commit/galaxy-central: greg: Refactor code supporting setting metadata on repositories in the tool shed and installed in Galaxy - enables using same code across web apps. - galaxy-commits

26 Oct 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/50b1d7a65bd2/
changeset:   50b1d7a65bd2
user:        greg
date:        2012-10-26 21:39:50
summary:     Refactor code supporting setting metadata on repositories in the tool shed and installed in Galaxy - enables using same code across web apps.
affected #:  14 files

diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/util/shed_util.py

--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -3,9 +3,12 @@
 from datetime import date, datetime, timedelta
 from time import strftime, gmtime
 from galaxy import util
+from galaxy.web import url_for
+from galaxy.web.form_builder import SelectField
 from galaxy.tools import parameters
 from galaxy.datatypes.checkers import *
 from galaxy.util.json import *
+from galaxy.util import inflector
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment
 from galaxy.tool_shed.encoding_util import *
@@ -23,6 +26,7 @@
 
 log = logging.getLogger( __name__ )
 
+GALAXY_ADMIN_TOOL_SHED_CONTROLLER = 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER'
 INITIAL_CHANGELOG_HASH = '000000000000'
 # Characters that must be html escaped
 MAPPED_CHARS = { '>' :'>', 
@@ -33,6 +37,7 @@
 MAX_CONTENT_SIZE = 32768
 NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'tool_dependencies.xml' ]
 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" )
+TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER'
 
