decoded_group_id = trans.security.decode_id( group_id )
+        except TypeError:
+            trans.response.status = 400
+            return "Malformed group id ( %s ) specified, unable to decode." % str( group_id )
+        try:
+            group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id )
+        except:
+            group = None
+        if not group:
+            trans.response.status = 400
+            return "Invalid group id ( %s ) specified." % str( group_id )
+        name = payload.get( 'name', None )
+        if name:
+          group.name = name
+          trans.sa_session.add(group)
+        user_ids = payload.get( 'user_ids', [] )
+        users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ]
+        role_ids = payload.get( 'role_ids', [] )
+        roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ]
+        trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users,delete_existing_assocs=False )
+        trans.sa_session.flush()
+


diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/buildapp.py
--- a/lib/galaxy/web/buildapp.py
+++ b/lib/galaxy/web/buildapp.py
@@ -122,6 +122,18 @@
                                 'permissions',
                                 path_prefix='/api/libraries/:library_id',
                                 parent_resources=dict( member_name='library', collection_name='libraries' ) )      
+    webapp.api_mapper.resource( 'user',
+                                'users',
+                                controller='group_users',
+                                name_prefix='group_',
+                                path_prefix='/api/groups/:group_id',
+                                parent_resources=dict( member_name='group', collection_name='groups' ) )
+    webapp.api_mapper.resource( 'role',
+                                'roles',
+                                controller='group_roles',
+                                name_prefix='group_',
+                                path_prefix='/api/groups/:group_id',
+                                parent_resources=dict( member_name='group', collection_name='groups' ) )
     webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' )
     webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' )
@@ -129,6 +141,7 @@
     webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' )
     webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' )
     webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' )
+    webapp.api_mapper.resource( 'group', 'groups', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' )
     webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' )



https://bitbucket.org/galaxy/galaxy-central/changeset/966a9b393b85/
changeset:   966a9b393b85
branch:      add_requirement_tags_for_plink
user:        dannon
date:        2012-08-13 19:23:54
summary:     Branch close
affected #:  0 files

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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