commit/galaxy-central: 7 new changesets

11 Apr 2013

7 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/be5107c0321d/
Changeset:   be5107c0321d
Branch:      search
User:        kellrott
Date:        2013-01-15 07:39:31
Summary:     Adding in the starting work for a unified search system.
Affected #:  7 files

diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r be5107c0321d1a7e7ab0221e7feb711932488bb0 lib/galaxy/model/search.py

--- /dev/null
+++ b/lib/galaxy/model/search.py
@@ -0,0 +1,242 @@
+"""
+Classes for implmenting search methods for various data models
+"""
+
+import logging
+from galaxy.model.orm import *
+from galaxy.model import *
+
+from sqlalchemy import or_, and_
+
+log = logging.getLogger( __name__ )
+
+
+"""
+
+The search model is a simplified view of the SQL schema. A search domain 
+typicaly covers a base data table, but it's fields can be constructs of multiple 
+tables that are joined togeather. For example, a History dataset may have tags associated with it.
+The Search class simplifies the joining process between the history dataset and the tags table, 
+and presents the 'tag' field as a single concept that can be filtered against.
+
+
+"""
+
+class SearchField(object):
+
+    def __init__(self, name):
+        self.name = name
+        self.other = None
+        self.mode = None
+
+    def __eq__(self, other ):
+        self.other = other
+        self.mode = "=="
+        return self
+
+    def like(self, other):
+        self.other = other
+        self.mode = "like"
+        return self
+
+class QueryBaseClass(object):
+    OUTPUT_COLUMNS = []
+
+    def __init__(self, base_query):
+        self.query = base_query
+        self.do_query = False
+
+    def get_results(self, force_query=False):
+        if self.query is not None and (force_query or self.do_query):
+            print self.query
+            for row in self.query.distinct().all():
+                out = {}
+                for col in self.OUTPUT_COLUMNS:
+                    out[col] = getattr(row, col)
+                yield out
+
+
+class SearchBaseClass(object):
+
+    def get_field(self, name):
+        for f_obj in self.FIELDS:
+            if isinstance(f_obj, SearchField):
+                if f_obj.name == name:
+                    return f_obj
+            else:
+                print "Not SearchField", f_obj
+        return None
+
+    @staticmethod
+    def search(trans):
+        return None
+
+
+##################
+#Library Searching
+##################
+
+class LibraryQuery(QueryBaseClass):
+    OUTPUT_COLUMNS = [ 'extended_metadata', 'name', 'id' ]
+    def filter(self, arg):
+        if arg.name == 'extended_metadata':
+            self.do_query = True
+            self.query = self.query.join( ExtendedMetadata )
+            ex_meta = arg.other
+            for f in ex_meta:
+                alias = aliased( ExtendedMetadataIndex )
+                self.query = self.query.filter( 
+                    and_( 
+                        ExtendedMetadata.id == alias.extended_metadata_id, 
+                        alias.path == "/" + f,
+                        alias.value == str(ex_meta[f]) 
+                    )
+                )
+
+
+class LibrarySearch(SearchBaseClass):
+    FIELDS = [
+        SearchField("name"),
+        SearchField("id"),
+        SearchField("extended_metadata")
+    ]
+
+    @staticmethod
+    def search(trans):
+        query = trans.sa_session.query( LibraryDatasetDatasetAssociation )
+        return LibraryQuery(query)
+
+##################
+#History Dataset Searching
+##################
+
+
+class HistoryDatasetQuery(QueryBaseClass):
+    OUTPUT_COLUMNS = ['name', 'id']
+
+    def filter(self, arg):
+        if arg.name == 'name':
+            if arg.mode == "==":
+                self.do_query = True
+                self.query= self.query.filter( HistoryDatasetAssociation.name == arg.other )