 class ShedCounter( object ):
     def __init__( self, model ):
@@ -246,6 +251,27 @@
         except:
             pass
     return converter_path, display_path
+def build_repository_ids_select_field( trans, cntrller, name='repository_ids', multiple=True, display='checkboxes' ):
+    """Method called from both Galaxy and the Tool Shed to generate the current list of repositories for resetting metadata."""
+    repositories_select_field = SelectField( name=name, multiple=multiple, display=display )
+    if cntrller == TOOL_SHED_ADMIN_CONTROLLER:
+        for repository in trans.sa_session.query( trans.model.Repository ) \
+                                          .filter( trans.model.Repository.table.c.deleted == False ) \
+                                          .order_by( trans.model.Repository.table.c.name,
+                                                     trans.model.Repository.table.c.user_id ):
+            owner = repository.user.username
+            option_label = '%s (%s)' % ( repository.name, owner )
+            option_value = '%s' % trans.security.encode_id( repository.id )
+            repositories_select_field.add_option( option_label, option_value )
+    elif cntrller == GALAXY_ADMIN_TOOL_SHED_CONTROLLER:
+        for repository in trans.sa_session.query( trans.model.ToolShedRepository ) \
+                                          .filter( trans.model.ToolShedRepository.table.c.uninstalled == False ) \
+                                          .order_by( trans.model.ToolShedRepository.table.c.name,
+                                                     trans.model.ToolShedRepository.table.c.owner ):
+            option_label = '%s (%s)' % ( repository.name, repository.owner )
+            option_value = trans.security.encode_id( repository.id )
+            repositories_select_field.add_option( option_label, option_value )
+    return repositories_select_field
 def can_generate_tool_dependency_metadata( root, metadata_dict ):
     """
     Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml
@@ -339,6 +365,105 @@
                         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 ) )
     return invalid_files_and_errors_tups
+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 = []
+    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,
+                                                          trans.model.RepositoryMetadata.table.c.update_time.desc() ):
+        changeset_revision = repository_metadata.changeset_revision
+        can_delete = changeset_revision in changeset_revisions_checked or changeset_revision not in changeset_revisions
+        if can_delete:
+            trans.sa_session.delete( repository_metadata )
+            trans.sa_session.flush()
+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
+    # when this method returns the string 'not equal and not subset'.
+    ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] )
+    ancestor_tools = ancestor_metadata_dict.get( 'tools', [] )
+    ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ]
+    ancestor_guids.sort()
+    ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', [] )
+    ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] )
+    current_datatypes = current_metadata_dict.get( 'datatypes', [] )
+    current_tools = current_metadata_dict.get( 'tools', [] )
+    current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ]
+    current_guids.sort()
+    current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', [] ) 
+    current_workflows = current_metadata_dict.get( 'workflows', [] )
+    # Handle case where no metadata exists for either changeset.
+    if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes:
+        return 'no metadata'
+    workflow_comparison = compare_workflows( ancestor_workflows, current_workflows )
+    datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes )
+    # Handle case where all metadata is the same.
+    if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal':
+        return 'equal'
+    if workflow_comparison in [ 'equal', 'subset' ] and datatype_comparison in [ 'equal', 'subset' ]:
+        is_subset = True
+        for guid in ancestor_guids:
+            if guid not in current_guids:
+                is_subset = False
+                break
+        if is_subset:
+            return 'subset'
+    return 'not equal and not subset'
+def compare_datatypes( ancestor_datatypes, current_datatypes ):
+    # Determine if ancestor_datatypes is the same as current_datatypes
+    # or if ancestor_datatypes is a subset of current_datatypes.  Each
+    # datatype dict looks something like:
+    # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"}
+    if len( ancestor_datatypes ) <= len( current_datatypes ):
+        for ancestor_datatype in ancestor_datatypes:
+            # Currently the only way to differentiate datatypes is by name.
+            ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ]
+            ancestor_datatype_extension = ancestor_datatype[ 'extension' ]
+            ancestor_datatype_mimetype = ancestor_datatype.get( 'mimetype', None )
+            found_in_current = False
+            for current_datatype in current_datatypes:
+                if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \
+                    current_datatype[ 'extension' ] == ancestor_datatype_extension and \
+                    current_datatype.get( 'mimetype', None ) == ancestor_datatype_mimetype:
+                    found_in_current = True
+                    break
+            if not found_in_current:
+                return 'not equal and not subset'
+        if len( ancestor_datatypes ) == len( current_datatypes ):
+            return 'equal'
+        else:
+            return 'subset'
+    return 'not equal and not subset'
+def compare_workflows( ancestor_workflows, current_workflows ):
+    # Determine if ancestor_workflows is the same as current_workflows
+    # or if ancestor_workflows is a subset of current_workflows.
+    if len( ancestor_workflows ) <= len( current_workflows ):
+        for ancestor_workflow_tup in ancestor_workflows:
+            # ancestor_workflows is a list of tuples where each contained tuple is
+            # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
+            ancestor_workflow_dict = ancestor_workflow_tup[1]
+            # Currently the only way to differentiate workflows is by name.
+            ancestor_workflow_name = ancestor_workflow_dict[ 'name' ]
+            num_ancestor_workflow_steps = len( ancestor_workflow_dict[ 'steps' ] )
+            found_in_current = False
+            for current_workflow_tup in current_workflows:
+                current_workflow_dict = current_workflow_tup[1]
+                # Assume that if the name and number of steps are euqal,
+                # then the workflows are the same.  Of course, this may
+                # not be true...
+                if current_workflow_dict[ 'name' ] == ancestor_workflow_name and len( current_workflow_dict[ 'steps' ] ) == num_ancestor_workflow_steps:
+                    found_in_current = True
+                    break
+            if not found_in_current:
+                return 'not equal and not subset'
+        if len( ancestor_workflows ) == len( current_workflows ):
+            return 'equal'
+        else:
+            return 'subset'
+    return 'not equal and not subset'
 def concat_messages( msg1, msg2 ):
     if msg1:
         if msg2:
@@ -447,6 +572,20 @@
                  tool_dicts=tool_dicts,
                  converter_path=converter_path,
                  display_path=display_path )
+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=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 create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict,
                                            status, current_changeset_revision=None, owner='', dist_to_shed=False ):
     # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used
@@ -546,10 +685,19 @@
                                                                         set_status=set_status )
                     tool_dependency_objects.append( tool_dependency )
     return tool_dependency_objects
-def generate_clone_url( trans, repository ):
-    """Generate the URL for cloning a repository."""
+def generate_clone_url_for_installed_repository( trans, repository ):
+    """Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
     tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
     return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
+def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
+    """Generate the URL for cloning a repository that is in the tool shed."""
+    base_url = url_for( '/', qualified=True ).rstrip( '/' )
+    if trans.user:
+        protocol, base = base_url.split( '://' )
+        username = '%s@' % trans.user.username
+        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_datatypes_metadata( datatypes_config, metadata_dict ):
     """Update the received metadata_dict with information from the parsed datatypes_config."""
     tree = ElementTree.parse( datatypes_config )
@@ -750,6 +898,42 @@
     app.config.tool_data_path = original_tool_data_path
     app.config.tool_data_table_config_path = original_tool_data_table_config_path
     return metadata_dict, invalid_file_tups
+def generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False ):
+    if as_html:
+        new_line = '<br/>'
+        bold_start = '<b>'
+        bold_end = '</b>'
+    else:
+        new_line = '\n'
+        bold_start = ''
+        bold_end = ''
+    message = ''
+    if not displaying_invalid_tool:
+        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.%s" % new_line
+        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.%s" % new_line
+    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()
+            missing_file_items = exception_items[ 7 ].split( '/' )
+            missing_file = missing_file_items[ -1 ].rstrip( '\'' )
+            if missing_file.endswith( '.loc' ):
+                sample_ext = '%s.sample' % missing_file
+            else:
+                sample_ext = missing_file
+            correction_msg = "This file refers to a missing file %s%s%s.  " % ( bold_start, str( missing_file ), bold_end )
+            correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % ( bold_start, sample_ext, bold_end )
+        else:
+            if as_html:
+                correction_msg = exception_msg
+            else:
+                correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end )
+        message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line )
+    return message
 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 = {}
@@ -1158,6 +1342,9 @@
     ctx = get_changectx_for_changeset( repo, changeset_revision )
     named_tmp_file = get_named_tmpfile_from_ctx( ctx, file_name, dir )
     return named_tmp_file
+def get_installed_tool_shed_repository( trans, id ):
+    """Get a repository on the Galaxy side from the database via id"""
+    return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
 def get_list_of_copied_sample_files( repo, ctx, dir ):
     """
     Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx.  Copy
@@ -1211,6 +1398,24 @@
                 fh.close()
                 return tmp_filename
     return None
+def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ):
+    parent_id = None
+    # Compare from most recent to oldest.
+    changeset_revisions.reverse()
+    for changeset_revision in changeset_revisions:
+        repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+        metadata = repository_metadata.metadata
+        tools_dicts = metadata.get( 'tools', [] )
+        for tool_dict in tools_dicts:
+            if tool_dict[ 'guid' ] == guid:
+                # The tool has not changed between the compared changeset revisions.
+                continue
+            if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version:
+                # The tool version is different, so we've found the parent.
+                return tool_dict[ 'guid' ]
+    if parent_id is None:
+        # The tool did not change through all of the changeset revisions.
+        return old_id
 def get_repository_file_contents( file_path ):
     if is_gzip( file_path ):
         to_html = to_html_str( '\ngzip compressed file\n' )
@@ -1242,6 +1447,9 @@
     if contents:
         contents.sort()
     return contents
+def get_repository_in_tool_shed( trans, id ):
+    """Get a repository on the tool shed side from the database via id"""
+    return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) )
 def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ):
     """Get metadata for a specified repository change set from the database"""
     # Make sure there are no duplicate records, and return the single unique record for the changeset_revision.  Duplicate records were somehow
@@ -1635,6 +1843,8 @@
                                                                              parent_id=tool_version_using_parent_id.id )
                 sa_session.add( tool_version_association )
                 sa_session.flush()
+def is_downloadable( metadata_dict ):
+    return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict
 def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ):
     # Load or deactivate proprietary datatype converters
     app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=installed_repository_dict, deactivate=deactivate )
@@ -1739,6 +1949,12 @@
                    repo,
                    source=repository_clone_url,
                    rev=[ ctx_rev ] )
+def remove_dir( dir ):
+    if os.path.exists( dir ):
+        try:
+            shutil.rmtree( dir )
+        except:
+            pass
 def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ):
     # A tool shed repository is being uninstalled so change the shed_tool_conf file.  Parse the config file to generate the entire list
     # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have
@@ -1912,6 +2128,188 @@
         removed = True
         error_message = ''
     return removed, error_message
+def reset_all_metadata_on_installed_repository( trans, id ):
+    """Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
+    repository = get_installed_tool_shed_repository( trans, id )
+    tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
+    repository_clone_url = generate_clone_url_for_installed_repository( trans, repository )
+    tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
+    if relative_install_dir:
+        original_metadata_dict = repository.metadata
+        metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
+                                                                                     repository=repository,
+                                                                                     repository_clone_url=repository_clone_url,
+                                                                                     shed_config_dict = repository.get_shed_config_dict( trans.app ),
+                                                                                     relative_install_dir=relative_install_dir,
+                                                                                     repository_files_dir=None,
+                                                                                     resetting_all_metadata_on_repository=False,
+                                                                                     updating_installed_repository=False )
+        repository.metadata = metadata_dict
+        if metadata_dict != original_metadata_dict:
+            update_in_shed_tool_config( trans.app, repository )
+            trans.sa_session.add( repository )
+            trans.sa_session.flush()
+            log.debug( 'Metadata has been reset on repository %s.' % repository.name )
+        else:
+            log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name )
+    else:
+        log.debug( 'Error locating installation directory for repository %s.' % repository.name )
+    return invalid_file_tups, metadata_dict
+def reset_all_metadata_on_repository_in_tool_shed( trans, id ):
+    """Reset all metadata on a single repository in a tool shed."""
+    def reset_all_tool_versions( trans, id, repo ):
+        changeset_revisions = []
+        for changeset in repo.changelog:
+            changeset_revision = str( repo.changectx( changeset ) )
+            repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+            if repository_metadata:
+                metadata = repository_metadata.metadata
+                if metadata:
+                    if metadata.get( 'tools', None ):
+                        changeset_revisions.append( changeset_revision )
+        # The list of changeset_revisions is now filtered to contain only those that are downloadable and contain tools.
+        # 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 )
+            metadata = repository_metadata.metadata
+            tool_dicts = metadata[ '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.
+                for tool_dict in tool_dicts:
+                    tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ]
+            else:
+                for tool_dict in tool_dicts:
+                    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()
+    repository = get_repository_in_tool_shed( trans, id )
+    log.debug( "Resetting all metadata on repository: %s" % repository.name )
+    repo_dir = repository.repo_path
+    repo = hg.repository( get_configured_ui(), repo_dir )
+    repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository )
+    # The list of changeset_revisions refers to repository_metadata records that have been created or updated.  When the following loop
+    # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list.
+    changeset_revisions = []
+    # When a new repository_metadata record is created, it always uses the values of metadata_changeset_revision and metadata_dict.
+    metadata_changeset_revision = None
+    metadata_dict = None
+    ancestor_changeset_revision = None
+    ancestor_metadata_dict = None
+    invalid_file_tups = []
+    home_dir = os.getcwd()
+    for changeset in repo.changelog:
+        work_dir = tempfile.mkdtemp()
+        current_changeset_revision = str( repo.changectx( changeset ) )
+        ctx = repo.changectx( changeset )
+        log.debug( "Cloning repository revision: %s", str( ctx.rev() ) )
+        cloned_ok, error_message = clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) )
+        if cloned_ok:
+            log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) )
+            current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
+                                                                                                 repository=repository,
+                                                                                                 repository_clone_url=repository_clone_url,
+                                                                                                 relative_install_dir=repo_dir,
+                                                                                                 repository_files_dir=work_dir,
+                                                                                                 resetting_all_metadata_on_repository=True,
+                                                                                                 updating_installed_repository=False )
+            if current_metadata_dict:
+                if not metadata_changeset_revision and not metadata_dict:
+                    # We're at the first change set in the change log.
+                    metadata_changeset_revision = current_changeset_revision
+                    metadata_dict = current_metadata_dict
+                if ancestor_changeset_revision:
+                    # Compare metadata from ancestor and current.  The value of comparison will be one of:
+                    # 'no metadata' - no metadata for either ancestor or current, so continue from current
+                    # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current
+                    # 'subset' - ancestor metadata is a subset of current metadata, so continue from current
+                    # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata.
+                    comparison = compare_changeset_revisions( ancestor_changeset_revision,
+                                                              ancestor_metadata_dict,
+                                                              current_changeset_revision,
+                                                              current_metadata_dict )
+                    if comparison in [ 'no metadata', 'equal', 'subset' ]:
+                        ancestor_changeset_revision = current_changeset_revision
+                        ancestor_metadata_dict = current_metadata_dict
+                    elif comparison == 'not equal and not subset':
+                        metadata_changeset_revision = ancestor_changeset_revision
+                        metadata_dict = ancestor_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
+                else:
+                    # We're at the beginning of the change log.
+                    ancestor_changeset_revision = current_changeset_revision
+                    ancestor_metadata_dict = current_metadata_dict
+                if not ctx.children():
+                    metadata_changeset_revision = current_changeset_revision
+                    metadata_dict = current_metadata_dict
+                    # We're at the end of the change log.
+                    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
+            elif ancestor_metadata_dict:
+                # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not.
+                if not ctx.children():
+                    # We're at the end of the change log.
+                    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
+        remove_dir( work_dir )
+    # 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 )
+    # Set tool version information for all downloadable changeset revisions.  Get the list of changeset revisions from the changelog.
+    reset_all_tool_versions( trans, id, repo )
+    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
+    reset_tool_data_tables( trans.app )
+    return invalid_file_tups, metadata_dict
+def reset_metadata_on_selected_repositories( trans, **kwd ):
+    # This method is called from both Galaxy and the Tool Shed, so the cntrller param is required.
+    repository_ids = util.listify( kwd.get( 'repository_ids', None ) )
+    CONTROLLER = kwd[ 'CONTROLLER' ]
+    message = ''
+    status = 'done'
+    if repository_ids:
+        successful_count = 0
+        unsuccessful_count = 0
+        for repository_id in repository_ids:
+            try:
+                if CONTROLLER == 'TOOL_SHED_ADMIN_CONTROLLER':
+                    repository = get_repository_in_tool_shed( trans, repository_id )
+                    invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, repository_id )
+                elif CONTROLLER == 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER':
+                    repository = get_installed_tool_shed_repository( trans, repository_id )
+                    invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id )
+                if invalid_file_tups:
+                    message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False )
+                    log.debug( message )
+                    unsuccessful_count += 1
+                else:
+                    log.debug( "Successfully reset metadata on repository %s" % repository.name )
+                    successful_count += 1
+            except Exception, e:
+                log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) )
+                unsuccessful_count += 1
+        message = "Successfully reset metadata on %d %s.  " % ( successful_count, inflector.cond_plural( successful_count, "repository" ) )
+        if unsuccessful_count:
+            message += "Error setting metadata on %d %s - see the paster log for details.  " % ( unsuccessful_count,
+                                                                                                 inflector.cond_plural( unsuccessful_count, "repository" ) )
+    else:
+        message = 'Select at least one repository to on which to reset all metadata.'
+        status = 'error'
+    return message, status
 def reset_tool_data_tables( app ):
     # Reset the tool_data_tables to an empty dictionary.
     app.tool_data_tables.data_tables = {}
@@ -2061,7 +2459,7 @@
     
     tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository )
     repository_tools_tups = get_repository_tools_tups( app, repository.metadata )
-    cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url( trans, repository ) )
+    cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url_for_installed_repository( trans, repository ) )
     tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url )
     owner = repository.owner
     if not owner:


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/admin.py
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -5,7 +5,9 @@
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.web.form_builder import SelectField
 from galaxy.util import inflector
-from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui
+# TODO: re-factor shed_util to eliminate the following restricted imports
+from galaxy.util.shed_util import build_repository_ids_select_field, get_changectx_for_changeset, get_configured_ui, get_repository_in_tool_shed
+from galaxy.util.shed_util import reset_metadata_on_selected_repositories, TOOL_SHED_ADMIN_CONTROLLER
 from common import *
 from repository import RepositoryGrid, CategoryGrid
 
@@ -481,7 +483,7 @@
                     # The received id is the repository id, so we need to get the id of the user
                     # that uploaded the repository.
                     repository_id = kwd.get( 'id', None )
-                    repository = get_repository( trans, repository_id )
+                    repository = get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'f-email' ] = repository.user.email
             elif operation == "repositories_by_category":
                 # Eliminate the current filters if any exist.
@@ -513,7 +515,7 @@
             changset_revision_str = 'changeset_revision_'
             if k.startswith( changset_revision_str ):
                 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) )
-                repository = get_repository( trans, repository_id )
+                repository = get_repository_in_tool_shed( trans, repository_id )
                 if repository.tip != v:
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='browse_repositories',
@@ -586,7 +588,7 @@
             count = 0
             deleted_repositories = ""
             for repository_id in ids:
-                repository = get_repository( trans, repository_id )
+                repository = get_repository_in_tool_shed( trans, repository_id )
                 if not repository.deleted:
                     repository.deleted = True
                     trans.sa_session.add( repository )
@@ -715,57 +717,14 @@
                                     status=status )
     @web.expose
     @web.require_admin
-    def reset_metadata_on_selected_repositories( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        repository_names_by_owner = util.listify( kwd.get( 'repository_names_by_owner', None ) )
+    def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ):
         if 'reset_metadata_on_selected_repositories_button' in kwd:
-            if repository_names_by_owner:
-                successful_count = 0
-                unsuccessful_count = 0
-                for repository_name_owner_str in repository_names_by_owner:
-                    repository_name_owner_list = repository_name_owner_str.split( STRSEP )
-                    name = repository_name_owner_list[ 0 ]
-                    owner = repository_name_owner_list[ 1 ]
-                    repository = get_repository_by_name_and_owner( trans, name, owner )
-                    try:
-                        invalid_file_tups, metadata_dict = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) )
-                        if invalid_file_tups:
-                            message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False )
-                            log.debug( message )
-                            unsuccessful_count += 1
-                        else:
-                            log.debug( "Successfully reset metadata on repository %s" % repository.name )
-                            successful_count += 1
-                    except Exception, e:
-                        log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) )
-                        unsuccessful_count += 1
-                message = "Successfully reset metadata on %d %s.  " % ( successful_count,
-                                                                        inflector.cond_plural( successful_count, "repository" ) )
-                if unsuccessful_count:
-                    message += "Error setting metadata on %d %s - see the paster log for details.  " % ( unsuccessful_count,
-                                                                                                         inflector.cond_plural( unsuccessful_count,
-                                                                                                                                "repository" ) )
-                trans.response.send_redirect( web.url_for( controller='admin',
-                                                           action='browse_repository_metadata',
-                                                           message=util.sanitize_text( message ),
-                                                           status=status ) )
-            else:
-                'Select at least one repository to on which to reset all metadata.'
-                status = 'error'
-        repositories_select_field = SelectField( name='repository_names_by_owner', 
-                                                 multiple=True,
-                                                 display='checkboxes' )
-        for repository in trans.sa_session.query( trans.model.Repository ) \
-                                          .filter( and_( trans.model.Repository.table.c.deleted == False,
-                                                         trans.model.Repository.table.c.deprecated == False ) ) \
-                                          .order_by( trans.model.Repository.table.c.name,
-                                                     trans.model.Repository.table.c.user_id ):
-            owner = repository.user.username
-            option_label = '%s (%s)' % ( repository.name, owner )
-            option_value = '%s%s%s' % ( repository.name, STRSEP, owner )
-            repositories_select_field.add_option( option_label, option_value )
+            kwd[ 'CONTROLLER' ] = TOOL_SHED_ADMIN_CONTROLLER
+            message, status = reset_metadata_on_selected_repositories( trans, **kwd )
+        else:
+            message = util.restore_text( kwd.get( 'message', ''  ) )
+            status = kwd.get( 'status', 'done' )
+        repositories_select_field = build_repository_ids_select_field( trans, TOOL_SHED_ADMIN_CONTROLLER )
         return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako',
                                     repositories_select_field=repositories_select_field,
                                     message=message,
@@ -783,7 +742,7 @@
             count = 0
             undeleted_repositories = ""
             for repository_id in ids:
-                repository = get_repository( trans, repository_id )
+                repository = get_repository_in_tool_shed( trans, repository_id )
                 if repository.deleted:
                     repository.deleted = False
                     trans.sa_session.add( repository )


