commit/galaxy-central: greg: Refinements for locating desired files within a tool shed repository manifest and setting metadata on tool shed repositories. - galaxy-commits

5 Jun 2012

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f551610b6870/
changeset:   f551610b6870
user:        greg
date:        2012-06-05 17:15:14
summary:     Refinements for locating desired files within a tool shed repository manifest and setting metadata on tool shed repositories.
affected #:  5 files
diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/util/shed_util.py

--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -21,6 +21,7 @@
log = logging.getLogger( __name__ )
+INITIAL_CHANGELOG_HASH = '000000000000'
 # Characters that must be html escaped
 MAPPED_CHARS = { '>' :'&gt;', 
                  '<' :'&lt;',
@@ -771,28 +772,15 @@
         if str( ctx ) == changeset_revision:
             return ctx
     return None
-def get_config( config_file, repo, repo_dir, ctx, dir ):
-    """Return config_filename if it exists in some changeset of the repository."""
-    # First look on disk.
-    for root, dirs, files in os.walk( repo_dir ):
-        if root.find( '.hg' ) < 0:
-            for name in files:
-                if name == config_file:
-                    dest_file_name = os.path.join( dir, name )
-                    shutil.copy( os.path.abspath( os.path.join( root, name ) ), dest_file_name )
-                    return os.path.abspath( dest_file_name )
-    # Next look in the current change set.
-    for filename in ctx:
-        ctx_file_name = strip_path( filename )
-        if ctx_file_name == config_file:
-            return get_named_tmpfile_from_ctx( ctx, filename, dir )
-    # Finally look in the repository manifest.
-    for changeset in repo.changelog:
-        prev_ctx = repo.changectx( changeset )
-        for ctx_file in prev_ctx.files():
+def get_config( config_file, repo, ctx, dir ):
+    """Return the latest version of config_filename from the repository manifest."""
+    config_file = strip_path( config_file )
+    for changeset in reversed_upper_bounded_changelog( repo, ctx ):
+        changeset_ctx = repo.changectx( changeset )
+        for ctx_file in changeset_ctx.files():
             ctx_file_name = strip_path( ctx_file )
             if ctx_file_name == config_file:
-                return get_named_tmpfile_from_ctx( prev_ctx, filename, dir )
+                return get_named_tmpfile_from_ctx( changeset_ctx, ctx_file, dir )
     return None
 def get_config_from_disk( config_file, relative_install_dir ):
     for root, dirs, files in os.walk( relative_install_dir ):
@@ -808,7 +796,7 @@
     repo_files_dir = os.path.join( install_dir, repository.name )
     repo = hg.repository( get_configured_ui(), repo_files_dir )
     ctx = get_changectx_for_changeset( repo, changeset_revision )
-    config = get_config( config_file, repo, repo_files_dir, ctx, dir )
+    config = get_config( config_file, repo, ctx, dir )
     return config
 def get_configured_ui():
     # Configure any desired ui settings.
@@ -867,6 +855,15 @@
     ctx_rev = response.read()
     response.close()
     return ctx_rev
+def get_named_tmpfile_from_ctx( ctx, filename, dir ):
+    fctx = ctx[ filename ]
+    fh = tempfile.NamedTemporaryFile( 'wb', dir=dir )
+    tmp_filename = fh.name
+    fh.close()
+    fh = open( tmp_filename, 'wb' )
+    fh.write( fctx.data() )
+    fh.close()
+    return tmp_filename
 def get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ):
     sa_session = app.model.context.current
     if tool_shed.find( '//' ) > 0:
@@ -1383,6 +1380,31 @@
 def reset_tool_data_tables( app ):
     # Reset the tool_data_tables to an empty dictionary.
     app.tool_data_tables.data_tables = {}
+def reversed_lower_upper_bounded_changelog( repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision ):
+    """
+    Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and
+    including the included_upper_bounds_changeset_revision.  The value of excluded_lower_bounds_changeset_revision will be the value of
+    INITIAL_CHANGELOG_HASH if no valid changesets exist before included_upper_bounds_changeset_revision.
+    """
+    # To set excluded_lower_bounds_changeset_revision, calling methods should do the following, where the value of changeset_revision
+    # is a downloadable changeset_revision.
+    # excluded_lower_bounds_changeset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision )
+    if excluded_lower_bounds_changeset_revision == INITIAL_CHANGELOG_HASH:
+        appending_started = True
+    else:
+        appending_started = False
+    reversed_changelog = []
+    for changeset in repo.changelog:
+        changeset_hash = str( repo.changectx( changeset ) )
+        if appending_started:
+            reversed_changelog.insert( 0, changeset )
+        if changeset_hash == excluded_lower_bounds_changeset_revision and not appending_started:
+            appending_started = True
+        if changeset_hash == included_upper_bounds_changeset_revision:
+            break
+    return reversed_changelog
+def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revision ):
+    return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision )
 def strip_path( fpath ):
     file_path, file_name = os.path.split( fpath )
     return file_name
diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/admin.py
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -473,9 +473,12 @@
                                               .filter( trans.model.Repository.table.c.deleted == False ):
                 try:
                     error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) )
-                    if error_message:
+                    if status not in [ 'ok' ] and error_message:
                         log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, error_message ) )
                         unsuccessful_count += 1
+                    elif status in [ 'ok' ] and error_message:
+                        log.debug( "Successfully reset metadata on repository %s, but encountered this problem: %s" % ( repository.name, error_message ) )
+                        successful_count += 1
                     else:
                         log.debug( "Successfully reset metadata on repository %s" % repository.name )
                         successful_count += 1
diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -6,8 +6,9 @@
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.hash_util import *
 from galaxy.util.shed_util import copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata
-from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, handle_sample_tool_data_table_conf_file
-from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, strip_path, to_html_escaped, to_html_str, update_repository
+from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, get_named_tmpfile_from_ctx
+from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables
+from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path, to_html_escaped, to_html_str, update_repository
 from galaxy.web.base.controller import *
 from galaxy.webapps.community import model
 from galaxy.model.orm import *
@@ -201,7 +202,7 @@
             if options:
                 if options.tool_data_table or options.missing_tool_data_table_name:
                     # Make sure the repository contains a tool_data_table_conf.xml.sample file.
-                    sample_tool_data_table_conf = get_config( 'tool_data_table_conf.xml.sample', repo, repo_dir, ctx, dir )
+                    sample_tool_data_table_conf = get_config( 'tool_data_table_conf.xml.sample', repo, ctx, dir )
                     if sample_tool_data_table_conf:
                         error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, sample_tool_data_table_conf )
                         if error:
@@ -254,9 +255,9 @@
     # 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.
     #
-    # TODO: a new repository_metadata record will be created only when this method returns the string 'not equal and not subset'.  However,
-    # we're currently also returning the strings 'no metadata', 'equal' and 'subset', depending upon how the 2 change sets compare.  We'll
-    # leave things this way for the current time in case we discover a use for these additional result strings.
+    # A new repository_metadata record will be created only when this method returns the string 'not equal and not subset'.  However, we're
+    # currently also returning the strings 'no metadata', 'equal' and 'subset', depending upon how the 2 change sets compare.  We'll leave
+    # things this way for the current time in case we discover a use for these additional result strings.
     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 ]
@@ -357,41 +358,18 @@
         tmp_filename = None
     return tmp_filename
 def copy_file_from_manifest( repo, ctx, filename, dir ):
-    """Copy a file named filename from somewhere in the repository manifest to the directory to which dir refers."""
-    filename = strip_path( filename )
-    fctx = None
-    found = False
-    # First see if the file is in ctx.  We have to be careful in determining if we found the correct file because multiple files
-    # with the same name may be in different directories within ctx if the repository owner moved the files as part of the change set.
-    # For example, in the following ctx.files() list, the former may have been moved to the latter:
-    # ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']
-    for ctx_file in ctx.files():
-        ctx_file_name = strip_path( ctx_file )
-        if filename == ctx_file_name:
-            try:
-                fctx = ctx[ ctx_file ]
-                found = True
-                break
-            except:
-                continue
-    if not found:
-        # Find the file in the repository manifest.
-        for changeset in repo.changelog:
-            prev_ctx = repo.changectx( changeset )
-            for ctx_file in prev_ctx.files():
-                ctx_file_name = strip_path( ctx_file )
-                if filename == ctx_file_name:
-                    try:
-                        fctx = prev_ctx[ ctx_file ]
-                        break
-                    except:
-                        continue
-    if fctx:
-        file_path = os.path.join( dir, filename )
-        fh = open( file_path, 'wb' )
-        fh.write( fctx.data() )
-        fh.close()
-        return file_path
+    """
+    Copy the latest version of the file named filename from the repository manifest to the directory to which dir refers.
+    """
+    for changeset in reversed_upper_bounded_changelog( repo, ctx ):
+        changeset_ctx = repo.changectx( changeset )
+        fctx = get_file_context_from_ctx( changeset_ctx, filename )
+        if fctx and fctx not in [ 'DELETED' ]:
+            file_path = os.path.join( dir, filename )
+            fh = open( file_path, 'wb' )
+            fh.write( fctx.data() )
+            fh.close()
+            return file_path
     return None
 def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ):
     repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
@@ -444,10 +422,10 @@
     invalid_tool_configs = []
     original_tool_data_path = trans.app.config.tool_data_path
     work_dir = make_tmp_directory()
-    datatypes_config = get_config( 'datatypes_conf.xml', repo, repo_dir, ctx, work_dir  )
+    datatypes_config = get_config( 'datatypes_conf.xml', repo, ctx, work_dir  )
     if datatypes_config:
         metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )    
-    sample_files = get_sample_files( repo, repo_dir, dir=work_dir )
+    sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir )
     # Handle the tool_data_table_conf.xml.sample file if it is included in the repository.
     if 'tool_data_table_conf.xml.sample' in sample_files:
         tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir )
@@ -515,7 +493,7 @@
                 invalid_files.append( ( ctx_file_name, str( e ) ) )
     if 'tools' in metadata_dict:
         # Find tool_dependencies.xml if it exists.  This step must be done after metadata for tools has been defined.
-        tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir )
+        tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, ctx, work_dir )
         if tool_dependencies_config:
             metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict )
     if invalid_tool_configs:
@@ -529,7 +507,7 @@
         shutil.rmtree( work_dir )
     except:
         pass
-    return metadata_dict, invalid_files
+    return metadata_dict, invalid_files, deleted_sample_files
 def generate_tool_guid( trans, repository, tool ):
     """
     Generate a guid for the received tool.  The form of the guid is    
@@ -548,21 +526,59 @@
     return trans.sa_session.query( trans.model.Category ) \
                            .filter( trans.model.Category.table.c.deleted==False ) \
                            .order_by( trans.model.Category.table.c.name ).all()
+def get_file_context_from_ctx( ctx, filename ):
+    # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories
+    # within ctx if the files were moved within the change set.  For example, in the following ctx.files() list, the former may have been moved to
+    # the latter:
+    # ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']
+    filename = strip_path( filename )
+    for ctx_file in ctx.files():
+        ctx_file_name = strip_path( ctx_file )
+        if filename == ctx_file_name:
+            try:
+                fctx = ctx[ ctx_file ]
+                return fctx
+            except LookupError, e:
+                return 'DELETED'
+    return None
 def get_latest_repository_metadata( trans, id ):
     """Get last metadata defined for a specified repository from the database"""
     return 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.id.desc() ) \
                            .first()
-def get_named_tmpfile_from_ctx( ctx, filename, dir ):
-    fctx = ctx[ filename ]
-    fh = tempfile.NamedTemporaryFile( 'wb', dir=dir )
-    tmp_filename = fh.name
-    fh.close()
-    fh = open( tmp_filename, 'wb' )
-    fh.write( fctx.data() )
-    fh.close()
-    return tmp_filename
+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
+    each discovered file to dir and return the list of filenames.  If a .sample file was added in a changeset and then deleted in a later
+    changeset, it will be returned in the deleted_sample_files list.  The caller will set the value of app.config.tool_data_path to dir in
+    order to load the tools and generate metadata for them.
+    """
+    deleted_sample_files = []
+    sample_files = []
+    for changeset in reversed_upper_bounded_changelog( repo, ctx ):
+        changeset_ctx = repo.changectx( changeset )
+        for ctx_file in changeset_ctx.files():
+            ctx_file_name = strip_path( ctx_file )
+            # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement.
+            # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files:
+            if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files:
+                fctx = get_file_context_from_ctx( changeset_ctx, ctx_file )
+                if fctx in [ 'DELETED' ]:
+                    # Since the possibly future used if statement above is commented out, the same file that was initially added will be
+                    # discovered in an earlier changeset in the change log and fall through to the else block below.  In other words, if
+                    # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset
+                    # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below.  In this
+                    # way, the file contents will always be found for future tools even though the file was deleted.
+                    if ctx_file_name not in deleted_sample_files:
+                        deleted_sample_files.append( ctx_file_name )
+                else:
+                    sample_files.append( ctx_file_name )
+                    tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) )
+                    fh = open( tmp_ctx_file_name, 'wb' )
+                    fh.write( fctx.data() )
+                    fh.close()
+    return sample_files, deleted_sample_files
 def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ):
     parent_id = None
     # Compare from most recent to oldest.
@@ -582,6 +598,10 @@
         # The tool did not change through all of the changeset revisions.
         return old_id
 def get_previous_valid_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
+    refers.  If there isn't one, return the hash value of an empty repository changlog, INITIAL_CHANGELOG_HASH.
+    """
     changeset_tups = []
     for repository_metadata in repository.downloadable_revisions:
         changeset_revision = repository_metadata.changeset_revision
@@ -600,7 +620,7 @@
                 return previous_changeset_revision
             else:
                 # Return the hash value of an empty repository changlog - note that this will not be a valid changset revision.
-                return '000000000000'
+                return INITIAL_CHANGELOG_HASH
         else:
             previous_changeset_revision = current_changeset_revision
 def get_repository( trans, id ):
@@ -640,29 +660,6 @@
         return "%s:%s" % ( str( ctx.rev() ), changeset_revision )
     else:
         return "-1:%s" % changeset_revision
-def get_sample_files( repo, repo_dir, dir ):
-    """Return a list of all files in the repository with the special .sample extension"""
-    sample_files = []
-    # Copy all discovered sample files to dir, and the caller will set the value of app.config.tool_data_path to dir
-    # in order to load the tools and generate metadata for them.  First look on disk.
-    for root, dirs, files in os.walk( repo_dir ):
-        if root.find( '.hg' ) < 0:
-            for name in files:
-                if name.endswith( '.sample' ) and name not in sample_files:
-                    new_name = name.replace( '.sample', '' )
-                    file_path = os.path.join( dir, new_name )
-                    shutil.copy( os.path.abspath( os.path.join( root, name ) ), file_path )
-                    sample_files.append( name )
-    # Next look in the repository manifest.