+            if arg.mode == "like":
+                self.do_query = True
+                self.query= self.query.filter( HistoryDatasetAssociation.name.like(arg.other) )
+
+class HistoryDatasetSearch(SearchBaseClass):
+    FIELDS = [
+        SearchField("name")
+    ]
+    @staticmethod
+    def search(trans):
+        query = trans.sa_session.query( HistoryDatasetAssociation )
+        return HistoryDatasetQuery(query)
+
+
+##################
+#History Searching
+##################
+
+
+class HistoryQuery(QueryBaseClass):
+    OUTPUT_COLUMNS = ['name', 'id']
+
+    def filter(self, arg):
+        if arg.name == 'name':
+            if arg.mode == "==":
+                self.do_query = True
+                self.query = self.query.filter( History.name == arg.other )
+            if arg.mode == "like":
+                self.do_query = True
+                self.query = self.query.filter( History.name.like(arg.other) )
+
+        if arg.name == 'tag':
+            self.do_query = True
+            self.query = self.query.filter(
+               History.id == HistoryTagAssociation.history_id
+            )
+            tmp = arg.other.split(":")
+            self.query = self.query.filter( HistoryTagAssociation.user_tname == tmp[0] )
+            if len(tmp) > 1:
+                self.query = self.query.filter( HistoryTagAssociation.user_value == tmp[1] )
+
+        if arg.name == 'annotation':
+            if arg.mode == "==":
+                self.do_query = True
+                self.query = self.query.filter( and_(
+                    HistoryAnnotationAssociation.history_id == History.id,
+                    HistoryAnnotationAssociation.annotation == arg.other
+                    )
+                )
+
+            if arg.mode == "like":
+                self.do_query = True
+                self.query = self.query.filter( and_(
+                    HistoryAnnotationAssociation.history_id == History.id,
+                    HistoryAnnotationAssociation.annotation.like( arg.other )
+                    )
+                )
+
+
+class HistorySearch(SearchBaseClass):
+    FIELDS = [
+        SearchField("name"),
+        SearchField("tag"),
+        SearchField("annotation")
+    ]
+
+    @staticmethod
+    def search(trans):
+        query = trans.sa_session.query( History )
+        return HistoryQuery(query)
+
+##################
+#Workflow Searching
+##################
+
+
+
+class WorkflowQuery(QueryBaseClass):
+    OUTPUT_COLUMNS = ['name', 'id']
+
+    def filter(self, arg):
+        if arg.name == 'name':
+            self.do_query = True
+            self.query = self.query.filter( StoredWorkflow.name == arg.other )
+        if arg.name == 'tag':
+            self.do_query = True
+            self.query = self.query.filter( and_(
+                Tag.name == arg.other, 
+                Tag.id == StoredWorkflowTagAssociation.tag_id, 
+                StoredWorkflowTagAssociation.stored_workflow_id == StoredWorkflow.id )
+            )
+            self.query = self.query.filter(
+               Workflow.id == StoredWorkflowTagAssociation.workflow_id
+            )
+            tmp = arg.other.split(":")
+            self.query = self.query.filter( StoredWorkflowTagAssociation.user_tname == tmp[0] )
+            if len(tmp) > 1:
+                self.query = self.query.filter( StoredWorkflowTagAssociation.user_value == tmp[1] )
+
+        
+class WorkflowSearch(SearchBaseClass):
+
+    FIELDS = [
+        SearchField("name"),
+        SearchField("tag")
+    ]
+
+    @staticmethod
+    def search(trans):
+        query = trans.sa_session.query( StoredWorkflow )
+        return WorkflowQuery(query)
+
+
+search_mapping = {
+    'library' : LibrarySearch,
+    'history_dataset' : HistoryDatasetSearch,
+    'history' : HistorySearch,
+    'workflow' : WorkflowSearch
+}
+
+

diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r be5107c0321d1a7e7ab0221e7feb711932488bb0 lib/galaxy/webapps/galaxy/api/search.py
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/api/search.py
@@ -0,0 +1,113 @@
+"""
+API for searching Galaxy Datasets
+"""
+import logging, os, string, shutil, urllib, re, socket
+from cgi import escape, FieldStorage
+from galaxy import util, datatypes, jobs, web, util
+from galaxy.web.base.controller import *
+from galaxy.util.sanitize_html import sanitize_html
+from galaxy.model.orm import *
+from galaxy.model.search import *
+
+
+from galaxy.model import *
+
+from sqlalchemy import or_, and_
+
+log = logging.getLogger( __name__ )
+
+class SearchController( BaseAPIController ):
+    """
+    The search API accepts a POST with a payload of:
+     - search_type : The type of data to be searched, "library", "history_dataset", "history", "workflow"
+     - result_fields : The fields in the return structure that should be populated, includes:
+       "name", "id", "extended_metadata", "annotation", "tags"
+     - query : The query structure to be used
+
+    Example query data structures:
+
+    Find elements such that name == "test"
+    {
+        "name" : "test"
+    }
+
+
+    Find elements such that annotation contains the work 'world'
+
+    {
+        "annotation" : { "$like" : "%world%" }
+    }
+
+    Find elements such that the extended metadata field dataSubType/@id == 'geneExp'
+
+    {
+        "extended_metadata" : {
+            "dataSubType/@id" : "geneExp"
+        }
+    }
+
+    """
+
+    FIELD_NAME = "name"
+    FIELD_ID = "id"
+    FIELD_EXTENDED_METADATA = "extended_metadata"
+    FIELD_ANNOTATION = "annotation"
+    FIELD_TAGS = "tags"
+
+    @web.expose_api
+    def create( self, trans, payload, **kwd ):
+        """
+        POST /api/search
+        Do a search of the various elements of Galaxy.
+        """
+        domains = payload.get("domain", [])
+        result_fields = payload.get("result_fields", [self.FIELD_EXTENDED_METADATA])
+        query = payload.get("query", {})
+        print payload
+        out = []
+        for domain in domains:
+            if domain in search_mapping:
+                search_base = search_mapping[domain]()
+                search_query = search_base.search(trans)
+                for field in query:
+                    search_field = search_base.get_field(field)
+                    if search_field is not None:
+                        if isinstance(query[field], dict) and '$like' in query[field]:
+                            search_query.filter( search_field.like(query[field]['$like']) )
+                        else:
+                            search_query.filter( search_field == query[field] )
+                out += list(search_query.get_results())
+
+        return self._create_response(trans, out, result_fields)
+
+    def _create_response(self, trans, rows, result_fields):
+        out = []
+        for row in rows:
+            o = {}
+            o[ self.FIELD_ID ] =  trans.security.encode_id(row['id'])
+            o[ self.FIELD_NAME ] = row['name']
+
+            if self.FIELD_EXTENDED_METADATA in result_fields and 'extended_metadata' in row:
+                o[ self.FIELD_EXTENDED_METADATA ] = row['extended_metadata.data']
+
+            if self.FIELD_ANNOTATION in result_fields:
+                try:
+                    o[self.FIELD_ANNOTATION] = []
+                    for a in row['annotations']:
+                        o[self.FIELD_ANNOTATION].append(a.annotation)
+                except AttributeError:
+                    del o[self.FIELD_ANNOTATION]
+
+            if self.FIELD_TAGS in result_fields:
+                try:
+                    o[self.FIELD_TAGS] = []
+                    for t in row['tags']:
+                        s = t.user_tname
+                        if t.user_value is not None:
+                            s += ":" + t.user_value
+                        o[self.FIELD_TAGS].append(s)
+                except AttributeError:
+                    del o[self.FIELD_TAGS]
+
+            out.append(o)
+        return out        

diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r be5107c0321d1a7e7ab0221e7feb711932488bb0 lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -59,6 +59,7 @@
     webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' )
     webapp.add_route( '/u/:username/w/:slug', controller='workflow', action='display_by_username_and_slug' )
     webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' )
+    webapp.add_route( '/search', controller='search', action='index' )
     
     # Add the web API
     webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app )
@@ -122,6 +123,7 @@
     webapp.api_mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
     webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
     webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
+    webapp.api_mapper.resource( 'search', 'search', path_prefix='/api' )    
     webapp.api_mapper.resource( 'configuration', 'configuration', path_prefix='/api' )
     #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) )
 

diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r be5107c0321d1a7e7ab0221e7feb711932488bb0 lib/galaxy/webapps/galaxy/controllers/search.py
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/controllers/search.py
@@ -0,0 +1,18 @@
+
+"""
+Contains the main interface in the Universe class
+"""
+import logging, os, string, shutil, urllib, re, socket
+from cgi import escape, FieldStorage
+from galaxy import util, datatypes, jobs, web, util
+from galaxy.web.base.controller import *
+from galaxy.util.sanitize_html import sanitize_html
+from galaxy.model.orm import *
+from galaxy.model.item_attrs import UsesAnnotations
+
+log = logging.getLogger( __name__ )
+
+class SearchController( BaseUIController ):
+    @web.expose
+    def index(self, trans):
+        return trans.fill_template( "search/index.mako")
\ No newline at end of file

diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r be5107c0321d1a7e7ab0221e7feb711932488bb0 templates/search/index.mako
--- /dev/null
+++ b/templates/search/index.mako
@@ -0,0 +1,21 @@
+
+<%inherit file="/webapps/galaxy/base_panels.mako"/>
+<%namespace file="/search/search.mako" import="search_init" />
+<%namespace file="/search/search.mako" import="search_dialog" />
+
+<%def name="init()">
+<%
+    self.has_left_panel = False
+    self.has_right_panel = False
+    self.active_view = "profile"
+%>
+</%def>
+
+<%def name="center_panel()">
+
+${search_init()}
+
+${search_dialog()}
+
+</%def>
+

diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r be5107c0321d1a7e7ab0221e7feb711932488bb0 templates/search/search.mako
--- /dev/null
+++ b/templates/search/search.mako
@@ -0,0 +1,146 @@
+
+<%def name="search_init()">
+
+ ${h.js(
+	'libs/jquery/jquery',
+    'libs/json2'
+)}
+
+</%def>
+
+<%def name="search_dialog()">
+
+<script type="text/javascript">
+
+function doSearch(query) {
+	if (query.length > 1) {
+		var url = "/api/search";	
+		var query_struct = {};
+		var domain_array = [];
+		var field = $("#field_type").val();
+		if (field == "name") {
+			query_struct["name"] = { "$like" : "%" + $("#search_text").val() + "%" };
+		}
+
+		if ($("#history_search").val()) {
+			domain_array[domain_array.length] = "history"
+		}
+		if ($("#history_dataset_search").val()) {
+			domain_array[domain_array.length] = "history_dataset"
+		}
+		if ($("#library_dataset_search").val()) {
+			domain_array[domain_array.length] = "library_dataset"
+		}
+
+		$.ajax({ 
+			type : 'POST',
+			url: url, 
+			data: JSON.stringify({ "domain" : domain_array, "query" : query_struct }),
+			contentType : 'application/json',
+			dataType : 'json',
+			success : function(data) { 
+				$("#output").empty();
+				var p = $("#output");
+				p.empty();
+				for(var i in data) {
+					p.append( $("<div style='margin: 20px;'>").append(
+						$("<a href='/file/" + data[i]['id'] + "'>" + data[i]['name'] + "</a>")
+					)).append( 
+						$("<div class='quote'>").append( 
+							data[i]['name']
+						)
+					);
+				}
+			}
+		});
+	}
+};
+
+$(document).ready( function() {
+	$("#search_button").click(function() {
+		doSearch($("#search_text").val());
+	});
+	$('#search_text').keyup(function(e){
+		if(e.keyCode == 13) {
+			doSearch($("#search_text").val());
+		}
+	});
+	doSearch($("#search_text").val());	
+});
+
+var queryURL = function (query) {
+	var url = "/api/search" + encodeURIComponent(query);
+	url = url + "&field=" + $("#searchFields").val();
+	if ($("#fileType").val() != "All") {
+		url = url + "&type=" +  $("#fileType").val()
+	}
+	return url;
+}
+
+var suggestURL = function (query) {
+	var url = "/api/search" + encodeURIComponent(query);
+	url = url + "&field=" + $("#searchFields").val();
+	if ($("#fileType").val() != "All") {
+		url = url + "&type=" +  $("#fileType").val()
+	}
+	return url;	
+}
+
+var postClick = function(data) {
+	$("#name").attr("value", data.data[0]);
+	$("#type").attr("value", data.data[1]);	
+	$("#uuid").attr("value", data.data[2]);
+	document.getElementById('galaxy_form').submit();
+}
+
+var formatLink = function(doc) {
+	return $("<a href='/file/" + doc['_id'] + "'>" + doc['@id'] + "</a>");
+}
+
+var formatDesc = function(doc) {
+	var out = "<div>" + doc['md5'] +"</div>";
+	if (doc['description'] != null) {
+		return out + doc['description'].substring(0, 350)
+	} else {
+		return out + "<div>No Description</div>";
+	}
+}
+
+
+</script>
+
+
+<div style="margin: 20px; position: absolute; width: 100%; height: 100%">
+
+<div id="search_box">
+<input type="text" id="search_text" size="90"/>
+
+<div align="left">
+<h3>Domain</h3>
+<input type="checkbox" checked="true" id="history_search">History</input><br/>
+<input type="checkbox" checked="true" id="history_dataset_search">History Dataset</input><br/>
+<input type="checkbox" checked="true" id="library_dataset_search">Library Dataset</input><br/>
+</div>
+
+
+<div>
+<h3>Fields</h3>
+<select id="field_type">
+<option value="name">Name</a>
+<option value="datatype">Data Type</a>
+<option value="tag">Tags</a>
+<option value="annotations">Annotations</a>
+<option value="extended_metadata">Extended Metadata</a>
+</select>
+</div>
+<div style="margin: 20px;">
+<input type="button" id="search_button" value="Search"/>
+</div>
+
+<div id="output"></div>
+
+</div>
+
+</div>
+
+</%def>
\ No newline at end of file

diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r be5107c0321d1a7e7ab0221e7feb711932488bb0 templates/webapps/galaxy/base_panels.mako
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -80,7 +80,9 @@
                         [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ],
                         [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ],
                         [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ],
-                        [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ]
+                        [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ],
+                        None,
+                        [ _('Search'),  h.url_for( controller='/search', action='index' ) ]
                        ] 
         tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options )
     %>


https://bitbucket.org/galaxy/galaxy-central/commits/bd6d97447ef8/
Changeset:   bd6d97447ef8
Branch:      search
User:        Kyle Ellrott
Date:        2013-01-25 00:59:19
Summary:     default merge
Affected #:  84 files

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -16,6 +16,7 @@
 database/community_files
 database/compiled_templates
 database/files
+database/job_working_directory
 database/pbs
 database/tmp
 database/*.sqlite
@@ -23,6 +24,11 @@
 # Python bytecode
 *.pyc
 
+# Tool Shed Runtime Files
+community_webapp.log
+community_webapp.pid
+hgweb.config*
+
 # Config files
 universe_wsgi.ini
 reports_wsgi.ini

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 doc/source/lib/galaxy.webapps.galaxy.api.rst
--- a/doc/source/lib/galaxy.webapps.galaxy.api.rst
+++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst
@@ -23,10 +23,6 @@
 Quickstart
 ==========
 
-Set the following option in universe_wsgi.ini and start the server::
-
-        enable_api = True
-
 Log in as your user, navigate to the API Keys page in the User menu, and
 generate a new API key.  Make a note of the API key, and then pull up a
 terminal.  Now we'll use the display.py script in your galaxy/scripts/api

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -13,7 +13,7 @@
 from galaxy.datatypes import metadata
 from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes.sniff import get_headers
+from galaxy.datatypes.sniff import get_headers, get_test_fname
 from galaxy.util.json import to_json_string
 
 log = logging.getLogger(__name__)

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -346,7 +346,7 @@
         Return an id tag suitable for identifying the task.
         This combines the task's job id and the task's own id.
         """
-        return "%s:%s" % ( self.job.get_id(), self.get_id() )
+        return "%s_%s" % ( self.job.get_id(), self.get_id() )
     def get_command_line( self ):
         return self.command_line
     def get_parameters( self ):