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -5,11 +5,14 @@
 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 check_tool_input_params, clone_repository, concat_messages, copy_sample_file, generate_metadata_for_changeset_revision
+# TODO: re-factor shed_util to eliminate the following restricted imports
+from galaxy.util.shed_util import check_tool_input_params, clone_repository, concat_messages, copy_sample_file, create_or_update_repository_metadata
+from galaxy.util.shed_util import generate_clone_url_for_repository_in_tool_shed, generate_message_for_invalid_tools, generate_metadata_for_changeset_revision
 from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_file_context_from_ctx, get_named_tmpfile_from_ctx
-from galaxy.util.shed_util import get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk
-from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH
-from galaxy.util.shed_util import load_tool_from_config, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path
+from galaxy.util.shed_util import get_parent_id, get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision
+from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config
+from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, is_downloadable, load_tool_from_config, remove_dir
+from galaxy.util.shed_util import reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path
 from galaxy.web.base.controller import *
 from galaxy.web.base.controllers.admin import *
 from galaxy.webapps.community import model
@@ -171,105 +174,6 @@
             if user_email in admin_users:
                 return True
     return False
-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 = []
-    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,
-                                                          trans.model.RepositoryMetadata.table.c.update_time.desc() ):
-        changeset_revision = repository_metadata.changeset_revision
-        can_delete = changeset_revision in changeset_revisions_checked or changeset_revision not in changeset_revisions
-        if can_delete:
-            trans.sa_session.delete( repository_metadata )
-            trans.sa_session.flush()
-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
-    # when this method returns the string 'not equal and not subset'.
-    ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] )
-    ancestor_tools = ancestor_metadata_dict.get( 'tools', [] )
-    ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ]
-    ancestor_guids.sort()
-    ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', [] )
-    ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] )
-    current_datatypes = current_metadata_dict.get( 'datatypes', [] )
-    current_tools = current_metadata_dict.get( 'tools', [] )
-    current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ]
-    current_guids.sort()
-    current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', [] ) 
-    current_workflows = current_metadata_dict.get( 'workflows', [] )
-    # Handle case where no metadata exists for either changeset.
-    if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes:
-        return 'no metadata'
-    workflow_comparison = compare_workflows( ancestor_workflows, current_workflows )
-    datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes )
-    # Handle case where all metadata is the same.
-    if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal':
-        return 'equal'
-    if workflow_comparison in [ 'equal', 'subset' ] and datatype_comparison in [ 'equal', 'subset' ]:
-        is_subset = True
-        for guid in ancestor_guids:
-            if guid not in current_guids:
-                is_subset = False
-                break
-        if is_subset:
-            return 'subset'
-    return 'not equal and not subset'
-def compare_datatypes( ancestor_datatypes, current_datatypes ):
-    # Determine if ancestor_datatypes is the same as current_datatypes
-    # or if ancestor_datatypes is a subset of current_datatypes.  Each
-    # datatype dict looks something like:
-    # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"}
-    if len( ancestor_datatypes ) <= len( current_datatypes ):
-        for ancestor_datatype in ancestor_datatypes:
-            # Currently the only way to differentiate datatypes is by name.
-            ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ]
-            ancestor_datatype_extension = ancestor_datatype[ 'extension' ]
-            ancestor_datatype_mimetype = ancestor_datatype.get( 'mimetype', None )
-            found_in_current = False
-            for current_datatype in current_datatypes:
-                if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \
-                    current_datatype[ 'extension' ] == ancestor_datatype_extension and \
-                    current_datatype.get( 'mimetype', None ) == ancestor_datatype_mimetype:
-                    found_in_current = True
-                    break
-            if not found_in_current:
-                return 'not equal and not subset'
-        if len( ancestor_datatypes ) == len( current_datatypes ):
-            return 'equal'
-        else:
-            return 'subset'
-    return 'not equal and not subset'
-def compare_workflows( ancestor_workflows, current_workflows ):
-    # Determine if ancestor_workflows is the same as current_workflows
-    # or if ancestor_workflows is a subset of current_workflows.
-    if len( ancestor_workflows ) <= len( current_workflows ):
-        for ancestor_workflow_tup in ancestor_workflows:
-            # ancestor_workflows is a list of tuples where each contained tuple is
-            # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
-            ancestor_workflow_dict = ancestor_workflow_tup[1]
-            # Currently the only way to differentiate workflows is by name.
-            ancestor_workflow_name = ancestor_workflow_dict[ 'name' ]
-            num_ancestor_workflow_steps = len( ancestor_workflow_dict[ 'steps' ] )
-            found_in_current = False
-            for current_workflow_tup in current_workflows:
-                current_workflow_dict = current_workflow_tup[1]
-                # Assume that if the name and number of steps are euqal,
-                # then the workflows are the same.  Of course, this may
-                # not be true...
-                if current_workflow_dict[ 'name' ] == ancestor_workflow_name and len( current_workflow_dict[ 'steps' ] ) == num_ancestor_workflow_steps:
-                    found_in_current = True
-                    break
-            if not found_in_current:
-                return 'not equal and not subset'
-        if len( ancestor_workflows ) == len( current_workflows ):
-            return 'equal'
-        else:
-            return 'subset'
-    return 'not equal and not subset'
 def copy_file_from_disk( filename, repo_dir, dir ):
     file_path = None
     found = False
@@ -300,66 +204,6 @@
             fh.close()
             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=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 )
-    base_url = url_for( '/', qualified=True ).rstrip( '/' )
-    if trans.user:
-        protocol, base = base_url.split( '://' )
-        username = '%s@' % trans.user.username
-        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_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False ):
-    if as_html:
-        new_line = '<br/>'
-        bold_start = '<b>'
-        bold_end = '</b>'
-    else:
-        new_line = '\n'
-        bold_start = ''
-        bold_end = ''
-    message = ''
-    if not displaying_invalid_tool:
-        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.%s" % new_line
-        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.%s" % new_line
-    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()
-            missing_file_items = exception_items[ 7 ].split( '/' )
-            missing_file = missing_file_items[ -1 ].rstrip( '\'' )
-            if missing_file.endswith( '.loc' ):
-                sample_ext = '%s.sample' % missing_file
-            else:
-                sample_ext = missing_file
-            correction_msg = "This file refers to a missing file %s%s%s.  " % ( bold_start, str( missing_file ), bold_end )
-            correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % ( bold_start, sample_ext, bold_end )
-        else:
-            if as_html:
-                correction_msg = exception_msg
-            else:
-                correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end )
-        message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line )
-    return message
 def generate_tool_guid( trans, repository, tool ):
     """
     Generate a guid for the received tool.  The form of the guid is    
@@ -450,24 +294,6 @@
                 fh.close()
                 return tmp_filename
     return None
-def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ):
-    parent_id = None
-    # Compare from most recent to oldest.
-    changeset_revisions.reverse()
-    for changeset_revision in changeset_revisions:
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
-        metadata = repository_metadata.metadata
-        tools_dicts = metadata.get( 'tools', [] )
-        for tool_dict in tools_dicts:
-            if tool_dict[ 'guid' ] == guid:
-                # The tool has not changed between the compared changeset revisions.
-                continue
-            if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version:
-                # The tool version is different, so we've found the parent.
-                return tool_dict[ 'guid' ]
-    if parent_id is None:
-        # The tool did not change through all of the changeset revisions.
-        return old_id
 def get_previous_downloadable_changset_revision( repository, repo, before_changeset_revision ):
     """
     Return the downloadable changeset_revision in the repository changelog just prior to the changeset to which before_changeset_revision
@@ -542,9 +368,6 @@
     for changeset in repo.changelog:
         reversed_changelog.insert( 0, changeset )
     return reversed_changelog
-def get_repository( trans, id ):
-    """Get a repository from the database via id"""
-    return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) )
 def get_repository_by_name( trans, name ):
     """Get a repository from the database via name"""
     return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one()
@@ -707,8 +530,6 @@
         if previous_changeset_revision in reviewed_revision_hashes:
             return True
     return False
-def is_downloadable( metadata_dict ):
-    return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict
 def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ):
     """
     Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename.  The value of changeset_revision
@@ -716,7 +537,7 @@
     revision and the first changeset revision in the repository, searching backwards.
     """
     original_tool_data_path = trans.app.config.tool_data_path
-    repository = get_repository( trans, repository_id )
+    repository = get_repository_in_tool_shed( trans, repository_id )
     repo_files_dir = repository.repo_path
     repo = hg.repository( get_configured_ui(), repo_files_dir )
     message = ''
@@ -802,134 +623,6 @@
             return True
     # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed.
     return False
-def remove_dir( dir ):
-    if os.path.exists( dir ):
-        try:
-            shutil.rmtree( dir )
-        except:
-            pass
-def reset_all_metadata_on_repository( trans, id, **kwd ):
-    def reset_all_tool_versions( trans, id, repo ):
-        changeset_revisions = []
-        for changeset in repo.changelog:
-            changeset_revision = str( repo.changectx( changeset ) )
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
-            if repository_metadata:
-                metadata = repository_metadata.metadata
-                if metadata:
-                    if metadata.get( 'tools', None ):
-                        changeset_revisions.append( changeset_revision )
-        # The list of changeset_revisions is now filtered to contain only those that are downloadable and contain tools.
-        # 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 )
-            metadata = repository_metadata.metadata
-            tool_dicts = metadata[ '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.
-                for tool_dict in tool_dicts:
-                    tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ]
-            else:
-                for tool_dict in tool_dicts:
-                    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()
-    params = util.Params( kwd )
-    message = util.restore_text( params.get( 'message', ''  ) )
-    status = params.get( 'status', 'done' )
-    repository = get_repository( trans, id )
-    log.debug( "Resetting all metadata on repository: %s" % repository.name )
-    repo_dir = repository.repo_path
-    repo = hg.repository( get_configured_ui(), repo_dir )
-    repository_clone_url = generate_clone_url( trans, id )
-    # The list of changeset_revisions refers to repository_metadata records that have been created or updated.  When the following loop
-    # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list.
-    changeset_revisions = []
-    # When a new repository_metadata record is created, it always uses the values of metadata_changeset_revision and metadata_dict.
-    metadata_changeset_revision = None
-    metadata_dict = None
-    ancestor_changeset_revision = None
-    ancestor_metadata_dict = None
-    invalid_file_tups = []
-    home_dir = os.getcwd()
-    for changeset in repo.changelog:
-        work_dir = tempfile.mkdtemp()
-        current_changeset_revision = str( repo.changectx( changeset ) )
-        ctx = repo.changectx( changeset )
-        log.debug( "Cloning repository revision: %s", str( ctx.rev() ) )
-        cloned_ok, error_message = clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) )
-        if cloned_ok:
-            log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) )
-            current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
-                                                                                                 repository=repository,
-                                                                                                 repository_clone_url=repository_clone_url,
-                                                                                                 relative_install_dir=repo_dir,
-                                                                                                 repository_files_dir=work_dir,
-                                                                                                 resetting_all_metadata_on_repository=True,
-                                                                                                 updating_installed_repository=False )
-            if current_metadata_dict:
-                if not metadata_changeset_revision and not metadata_dict:
-                    # We're at the first change set in the change log.
-                    metadata_changeset_revision = current_changeset_revision
-                    metadata_dict = current_metadata_dict
-                if ancestor_changeset_revision:
-                    # Compare metadata from ancestor and current.  The value of comparison will be one of:
-                    # 'no metadata' - no metadata for either ancestor or current, so continue from current
-                    # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current
-                    # 'subset' - ancestor metadata is a subset of current metadata, so continue from current
-                    # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata.
-                    comparison = compare_changeset_revisions( ancestor_changeset_revision,
-                                                              ancestor_metadata_dict,
-                                                              current_changeset_revision,
-                                                              current_metadata_dict )
-                    if comparison in [ 'no metadata', 'equal', 'subset' ]:
-                        ancestor_changeset_revision = current_changeset_revision
-                        ancestor_metadata_dict = current_metadata_dict
-                    elif comparison == 'not equal and not subset':
-                        metadata_changeset_revision = ancestor_changeset_revision
-                        metadata_dict = ancestor_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
-                else:
-                    # We're at the beginning of the change log.
-                    ancestor_changeset_revision = current_changeset_revision
-                    ancestor_metadata_dict = current_metadata_dict
-                if not ctx.children():
-                    metadata_changeset_revision = current_changeset_revision
-                    metadata_dict = current_metadata_dict
-                    # We're at the end of the change log.
-                    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
-            elif ancestor_metadata_dict:
-                # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not.
-                if not ctx.children():
-                    # We're at the end of the change log.
-                    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
-        remove_dir( work_dir )
-    # 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 )
-    # Set tool version information for all downloadable changeset revisions.  Get the list of changeset revisions from the changelog.
-    reset_all_tool_versions( trans, id, repo )
-    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-    reset_tool_data_tables( trans.app )
-    return invalid_file_tups, metadata_dict
 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
@@ -938,7 +631,7 @@
     message = ''
     status = 'done'
     encoded_id = trans.security.encode_id( repository.id )
-    repository_clone_url = generate_clone_url( trans, encoded_id )
+    repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository )
     repo_dir = repository.repo_path
     repo = hg.repository( get_configured_ui(), repo_dir )
     metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -9,11 +9,14 @@
 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_file_from_changeset_revision
-from galaxy.util.shed_util import get_repository_file_contents, get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk
+# TODO: re-factor shed_util to eliminate the following restricted imports
+from galaxy.util.shed_util import create_repo_info_dict, generate_clone_url_for_repository_in_tool_shed, generate_message_for_invalid_tools
+from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_file_from_changeset_revision, get_repository_file_contents
+from galaxy.util.shed_util import get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk
 from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS
-from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path
-from galaxy.util.shed_util import to_html_escaped, update_repository, url_join
+from galaxy.util.shed_util import open_repository_files_folder, remove_dir, reset_all_metadata_on_repository_in_tool_shed
+from galaxy.util.shed_util import reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path, to_html_escaped
+from galaxy.util.shed_util import update_repository, url_join
 from galaxy.tool_shed.encoding_util import *
 from common import *
 