-    for changeset in repo.changelog:
-        ctx = repo.changectx( changeset )
-        for ctx_file in ctx.files():
-            ctx_file_name = strip_path( ctx_file )
-            if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files:
-                new_ctx_file_name = ctx_file_name.replace( '.sample', '' )
-                copy_file_from_manifest( repo, ctx, ctx_file, dir )
-                sample_files.append( ctx_file_name )
-    return sample_files
 def get_user( trans, id ):
     """Get a user from the database by id"""
     return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) )
@@ -796,7 +793,7 @@
             tool = load_tool( trans, tmp_tool_config )
         except Exception, e:
             tool = None
-            message = "Error loading tool: %s.  Clicking <b>Reset metadata</b> may correct this error." % str( e )
+            message = "Error loading tool: %s.  " % str( e )
         for tmp_code_file in tmp_code_files:
             try:
                 os.unlink( tmp_code_file )
@@ -819,40 +816,19 @@
     tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir )
     if tool_data_table_config:
         error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config )
-    if changeset_revision == repository.tip:
-        # Load the tool fron it's config file on disk.
-        try:
-            copied_tool_config = copy_file_from_disk( tool_config_filename, repo_files_dir, work_dir )
-            tool = load_tool( trans, copied_tool_config )
-        except Exception, e:
-            tool = None
-            message = "Error loading tool from config '%s': %s." % ( tool_config_filename, str( e ) )
-    else:
-        found = False
-        tool = None
-        # Get the tool config from ctx if present.
-        for ctx_file in ctx.files():
+    found = False
+    # Get the latest revision of the tool config from the repository manifest up to the value of changeset_revision.
+    for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
+        manifest_changeset_revision = str( repo.changectx( changeset ) )
+        manifest_ctx = repo.changectx( changeset )
+        for ctx_file in manifest_ctx.files():
             ctx_file_name = strip_path( ctx_file )
             if ctx_file_name == tool_config_filename:
                 found = True
                 break
         if found:
-            if found:
-                tool, message = load_from_tmp_config( ctx, ctx_file, work_dir )
-        else:
-            # Get the tool config from the repository manifest between valid changeset revisions.
-            previous_valid_changset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision )
-            for changeset in reversed_filtered_changelog( repo, previous_valid_changset_revision, changeset_revision ):
-                manifest_changeset_revision = str( repo.changectx( changeset ) )
-                manifest_ctx = repo.changectx( changeset )
-                for ctx_file in manifest_ctx.files():
-                    ctx_file_name = strip_path( ctx_file )
-                    if ctx_file_name == tool_config_filename:
-                        found = True
-                        break
-                if found:
-                    tool, message = load_from_tmp_config( manifest_ctx, ctx_file, work_dir )
-                    break
+            tool, message = load_from_tmp_config( manifest_ctx, ctx_file, work_dir )
+            break
     # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
     reset_tool_data_tables( trans.app )
     try:
@@ -968,6 +944,7 @@
     log.debug( "Resetting all metadata on repository: %s" % repository.name )
     repo_dir = repository.repo_path
     repo = hg.repository( get_configured_ui(), repo_dir )
+    missing_sample_files = []
     if len( repo ) == 1:
         error_message, status = set_repository_metadata( trans, id, repository.tip, **kwd )
         if error_message:
@@ -983,13 +960,16 @@
         for changeset in repo.changelog:
             current_changeset_revision = str( repo.changectx( changeset ) )
             ctx = get_changectx_for_changeset( repo, current_changeset_revision )
-            current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans,
-                                                                                             repo,
-                                                                                             id,
-                                                                                             ctx,
-                                                                                             current_changeset_revision,
-                                                                                             repo_dir,
-                                                                                             updating_tip=current_changeset_revision==repository.tip )
+            current_metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans,
+                                                                                                                   repo,
+                                                                                                                   id,
+                                                                                                                   ctx,
+                                                                                                                   current_changeset_revision,
+                                                                                                                   repo_dir,
+                                                                                                                   updating_tip=current_changeset_revision==repository.tip )
+            for deleted_sample_file in deleted_sample_files:
+                if deleted_sample_file not in missing_sample_files:
+                    missing_sample_files.append( deleted_sample_file )
             if current_metadata_dict:
                 if ancestor_changeset_revision:
                     # Compare metadata from ancestor and current.  The value of comparsion will be one of:
@@ -1032,27 +1012,12 @@
                 ancestor_metadata_dict = None
         clean_repository_metadata( trans, id, changeset_revisions )
         add_repository_metadata_tool_versions( trans, id, changeset_revisions )
+    if missing_sample_files:
+        message += "Metadata was successfully reset, but the following required sample files have been deleted from the repository so the version "
+        message += "of each file just prior to its deletion is being used.  These files should be re-added to the repository as soon as possible:  "
+        message += "<b>%s</b><br/>" % ', '.join( missing_sample_files )
+        return message, 'ok'
     return '', 'ok'
-def reversed_filtered_changelog( repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision ):
-    """
-    Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and
-    including the included_upper_bounds_changeset_revision.  The value of excluded_lower_bounds_changeset_revision will be '000000000000'
-    if no valid changesets exist before included_upper_bounds_changeset_revision.
-    """
-    if excluded_lower_bounds_changeset_revision == '000000000000':
-        appending_started = True
-    else:
-        appending_started = False
-    reversed_changelog = []
-    for changeset in repo.changelog:
-        changeset_hash = str( repo.changectx( changeset ) )
-        if appending_started:
-            reversed_changelog.insert( 0, changeset )
-        if changeset_hash == excluded_lower_bounds_changeset_revision and not appending_started:
-            appending_started = True
-        if changeset_hash == included_upper_bounds_changeset_revision:
-            break
-    return reversed_changelog
 def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ):
     """
     Set repository metadata on the repository tip, returning specific error messages (if any) to alert the repository owner that the changeset
@@ -1068,13 +1033,13 @@
     invalid_files = []
     updating_tip = changeset_revision == repository.tip
     if ctx is not None:
-        metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans,
-                                                                                 repo,
-                                                                                 id,
-                                                                                 ctx,
-                                                                                 changeset_revision,
-                                                                                 repo_dir,
-                                                                                 updating_tip=updating_tip )
+        metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans,
+                                                                                                       repo,
+                                                                                                       id,
+                                                                                                       ctx,
+                                                                                                       changeset_revision,
+                                                                                                       repo_dir,
+                                                                                                       updating_tip=updating_tip )
         if metadata_dict:
             if updating_tip:
                 if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ):
@@ -1120,6 +1085,10 @@
         # Here ctx is None.
         message = "This repository does not include revision '%s'." % str( changeset_revision )
         status = 'error'
+    if deleted_sample_files:
+        message += "Metadata was successfully reset, but the following required sample files have been deleted from the repository so the version "
+        message += "of each file just prior to its deletion is being used.  These files should be re-added to the repository as soon as possible:  "
+        message += "<b>%s</b><br/>" % ', '.join( deleted_sample_files )
     if invalid_files:
         if metadata_dict:
             message = "Metadata was defined for some items in revision '%s'.  " % str( changeset_revision )
diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/hg.py
--- a/lib/galaxy/webapps/community/controllers/hg.py
+++ b/lib/galaxy/webapps/community/controllers/hg.py
@@ -27,8 +27,10 @@
                 repository = get_repository_by_name_and_owner( trans, name, owner )
                 if repository:
                     error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) )
-                    if error_message:
-                        log.debug( "Error resetting all metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) )
+                    if status not in [ 'ok' ] and error_message:
+                        log.debug( "Error resetting metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) )
+                    elif status in [ 'ok' ] and error_message:
+                        log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( str( repository.name ), str( error_message ) ) )
         return wsgi_app
def make_web_app():
diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -10,7 +10,7 @@
 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 get_changectx_for_changeset, get_configured_ui, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path
+from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_named_tmpfile_from_ctx, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path
 from galaxy.tool_shed.encoding_util import *
 from common import *
@@ -323,17 +323,26 @@
     email_alerts_repository_list_grid = EmailAlertsRepositoryListGrid()
     category_list_grid = CategoryListGrid()
-    @web.expose
-    def index( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        # See if there are any RepositoryMetadata records since menu items require them.
-        repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first()
-        return trans.fill_template( '/webapps/community/index.mako',
-                                    repository_metadata=repository_metadata,
-                                    message=message,
-                                    status=status )
+    def __add_hgweb_config_entry( self, trans, repository, repository_path ):
+        # Add an entry in the hgweb.config file for a new repository.  An entry looks something like:
+        # repos/test/mira_assembler = database/community_files/000/repo_123.
+        hgweb_config = "%s/hgweb.config" %  trans.app.config.root
+        if repository_path.startswith( './' ):
+            repository_path = repository_path.replace( './', '', 1 )
+        entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path )
+        tmp_fd, tmp_fname = tempfile.mkstemp()
+        if os.path.exists( hgweb_config ):
+            # Make a backup of the hgweb.config file since we're going to be changing it.
+            self.__make_hgweb_config_copy( trans, hgweb_config )
+            new_hgweb_config = open( tmp_fname, 'wb' )
+            for i, line in enumerate( open( hgweb_config ) ):
+                new_hgweb_config.write( line )
+        else:
+            new_hgweb_config = open( tmp_fname, 'wb' )
+            new_hgweb_config.write( '[paths]\n' )
+        new_hgweb_config.write( "%s\n" % entry )
+        new_hgweb_config.flush()
+        shutil.move( tmp_fname, os.path.abspath( hgweb_config ) )
     @web.expose
     def browse_categories( self, trans, **kwd ):
         if 'f-free-text-search' in kwd:
@@ -360,9 +369,146 @@
                 return trans.response.send_redirect( web.url_for( controller='repository',
                                                                   action='browse_repositories',
                                                                   **kwd ) )
-        # Render the list view
         return self.category_list_grid( trans, **kwd )
     @web.expose
+    def browse_invalid_tools( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
+        cntrller = params.get( 'cntrller', 'repository' )
+        is_admin = trans.user_is_admin()
+        invalid_tools_dict = odict()
+        if is_admin and cntrller == 'admin':
+            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 ):
+                for downloadable_revision in repository.downloadable_revisions:
+                    metadata = downloadable_revision.metadata
+                    invalid_tools = metadata.get( 'invalid_tools', [] )
+                    for invalid_tool_config in invalid_tools:
+                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
+        else:
+            for repository in trans.sa_session.query( trans.model.Repository ) \
+                                              .filter( and_( trans.model.Repository.table.c.deleted == False,
+                                                             trans.model.Repository.table.c.user_id == trans.user.id ) ) \
+                                              .order_by( trans.model.Repository.table.c.name ):
+                for downloadable_revision in repository.downloadable_revisions:
+                    metadata = downloadable_revision.metadata
+                    invalid_tools = metadata.get( 'invalid_tools', [] )
+                    for invalid_tool_config in invalid_tools:
+                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
+        return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako',
+                                    cntrller=cntrller,
+                                    invalid_tools_dict=invalid_tools_dict,
+                                    webapp=webapp,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    def browse_repositories( self, trans, **kwd ):
+        # We add params to the keyword dict in this method in order to rename the param
+        # with an "f-" prefix, simulating filtering by clicking a search link.  We have
+        # to take this approach because the "-" character is illegal in HTTP requests.
+        if 'webapp' not in kwd:
+            kwd[ 'webapp' ] = 'community'
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if operation == "view_or_manage_repository":
+                repository_id = kwd[ 'id' ]
+                repository = get_repository( trans, repository_id )
+                is_admin = trans.user_is_admin()
+                if is_admin or repository.user == trans.user:
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action='manage_repository',
+                                                                      **kwd ) )
+                else:
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action='view_repository',
+                                                                      **kwd ) )
+            elif operation == "edit_repository":
+                return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                  action='edit_repository',
+                                                                  **kwd ) )
+            elif operation == "repositories_by_user":
+                # Eliminate the current filters if any exist.
+                for k, v in kwd.items():
+                    if k.startswith( 'f-' ):
+                        del kwd[ k ]
+                if 'user_id' in kwd:
+                    user = get_user( trans, kwd[ 'user_id' ] )
+                    kwd[ 'f-email' ] = user.email
+                    del kwd[ 'user_id' ]
+                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 )
+                    kwd[ 'f-email' ] = repository.user.email
+            elif operation == "my_repositories":
+                # Eliminate the current filters if any exist.
+                for k, v in kwd.items():
+                    if k.startswith( 'f-' ):
+                        del kwd[ k ]
+                kwd[ 'f-email' ] = trans.user.email
+            elif operation == "repositories_by_category":
+                # Eliminate the current filters if any exist.
+                for k, v in kwd.items():
+                    if k.startswith( 'f-' ):
+                        del kwd[ k ]
+                category_id = kwd.get( 'id', None )
+                category = get_category( trans, category_id )
+                kwd[ 'f-Category.name' ] = category.name
+            elif operation == "receive email alerts":
+                if trans.user:
+                    if kwd[ 'id' ]:
+                        kwd[ 'caller' ] = 'browse_repositories'
+                        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                          action='set_email_alerts',
+                                                                          **kwd ) )
+                else:
+                    kwd[ 'message' ] = 'You must be logged in to set email alerts.'
+                    kwd[ 'status' ] = 'error'
+                    del kwd[ 'operation' ]
+        # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change
+        # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc.  One
+        # of the many select fields on the grid performed the refresh_on_change, so we loop through 
+        # all of the received values to see which value is not the repository tip.  If we find it, we
+        # know the refresh_on_change occurred, and we have the necessary repository id and change set
+        # revision to pass on.
+        for k, v in kwd.items():
+            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 )
+                if repository.tip != v:
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action='browse_repositories',
+                                                                      operation='view_or_manage_repository',
+                                                                      id=trans.security.encode_id( repository.id ),
+                                                                      changeset_revision=v ) )
+        return self.repository_list_grid( trans, **kwd )
+    @web.expose
+    def browse_repository( self, trans, id, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
+        commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
+        repository = get_repository( trans, id )
+        repo = hg.repository( get_configured_ui(), repository.repo_path )
+        current_working_dir = os.getcwd()
+        # Update repository files for browsing.