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/model/item_attrs.py
--- a/lib/galaxy/model/item_attrs.py
+++ b/lib/galaxy/model/item_attrs.py
@@ -137,6 +137,12 @@
         # Set annotation.
         annotation_assoc.annotation = annotation
         return annotation_assoc
+
+    def delete_item_annotation( self, db_session, user, item):
+        annotation_assoc = self.get_item_annotation_obj( db_session, user, item )
+        if annotation_assoc:
+            db_session.delete(annotation_assoc)
+            db_session.flush()
         
     def copy_item_annotation( self, db_session, source_user, source_item, target_user, target_item ):
         """ Copy an annotation from a user/item source to a user/item target. """

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
--- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
+++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
@@ -61,13 +61,20 @@
 
 def downgrade():
     metadata.reflect()
-    ExtendedMetadata_table.drop()
-    ExtendedMetadataIndex_table.drop()
+    try:
+        ExtendedMetadataIndex_table.drop()
+    except Exception, e:
+        log.debug( "Dropping 'extended_metadata_index' table failed: %s" % ( str( e ) ) )
+
+    try:   
+        ExtendedMetadata_table.drop()
+    except Exception, e:
+        log.debug( "Dropping 'extended_metadata' table failed: %s" % ( str( e ) ) )
     
-    # Drop the Job table's exit_code column. 
+    # Drop the LDDA table's extended metadata ID column. 
     try:
-        job_table = Table( "library_dataset_dataset_association", metadata, autoload=True )
-        extended_metadata_id = job_table.c.extended_metadata_id
+        ldda_table = Table( "library_dataset_dataset_association", metadata, autoload=True )
+        extended_metadata_id = ldda_table.c.extended_metadata_id
         extended_metadata_id.drop()
     except Exception, e:
         log.debug( "Dropping 'extended_metadata_id' column from library_dataset_dataset_association table failed: %s" % ( str( e ) ) )

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/tool_shed/update_manager.py
--- a/lib/galaxy/tool_shed/update_manager.py
+++ b/lib/galaxy/tool_shed/update_manager.py
@@ -4,6 +4,7 @@
 import threading, urllib2, logging
 from galaxy.util import string_as_bool
 import galaxy.util.shed_util as shed_util
+from galaxy.model.orm import and_
 
 log = logging.getLogger( __name__ )
 

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -813,7 +813,7 @@
             self.attributes['split_size'] = 20
             self.attributes['split_mode'] = 'number_of_parts'
 
-class Tool:
+class Tool( object ):
     """
     Represents a computational tool that can be executed through Galaxy. 
     """

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -2,7 +2,7 @@
 Utility functions used systemwide.
 
 """
-import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib
+import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib, errno
 from email.MIMEText import MIMEText
 
 # Older py compatibility

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -350,7 +350,7 @@
                     # Keep the one-to-one mapping between items in 3 lists.
                     created_or_updated_tool_shed_repositories.append( tool_shed_repository )
                     tool_panel_section_keys.append( tool_panel_section_key )
-                    filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) )
+                    filtered_repo_info_dicts.append( repo_info_dict )
     # Build repository dependency relationships even if the user chose to not install repository dependencies.
     suc.build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories )                     
     return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message
@@ -596,8 +596,7 @@
         # In this case, a record for the repository will exist in the database with the status of 'New'.
         repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision )
         if repository and repository.metadata:
-            installed_rd, missing_rd = \
-                get_installed_and_missing_repository_dependencies( trans, repository )
+            installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository )
         else:
             installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
         # Discover all repository dependencies and retrieve information for installing them.