@@ -639,7 +642,7 @@
                 else:
                     # The received id is the repository id, so we need to get the id of the user that uploaded the repository.
                     repository_id = kwd.get( 'id', None )
-                    repository = get_repository( trans, repository_id )
+                    repository = get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'f-email' ] = repository.user.email
             elif operation == "repositories_i_own":
                 # Eliminate the current filters if any exist.
@@ -696,7 +699,7 @@
             changset_revision_str = 'changeset_revision_'
             if k.startswith( changset_revision_str ):
                 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) )
-                repository = get_repository( trans, repository_id )
+                repository = get_repository_in_tool_shed( trans, repository_id )
                 if repository.tip != v:
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='browse_repositories',
@@ -710,7 +713,7 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
         # Update repository files for browsing.
         update_repository( repo )
@@ -771,7 +774,7 @@
             operation = kwd[ 'operation' ].lower()
             if operation == "preview_tools_in_changeset":
                 repository_id = kwd.get( 'id', None )
-                repository = get_repository( trans, repository_id )
+                repository = get_repository_in_tool_shed( trans, repository_id )
                 repository_metadata = get_latest_repository_metadata( trans, repository.id )
                 latest_installable_changeset_revision = repository_metadata.changeset_revision
                 return trans.response.send_redirect( web.url_for( controller='repository',
@@ -795,7 +798,7 @@
             changset_revision_str = 'changeset_revision_'
             if k.startswith( changset_revision_str ):
                 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) )
-                repository = get_repository( trans, repository_id )
+                repository = get_repository_in_tool_shed( trans, repository_id )
                 if repository.tip != v:
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='preview_tools_in_changeset',
@@ -922,7 +925,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         metadata = self.get_metadata( trans, id, repository.tip )
         if trans.user and trans.user.email:
             return trans.fill_template( "/webapps/community/repository/contact_owner.mako",
@@ -1033,7 +1036,7 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         repository_id = params.get( 'id', None )
-        repository = get_repository( trans, repository_id )
+        repository = get_repository_in_tool_shed( trans, repository_id )
         mark_deprecated = util.string_as_bool( params.get( 'mark_deprecated', False ) )
         repository.deprecated = mark_deprecated
         trans.sa_session.add( repository )
@@ -1086,7 +1089,7 @@
     def download( self, trans, repository_id, changeset_revision, file_type, **kwd ):
         # Download an archive of the repository files compressed as zip, gz or bz2.
         params = util.Params( kwd )
-        repository = get_repository( trans, repository_id )
+        repository = get_repository_in_tool_shed( trans, repository_id )
         # Allow hgweb to handle the download.  This requires the tool shed
         # server account's .hgrc file to include the following setting:
         # [web]
@@ -1119,7 +1122,7 @@
                     # The received id is a RepositoryMetadata id, so we have to get the repository id.
                     repository_metadata = get_repository_metadata_by_id( trans, item_id )
                     repository_id = trans.security.encode_id( repository_metadata.repository.id )
-                    repository = get_repository( trans, repository_id )
+                    repository = get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'id' ] = repository_id
                     kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
                     if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ):
@@ -1204,7 +1207,7 @@
                     # The received id is a RepositoryMetadata id, so we have to get the repository id.
                     repository_metadata = get_repository_metadata_by_id( trans, item_id )
                     repository_id = trans.security.encode_id( repository_metadata.repository.id )
-                    repository = get_repository( trans, repository_id )
+                    repository = get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'id' ] = repository_id
                     kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
                     if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ):
@@ -1309,8 +1312,8 @@
         repo_info_dicts = []
         for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ):
             repository_id, changeset_revision = tup
-            repository_clone_url = generate_clone_url( trans, repository_id )
-            repository = get_repository( trans, repository_id )
+            repository = get_repository_in_tool_shed( trans, repository_id )
+            repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository )
             repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
             metadata = repository_metadata.metadata
             if not includes_tools and 'tools' in metadata:
@@ -1668,7 +1671,7 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         cntrller = params.get( 'cntrller', 'repository' )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repo_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_dir )
         repo_name = util.restore_text( params.get( 'repo_name', repository.name ) )
@@ -1892,7 +1895,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, repository_id )
+        repository = get_repository_in_tool_shed( trans, repository_id )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata:
@@ -1957,7 +1960,7 @@
                                                               action='browse_repositories',
                                                               message='Select a repository to rate',
                                                               status='error' ) )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
         if repository.user == trans.user:
             return trans.response.send_redirect( web.url_for( controller='repository',
@@ -1985,9 +1988,11 @@
                                     status=status )
     @web.expose
     def reset_all_metadata( self, trans, id, **kwd ):
-        invalid_file_tups, metadata_dict = reset_all_metadata_on_repository( trans, id, **kwd )
+        # This method is called only from the ~/templates/webapps/community/repository/manage_repository.mako template.
+        # It resets all metadata on the complete changelog for a single repository in the tool shed.
+        invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd )
         if invalid_file_tups:
-            repository = get_repository( trans, id )
+            repository = get_repository_in_tool_shed( trans, id )
             message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict )
             status = 'error'
         else:
@@ -2093,7 +2098,7 @@
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )
         commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repo_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_dir )
         selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) )
@@ -2155,7 +2160,7 @@
                                     status=status )
     @web.expose
     def send_to_owner( self, trans, id, message='' ):
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         if not message:
             message = 'Enter a message'
             status = 'error'
@@ -2205,7 +2210,7 @@
             total_alerts_removed = 0
             flush_needed = False
             for repository_id in repository_ids:
-                repository = get_repository( trans, repository_id )
+                repository = get_repository_in_tool_shed( trans, repository_id )
                 if repository.email_alerts:
                     email_alerts = from_json_string( repository.email_alerts )
                 else:
@@ -2277,7 +2282,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
         changesets = []
         for changeset in repo.changelog:
@@ -2314,7 +2319,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
         ctx = get_changectx_for_changeset( repo, ctx_str )
         if ctx is None:
@@ -2351,7 +2356,7 @@
                                     status=status )
     @web.expose
     def view_or_manage_repository( self, trans, **kwd ):
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] )
         if trans.user_is_admin() or repository.user == trans.user:
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='manage_repository',
@@ -2366,7 +2371,7 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         cntrller = params.get( 'cntrller', 'repository' )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )
         if repository_metadata:
             metadata = repository_metadata.metadata
@@ -2417,7 +2422,7 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         cntrller = params.get( 'cntrller', 'repository' )
-        repository = get_repository( trans, id )
+        repository = get_repository_in_tool_shed( trans, id )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
         avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
@@ -2499,7 +2504,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, repository_id )
+        repository = get_repository_in_tool_shed( trans, repository_id )
         repo_files_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_files_dir )
         tool_metadata_dict = {}