+        update_repository( repo )
+        is_malicious = changeset_is_malicious( trans, id, repository.tip )
+        return trans.fill_template( '/webapps/community/repository/browse_repository.mako',
+                                    repo=repo,
+                                    repository=repository,
+                                    commit_message=commit_message,
+                                    is_malicious=is_malicious,
+                                    webapp=webapp,
+                                    message=message,
+                                    status=status )
+    @web.expose
     def browse_valid_repositories( self, trans, **kwd ):
         webapp = kwd.get( 'webapp', 'community' )
         galaxy_url = kwd.get( 'galaxy_url', None )
@@ -404,40 +550,400 @@
                                                                             allow_multiple=False,
                                                                             async_compatible=False ) ]
         return self.valid_repository_list_grid( trans, **kwd )
+    def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ):
+        options = []
+        for user in trans.sa_session.query( trans.model.User ):
+            if user.username not in current_push_list:
+                options.append( user )
+        return build_select_field( trans,
+                                   objs=options,
+                                   label_attr='username',
+                                   select_field_name='allow_push',
+                                   selected_value=selected_value,
+                                   refresh_on_change=False,
+                                   multiple=True )
+    def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ):
+        # Change an entry in the hgweb.config file for a repository.  This only happens when
+        # the owner changes the name of the repository.  An entry looks something like:
+        # repos/test/mira_assembler = database/community_files/000/repo_123.
+        hgweb_config = "%s/hgweb.config" % trans.app.config.root
+        # Make a backup of the hgweb.config file since we're going to be changing it.
+        self.__make_hgweb_config_copy( trans, hgweb_config )
+        repo_dir = repository.repo_path
+        old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name )
+        new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir )
+        tmp_fd, tmp_fname = tempfile.mkstemp()
+        new_hgweb_config = open( tmp_fname, 'wb' )
+        for i, line in enumerate( open( hgweb_config ) ):
+            if line.startswith( old_lhs ):
+                new_hgweb_config.write( new_entry )
+            else:
+                new_hgweb_config.write( line )
+        new_hgweb_config.flush()
+        shutil.move( tmp_fname, os.path.abspath( hgweb_config ) )
     @web.expose
-    def browse_invalid_tools( self, trans, **kwd ):
+    def check_for_updates( self, trans, **kwd ):
+        """
+        Handle a request from a local Galaxy instance.  If the request originated with the Galaxy instances' UpdateManager, the value of 'webapp'
+        will be 'update_manager'.
+        """
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        # If the request originated with the UpdateManager, it will not include a galaxy_url.
+        galaxy_url = kwd.get( 'galaxy_url', '' )
+        name = params.get( 'name', None )
+        owner = params.get( 'owner', None )
+        changeset_revision = params.get( 'changeset_revision', None )
+        webapp = params.get( 'webapp', 'community' )
+        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repo_dir = repository.repo_path
+        repo = hg.repository( get_configured_ui(), repo_dir )
+        from_update_manager = webapp == 'update_manager'
+        if from_update_manager:
+            update = 'true'
+            no_update = 'false'
+        else:
+            # Start building up the url to redirect back to the calling Galaxy instance.
+            url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) )
+            url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % ( repository.name, repository.user.username, changeset_revision )
+        if changeset_revision == repository.tip:
+            # If changeset_revision is the repository tip, we know there are no additional updates for the tools.
+            if from_update_manager:
+                return no_update
+            # Return the same value for changeset_revision and latest_changeset_revision.
+            url += repository.tip
+        else:
+            repository_metadata = get_repository_metadata_by_changeset_revision( trans, 
+                                                                                 trans.security.encode_id( repository.id ),
+                                                                                 changeset_revision )
+            if repository_metadata:
+                # If changeset_revision is in the repository_metadata table for this repository, then we know there are no additional updates
+                # for the tools.
+                if from_update_manager:
+                    return no_update
+                else:
+                    # Return the same value for changeset_revision and latest_changeset_revision.
+                    url += changeset_revision
+            else:
+                # TODO: Re-engineer this to define the change set for update to be the one just before the next change set in the repository_metadata
+                # table for this repository.
+                # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the
+                # repository was cloned.  Load each tool in the repository's changeset_revision to generate a list of tool guids, since guids
+                # differentiate tools by id and version.
+                ctx = get_changectx_for_changeset( repo, changeset_revision )
+                if ctx is not None:
+                    work_dir = make_tmp_directory()
+                    tool_guids = []
+                    for filename in ctx:
+                        # Find all tool configs in this repository changeset_revision.
+                        if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ):
+                            is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans,
+                                                                                                       repo,
+                                                                                                       repo_dir,
+                                                                                                       ctx,
+                                                                                                       filename,
+                                                                                                       work_dir )
+                            if valid and tool is not None:
+                                tool_guids.append( generate_tool_guid( trans, repository, tool ) )
+                    tool_guids.sort()
+                    if tool_guids:
+                        # Compare our list of tool guids against those in each repository_metadata record for the repository to find the
+                        # repository_metadata record with the changeset_revision value we want to pass back to the caller.
+                        found = False
+                        for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ):
+                            metadata = repository_metadata.metadata
+                            metadata_tool_guids = []
+                            for tool_dict in metadata[ 'tools' ]:
+                                metadata_tool_guids.append( tool_dict[ 'guid' ] )
+                            metadata_tool_guids.sort()
+                            if tool_guids == metadata_tool_guids:
+                                # We've found the repository_metadata record whose changeset_revision value has been updated.
+                                if from_update_manager:
+                                    return update
+                                url += repository_metadata.changeset_revision
+                                # Get the ctx_rev for the discovered changeset_revision.
+                                latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
+                                found = True
+                                break
+                        if not found:
+                            # There must be a problem in the data, so we'll just send back the received changeset_revision.
+                            log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id )
+                            if from_update_manager:
+                                return no_update
+                            url += changeset_revision
+                    else:
+                        # There are no tools in the changeset_revision, so no tool updates are possible.
+                        if from_update_manager:
+                            return no_update
+                        url += changeset_revision
+                    try:
+                        shutil.rmtree( work_dir )
+                    except:
+                        pass
+        url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
+        return trans.response.send_redirect( url )
+    @web.expose
+    def contact_owner( self, trans, id, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        repository = get_repository( trans, id )
+        if trans.user and trans.user.email:
+            return trans.fill_template( "/webapps/community/repository/contact_owner.mako",
+                                        repository=repository,
+                                        message=message,
+                                        status=status )
+        else:
+            # Do all we can to eliminate spam.
+            return trans.show_error_message( "You must be logged in to contact the owner of a repository." )
+    def __create_hgrc_file( self, repository ):
+        # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path.
+        # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api.
+        # The hg purge extension purges all files and directories not being tracked by mercurial in the current repository.  It'll
+        # remove unknown files and empty directories.  This is not currently used because it is not supported in the mercurial API.
+        repo = hg.repository( get_configured_ui(), path=repository.repo_path )
+        fp = repo.opener( 'hgrc', 'wb' )
+        fp.write( '[paths]\n' )
+        fp.write( 'default = .\n' )
+        fp.write( 'default-push = .\n' )
+        fp.write( '[web]\n' )
+        fp.write( 'allow_push = %s\n' % repository.user.username )
+        fp.write( 'name = %s\n' % repository.name )
+        fp.write( 'push_ssl = false\n' )
+        fp.write( '[extensions]\n' )
+        fp.write( 'hgext.purge=' )
+        fp.close()
+    @web.expose
+    def create_repository( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        categories = get_categories( trans )
+        if not categories:
+            message = 'No categories have been configured in this instance of the Galaxy Tool Shed.  ' + \
+                'An administrator needs to create some via the Administrator control panel before creating repositories.',
+            status = 'error'
+            return trans.response.send_redirect( web.url_for( controller='repository',
+                                                              action='browse_repositories',
+                                                              message=message,
+                                                              status=status ) )
+        name = util.restore_text( params.get( 'name', '' ) )
+        description = util.restore_text( params.get( 'description', '' ) )
+        long_description = util.restore_text( params.get( 'long_description', '' ) )
+        category_ids = util.listify( params.get( 'category_id', '' ) )
+        selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
+        if params.get( 'create_repository_button', False ):
+            error = False
+            message = self.__validate_repository_name( name, trans.user )
+            if message:
+                error = True
+            if not description:
+                message = 'Enter a description.'
+                error = True
+            if not error:
+                # Add the repository record to the db
+                repository = trans.app.model.Repository( name=name,
+                                                         description=description,
+                                                         long_description=long_description,
+                                                         user_id=trans.user.id )
+                # Flush to get the id
+                trans.sa_session.add( repository )
+                trans.sa_session.flush()
+                # Determine the repository's repo_path on disk
+                dir = os.path.join( trans.app.config.file_path, *directory_hash_id( repository.id ) )
+                # Create directory if it does not exist
+                if not os.path.exists( dir ):
+                    os.makedirs( dir )
+                # Define repo name inside hashed directory
+                repository_path = os.path.join( dir, "repo_%d" % repository.id )
+                # Create local repository directory
+                if not os.path.exists( repository_path ):
+                    os.makedirs( repository_path )
+                # Create the local repository
+                repo = hg.repository( get_configured_ui(), repository_path, create=True )
+                # Add an entry in the hgweb.config file for the local repository
+                # This enables calls to repository.repo_path
+                self.__add_hgweb_config_entry( trans, repository, repository_path )
+                # Create a .hg/hgrc file for the local repository
+                self.__create_hgrc_file( repository )
+                flush_needed = False
+                if category_ids:
+                    # Create category associations
+                    for category_id in category_ids:
+                        category = trans.app.model.Category.get( trans.security.decode_id( category_id ) )
+                        rca = trans.app.model.RepositoryCategoryAssociation( repository, category )
+                        trans.sa_session.add( rca )
+                        flush_needed = True
+                if flush_needed:
+                    trans.sa_session.flush()
+                message = "Repository '%s' has been created." % repository.name
+                trans.response.send_redirect( web.url_for( controller='repository',
+                                                           action='view_repository',
+                                                           webapp='community',
+                                                           message=message,
+                                                           id=trans.security.encode_id( repository.id ) ) )
+        return trans.fill_template( '/webapps/community/repository/create_repository.mako',
+                                    name=name,
+                                    description=description,
+                                    long_description=long_description,
+                                    selected_categories=selected_categories,
+                                    categories=categories,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         webapp = params.get( 'webapp', 'community' )
-        cntrller = params.get( 'cntrller', 'repository' )
-        is_admin = trans.user_is_admin()
-        invalid_tools_dict = odict()
-        if is_admin and cntrller == 'admin':
-            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 ):
-                for downloadable_revision in repository.downloadable_revisions:
-                    metadata = downloadable_revision.metadata
-                    invalid_tools = metadata.get( 'invalid_tools', [] )
-                    for invalid_tool_config in invalid_tools:
-                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
-        else:
-            for repository in trans.sa_session.query( trans.model.Repository ) \
-                                              .filter( and_( trans.model.Repository.table.c.deleted == False,
-                                                             trans.model.Repository.table.c.user_id == trans.user.id ) ) \
-                                              .order_by( trans.model.Repository.table.c.name ):
-                for downloadable_revision in repository.downloadable_revisions:
-                    metadata = downloadable_revision.metadata
-                    invalid_tools = metadata.get( 'invalid_tools', [] )
-                    for invalid_tool_config in invalid_tools:
-                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
-        return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako',
-                                    cntrller=cntrller,
-                                    invalid_tools_dict=invalid_tools_dict,
+        repository = get_repository( trans, repository_id )
+        tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
+        tool_state = self.__new_state( trans )
+        is_malicious = changeset_is_malicious( trans, repository_id, repository.tip )
+        try:
+            return trans.fill_template( "/webapps/community/repository/tool_form.mako",
+                                        repository=repository,
+                                        changeset_revision=changeset_revision,
+                                        tool=tool,
+                                        tool_state=tool_state,
+                                        is_malicious=is_malicious,
+                                        webapp=webapp,
+                                        message=message,
+                                        status=status )
+        except Exception, e:
+            message = "Error displaying tool, probably due to a problem in the tool config.  The exception is: %s." % str( e )
+        if webapp == 'galaxy':
+            return trans.response.send_redirect( web.url_for( controller='repository',
+                                                              action='preview_tools_in_changeset',
+                                                              repository_id=repository_id,
+                                                              changeset_revision=changeset_revision,
+                                                              message=message,
+                                                              status='error' ) )
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action='browse_repositories',
+                                                          operation='view_or_manage_repository',
+                                                          id=repository_id,
+                                                          changeset_revision=changeset_revision,
+                                                          message=message,
+                                                          status='error' ) )
+    @web.expose
+    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 )
+        # Allow hgweb to handle the download.  This requires the tool shed
+        # server account's .hgrc file to include the following setting:
+        # [web]
+        # allow_archive = bz2, gz, zip
+        if file_type == 'zip':
+            file_type_str = '%s.zip' % changeset_revision
+        elif file_type == 'bz2':
+            file_type_str = '%s.tar.bz2' % changeset_revision
+        elif file_type == 'gz':
+            file_type_str = '%s.tar.gz' % changeset_revision
+        repository.times_downloaded += 1
+        trans.sa_session.add( repository )
+        trans.sa_session.flush()
+        download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str )
+        return trans.response.send_redirect( download_url )
+    def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ):
+        repo_info_dict = {}
+        includes_tools = False
+        for repository_metadata_id in repository_metadata_ids:
+            repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+            if not includes_tools and 'tools' in repository_metadata.metadata:
+                includes_tools = True
+            repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+            # Get the changelog rev for this changeset_revision.
+            repo_dir = repository.repo_path
+            repo = hg.repository( get_configured_ui(), repo_dir )
+            changeset_revision = repository_metadata.changeset_revision
+            ctx = get_changectx_for_changeset( repo, changeset_revision )
+            repository_id = trans.security.encode_id( repository.id )
+            repository_clone_url = generate_clone_url( trans, repository_id )
+            repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) )
+        return encode( repo_info_dict ), includes_tools
+    @web.expose
+    def find_tools( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', '' ) )
+        status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
+        galaxy_url = kwd.get( 'galaxy_url', None )
+        if galaxy_url:
+            trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
+        if 'operation' in kwd:
+            item_id = kwd.get( 'id', '' )
+            if item_id:
+                operation = kwd[ 'operation' ].lower()
+                is_admin = trans.user_is_admin()
+                if operation == "view_or_manage_repository":
+                    # 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 )
+                    kwd[ 'id' ] = repository_id
+                    kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
+                    if webapp == 'community' and ( is_admin or repository.user == trans.user ):
+                        a = 'manage_repository'
+                    else:
+                        a = 'view_repository'
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action=a,
+                                                                      **kwd ) )
+                if operation == "install":
+                    galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
+                    encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
+                    url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \
+                        ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) )
+                    return trans.response.send_redirect( url )
+            else:
+                # This can only occur when there is a multi-select grid with check boxes and an operation,
+                # and the user clicked the operation button without checking any of the check boxes.