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -1,12 +1,16 @@
 import os, shutil, tempfile, logging, string, threading, urllib2, filecmp
-from galaxy import util
+from datetime import datetime
+from time import gmtime, strftime
+from galaxy import web, util
 from galaxy.tools import parameters
 from galaxy.util import inflector, json
+from galaxy.util.odict import odict
 from galaxy.web import url_for
 from galaxy.web.form_builder import SelectField
 from galaxy.webapps.community.util import container_util
 from galaxy.datatypes import checkers
 from galaxy.model.orm import and_
+import sqlalchemy.orm.exc
 from galaxy.tools.parameters import dynamic_options
 from galaxy.tool_shed import encoding_util
 
@@ -38,6 +42,60 @@
 TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER'
 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" )
 
+new_repo_email_alert_template = """
+Repository name:       ${repository_name}
+Revision:              ${revision}
+Change description:
+${description}
+
+Uploaded by:           ${username}
+Date content uploaded: ${display_date}
+
+${content_alert_str}
+
+-----------------------------------------------------------------------------
+This change alert was sent from the Galaxy tool shed hosted on the server
+"${host}"
+-----------------------------------------------------------------------------
+You received this alert because you registered to receive email when
+new repositories were created in the Galaxy tool shed named "${host}".
+-----------------------------------------------------------------------------
+"""
+
+email_alert_template = """
+Repository name:       ${repository_name}
+Revision: ${revision}
+Change description:
+${description}
+
+Changed by:     ${username}
+Date of change: ${display_date}
+
+${content_alert_str}
+
+-----------------------------------------------------------------------------
+This change alert was sent from the Galaxy tool shed hosted on the server
+"${host}"
+-----------------------------------------------------------------------------
+You received this alert because you registered to receive email whenever
+changes were made to the repository named "${repository_name}".
+-----------------------------------------------------------------------------
+"""
+
+contact_owner_template = """
+GALAXY TOOL SHED REPOSITORY MESSAGE
+------------------------
+
+The user '${username}' sent you the following message regarding your tool shed
+repository named '${repository_name}'.  You can respond by sending a reply to
+the user's email address: ${email}.
+-----------------------------------------------------------------------------
+${message}
+-----------------------------------------------------------------------------
+This message was sent from the Galaxy Tool Shed instance hosted on the server
+'${host}'
+"""
+
 def add_installation_directories_to_tool_dependencies( trans, tool_dependencies ):
     """
     Determine the path to the installation directory for each of the received tool dependencies.  This path will be displayed within the tool dependencies
@@ -65,8 +123,20 @@
             requirements_dict[ 'install_dir' ] = install_dir
             tool_dependencies[ dependency_key ] = requirements_dict
     return tool_dependencies
+def add_tool_versions( trans, id, repository_metadata, changeset_revisions ):
+    # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata.
+    metadata = repository_metadata.metadata
+    tool_versions_dict = {}
+    for tool_dict in metadata.get( 'tools', [] ):
+        # We have at least 2 changeset revisions to compare tool guids and tool ids.
+        parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions )
+        tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id
+    if tool_versions_dict:
+        repository_metadata.tool_versions = tool_versions_dict
+        trans.sa_session.add( repository_metadata )
+        trans.sa_session.flush()
 def build_readme_files_dict( metadata, tool_path=None ):
-    """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received repository_metadata."""
+    """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received metadata."""
     readme_files_dict = {}
     if metadata:
         if 'readme_files' in metadata:
@@ -128,10 +198,14 @@
             containers_dict[ 'readme_files' ] = readme_files_root_folder
         # Installed repository dependencies container.
         if repository_dependencies:
+            if new_install:
+                label = 'Repository dependencies'
+            else:
+                label = 'Installed repository dependencies'
             folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( trans=trans,
                                                                                                                   folder_id=folder_id,
                                                                                                                   repository_dependencies=repository_dependencies,
-                                                                                                                  label='Installed repository dependencies',
+                                                                                                                  label=label,
                                                                                                                   installed=True )
             containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder
         # Missing repository dependencies container.
@@ -435,6 +509,30 @@
     except:
         pass
     return can_use_disk_file
+def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
+    """Check the malicious flag in repository metadata for a specified change set"""
+    repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+    if repository_metadata:
+        return repository_metadata.malicious
+    return False
+def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ):
+    """Determine if the current changeset revision has been reviewed by the current user."""
+    for review in repository.reviews:
+        if review.changeset_revision == changeset_revision and review.user == user:
+            return True
+    return False
+def check_file_contents( trans ):
+    """See if any admin users have chosen to receive email alerts when a repository is updated.  If so, the file contents of the update must be
+    checked for inappropriate content.
+    """
+    admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
+    for repository in trans.sa_session.query( trans.model.Repository ) \
+                                      .filter( trans.model.Repository.table.c.email_alerts != None ):
+        email_alerts = json.from_json_string( repository.email_alerts )
+        for user_email in email_alerts:
+            if user_email in admin_users:
+                return True
+    return False
 def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ):
     """
     Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make 
@@ -777,17 +875,20 @@
     sa_session.flush()
     return tool_shed_repository
 def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, repository=None,
-                           repository_metadata=None, metadata=None, repository_dependencies=None ):
+                           repository_metadata=None, tool_dependencies=None, repository_dependencies=None ):
     """
     Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance.  The dictionary will also
     contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies.  
     