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/repository_review.py
--- a/lib/galaxy/webapps/community/controllers/repository_review.py
+++ b/lib/galaxy/webapps/community/controllers/repository_review.py
@@ -8,7 +8,8 @@
 from sqlalchemy.sql.expression import func
 from common import *
 from repository import RepositoryGrid
-from galaxy.util.shed_util import get_configured_ui
+# TODO: re-factor shed_util to eliminate the following restricted imports
+from galaxy.util.shed_util import get_configured_ui, get_repository_in_tool_shed
 from galaxy.util.odict import odict
 
 from galaxy import eggs
@@ -381,7 +382,7 @@
                     message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, repository.name )
                     status = "error"
                 else:
-                    repository = get_repository( trans, repository_id )
+                    repository = get_repository_in_tool_shed( trans, repository_id )
                     # See if there are any reviews for previous changeset revisions that the user can copy.
                     if not create_without_copying and not previous_review_id and has_previous_repository_reviews( trans, repository, changeset_revision ):
                         return trans.response.send_redirect( web.url_for( controller='repository_review',
@@ -650,7 +651,7 @@
         status = params.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         if repository_id:
-            repository = get_repository( trans, repository_id )
+            repository = get_repository_in_tool_shed( trans, repository_id )
             repo_dir = repository.repo_path
             repo = hg.repository( get_configured_ui(), repo_dir )
             metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
@@ -697,7 +698,7 @@
         status = params.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         changeset_revision = kwd.get( 'changeset_revision', None )
-        repository = get_repository( trans, repository_id )
+        repository = get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_dir )
         installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
@@ -762,7 +763,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] )
         changeset_revision = kwd.get( 'changeset_revision', None )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
         previous_reviews_dict = get_previous_repository_reviews( trans, repository, changeset_revision )
@@ -777,7 +778,7 @@
     @web.expose
     @web.require_login( "view or manage repository" )
     def view_or_manage_repository( self, trans, **kwd ):
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] )
         if trans.user_is_admin() or repository.user == trans.user:
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='manage_repository',


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/upload.py
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -3,7 +3,9 @@
 from galaxy.model.orm import *
 from galaxy.datatypes.checkers import *
 from common import *
-from galaxy.util.shed_util import get_configured_ui, reset_tool_data_tables, handle_sample_tool_data_table_conf_file, update_repository
+# TODO: re-factor shed_util to eliminate the following restricted imports
+from galaxy.util.shed_util import get_configured_ui, get_repository_in_tool_shed, reset_tool_data_tables, handle_sample_tool_data_table_conf_file
+from galaxy.util.shed_util import update_repository
 
 from galaxy import eggs
 eggs.require('mercurial')
@@ -28,7 +30,7 @@
         category_ids = util.listify( params.get( 'category_id', '' ) )
         categories = get_categories( trans )
         repository_id = params.get( 'repository_id', '' )
-        repository = get_repository( trans, repository_id )
+        repository = get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_dir )
         uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) )