+                return trans.show_error_message( "No items were selected." )
+        tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ]
+        tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ]
+        tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ]
+        exact_matches = params.get( 'exact_matches', '' )
+        exact_matches_checked = CheckboxField.is_checked( exact_matches )
+        match_tuples = []
+        ok = True
+        if tool_ids or tool_names or tool_versions:
+            ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions )
+            if ok:
+                kwd[ 'match_tuples' ] = match_tuples
+                # Render the list view
+                if webapp == 'galaxy':
+                    # Our initial request originated from a Galaxy instance.
+                    global_actions = [ grids.GridAction( "Browse valid repositories",
+                                                         dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ),
+                                       grids.GridAction( "Search for valid tools",
+                                                         dict( controller='repository', action='find_tools', webapp=webapp ) ),
+                                       grids.GridAction( "Search for workflows",
+                                                         dict( controller='repository', action='find_workflows', webapp=webapp ) ) ]
+                    self.install_matched_repository_list_grid.global_actions = global_actions
+                    install_url_args = dict( controller='repository', action='find_tools', webapp=webapp )
+                    operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ]
+                    self.install_matched_repository_list_grid.operations = operations
+                    return self.install_matched_repository_list_grid( trans, **kwd )
+                else:
+                    kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
+                        ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) )
+                    self.matched_repository_list_grid.title = "Repositories with matching tools"
+                    return self.matched_repository_list_grid( trans, **kwd )
+            else:
+                message = "No search performed - each field must contain the same number of comma-separated items."
+                status = "error"
+        exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
+        return trans.fill_template( '/webapps/community/repository/find_tools.mako',
                                     webapp=webapp,
+                                    tool_id=self.__stringify( tool_ids ),
+                                    tool_name=self.__stringify( tool_names ),
+                                    tool_version=self.__stringify( tool_versions ),
+                                    exact_matches_check_box=exact_matches_check_box,
                                     message=message,
-                                    status=status )     
+                                    status=status )
     @web.expose
     def find_workflows( self, trans, **kwd ):
         params = util.Params( kwd )
@@ -521,160 +1027,127 @@
                                     message=message,
                                     status=status )
     @web.expose
-    def find_tools( self, trans, **kwd ):
+    def get_ctx_rev( self, trans, **kwd ):
+        """Given a repository and changeset_revision, return the correct ctx.rev() value."""
+        repository_name = kwd[ 'name' ]
+        repository_owner = kwd[ 'owner' ]
+        changeset_revision = kwd[ 'changeset_revision' ]
+        repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
+        repo_dir = repository.repo_path
+        repo = hg.repository( get_configured_ui(), repo_dir )
+        ctx = get_changectx_for_changeset( repo, changeset_revision )
+        if ctx:
+            return str( ctx.rev() )
+        return ''
+    @web.json
+    def get_file_contents( self, trans, file_path ):
+        # Avoid caching
+        trans.response.headers['Pragma'] = 'no-cache'
+        trans.response.headers['Expires'] = '0'
+        if is_gzip( file_path ):
+            to_html = to_html_str( '\ngzip compressed file\n' )
+        elif is_bz2( file_path ):
+            to_html = to_html_str( '\nbz2 compressed file\n' )
+        elif check_zip( file_path ):
+            to_html = to_html_str( '\nzip compressed file\n' )
+        elif check_binary( file_path ):
+            to_html = to_html_str( '\nBinary file\n' )
+        else:
+            to_html = ''
+            for i, line in enumerate( open( file_path ) ):
+                to_html = '%s%s' % ( to_html, to_html_str( line ) )
+                if len( to_html ) > MAX_CONTENT_SIZE:
+                    large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
+                    to_html = '%s%s' % ( to_html, to_html_str( large_str ) )
+                    break
+        return to_html
+    def __get_files( self, trans, folder_path ):
+        contents = []
+        for item in os.listdir( folder_path ):
+            # Skip .hg directories
+            if str( item ).startswith( '.hg' ):
+                continue
+            if os.path.isdir( os.path.join( folder_path, item ) ):
+                # Append a '/' character so that our jquery dynatree will
+                # function properly.
+                item = '%s/' % item
+            contents.append( item )
+        if contents:
+            contents.sort()
+        return contents
+    @web.expose
+    def get_readme( self, trans, **kwd ):
+        """If the received changeset_revision includes a file named readme (case ignored), return it's contents."""
+        repository_name = kwd[ 'name' ]
+        repository_owner = kwd[ 'owner' ]
+        changeset_revision = kwd[ 'changeset_revision' ]
+        valid_filenames = [ r for r in README_FILES ]
+        for r in README_FILES:
+            valid_filenames.append( '%s.txt' % r )
+        valid_filenames.append( '%s.txt' % repository_name )
+        repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
+        repo_dir = repository.repo_path
+        for root, dirs, files in os.walk( repo_dir ):
+            for name in files:
+                if name.lower() in valid_filenames:
+                    f = open( os.path.join( root, name ), 'r' )
+                    text = f.read()
+                    f.close()
+                    return str( text )
+        return ''
+    @web.expose
+    def get_tool_dependencies( self, trans, **kwd ):
+        # Handle a request from a local Galaxy instance.  If the request originated with the Galaxy instances' InstallManager, the value of 'webapp'
+        # will be 'install_manager'.
         params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', '' ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
+        # If the request originated with the UpdateManager, it will not include a galaxy_url.
+        galaxy_url = kwd.get( 'galaxy_url', '' )
+        name = params.get( 'name', None )
+        owner = params.get( 'owner', None )
+        changeset_revision = params.get( 'changeset_revision', None )
         webapp = params.get( 'webapp', 'community' )
-        galaxy_url = kwd.get( 'galaxy_url', None )
-        if galaxy_url:
-            trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
-        if 'operation' in kwd:
-            item_id = kwd.get( 'id', '' )
-            if item_id:
-                operation = kwd[ 'operation' ].lower()
-                is_admin = trans.user_is_admin()
-                if operation == "view_or_manage_repository":
-                    # 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 )
-                    kwd[ 'id' ] = repository_id
-                    kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
-                    if webapp == 'community' and ( is_admin or repository.user == trans.user ):
-                        a = 'manage_repository'
-                    else:
-                        a = 'view_repository'
-                    return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                      action=a,
-                                                                      **kwd ) )
-                if operation == "install":
-                    galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
-                    encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
-                    url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \
-                        ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) )
-                    return trans.response.send_redirect( url )
-            else:
-                # This can only occur when there is a multi-select grid with check boxes and an operation,
-                # and the user clicked the operation button without checking any of the check boxes.
-                return trans.show_error_message( "No items were selected." )
-        tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ]
-        tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ]
-        tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ]
-        exact_matches = params.get( 'exact_matches', '' )
-        exact_matches_checked = CheckboxField.is_checked( exact_matches )
-        match_tuples = []
-        ok = True
-        if tool_ids or tool_names or tool_versions:
-            ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions )
-            if ok:
-                kwd[ 'match_tuples' ] = match_tuples
-                # Render the list view
-                if webapp == 'galaxy':
-                    # Our initial request originated from a Galaxy instance.
-                    global_actions = [ grids.GridAction( "Browse valid repositories",
-                                                         dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ),
-                                       grids.GridAction( "Search for valid tools",
-                                                         dict( controller='repository', action='find_tools', webapp=webapp ) ),
-                                       grids.GridAction( "Search for workflows",
-                                                         dict( controller='repository', action='find_workflows', webapp=webapp ) ) ]
-                    self.install_matched_repository_list_grid.global_actions = global_actions
-                    install_url_args = dict( controller='repository', action='find_tools', webapp=webapp )
-                    operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ]
-                    self.install_matched_repository_list_grid.operations = operations
-                    return self.install_matched_repository_list_grid( trans, **kwd )
-                else:
-                    kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
-                        ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) )
-                    self.matched_repository_list_grid.title = "Repositories with matching tools"
-                    return self.matched_repository_list_grid( trans, **kwd )
-            else:
-                message = "No search performed - each field must contain the same number of comma-separated items."
-                status = "error"
-        exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
-        return trans.fill_template( '/webapps/community/repository/find_tools.mako',
-                                    webapp=webapp,
-                                    tool_id=self.__stringify( tool_ids ),
-                                    tool_name=self.__stringify( tool_names ),
-                                    tool_version=self.__stringify( tool_versions ),
-                                    exact_matches_check_box=exact_matches_check_box,
-                                    message=message,
-                                    status=status )
-    def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ):
-        match_tuples = []
-        ok = True
-        for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
-            metadata = repository_metadata.metadata
-            if tool_ids or tool_names or tool_versions:
-                if 'tools' in metadata:
-                    tools = metadata[ 'tools' ]
-                else:
-                    tools = []
-                for tool_dict in tools:
-                    if tool_ids and not tool_names and not tool_versions:
-                        for tool_id in tool_ids:
-                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
-                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                    elif tool_names and not tool_ids and not tool_versions:
-                        for tool_name in tool_names:
-                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
-                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                    elif tool_versions and not tool_ids and not tool_names:
-                        for tool_version in tool_versions:
-                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
-                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                    elif tool_ids and tool_names and not tool_versions:
-                        if len( tool_ids ) == len( tool_names ):
-                            match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
-                        elif len( tool_ids ) == 1 or len( tool_names ) == 1:
-                            tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names )
-                            match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
-                        else:
-                            ok = False
-                    elif tool_ids and tool_versions and not tool_names:
-                        if len( tool_ids )  == len( tool_versions ):
-                            match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
-                        elif len( tool_ids ) == 1 or len( tool_versions ) == 1:
-                            tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions )
-                            match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
-                        else:
-                            ok = False
-                    elif tool_versions and tool_names and not tool_ids:
-                        if len( tool_versions ) == len( tool_names ):
-                            match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
-                        elif len( tool_versions ) == 1 or len( tool_names ) == 1:
-                            tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names )
-                            match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
-                        else:
-                            ok = False
-                    elif tool_versions and tool_names and tool_ids:
-                        if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ):
-                            for i, tool_version in enumerate( tool_versions ):
-                                tool_name = tool_names[ i ]
-                                tool_id = tool_ids[ i ]
-                                if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ):
-                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                        else:
-                            ok = False
-            elif workflow_names:
-                if 'workflows' in metadata:
-                    # metadata[ 'workflows' ] is a list of tuples where each contained tuple is
-                    # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
-                    workflow_tups = metadata[ 'workflows' ]
-                    workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ]
-                else:
-                    workflows = []
-                for workflow_dict in workflows:
-                    for workflow_name in workflow_names:
-                        if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ):
-                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-            elif all_workflows and 'workflows' in metadata:
-                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-        return ok, match_tuples
-    def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ):
-        workflow_dict_workflow_name = workflow_dict[ 'name' ].lower()
-        return ( workflow_name == workflow_dict_workflow_name ) or \
-               ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 )
+        repository = get_repository_by_name_and_owner( trans, name, owner )
+        for downloadable_revision in repository.downloadable_revisions:
+            if downloadable_revision.changeset_revision == changeset_revision:
+                break
+        metadata = downloadable_revision.metadata
+        tool_dependencies = metadata.get( 'tool_dependencies', '' )
+        if webapp == 'install_manager':
+            if tool_dependencies:
+                return tool_shed_encode( tool_dependencies )
+            return ''
+        # TODO: future handler where request comes from some Galaxy admin feature.
+    @web.expose
+    def get_tool_versions( self, trans, **kwd ):
+        """
+        For each valid /downloadable change set (up to the received changeset_revision) in the repository's change log, append the change
+        set's tool_versions dictionary to the list that will be returned.
+        """
+        name = kwd[ 'name' ]
+        owner = kwd[ 'owner' ]
+        changeset_revision = kwd[ 'changeset_revision' ]
+        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repo_dir = repository.repo_path
+        repo = hg.repository( get_configured_ui(), repo_dir )
+        tool_version_dicts = []
+        for changeset in repo.changelog:
+            current_changeset_revision = str( repo.changectx( changeset ) )
+            repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision )
+            if repository_metadata and repository_metadata.tool_versions:
+                tool_version_dicts.append( repository_metadata.tool_versions )
+                if current_changeset_revision == changeset_revision:
+                    break
+        if tool_version_dicts:
+            return to_json_string( tool_version_dicts )
+        return ''
+    @web.expose
+    def help( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd )
     def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ):
         found = False
         if tool_id and not tool_name and not tool_version:
@@ -716,83 +1189,19 @@
                       tool_dict_tool_name.find( tool_name ) >= 0 and \
                       tool_dict_tool_id.find( tool_id ) >= 0 )
         return found
-    def __stringify( self, list ):
-        if list:
-            return ','.join( list )
-        return ''
-    def __make_same_length( self, list1, list2 ):
-        # If either list is 1 item, we'll append to it until its 
-        # length is the same as the other.
-        if len( list1 ) == 1:
-            for i in range( 1, len( list2 ) ):
-                list1.append( list1[ 0 ] )
-        elif len( list2 ) == 1:
-            for i in range( 1, len( list1 ) ):
-                list2.append( list2[ 0 ] )
-        return list1, list2
-    def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ):
-        for i, tool_id in enumerate( tool_ids ):
-            tool_name = tool_names[ i ]
-            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
-                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-        return match_tuples
-    def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ):
-        for i, tool_id in enumerate( tool_ids ):
-            tool_version = tool_versions[ i ]
-            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
-                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-        return match_tuples
-    def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ):
-        for i, tool_name in enumerate( tool_names ):
-            tool_version = tool_versions[ i ]
-            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ):
-                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-        return match_tuples
-    def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ):
-        repo_info_dict = {}
-        includes_tools = False
-        for repository_metadata_id in repository_metadata_ids:
-            repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
-            if not includes_tools and 'tools' in repository_metadata.metadata:
-                includes_tools = True
-            repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
-            # Get the changelog rev for this changeset_revision.
-            repo_dir = repository.repo_path
-            repo = hg.repository( get_configured_ui(), repo_dir )
-            changeset_revision = repository_metadata.changeset_revision
-            ctx = get_changectx_for_changeset( repo, changeset_revision )
-            repository_id = trans.security.encode_id( repository.id )
-            repository_clone_url = generate_clone_url( trans, repository_id )
-            repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) )
-        return encode( repo_info_dict ), includes_tools
+    def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ):
+        workflow_dict_workflow_name = workflow_dict[ 'name' ].lower()
+        return ( workflow_name == workflow_dict_workflow_name ) or \
+               ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 )
     @web.expose
-    def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
+    def index( self, trans, **kwd ):
         params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', '' ) )
+        message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        webapp = params.get( 'webapp', 'community' )
-        repository = get_repository( 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:
-            repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
-            metadata = repository_metadata.metadata
-        else:
-            repository_metadata_id = None
-            metadata = None
-        revision_label = get_revision_label( trans, repository, changeset_revision )
-        changeset_revision_select_field = build_changeset_revision_select_field( trans,
-                                                                                 repository,
-                                                                                 selected_value=changeset_revision,
-                                                                                 add_id_to_name=False )
-        return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako',
-                                    repository=repository,
-                                    repository_metadata_id=repository_metadata_id,
-                                    changeset_revision=changeset_revision,
-                                    revision_label=revision_label,
-                                    changeset_revision_select_field=changeset_revision_select_field,
-                                    metadata=metadata,
-                                    webapp=webapp,
+        # See if there are any RepositoryMetadata records since menu items require them.