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/workflow.py
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -10,6 +10,8 @@
 from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps
 from galaxy.model.orm import *
 from common import *
+# TODO: re-factor shed_util to eliminate the following restricted imports
+from galaxy.util.shed_util import get_repository_in_tool_shed
 from galaxy.tool_shed.encoding_util import *
 
 class RepoInputDataModule( InputDataModule ):
@@ -144,7 +146,7 @@
         message = kwd.get( 'message', '' )
         status = kwd.get( 'status', 'done' )
         repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
-        repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+        repository = get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) )
         return trans.fill_template( "/webapps/community/repository/view_workflow.mako",
                                     repository=repository,
                                     changeset_revision=repository_metadata.changeset_revision,


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -10,8 +10,6 @@
 
 log = logging.getLogger( __name__ )
 
-MAX_CONTENT_SIZE = 32768
-
 class InstalledRepositoryGrid( grids.Grid ):
     class NameColumn( grids.TextColumn ):
         def get_value( self, trans, grid, tool_shed_repository ):
@@ -300,7 +298,7 @@
         return query
 
 class AdminToolshed( AdminGalaxy ):
-    
+
     installed_repository_grid = InstalledRepositoryGrid()
     repository_installation_grid = RepositoryInstallationGrid()
     tool_dependency_grid = ToolDependencyGrid()
@@ -309,9 +307,9 @@
     @web.require_admin
     def activate_repository( self, trans, **kwd ):
         """Activate a repository that was deactivated but not uninstalled."""
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
         shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
-        repository_clone_url = self.__generate_clone_url( trans, repository )
+        repository_clone_url = generate_clone_url_for_installed_repository( trans, repository )
         repository.deleted = False
         repository.status = trans.model.ToolShedRepository.installation_status.INSTALLED
         if repository.includes_tools:
@@ -356,7 +354,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
         return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako',
                                     repository=repository,
                                     message=message,
@@ -380,7 +378,7 @@
                                                                   action='reset_to_install',
                                                                   **kwd ) )
             if operation == "activate or reinstall":
-                repository = get_repository( trans, kwd[ 'id' ] )
+                repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
                 if repository.uninstalled:
                     if repository.includes_tools:
                         # Only allow selecting a different section in the tool panel if the repository was uninstalled.
@@ -440,7 +438,7 @@
     @web.require_admin
     def check_for_updates( self, trans, **kwd ):
         # Send a request to the relevant tool shed to see if there are any updates.
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
         tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
         url = url_join( tool_shed_url,
                         'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
@@ -454,7 +452,7 @@
         status = params.get( 'status', 'done' )
         remove_from_disk = params.get( 'remove_from_disk', '' )
         remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk )
-        tool_shed_repository = get_repository( trans, kwd[ 'id' ] )
+        tool_shed_repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
         shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
         if relative_install_dir:
             if tool_path:
@@ -819,7 +817,7 @@
         status = params.get( 'status', 'done' )
         repository_id = kwd[ 'id' ]
         operation = kwd.get( 'operation', None )
-        repository = get_repository( trans, repository_id )
+        repository = get_installed_tool_shed_repository( trans, repository_id )
         if not repository:
             return trans.show_error_message( 'Invalid repository specified.' )
         if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]:
@@ -1237,14 +1235,14 @@
         message = kwd.get( 'message', '' )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd[ 'id' ]
-        tool_shed_repository = get_repository( trans, repository_id )
+        tool_shed_repository = get_installed_tool_shed_repository( trans, repository_id )
         no_changes = kwd.get( 'no_changes', '' )
         no_changes_checked = CheckboxField.is_checked( no_changes )
         install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
         new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
         tool_panel_section = kwd.get( 'tool_panel_section', '' )
         shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
-        repository_clone_url = generate_clone_url( trans, tool_shed_repository )
+        repository_clone_url = generate_clone_url_for_installed_repository( trans, tool_shed_repository )
         clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) )
         relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name )
         tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
@@ -1395,11 +1393,11 @@
     @web.expose
     @web.require_admin
     def reselect_tool_panel_section( self, trans, **kwd ):
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
         metadata = repository.metadata
         tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
         ctx_rev = get_ctx_rev( tool_shed_url, repository.name, repository.owner, repository.installed_changeset_revision )
-        repository_clone_url = generate_clone_url( trans, repository )
+        repository_clone_url = generate_clone_url_for_installed_repository( trans, repository )
         repo_info_dict = create_repo_info_dict( repository,
                                                 repository.owner,
                                                 repository_clone_url,
@@ -1460,63 +1458,25 @@
                                     status=status )
     @web.expose
     @web.require_admin
-    def reset_metadata_on_selected_repositories( self, trans, **kwd ):
-        # TODO: merge this with the similar method in the repository controller.
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        repository_ids = util.listify( kwd.get( 'repository_names_by_owner', None ) )
+    def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ):
         if 'reset_metadata_on_selected_repositories_button' in kwd:
-            if repository_ids:
-                successful_count = 0
-                unsuccessful_count = 0
-                for repository_id in repository_ids:
-                    repository = get_repository( trans, repository_id )
-                    try:
-                        invalid_file_tups, metadata_dict = self.reset_repository_metadata( trans,
-                                                                                           trans.security.encode_id( repository.id ),
-                                                                                           resetting_all_repositories=True )
-                        if invalid_file_tups:
-                            unsuccessful_count += 1
-                        else:
-                            successful_count += 1
-                    except Exception, e:
-                        log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) )
-                        unsuccessful_count += 1
-                message = "Successfully reset metadata on %d %s.  " % ( successful_count,
-                                                                        inflector.cond_plural( successful_count, "repository" ) )
-                if unsuccessful_count:
-                    message += "Error setting metadata on %d %s - see the paster log for details.  " % ( unsuccessful_count,
-                                                                                                         inflector.cond_plural( unsuccessful_count,
-                                                                                                                                "repository" ) )
-                trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                           action='browse_repositories',
-                                                           message=util.sanitize_text( message ),
-                                                           status=status ) )
-            else:
-                'Select at least one repository to on which to reset all metadata.'
-                status = 'error'
-        repositories_select_field = SelectField( name='repository_names_by_owner', 
-                                                 multiple=True,
-                                                 display='checkboxes' )
-        for repository in trans.sa_session.query( trans.model.ToolShedRepository ) \
-                                          .filter( trans.model.ToolShedRepository.table.c.uninstalled == False ) \
-                                          .order_by( trans.model.ToolShedRepository.table.c.name,
-                                                     trans.model.ToolShedRepository.table.c.owner ):
-            option_label = '%s (%s)' % ( repository.name, repository.owner )
-            option_value = trans.security.encode_id( repository.id )
-            repositories_select_field.add_option( option_label, option_value )
+            kwd[ 'CONTROLLER' ] = GALAXY_ADMIN_TOOL_SHED_CONTROLLER
+            message, status = reset_metadata_on_selected_repositories( trans, **kwd )
+        else:
+            message = util.restore_text( kwd.get( 'message', ''  ) )
+            status = kwd.get( 'status', 'done' )
+        repositories_select_field = build_repository_ids_select_field( trans, GALAXY_ADMIN_TOOL_SHED_CONTROLLER )
         return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
                                     repositories_select_field=repositories_select_field,
                                     message=message,
                                     status=status )
     @web.expose
     @web.require_admin
-    def reset_repository_metadata( self, trans, id, resetting_all_repositories=False ):
-        """Reset all metadata on the installed tool shed repository."""
-        repository = get_repository( trans, id )
+    def reset_repository_metadata( self, trans, id ):
+        """Reset all metadata on a single installed tool shed repository."""
+        repository = get_installed_tool_shed_repository( trans, id )
         tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-        repository_clone_url = self.__generate_clone_url( trans, repository )
+        repository_clone_url = generate_clone_url_for_installed_repository( trans, repository )
         tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
         if relative_install_dir:
             original_metadata_dict = repository.metadata
@@ -1533,35 +1493,24 @@
                 update_in_shed_tool_config( trans.app, repository )
                 trans.sa_session.add( repository )
                 trans.sa_session.flush()
-                if resetting_all_repositories:
-                    log.debug( 'Metadata has been reset on repository %s.' % repository.name )
-                else:
-                    message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name
-                    status = 'done'
+                message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name
+                status = 'done'
             else:
-                if resetting_all_repositories:
-                    log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name )
-                else:
-                    message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name
-                    status = 'done'
+                message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name
+                status = 'done'
         else:
-            if resetting_all_repositories:
-                log.debug( 'Error locating installation directory for repository %s.' % repository.name )
-            else:
-                message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name
-                status = 'error'
-        if resetting_all_repositories:
-            return invalid_file_tups, metadata_dict
-        else:
-            new_kwd = dict( id=id, message=message, status=status )
-            return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                              action='manage_repository',
-                                                              **new_kwd ) )
+            message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name
+            status = 'error'
+        return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                          action='manage_repository',
+                                                          id=id,
+                                                          message=message,
+                                                          status=status ) )
     @web.expose
     @web.require_admin
     def reset_to_install( self, trans, **kwd ):
         """An error occurred while cloning the repository, so reset everything necessary to enable another attempt."""
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
         if kwd.get( 'reset_repository', False ):
             self.set_repository_attributes( trans,
                                             repository,
@@ -1596,7 +1545,7 @@
     @web.require_admin
     def set_tool_versions( self, trans, **kwd ):
         # Get the tool_versions from the tool shed for each tool in the installed change set.
-        repository = get_repository( trans, kwd[ 'id' ] )
+        repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
         tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
         url = url_join( tool_shed_url,
                         'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
@@ -1756,7 +1705,7 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         cntrller = params.get( 'cntrller', 'admin_toolshed' )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, id )
+        repository = get_installed_tool_shed_repository( trans, id )
         metadata = repository.metadata
         shed_config_dict = repository.get_shed_config_dict( trans.app )
         tool_path = shed_config_dict.get( 'tool_path', None )
@@ -1790,7 +1739,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, repository_id )
+        repository = get_installed_tool_shed_repository( trans, repository_id )
         repository_metadata = repository.metadata
         shed_config_dict = repository.get_shed_config_dict( trans.app )
         tool_metadata = {}
@@ -1815,10 +1764,6 @@
                                     tool_lineage=tool_lineage,
                                     message=message,
                                     status=status )
-    def __generate_clone_url( self, trans, repository ):
-        """Generate the URL for cloning a repository."""
-        tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-        return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
 