+        repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first()
+        return trans.fill_template( '/webapps/community/index.mako',
+                                    repository_metadata=repository_metadata,
                                     message=message,
                                     status=status )
     @web.expose
@@ -838,633 +1247,117 @@
                 ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ) )
         return trans.response.send_redirect( url )
     @web.expose
-    def get_ctx_rev( self, trans, **kwd ):
-        """Given a repository and changeset_revision, return the correct ctx.rev() value."""
-        repository_name = kwd[ 'name' ]
-        repository_owner = kwd[ 'owner' ]
-        changeset_revision = kwd[ 'changeset_revision' ]
-        repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
+    def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'error' )
+        webapp = params.get( 'webapp', 'community' )
+        repository = get_repository( trans, repository_id )
         repo_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_dir )
         ctx = get_changectx_for_changeset( repo, changeset_revision )
-        if ctx:
-            return str( ctx.rev() )
-        return ''
-    @web.expose
-    def get_readme( self, trans, **kwd ):
-        """If the received changeset_revision includes a file named readme (case ignored), return it's contents."""
-        repository_name = kwd[ 'name' ]
-        repository_owner = kwd[ 'owner' ]
-        changeset_revision = kwd[ 'changeset_revision' ]
-        valid_filenames = [ r for r in README_FILES ]
-        for r in README_FILES:
-            valid_filenames.append( '%s.txt' % r )
-        valid_filenames.append( '%s.txt' % repository_name )
-        repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
-        repo_dir = repository.repo_path
-        for root, dirs, files in os.walk( repo_dir ):
-            for name in files:
-                if name.lower() in valid_filenames:
-                    f = open( os.path.join( root, name ), 'r' )
-                    text = f.read()
-                    f.close()
-                    return str( text )
-        return ''
-    @web.expose
-    def get_tool_versions( self, trans, **kwd ):
-        """
-        For each valid /downloadable change set (up to the received changeset_revision) in the repository's change log, append the change
-        set's tool_versions dictionary to the list that will be returned.
-        """
-        name = kwd[ 'name' ]
-        owner = kwd[ 'owner' ]
-        changeset_revision = kwd[ 'changeset_revision' ]
-        repository = get_repository_by_name_and_owner( trans, name, owner )
-        repo_dir = repository.repo_path
-        repo = hg.repository( get_configured_ui(), repo_dir )
-        tool_version_dicts = []
-        for changeset in repo.changelog:
-            current_changeset_revision = str( repo.changectx( changeset ) )
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision )
-            if repository_metadata and repository_metadata.tool_versions:
-                tool_version_dicts.append( repository_metadata.tool_versions )
-                if current_changeset_revision == changeset_revision:
-                    break
-        if tool_version_dicts:
-            return to_json_string( tool_version_dicts )
-        return ''
-    @web.expose
-    def check_for_updates( self, trans, **kwd ):
-        # Handle a request from a local Galaxy instance.  If the request originated with the
-        # Galaxy instances' UpdateManager, the value of 'webapp' will be 'update_manager'.
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        # If the request originated with the UpdateManager, it will not include a galaxy_url.
-        galaxy_url = kwd.get( 'galaxy_url', '' )
-        name = params.get( 'name', None )
-        owner = params.get( 'owner', None )
-        changeset_revision = params.get( 'changeset_revision', None )
-        webapp = params.get( 'webapp', 'community' )
-        repository = get_repository_by_name_and_owner( trans, name, owner )
-        repo_dir = repository.repo_path
-        repo = hg.repository( get_configured_ui(), repo_dir )
-        latest_ctx = get_changectx_for_changeset( repo, changeset_revision )
-        from_update_manager = webapp == 'update_manager'
-        if from_update_manager:
-            update = 'true'
-            no_update = 'false'
-        else:
-            # Start building up the url to redirect back to the calling Galaxy instance.
-            url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) )
-            url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
-                ( repository.name, repository.user.username, changeset_revision )
-        if changeset_revision == repository.tip:
-            # If changeset_revision is the repository tip, we know there are no additional updates for the tools.
-            if from_update_manager:
-                return no_update
-            # Return the same value for changeset_revision and latest_changeset_revision.
-            url += repository.tip
-        else:
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, 
-                                                                                 trans.security.encode_id( repository.id ),
-                                                                                 changeset_revision )
-            if repository_metadata:
-                # If changeset_revision is in the repository_metadata table for this repository, then we know there are no additional updates
-                # for the tools.
-                if from_update_manager:
-                    return no_update
-                else:
-                    # Return the same value for changeset_revision and latest_changeset_revision.
-                    url += changeset_revision
-            else:
-                # TODO: Re-engineer this to define the change set for update to be the one just before the next change set in the repository_metadata
-                # table for this repository.
-                # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the
-                # repository was cloned.  Load each tool in the repository's changeset_revision to generate a list of tool guids, since guids
-                # differentiate tools by id and version.
-                ctx = get_changectx_for_changeset( repo, changeset_revision )
-                if ctx is not None:
-                    work_dir = make_tmp_directory()
-                    tool_guids = []
-                    for filename in ctx:
-                        # Find all tool configs in this repository changeset_revision.
-                        if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ):
-                            is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans,
+        invalid_message = ''
+        work_dir = make_tmp_directory()
+        for filename in ctx:
+            ctx_file_name = strip_path( filename )
+            if ctx_file_name == tool_config:
+                tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir )
+                break
+        metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans,
                                                                                                        repo,
+                                                                                                       repository_id,
+                                                                                                       ctx,
+                                                                                                       changeset_revision,
                                                                                                        repo_dir,
-                                                                                                       ctx,
-                                                                                                       filename,
-                                                                                                       work_dir )
-                            if valid and tool is not None:
-                                tool_guids.append( generate_tool_guid( trans, repository, tool ) )
-                    tool_guids.sort()
-                    if tool_guids:
-                        # Compare our list of tool guids against those in each repository_metadata record for the repository to find the
-                        # repository_metadata record with the changeset_revision value we want to pass back to the caller.
-                        found = False
-                        for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ):
-                            metadata = repository_metadata.metadata
-                            metadata_tool_guids = []
-                            for tool_dict in metadata[ 'tools' ]:
-                                metadata_tool_guids.append( tool_dict[ 'guid' ] )
-                            metadata_tool_guids.sort()
-                            if tool_guids == metadata_tool_guids:
-                                # We've found the repository_metadata record whose changeset_revision value has been updated.
-                                if from_update_manager:
-                                    return update
-                                url += repository_metadata.changeset_revision
-                                # Get the ctx_rev for the discovered changeset_revision.
-                                latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
-                                found = True
-                                break
-                        if not found:
-                            # There must be a problem in the data, so we'll just send back the received changeset_revision.
-                            log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id )
-                            if from_update_manager:
-                                return no_update
-                            url += changeset_revision
-                    else:
-                        # There are no tools in the changeset_revision, so no tool updates are possible.
-                        if from_update_manager:
-                            return no_update
-                        url += changeset_revision
-                    try:
-                        shutil.rmtree( work_dir )
-                    except:
-                        pass
-        url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
-        return trans.response.send_redirect( url )
-    @web.expose
-    def get_tool_dependencies( self, trans, **kwd ):
-        # Handle a request from a local Galaxy instance.  If the request originated with the Galaxy instances' InstallManager, the value of 'webapp'
-        # will be 'install_manager'.
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        # If the request originated with the UpdateManager, it will not include a galaxy_url.
-        galaxy_url = kwd.get( 'galaxy_url', '' )
-        name = params.get( 'name', None )
-        owner = params.get( 'owner', None )
-        changeset_revision = params.get( 'changeset_revision', None )
-        webapp = params.get( 'webapp', 'community' )
-        repository = get_repository_by_name_and_owner( trans, name, owner )
-        for downloadable_revision in repository.downloadable_revisions:
-            if downloadable_revision.changeset_revision == changeset_revision:
-                break
-        metadata = downloadable_revision.metadata
-        tool_dependencies = metadata.get( 'tool_dependencies', '' )
-        if webapp == 'install_manager':
-            if tool_dependencies:
-                return tool_shed_encode( tool_dependencies )
-            return ''
-        # TODO: future handler where request comes from some Galaxy admin feature.
-    @web.expose
-    def browse_repositories( self, trans, **kwd ):
-        # We add params to the keyword dict in this method in order to rename the param
-        # with an "f-" prefix, simulating filtering by clicking a search link.  We have
-        # to take this approach because the "-" character is illegal in HTTP requests.
-        if 'webapp' not in kwd:
-            kwd[ 'webapp' ] = 'community'
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
-            if operation == "view_or_manage_repository":
-                repository_id = kwd[ 'id' ]
-                repository = get_repository( trans, repository_id )
-                is_admin = trans.user_is_admin()
-                if is_admin or repository.user == trans.user:
-                    return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                      action='manage_repository',
-                                                                      **kwd ) )
-                else:
-                    return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                      action='view_repository',
-                                                                      **kwd ) )
-            elif operation == "edit_repository":
-                return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                  action='edit_repository',
-                                                                  **kwd ) )
-            elif operation == "repositories_by_user":
-                # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
-                    if k.startswith( 'f-' ):
-                        del kwd[ k ]
-                if 'user_id' in kwd:
-                    user = get_user( trans, kwd[ 'user_id' ] )
-                    kwd[ 'f-email' ] = user.email
-                    del kwd[ 'user_id' ]
-                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 )
-                    kwd[ 'f-email' ] = repository.user.email
-            elif operation == "my_repositories":
-                # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
-                    if k.startswith( 'f-' ):
-                        del kwd[ k ]
-                kwd[ 'f-email' ] = trans.user.email
-            elif operation == "repositories_by_category":
-                # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
-                    if k.startswith( 'f-' ):
-                        del kwd[ k ]
-                category_id = kwd.get( 'id', None )
-                category = get_category( trans, category_id )
-                kwd[ 'f-Category.name' ] = category.name
-            elif operation == "receive email alerts":
-                if trans.user:
-                    if kwd[ 'id' ]:
-                        kwd[ 'caller' ] = 'browse_repositories'
-                        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                          action='set_email_alerts',
-                                                                          **kwd ) )
-                else:
-                    kwd[ 'message' ] = 'You must be logged in to set email alerts.'
-                    kwd[ 'status' ] = 'error'
-                    del kwd[ 'operation' ]
-        # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change
-        # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc.  One
-        # of the many select fields on the grid performed the refresh_on_change, so we loop through 
-        # all of the received values to see which value is not the repository tip.  If we find it, we
-        # know the refresh_on_change occurred, and we have the necessary repository id and change set
-        # revision to pass on.
-        for k, v in kwd.items():
-            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 )
-                if repository.tip != v:
-                    return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                      action='browse_repositories',
-                                                                      operation='view_or_manage_repository',
-                                                                      id=trans.security.encode_id( repository.id ),
-                                                                      changeset_revision=v ) )
-        # Render the list view
-        return self.repository_list_grid( trans, **kwd )
-    @web.expose
-    def create_repository( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        categories = get_categories( trans )
-        if not categories:
-            message = 'No categories have been configured in this instance of the Galaxy Tool Shed.  ' + \
-                'An administrator needs to create some via the Administrator control panel before creating repositories.',
-            status = 'error'
+                                                                                                       updating_tip=changeset_revision==repository.tip )
+        for invalid_file_tup in invalid_files:
+            invalid_tool_config, invalid_msg = invalid_file_tup
+            invalid_tool_config_name = strip_path( invalid_tool_config )
+            if tool_config == invalid_tool_config_name:
+                invalid_message = invalid_msg
+                break 
+        tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
+        #if error_message:
+        #    message += error_message
+        tool_state = self.__new_state( trans )
+        is_malicious = changeset_is_malicious( trans, repository_id, repository.tip )
+        try:
+            shutil.rmtree( work_dir )
+        except:
+            pass
+        try:
+            if invalid_message:
+                message = invalid_message
+            return trans.fill_template( "/webapps/community/repository/tool_form.mako",
+                                        repository=repository,
+                                        changeset_revision=changeset_revision,
+                                        tool=tool,
+                                        tool_state=tool_state,
+                                        is_malicious=is_malicious,
+                                        webapp=webapp,
+                                        message=message,
+                                        status='error' )
+        except Exception, e:
+            message = "This tool is invalid because: %s." % str( e )
+        if webapp == 'galaxy':
             return trans.response.send_redirect( web.url_for( controller='repository',
-                                                              action='browse_repositories',
+                                                              action='preview_tools_in_changeset',
+                                                              repository_id=repository_id,
+                                                              changeset_revision=changeset_revision,
                                                               message=message,
-                                                              status=status ) )
-        name = util.restore_text( params.get( 'name', '' ) )
-        description = util.restore_text( params.get( 'description', '' ) )
-        long_description = util.restore_text( params.get( 'long_description', '' ) )
-        category_ids = util.listify( params.get( 'category_id', '' ) )
-        selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
-        if params.get( 'create_repository_button', False ):
-            error = False
-            message = self.__validate_repository_name( name, trans.user )
-            if message:
-                error = True
-            if not description:
-                message = 'Enter a description.'
-                error = True
-            if not error:
-                # Add the repository record to the db
-                repository = trans.app.model.Repository( name=name,
-                                                         description=description,
-                                                         long_description=long_description,
-                                                         user_id=trans.user.id )
-                # Flush to get the id
-                trans.sa_session.add( repository )
-                trans.sa_session.flush()
-                # Determine the repository's repo_path on disk
-                dir = os.path.join( trans.app.config.file_path, *directory_hash_id( repository.id ) )
-                # Create directory if it does not exist
-                if not os.path.exists( dir ):
-                    os.makedirs( dir )
-                # Define repo name inside hashed directory
-                repository_path = os.path.join( dir, "repo_%d" % repository.id )
-                # Create local repository directory
-                if not os.path.exists( repository_path ):
-                    os.makedirs( repository_path )
-                # Create the local repository
-                repo = hg.repository( get_configured_ui(), repository_path, create=True )
-                # Add an entry in the hgweb.config file for the local repository
-                # This enables calls to repository.repo_path
-                self.__add_hgweb_config_entry( trans, repository, repository_path )
-                # Create a .hg/hgrc file for the local repository
-                self.__create_hgrc_file( repository )
-                flush_needed = False
-                if category_ids:
-                    # Create category associations
-                    for category_id in category_ids:
-                        category = trans.app.model.Category.get( trans.security.decode_id( category_id ) )
-                        rca = trans.app.model.RepositoryCategoryAssociation( repository, category )
-                        trans.sa_session.add( rca )
-                        flush_needed = True
-                if flush_needed:
-                    trans.sa_session.flush()
-                message = "Repository '%s' has been created." % repository.name
-                trans.response.send_redirect( web.url_for( controller='repository',
-                                                           action='view_repository',
-                                                           webapp='community',
-                                                           message=message,
-                                                           id=trans.security.encode_id( repository.id ) ) )
-        return trans.fill_template( '/webapps/community/repository/create_repository.mako',
-                                    name=name,
-                                    description=description,
-                                    long_description=long_description,
-                                    selected_categories=selected_categories,
-                                    categories=categories,
-                                    message=message,
-                                    status=status )
-    def __validate_repository_name( self, name, user ):
-        # Repository names must be unique for each user, must be at least four characters
-        # in length and must contain only lower-case letters, numbers, and the '_' character.
-        if name in [ 'None', None, '' ]:
-            return 'Enter the required repository name.'
-        for repository in user.active_repositories:
-            if repository.name == name:
-                return "You already have a repository named '%s', so choose a different name." % name
-        if len( name ) < 4:
-            return "Repository names must be at least 4 characters in length."
-        if len( name ) > 80:
-            return "Repository names cannot be more than 80 characters in length."
-        if not( VALID_REPOSITORYNAME_RE.match( name ) ):
-            return "Repository names must contain only lower-case letters, numbers and underscore '_'."
-        return ''
+                                                              status='error' ) )
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action='browse_repositories',
+                                                          operation='view_or_manage_repository',
+                                                          id=repository_id,
+                                                          changeset_revision=changeset_revision,
+                                                          message=message,
+                                                          status='error' ) )
     def __make_hgweb_config_copy( self, trans, hgweb_config ):
         # Make a backup of the hgweb.config file
         today = date.today()
         backup_date = today.strftime( "%Y_%m_%d" )
         hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date )
         shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) )
-    def __add_hgweb_config_entry( self, trans, repository, repository_path ):
-        # Add an entry in the hgweb.config file for a new repository.  An entry looks something like:
-        # repos/test/mira_assembler = database/community_files/000/repo_123.
-        hgweb_config = "%s/hgweb.config" %  trans.app.config.root
-        if repository_path.startswith( './' ):
-            repository_path = repository_path.replace( './', '', 1 )
-        entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path )
-        tmp_fd, tmp_fname = tempfile.mkstemp()
-        if os.path.exists( hgweb_config ):
-            # Make a backup of the hgweb.config file since we're going to be changing it.
-            self.__make_hgweb_config_copy( trans, hgweb_config )
-            new_hgweb_config = open( tmp_fname, 'wb' )
-            for i, line in enumerate( open( hgweb_config ) ):
-                new_hgweb_config.write( line )
-        else:
-            new_hgweb_config = open( tmp_fname, 'wb' )
-            new_hgweb_config.write( '[paths]\n' )
-        new_hgweb_config.write( "%s\n" % entry )
-        new_hgweb_config.flush()
-        shutil.move( tmp_fname, os.path.abspath( hgweb_config ) )
-    def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ):
-        # Change an entry in the hgweb.config file for a repository.  This only happens when
-        # the owner changes the name of the repository.  An entry looks something like:
-        # repos/test/mira_assembler = database/community_files/000/repo_123.
-        hgweb_config = "%s/hgweb.config" % trans.app.config.root
-        # Make a backup of the hgweb.config file since we're going to be changing it.
-        self.__make_hgweb_config_copy( trans, hgweb_config )
-        repo_dir = repository.repo_path
-        old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name )
-        new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir )
-        tmp_fd, tmp_fname = tempfile.mkstemp()
-        new_hgweb_config = open( tmp_fname, 'wb' )
-        for i, line in enumerate( open( hgweb_config ) ):
-            if line.startswith( old_lhs ):
-                new_hgweb_config.write( new_entry )
-            else:
-                new_hgweb_config.write( line )
-        new_hgweb_config.flush()
-        shutil.move( tmp_fname, os.path.abspath( hgweb_config ) )
-    def __create_hgrc_file( self, repository ):
-        # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path.
-        # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api.
-        # The hg purge extension purges all files and directories not being tracked by mercurial in the current repository.  It'll
-        # remove unknown files and empty directories.  This is not currently used because it is not supported in the mercurial API.
-        repo = hg.repository( get_configured_ui(), path=repository.repo_path )
-        fp = repo.opener( 'hgrc', 'wb' )
-        fp.write( '[paths]\n' )
-        fp.write( 'default = .\n' )
-        fp.write( 'default-push = .\n' )
-        fp.write( '[web]\n' )
-        fp.write( 'allow_push = %s\n' % repository.user.username )
-        fp.write( 'name = %s\n' % repository.name )
-        fp.write( 'push_ssl = false\n' )
-        fp.write( '[extensions]\n' )
-        fp.write( 'hgext.purge=' )
-        fp.close()
+    def __make_same_length( self, list1, list2 ):
+        # If either list is 1 item, we'll append to it until its length is the same as the other.
+        if len( list1 ) == 1:
+            for i in range( 1, len( list2 ) ):
+                list1.append( list1[ 0 ] )
+        elif len( list2 ) == 1:
+            for i in range( 1, len( list1 ) ):
+                list2.append( list2[ 0 ] )
+        return list1, list2
     @web.expose
-    def browse_repository( self, trans, id, **kwd ):
+    @web.require_login( "manage email alerts" )
+    def manage_email_alerts( self, trans, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        webapp = params.get( 'webapp', 'community' )
-        commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
-        repository = get_repository( trans, id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path )
-        current_working_dir = os.getcwd()
-        # Update repository files for browsing.
-        update_repository( repo )
-        is_malicious = changeset_is_malicious( trans, id, repository.tip )
-        return trans.fill_template( '/webapps/community/repository/browse_repository.mako',
-                                    repo=repo,
-                                    repository=repository,
-                                    commit_message=commit_message,
-                                    is_malicious=is_malicious,
-                                    webapp=webapp,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    def contact_owner( self, trans, id, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        repository = get_repository( trans, id )
-        if trans.user and trans.user.email:
-            return trans.fill_template( "/webapps/community/repository/contact_owner.mako",
-                                        repository=repository,
-                                        message=message,
-                                        status=status )
-        else:
-            # Do all we can to eliminate spam.
-            return trans.show_error_message( "You must be logged in to contact the owner of a repository." )
-    @web.expose
-    def send_to_owner( self, trans, id, message='' ):
-        repository = get_repository( trans, id )
-        if not message:
-            message = 'Enter a message'
-            status = 'error'
-        elif trans.user and trans.user.email:
-            smtp_server = trans.app.config.smtp_server
-            from_address = trans.app.config.email_from
-            if smtp_server is None or from_address is None:
-                return trans.show_error_message( "Mail is not configured for this Galaxy tool shed instance" )
-            to_address = repository.user.email
-            # Get the name of the server hosting the tool shed instance.
-            host = trans.request.host
-            # Build the email message
-            body = string.Template( contact_owner_template ) \
-                .safe_substitute( username=trans.user.username,
-                                  repository_name=repository.name,
-                                  email=trans.user.email,
-                                  message=message,
-                                  host=host )
-            subject = "Regarding your tool shed repository named %s" % repository.name
-            # Send it
-            try:
-                util.send_mail( from_address, to_address, subject, body, trans.app.config )
-                message = "Your message has been sent"
-                status = "done"
-            except Exception, e:
-                message = "An error occurred sending your message by email: %s" % str( e )
-                status = "error"
-        else:
-            # Do all we can to eliminate spam.
-            return trans.show_error_message( "You must be logged in to contact the owner of a repository." )
-        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action='contact_owner',
-                                                          id=id,
-                                                          message=message,
-                                                          status=status ) )
-    @web.expose
-    def select_files_to_delete( self, trans, id, **kwd ):
-        params = util.Params( kwd )
-        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 )
-        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', '' ) )
-        if params.get( 'select_files_to_delete_button', False ):
-            if selected_files_to_delete:
-                selected_files_to_delete = selected_files_to_delete.split( ',' )
-                current_working_dir = os.getcwd()
-                # Get the current repository tip.
-                tip = repository.tip
-                for selected_file in selected_files_to_delete:
-                    try:
-                        commands.remove( repo.ui, repo, selected_file, force=True )
-                    except Exception, e:
-                        log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e ))
-                        relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' )
-                        repo.dirstate.remove( relative_selected_file )
-                        repo.dirstate.write()
-                        absolute_selected_file = os.path.abspath( selected_file )
-                        if os.path.isdir( absolute_selected_file ):
-                            try:
-                                os.rmdir( absolute_selected_file )
-                            except OSError, e:
-                                # The directory is not empty
-                                pass
-                        elif os.path.isfile( absolute_selected_file ):
-                            os.remove( absolute_selected_file )
-                            dir = os.path.split( absolute_selected_file )[0]
-                            try:
-                                os.rmdir( dir )
-                            except OSError, e:
-                                # The directory is not empty
-                                pass
-                # Commit the change set.
-                if not commit_message:
-                    commit_message = 'Deleted selected files'
-                commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message )
-                handle_email_alerts( trans, repository )
-                # Update the repository files for browsing.
-                update_repository( repo )
-                # Get the new repository tip.
-                repo = hg.repository( get_configured_ui(), repo_dir )
-                if tip == repository.tip:
-                    message += 'No changes to repository.  '
-                    kwd[ 'message' ] = message
-                    
-                else:
-                    message += 'The selected files were deleted from the repository.  '
-                    kwd[ 'message' ] = message
-                    set_repository_metadata_due_to_new_tip( trans, id, repository, **kwd )
+        new_repo_alert = params.get( 'new_repo_alert', '' )
+        new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert )
+        user = trans.user
+        if params.get( 'new_repo_alert_button', False ):
+            user.new_repo_alert = new_repo_alert_checked
+            trans.sa_session.add( user )
+            trans.sa_session.flush()
+            if new_repo_alert_checked:
+                message = 'You will receive email alerts for all new valid tool shed repositories.'
             else:
-                message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>."
-                status = "error"
-        is_malicious = changeset_is_malicious( trans, id, repository.tip )
-        return trans.fill_template( '/webapps/community/repository/browse_repository.mako',
-                                    repo=repo,
-                                    repository=repository,
-                                    commit_message=commit_message,
-                                    is_malicious=is_malicious,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    def view_repository( self, trans, id, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        repository = get_repository( trans, id )
-        webapp = params.get( 'webapp', 'community' )
-        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 ) )
-        display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) )
-        alerts = params.get( 'alerts', '' )
-        alerts_checked = CheckboxField.is_checked( alerts )
-        if repository.email_alerts:
-            email_alerts = from_json_string( repository.email_alerts )
-        else:
-            email_alerts = []
-        user = trans.user
-        if user and params.get( 'receive_email_alerts_button', False ):
-            flush_needed = False
-            if alerts_checked:
-                if user.email not in email_alerts:
-                    email_alerts.append( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
-                    flush_needed = True
-            else:
-                if user.email in email_alerts:
-                    email_alerts.remove( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
-                    flush_needed = True
-            if flush_needed:
-                trans.sa_session.add( repository )
-                trans.sa_session.flush()
-        checked = alerts_checked or ( user and user.email in email_alerts )
-        alerts_check_box = CheckboxField( 'alerts', checked=checked )
-        changeset_revision_select_field = build_changeset_revision_select_field( trans,
-                                                                                 repository,
-                                                                                 selected_value=changeset_revision,
-                                                                                 add_id_to_name=False )
-        revision_label = get_revision_label( trans, repository, changeset_revision )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
-        if repository_metadata:
-            repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
-            metadata = repository_metadata.metadata
-        else:
-            repository_metadata_id = None
-            metadata = None
-        is_malicious = changeset_is_malicious( trans, id, repository.tip )
-        if is_malicious:
-            if trans.app.security_agent.can_push( trans.user, repository ):
-                message += malicious_error_can_push
-            else:
-                message += malicious_error
-            status = 'error'
-        return trans.fill_template( '/webapps/community/repository/view_repository.mako',
-                                    repo=repo,
-                                    repository=repository,
-                                    repository_metadata_id=repository_metadata_id,
-                                    metadata=metadata,
-                                    avg_rating=avg_rating,
-                                    display_reviews=display_reviews,
-                                    num_ratings=num_ratings,
-                                    alerts_check_box=alerts_check_box,
-                                    changeset_revision=changeset_revision,
-                                    changeset_revision_select_field=changeset_revision_select_field,
-                                    revision_label=revision_label,
-                                    is_malicious=is_malicious,
-                                    webapp=webapp,
+                message = 'You will not receive any email alerts for new valid tool shed repositories.'
+        checked = new_repo_alert_checked or ( user and user.new_repo_alert )
+        new_repo_alert_check_box = CheckboxField( 'new_repo_alert', checked=checked )
+        email_alert_repositories = []
+        for repository in trans.sa_session.query( trans.model.Repository ) \
+                                          .filter( and_( trans.model.Repository.table.c.deleted == False,
+                                                         trans.model.Repository.table.c.email_alerts != None ) ) \
+                                          .order_by( trans.model.Repository.table.c.name ):
+            if user.email in repository.email_alerts:
+                email_alert_repositories.append( repository )
+        return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako",
+                                    webapp='community',
+                                    new_repo_alert_check_box=new_repo_alert_check_box,
+                                    email_alert_repositories=email_alert_repositories,
                                     message=message,
                                     status=status )
     @web.expose
@@ -1621,6 +1514,429 @@
                                     message=message,
                                     status=status )
     @web.expose
+    @web.require_login( "multi select email alerts" )
+    def multi_select_email_alerts( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        if 'webapp' not in kwd:
+            kwd[ 'webapp' ] = 'community'
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if operation == "receive email alerts":
+                if trans.user:
+                    if kwd[ 'id' ]:
+                        kwd[ 'caller' ] = 'multi_select_email_alerts'
+                        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                          action='set_email_alerts',
+                                                                          **kwd ) )
+                else:
+                    kwd[ 'message' ] = 'You must be logged in to set email alerts.'