 ## ---- Utility methods -------------------------------------------------------
 
@@ -1847,9 +1792,6 @@
     for option_tup in options:
         select_field.add_option( option_tup[0], option_tup[1] )
     return select_field
-def get_repository( trans, id ):
-    """Get a tool_shed_repository from the database via id"""
-    return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
 def get_tool_dependency( trans, id ):
     """Get a tool_dependency from the database via id"""
     return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) )


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
--- a/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
+++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
@@ -1,42 +1,10 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
-
-<%def name="local_javascripts()">
-    <script type="text/javascript">
-        function checkAllFields()
-        {
-            var chkAll = document.getElementById('checkAll');
-            var checks = document.getElementsByTagName('input');
-            var boxLength = checks.length;
-            var allChecked = false;
-            var totalChecked = 0;
-            if ( chkAll.checked == true )
-            {
-                for ( i=0; i < boxLength; i++ )
-                {
-                    if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1)
-                    {
-                       checks[i].checked = true;
-                    }
-                }
-            }
-            else
-            {
-                for ( i=0; i < boxLength; i++ )
-                {
-                    if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1)
-                    {
-                       checks[i].checked = false
-                    }
-                }
-            }
-        }
-    </script>
-</%def>
+<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /><%def name="javascripts()">
     ${parent.javascripts()}
-    ${local_javascripts()}
+    ${common_misc_javascripts()}
 </%def>
 
 %if message:
@@ -50,13 +18,13 @@
 
 <div class="toolForm"><div class="toolFormTitle">Reset all metadata on each selected tool shed repository</div>
-        <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" method="post" >
+        <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_installed_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.
             </div><div style="clear: both"></div><div class="form-row">
-                <input type="checkbox" id="checkAll" name=select_all_repositories_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_repositories_checkbox value="true"/><b>Select/unselect all repositories</b>
+                <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b></div><div style="clear: both"></div><div class="form-row">


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/community/admin/index.mako
--- a/templates/webapps/community/admin/index.mako
+++ b/templates/webapps/community/admin/index.mako
@@ -55,7 +55,7 @@
                             <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a></div><div class="toolTitle">
-                            <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}">Reset selected metadata</a>
+                            <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}">Reset selected metadata</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a>


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a 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
@@ -1,42 +1,10 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
-
-<%def name="local_javascripts()">
-    <script type="text/javascript">
-        function checkAllFields()
-        {
-            var chkAll = document.getElementById('checkAll');
-            var checks = document.getElementsByTagName('input');
-            var boxLength = checks.length;
-            var allChecked = false;
-            var totalChecked = 0;
-            if ( chkAll.checked == true )
-            {
-                for ( i=0; i < boxLength; i++ )
-                {
-                    if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1)
-                    {
-                       checks[i].checked = true;
-                    }
-                }
-            }
-            else
-            {
-                for ( i=0; i < boxLength; i++ )
-                {
-                    if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1)
-                    {
-                       checks[i].checked = false
-                    }
-                }
-            }
-        }
-    </script>
-</%def>
+<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /><%def name="javascripts()">
     ${parent.javascripts()}
-    ${local_javascripts()}
+    ${common_misc_javascripts()}
 </%def>
 
 %if message:
@@ -51,13 +19,13 @@
 
 <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="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}" method="post" >
+        <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}" method="post" ><div class="form-row">
                 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">
-                <input type="checkbox" id="checkAll" name=select_all_repositories_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_repositories_checkbox value="true"/><b>Select/unselect all repositories</b>
+                <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b></div><div style="clear: both"></div><div class="form-row">


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/community/common/common.mako
--- a/templates/webapps/community/common/common.mako
+++ b/templates/webapps/community/common/common.mako
@@ -1,3 +1,36 @@
+<%def name="common_misc_javascripts()">
+    <script type="text/javascript">
+        function checkAllFields( name )
+        {
+            var chkAll = document.getElementById( 'checkAll' );
+            var checks = document.getElementsByTagName( 'input' );
+            var boxLength = checks.length;
+            var allChecked = false;
+            var totalChecked = 0;
+            if ( chkAll.checked == true )
+            {
+                for ( i=0; i < boxLength; i++ )
+                {
+                    if ( checks[i].name.indexOf( name ) != -1 )
+                    {
+                       checks[i].checked = true;
+                    }
+                }
+            }
+            else
+            {
+                for ( i=0; i < boxLength; i++ )
+                {
+                    if ( checks[i].name.indexOf( name ) != -1 )
+                    {
+                       checks[i].checked = false
+                    }
+                }
+            }
+        }
+    </script>
+</%def>
+
 <%def name="escape_html_add_breaks( value )"><%
         from galaxy import eggs


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/community/repository/common.mako
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -77,8 +77,8 @@
 
 <%def name="render_clone_str( repository )"><%
-        from galaxy.webapps.community.controllers.common import generate_clone_url
-        clone_str = generate_clone_url( trans, trans.security.encode_id( repository.id ) )
+        from galaxy.util.shed_util import generate_clone_url_for_repository_in_tool_shed
+        clone_str = generate_clone_url_for_repository_in_tool_shed( trans, repository )
     %>
     hg clone <a href="${clone_str}">${clone_str}</a></%def>


diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/galaxy/admin/index.mako
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -75,7 +75,7 @@
                             <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=installing_repository_ids )}" target="galaxy_main">Monitor installing tool shed repositories</a></div>
                         %endif
                         %if installed_repositories:
-                            <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" target="galaxy_main">Reset metadata for tool shed repositories</a></div>
+                            <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_installed_repositories' )}" target="galaxy_main">Reset metadata for tool shed repositories</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div>
                         %endif
                     </div>

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

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commit/galaxy-central: greg: Refactor code supporting setting metadata on repositories in the tool shed and installed in Galaxy - enables using same code across web apps.

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