+                    kwd[ 'status' ] = 'error'
+                    del kwd[ 'operation' ]
+        return self.email_alerts_repository_list_grid( trans, **kwd )
+    def __new_state( self, trans, all_pages=False ):
+        """
+        Create a new `DefaultToolState` for this tool. It will not be initialized
+        with default values for inputs. 
+        
+        Only inputs on the first page will be initialized unless `all_pages` is
+        True, in which case all inputs regardless of page are initialized.
+        """
+        state = DefaultToolState()
+        state.inputs = {}
+        return state
+    @web.json
+    def open_folder( self, trans, repository_id, key ):
+        # The tool shed includes a repository source file browser, which currently depends upon
+        # copies of the hg repository file store in the repo_path for browsing.
+        # Avoid caching
+        trans.response.headers['Pragma'] = 'no-cache'
+        trans.response.headers['Expires'] = '0'
+        repository = trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( repository_id ) )
+        folder_path = key
+        try:
+            files_list = self.__get_files( trans, folder_path )
+        except OSError, e:
+            if str( e ).find( 'No such file or directory' ) >= 0:
+                # We have a repository with no contents.
+                return []
+        folder_contents = []
+        for filename in files_list:
+            is_folder = False
+            if filename and filename[-1] == os.sep:
+                is_folder = True
+            if filename:
+                full_path = os.path.join( folder_path, filename )
+                node = { "title": filename,
+                         "isFolder": is_folder,
+                         "isLazy": is_folder,
+                         "tooltip": full_path,
+                         "key": full_path }
+                folder_contents.append( node )
+        return folder_contents
+    @web.expose
+    def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', '' ) )
+        status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
+        repository = get_repository( 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:
+            repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
+            metadata = repository_metadata.metadata
+        else:
+            repository_metadata_id = None
+            metadata = None
+        revision_label = get_revision_label( trans, repository, changeset_revision )
+        changeset_revision_select_field = build_changeset_revision_select_field( trans,
+                                                                                 repository,
+                                                                                 selected_value=changeset_revision,
+                                                                                 add_id_to_name=False )
+        return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako',
+                                    repository=repository,
+                                    repository_metadata_id=repository_metadata_id,
+                                    changeset_revision=changeset_revision,
+                                    revision_label=revision_label,
+                                    changeset_revision_select_field=changeset_revision_select_field,
+                                    metadata=metadata,
+                                    webapp=webapp,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_login( "rate repositories" )
+    def rate_repository( self, trans, **kwd ):
+        """ Rate a repository and return updated rating data. """
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        id = params.get( 'id', None )
+        if not id:
+            return trans.response.send_redirect( web.url_for( controller='repository',
+                                                              action='browse_repositories',
+                                                              message='Select a repository to rate',
+                                                              status='error' ) )
+        repository = get_repository( 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',
+                                                              action='browse_repositories',
+                                                              message="You are not allowed to rate your own repository",
+                                                              status='error' ) )
+        if params.get( 'rate_button', False ):
+            rating = int( params.get( 'rating', '0' ) )
+            comment = util.restore_text( params.get( 'comment', '' ) )
+            rating = self.rate_item( trans, trans.user, repository, rating, comment )
+        avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model )
+        display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) )
+        rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model )
+        is_malicious = changeset_is_malicious( trans, id, repository.tip )
+        return trans.fill_template( '/webapps/community/repository/rate_repository.mako', 
+                                    repository=repository,
+                                    avg_rating=avg_rating,
+                                    display_reviews=display_reviews,
+                                    num_ratings=num_ratings,
+                                    rra=rra,
+                                    is_malicious=is_malicious,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    def reset_all_metadata( self, trans, id, **kwd ):
+        error_message, status = reset_all_metadata_on_repository( trans, id, **kwd )
+        if error_message:
+            message = error_message
+            status = 'error'
+        else:
+            message = "All repository metadata has been reset."
+            status = 'done'
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action='manage_repository',
+                                                          id=id,
+                                                          message=message,
+                                                          status=status ) )
+    def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ):
+        for i, tool_id in enumerate( tool_ids ):
+            tool_name = tool_names[ i ]
+            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
+                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+        return match_tuples
+    def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ):
+        for i, tool_id in enumerate( tool_ids ):
+            tool_version = tool_versions[ i ]
+            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
+                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+        return match_tuples
+    def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ):
+        for i, tool_name in enumerate( tool_names ):
+            tool_version = tool_versions[ i ]
+            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ):
+                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+        return match_tuples
+    def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ):
+        match_tuples = []
+        ok = True
+        for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
+            metadata = repository_metadata.metadata
+            if tool_ids or tool_names or tool_versions:
+                if 'tools' in metadata:
+                    tools = metadata[ 'tools' ]
+                else:
+                    tools = []
+                for tool_dict in tools:
+                    if tool_ids and not tool_names and not tool_versions:
+                        for tool_id in tool_ids:
+                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_names and not tool_ids and not tool_versions:
+                        for tool_name in tool_names:
+                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_versions and not tool_ids and not tool_names:
+                        for tool_version in tool_versions:
+                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_ids and tool_names and not tool_versions:
+                        if len( tool_ids ) == len( tool_names ):
+                            match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                        elif len( tool_ids ) == 1 or len( tool_names ) == 1:
+                            tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names )
+                            match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                        else:
+                            ok = False
+                    elif tool_ids and tool_versions and not tool_names:
+                        if len( tool_ids )  == len( tool_versions ):
+                            match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                        elif len( tool_ids ) == 1 or len( tool_versions ) == 1:
+                            tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions )
+                            match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                        else:
+                            ok = False
+                    elif tool_versions and tool_names and not tool_ids:
+                        if len( tool_versions ) == len( tool_names ):
+                            match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                        elif len( tool_versions ) == 1 or len( tool_names ) == 1:
+                            tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names )
+                            match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                        else:
+                            ok = False
+                    elif tool_versions and tool_names and tool_ids:
+                        if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ):
+                            for i, tool_version in enumerate( tool_versions ):
+                                tool_name = tool_names[ i ]
+                                tool_id = tool_ids[ i ]
+                                if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ):
+                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                        else:
+                            ok = False
+            elif workflow_names:
+                if 'workflows' in metadata:
+                    # metadata[ 'workflows' ] is a list of tuples where each contained tuple is
+                    # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
+                    workflow_tups = metadata[ 'workflows' ]
+                    workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ]
+                else:
+                    workflows = []
+                for workflow_dict in workflows:
+                    for workflow_name in workflow_names:
+                        if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ):
+                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+            elif all_workflows and 'workflows' in metadata:
+                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+        return ok, match_tuples
+    @web.expose
+    def select_files_to_delete( self, trans, id, **kwd ):
+        params = util.Params( kwd )
+        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 )
+        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', '' ) )
+        if params.get( 'select_files_to_delete_button', False ):
+            if selected_files_to_delete:
+                selected_files_to_delete = selected_files_to_delete.split( ',' )
+                current_working_dir = os.getcwd()
+                # Get the current repository tip.
+                tip = repository.tip
+                for selected_file in selected_files_to_delete:
+                    try:
+                        commands.remove( repo.ui, repo, selected_file, force=True )
+                    except Exception, e:
+                        log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e ))
+                        relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' )
+                        repo.dirstate.remove( relative_selected_file )
+                        repo.dirstate.write()
+                        absolute_selected_file = os.path.abspath( selected_file )
+                        if os.path.isdir( absolute_selected_file ):
+                            try:
+                                os.rmdir( absolute_selected_file )
+                            except OSError, e:
+                                # The directory is not empty
+                                pass
+                        elif os.path.isfile( absolute_selected_file ):
+                            os.remove( absolute_selected_file )
+                            dir = os.path.split( absolute_selected_file )[0]
+                            try:
+                                os.rmdir( dir )
+                            except OSError, e:
+                                # The directory is not empty
+                                pass
+                # Commit the change set.
+                if not commit_message:
+                    commit_message = 'Deleted selected files'
+                commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message )
+                handle_email_alerts( trans, repository )
+                # Update the repository files for browsing.
+                update_repository( repo )
+                # Get the new repository tip.
+                repo = hg.repository( get_configured_ui(), repo_dir )
+                if tip == repository.tip:
+                    message += 'No changes to repository.  '
+                    kwd[ 'message' ] = message
+                    
+                else:
+                    message += 'The selected files were deleted from the repository.  '
+                    kwd[ 'message' ] = message
+                    set_repository_metadata_due_to_new_tip( trans, id, repository, **kwd )
+            else:
+                message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>."
+                status = "error"
+        is_malicious = changeset_is_malicious( trans, id, repository.tip )
+        return trans.fill_template( '/webapps/community/repository/browse_repository.mako',
+                                    repo=repo,
+                                    repository=repository,
+                                    commit_message=commit_message,
+                                    is_malicious=is_malicious,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    def send_to_owner( self, trans, id, message='' ):
+        repository = get_repository( trans, id )
+        if not message:
+            message = 'Enter a message'
+            status = 'error'
+        elif trans.user and trans.user.email:
+            smtp_server = trans.app.config.smtp_server
+            from_address = trans.app.config.email_from
+            if smtp_server is None or from_address is None:
+                return trans.show_error_message( "Mail is not configured for this Galaxy tool shed instance" )
+            to_address = repository.user.email
+            # Get the name of the server hosting the tool shed instance.
+            host = trans.request.host
+            # Build the email message
+            body = string.Template( contact_owner_template ) \
+                .safe_substitute( username=trans.user.username,
+                                  repository_name=repository.name,
+                                  email=trans.user.email,
+                                  message=message,
+                                  host=host )
+            subject = "Regarding your tool shed repository named %s" % repository.name
+            # Send it
+            try:
+                util.send_mail( from_address, to_address, subject, body, trans.app.config )
+                message = "Your message has been sent"
+                status = "done"
+            except Exception, e:
+                message = "An error occurred sending your message by email: %s" % str( e )
+                status = "error"
+        else:
+            # Do all we can to eliminate spam.
+            return trans.show_error_message( "You must be logged in to contact the owner of a repository." )
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action='contact_owner',
+                                                          id=id,
+                                                          message=message,
+                                                          status=status ) )
+    @web.expose
+    @web.require_login( "set email alerts" )
+    def set_email_alerts( self, trans, **kwd ):
+        # Set email alerts for selected repositories
+        # This method is called from multiple grids, so
+        # the caller must be passed.
+        caller = kwd[ 'caller' ]
+        user = trans.user
+        if user:
+            repository_ids = util.listify( kwd.get( 'id', '' ) )
+            total_alerts_added = 0
+            total_alerts_removed = 0
+            flush_needed = False
+            for repository_id in repository_ids:
+                repository = get_repository( trans, repository_id )
+                if repository.email_alerts:
+                    email_alerts = from_json_string( repository.email_alerts )
+                else:
+                    email_alerts = []
+                if user.email in email_alerts:
+                    email_alerts.remove( user.email )
+                    repository.email_alerts = to_json_string( email_alerts )
+                    trans.sa_session.add( repository )
+                    flush_needed = True
+                    total_alerts_removed += 1
+                else:
+                    email_alerts.append( user.email )
+                    repository.email_alerts = to_json_string( email_alerts )
+                    trans.sa_session.add( repository )
+                    flush_needed = True
+                    total_alerts_added += 1
+            if flush_needed:
+                trans.sa_session.flush()
+            message = 'Total alerts added: %d, total alerts removed: %d' % ( total_alerts_added, total_alerts_removed )
+            kwd[ 'message' ] = message
+            kwd[ 'status' ] = 'done'
+        del kwd[ 'operation' ]
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action=caller,
+                                                          **kwd ) )
+    @web.expose
+    @web.require_login( "set repository metadata" )
+    def set_metadata( self, trans, id, ctx_str, **kwd ):
+        malicious = kwd.get( 'malicious', '' )
+        if kwd.get( 'malicious_button', False ):
+            repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, ctx_str )
+            malicious_checked = CheckboxField.is_checked( malicious )
+            repository_metadata.malicious = malicious_checked
+            trans.sa_session.add( repository_metadata )
+            trans.sa_session.flush()
+            if malicious_checked:
+                message = "The repository tip has been defined as malicious."
+            else:
+                message = "The repository tip has been defined as <b>not</b> malicious."
+            status = 'done'
+        else:
+            # The set_metadata_button was clicked
+            message, status = set_repository_metadata( trans, id, ctx_str, **kwd )
+            if not message:
+                message = "Metadata for change set revision '%s' has been reset." % str( ctx_str )
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action='manage_repository',
+                                                          id=id,
+                                                          changeset_revision=ctx_str,
+                                                          malicious=malicious,
+                                                          message=message,
+                                                          status=status ) )
+    def __stringify( self, list ):
+        if list:
+            return ','.join( list )
+        return ''
+    def __validate_repository_name( self, name, user ):
+        # Repository names must be unique for each user, must be at least four characters
+        # in length and must contain only lower-case letters, numbers, and the '_' character.
+        if name in [ 'None', None, '' ]:
+            return 'Enter the required repository name.'
+        for repository in user.active_repositories:
+            if repository.name == name:
+                return "You already have a repository named '%s', so choose a different name." % name
+        if len( name ) < 4:
+            return "Repository names must be at least 4 characters in length."
+        if len( name ) > 80:
+            return "Repository names cannot be more than 80 characters in length."
+        if not( VALID_REPOSITORYNAME_RE.match( name ) ):
+            return "Repository names must contain only lower-case letters, numbers and underscore '_'."
+        return ''
+    @web.expose
     def view_changelog( self, trans, id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
@@ -1694,291 +2010,76 @@
                                     message=message,
                                     status=status )
     @web.expose
-    @web.require_login( "rate repositories" )
-    def rate_repository( self, trans, **kwd ):
-        """ Rate a repository and return updated rating data. """
+    def view_repository( self, trans, id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        id = params.get( 'id', None )
-        if not id:
-            return trans.response.send_redirect( web.url_for( controller='repository',
-                                                              action='browse_repositories',
-                                                              message='Select a repository to rate',
-                                                              status='error' ) )
         repository = get_repository( trans, id )
+        webapp = params.get( 'webapp', 'community' )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
-        if repository.user == trans.user:
-            return trans.response.send_redirect( web.url_for( controller='repository',
-                                                              action='browse_repositories',
-                                                              message="You are not allowed to rate your own repository",
-                                                              status='error' ) )
-        if params.get( 'rate_button', False ):
-            rating = int( params.get( 'rating', '0' ) )
-            comment = util.restore_text( params.get( 'comment', '' ) )
-            rating = self.rate_item( trans, trans.user, repository, rating, comment )
         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 ) )
         display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) )
-        rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model )
+        alerts = params.get( 'alerts', '' )
+        alerts_checked = CheckboxField.is_checked( alerts )
+        if repository.email_alerts:
+            email_alerts = from_json_string( repository.email_alerts )
+        else:
+            email_alerts = []
+        user = trans.user
+        if user and params.get( 'receive_email_alerts_button', False ):
+            flush_needed = False
+            if alerts_checked:
+                if user.email not in email_alerts:
+                    email_alerts.append( user.email )
+                    repository.email_alerts = to_json_string( email_alerts )
+                    flush_needed = True
+            else:
+                if user.email in email_alerts:
+                    email_alerts.remove( user.email )
+                    repository.email_alerts = to_json_string( email_alerts )
+                    flush_needed = True
+            if flush_needed:
+                trans.sa_session.add( repository )
+                trans.sa_session.flush()
+        checked = alerts_checked or ( user and user.email in email_alerts )
+        alerts_check_box = CheckboxField( 'alerts', checked=checked )
+        changeset_revision_select_field = build_changeset_revision_select_field( trans,
+                                                                                 repository,
+                                                                                 selected_value=changeset_revision,
+                                                                                 add_id_to_name=False )
+        revision_label = get_revision_label( trans, repository, changeset_revision )
+        repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+        if repository_metadata:
+            repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
+            metadata = repository_metadata.metadata
+        else:
+            repository_metadata_id = None
+            metadata = None
         is_malicious = changeset_is_malicious( trans, id, repository.tip )
-        return trans.fill_template( '/webapps/community/repository/rate_repository.mako', 
+        if is_malicious:
+            if trans.app.security_agent.can_push( trans.user, repository ):
+                message += malicious_error_can_push
+            else:
+                message += malicious_error
+            status = 'error'
+        return trans.fill_template( '/webapps/community/repository/view_repository.mako',
+                                    repo=repo,
                                     repository=repository,
+                                    repository_metadata_id=repository_metadata_id,
+                                    metadata=metadata,
                                     avg_rating=avg_rating,
                                     display_reviews=display_reviews,
                                     num_ratings=num_ratings,
-                                    rra=rra,
+                                    alerts_check_box=alerts_check_box,
+                                    changeset_revision=changeset_revision,
+                                    changeset_revision_select_field=changeset_revision_select_field,
+                                    revision_label=revision_label,
                                     is_malicious=is_malicious,
+                                    webapp=webapp,
                                     message=message,
                                     status=status )
     @web.expose
-    @web.require_login( "set email alerts" )
-    def set_email_alerts( self, trans, **kwd ):
-        # Set email alerts for selected repositories
-        # This method is called from multiple grids, so
-        # the caller must be passed.
-        caller = kwd[ 'caller' ]
-        user = trans.user
-        if user:
-            repository_ids = util.listify( kwd.get( 'id', '' ) )
-            total_alerts_added = 0
-            total_alerts_removed = 0
-            flush_needed = False
-            for repository_id in repository_ids:
-                repository = get_repository( trans, repository_id )
-                if repository.email_alerts:
-                    email_alerts = from_json_string( repository.email_alerts )
-                else:
-                    email_alerts = []
-                if user.email in email_alerts:
-                    email_alerts.remove( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
-                    trans.sa_session.add( repository )
-                    flush_needed = True
-                    total_alerts_removed += 1
-                else:
-                    email_alerts.append( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
-                    trans.sa_session.add( repository )
-                    flush_needed = True
-                    total_alerts_added += 1
-            if flush_needed:
-                trans.sa_session.flush()
-            message = 'Total alerts added: %d, total alerts removed: %d' % ( total_alerts_added, total_alerts_removed )
-            kwd[ 'message' ] = message
-            kwd[ 'status' ] = 'done'
-        del kwd[ 'operation' ]
-        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action=caller,
-                                                          **kwd ) )
-    @web.expose
-    @web.require_login( "manage email alerts" )
-    def manage_email_alerts( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        new_repo_alert = params.get( 'new_repo_alert', '' )
-        new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert )
-        user = trans.user
-        if params.get( 'new_repo_alert_button', False ):
-            user.new_repo_alert = new_repo_alert_checked
-            trans.sa_session.add( user )
-            trans.sa_session.flush()
-            if new_repo_alert_checked:
-                message = 'You will receive email alerts for all new valid tool shed repositories.'
-            else:
-                message = 'You will not receive any email alerts for new valid tool shed repositories.'
-        checked = new_repo_alert_checked or ( user and user.new_repo_alert )
-        new_repo_alert_check_box = CheckboxField( 'new_repo_alert', checked=checked )
-        email_alert_repositories = []
-        for repository in trans.sa_session.query( trans.model.Repository ) \
-                                          .filter( and_( trans.model.Repository.table.c.deleted == False,
-                                                         trans.model.Repository.table.c.email_alerts != None ) ) \
-                                          .order_by( trans.model.Repository.table.c.name ):
-            if user.email in repository.email_alerts:
-                email_alert_repositories.append( repository )
-        return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako",
-                                    webapp='community',
-                                    new_repo_alert_check_box=new_repo_alert_check_box,
-                                    email_alert_repositories=email_alert_repositories,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    @web.require_login( "manage email alerts" )
-    def multi_select_email_alerts( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        if 'webapp' not in kwd:
-            kwd[ 'webapp' ] = 'community'
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
-            if operation == "receive email alerts":
-                if trans.user:
-                    if kwd[ 'id' ]:
-                        kwd[ 'caller' ] = 'multi_select_email_alerts'
-                        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                          action='set_email_alerts',
-                                                                          **kwd ) )
-                else:
-                    kwd[ 'message' ] = 'You must be logged in to set email alerts.'
-                    kwd[ 'status' ] = 'error'
-                    del kwd[ 'operation' ]
-        return self.email_alerts_repository_list_grid( trans, **kwd )
-    @web.expose
-    @web.require_login( "set repository metadata" )
-    def set_metadata( self, trans, id, ctx_str, **kwd ):
-        malicious = kwd.get( 'malicious', '' )
-        if kwd.get( 'malicious_button', False ):
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, ctx_str )
-            malicious_checked = CheckboxField.is_checked( malicious )
-            repository_metadata.malicious = malicious_checked
-            trans.sa_session.add( repository_metadata )
-            trans.sa_session.flush()
-            if malicious_checked:
-                message = "The repository tip has been defined as malicious."
-            else:
-                message = "The repository tip has been defined as <b>not</b> malicious."
-            status = 'done'
-        else:
-            # The set_metadata_button was clicked
-            message, status = set_repository_metadata( trans, id, ctx_str, **kwd )
-            if not message:
-                message = "Metadata for change set revision '%s' has been reset." % str( ctx_str )
-        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action='manage_repository',
-                                                          id=id,
-                                                          changeset_revision=ctx_str,
-                                                          malicious=malicious,
-                                                          message=message,
-                                                          status=status ) )
-    @web.expose
-    def reset_all_metadata( self, trans, id, **kwd ):
-        error_message, status = reset_all_metadata_on_repository( trans, id, **kwd )
-        if error_message:
-            message = error_message
-        else:
-            message = "All repository metadata has been reset."
-            status = 'done'
-        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action='manage_repository',
-                                                          id=id,
-                                                          message=message,
-                                                          status=status ) )
-    @web.expose
-    def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        webapp = params.get( 'webapp', 'community' )
-        repository = get_repository( trans, repository_id )
-        tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
-        tool_state = self.__new_state( trans )
-        is_malicious = changeset_is_malicious( trans, repository_id, repository.tip )
-        try:
-            return trans.fill_template( "/webapps/community/repository/tool_form.mako",
-                                        repository=repository,
-                                        changeset_revision=changeset_revision,
-                                        tool=tool,
-                                        tool_state=tool_state,
-                                        is_malicious=is_malicious,
-                                        webapp=webapp,
-                                        message=message,
-                                        status=status )
-        except Exception, e:
-            message = "Error displaying tool, probably due to a problem in the tool config.  The exception is: %s." % str( e )
-        if webapp == 'galaxy':
-            return trans.response.send_redirect( web.url_for( controller='repository',
-                                                              action='preview_tools_in_changeset',
-                                                              repository_id=repository_id,
-                                                              changeset_revision=changeset_revision,
-                                                              message=message,
-                                                              status='error' ) )
-        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action='browse_repositories',
-                                                          operation='view_or_manage_repository',
-                                                          id=repository_id,
-                                                          changeset_revision=changeset_revision,
-                                                          message=message,
-                                                          status='error' ) )
-    @web.expose
-    def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'error' )
-        webapp = params.get( 'webapp', 'community' )
-        repository = get_repository( trans, repository_id )
-        repo_dir = repository.repo_path
-        repo = hg.repository( get_configured_ui(), repo_dir )
-        ctx = get_changectx_for_changeset( repo, changeset_revision )
-        invalid_message = ''
-        work_dir = make_tmp_directory()
-        for filename in ctx:
-            ctx_file_name = strip_path( filename )
-            if ctx_file_name == tool_config:
-                tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir )
-                break
-        metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans,
-                                                                                 repo,
-                                                                                 repository_id,
-                                                                                 ctx,
-                                                                                 changeset_revision,
-                                                                                 repo_dir,
-                                                                                 updating_tip=changeset_revision==repository.tip )
-        for invalid_file_tup in invalid_files:
-            invalid_tool_config, invalid_msg = invalid_file_tup
-            invalid_tool_config_name = strip_path( invalid_tool_config )
-            if tool_config == invalid_tool_config_name:
-                invalid_message = invalid_msg
-                break 
-        tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
-        if error_message:
-            message += error_message
-        tool_state = self.__new_state( trans )
-        is_malicious = changeset_is_malicious( trans, repository_id, repository.tip )
-        try:
-            shutil.rmtree( work_dir )
-        except:
-            pass
-        try:
-            if invalid_message:
-                message = invalid_message
-            return trans.fill_template( "/webapps/community/repository/tool_form.mako",
-                                        repository=repository,
-                                        changeset_revision=changeset_revision,
-                                        tool=tool,
-                                        tool_state=tool_state,
-                                        is_malicious=is_malicious,
-                                        webapp=webapp,
-                                        message=message,
-                                        status='error' )
-        except Exception, e:
-            message = "This tool is invalid because: %s." % str( e )
-        if webapp == 'galaxy':
-            return trans.response.send_redirect( web.url_for( controller='repository',
-                                                              action='preview_tools_in_changeset',
-                                                              repository_id=repository_id,
-                                                              changeset_revision=changeset_revision,
-                                                              message=message,
-                                                              status='error' ) )
-        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action='browse_repositories',
-                                                          operation='view_or_manage_repository',
-                                                          id=repository_id,
-                                                          changeset_revision=changeset_revision,
-                                                          message=message,
-                                                          status='error' ) )
-    def __new_state( self, trans, all_pages=False ):
-        """
-        Create a new `DefaultToolState` for this tool. It will not be initialized
-        with default values for inputs. 
-        
-        Only inputs on the first page will be initialized unless `all_pages` is
-        True, in which case all inputs regardless of page are initialized.
-        """
-        state = DefaultToolState()
-        state.inputs = {}
-        return state
-    @web.expose
     def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
@@ -2015,106 +2116,3 @@
                                     webapp=webapp,
                                     message=message,
                                     status=status )
-    @web.expose
-    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 )
-        # Allow hgweb to handle the download.  This requires the tool shed
-        # server account's .hgrc file to include the following setting:
-        # [web]
-        # allow_archive = bz2, gz, zip
-        if file_type == 'zip':
-            file_type_str = '%s.zip' % changeset_revision
-        elif file_type == 'bz2':
-            file_type_str = '%s.tar.bz2' % changeset_revision
-        elif file_type == 'gz':
-            file_type_str = '%s.tar.gz' % changeset_revision
-        repository.times_downloaded += 1
-        trans.sa_session.add( repository )
-        trans.sa_session.flush()
-        download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str )
-        return trans.response.send_redirect( download_url )
-    @web.json
-    def open_folder( self, trans, repository_id, key ):
-        # The tool shed includes a repository source file browser, which currently depends upon
-        # copies of the hg repository file store in the repo_path for browsing.
-        # Avoid caching
-        trans.response.headers['Pragma'] = 'no-cache'
-        trans.response.headers['Expires'] = '0'
-        repository = trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( repository_id ) )
-        folder_path = key
-        try:
-            files_list = self.__get_files( trans, folder_path )
-        except OSError, e:
-            if str( e ).find( 'No such file or directory' ) >= 0:
-                # We have a repository with no contents.
-                return []
-        folder_contents = []
-        for filename in files_list:
-            is_folder = False
-            if filename and filename[-1] == os.sep:
-                is_folder = True
-            if filename:
-                full_path = os.path.join( folder_path, filename )
-                node = { "title": filename,
-                         "isFolder": is_folder,
-                         "isLazy": is_folder,
-                         "tooltip": full_path,
-                         "key": full_path }
-                folder_contents.append( node )
-        return folder_contents
-    def __get_files( self, trans, folder_path ):
-        contents = []
-        for item in os.listdir( folder_path ):
-            # Skip .hg directories
-            if str( item ).startswith( '.hg' ):
-                continue
-            if os.path.isdir( os.path.join( folder_path, item ) ):
-                # Append a '/' character so that our jquery dynatree will
-                # function properly.
-                item = '%s/' % item
-            contents.append( item )
-        if contents:
-            contents.sort()
-        return contents
-    @web.json
-    def get_file_contents( self, trans, file_path ):
-        # Avoid caching
-        trans.response.headers['Pragma'] = 'no-cache'
-        trans.response.headers['Expires'] = '0'
-        if is_gzip( file_path ):
-            to_html = to_html_str( '\ngzip compressed file\n' )
-        elif is_bz2( file_path ):
-            to_html = to_html_str( '\nbz2 compressed file\n' )
-        elif check_zip( file_path ):
-            to_html = to_html_str( '\nzip compressed file\n' )
-        elif check_binary( file_path ):
-            to_html = to_html_str( '\nBinary file\n' )
-        else:
-            to_html = ''
-            for i, line in enumerate( open( file_path ) ):
-                to_html = '%s%s' % ( to_html, to_html_str( line ) )
-                if len( to_html ) > MAX_CONTENT_SIZE:
-                    large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
-                    to_html = '%s%s' % ( to_html, to_html_str( large_str ) )
-                    break
-        return to_html
-    @web.expose
-    def help( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd )
-    def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ):
-        options = []
-        for user in trans.sa_session.query( trans.model.User ):
-            if user.username not in current_push_list:
-                options.append( user )
-        return build_select_field( trans,
-                                   objs=options,
-                                   label_attr='username',
-                                   select_field_name='allow_push',
-                                   selected_value=selected_value,
-                                   refresh_on_change=False,
-                                   multiple=True )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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