-    This method is called from Galaxy in two places:
-    1. During the tool shed repository installation process (via the tool shed's get_repository_information() method)- in this case both the received
-    repository and repository_metadata will be objects.
-    2. When a tool shed repository that was uninstalled from a Galaxy instance is being re-installed - in this case, both repository and
-    repository_metadata will be None, but metadata will be the tool_shed_repository metadata on the Galaxy side, and the repository_dependencies will
-    be an object previously retrieved from the tool shed.
+    This method is called from Galaxy unser three scenarios:
+    1. During the tool shed repository installation process via the tool shed's get_repository_information() method.  In this case both the received
+    repository and repository_metadata will be objects., but tool_dependencies and repository_dependencies will be None
+    2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no updates available.  In this case, both
+    repository and repository_metadata will be None, but tool_dependencies and repository_dependencies will be objects previously retrieved from the
+    tool shed if the repository includes definitions for them.
+    3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates available.  In this case, this
+    method is reached via the tool shed's get_updated_repository_information() method, and both repository and repository_metadata will be objects
+    but tool_dependencies and repository_dependencies will be None.
     """
     repo_info_dict = {}
     repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
@@ -806,27 +907,24 @@
                                                                                               all_repository_dependencies=None,
                                                                                               handled_key_rd_dicts=None,
                                                                                               circular_repository_dependencies=None )
-    if metadata:
-        tool_dependencies = metadata.get( 'tool_dependencies', None )
-        if tool_dependencies:
-            new_tool_dependencies = {}
-            for dependency_key, requirements_dict in tool_dependencies.items():
-                if dependency_key in [ 'set_environment' ]:
-                    new_set_environment_dict_list = []
-                    for set_environment_dict in requirements_dict:
-                        set_environment_dict[ 'repository_name' ] = repository_name
-                        set_environment_dict[ 'repository_owner' ] = repository_owner
-                        set_environment_dict[ 'changeset_revision' ] = changeset_revision
-                        new_set_environment_dict_list.append( set_environment_dict )
-                    new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list
-                else:
-                    requirements_dict[ 'repository_name' ] = repository_name
-                    requirements_dict[ 'repository_owner' ] = repository_owner
-                    requirements_dict[ 'changeset_revision' ] = changeset_revision
-                    new_tool_dependencies[ dependency_key ] = requirements_dict
-            tool_dependencies = new_tool_dependencies
-    else:
-        tool_dependencies = None
+                tool_dependencies = metadata.get( 'tool_dependencies', None )
+    if tool_dependencies:
+        new_tool_dependencies = {}
+        for dependency_key, requirements_dict in tool_dependencies.items():
+            if dependency_key in [ 'set_environment' ]:
+                new_set_environment_dict_list = []
+                for set_environment_dict in requirements_dict:
+                    set_environment_dict[ 'repository_name' ] = repository_name
+                    set_environment_dict[ 'repository_owner' ] = repository_owner
+                    set_environment_dict[ 'changeset_revision' ] = changeset_revision
+                    new_set_environment_dict_list.append( set_environment_dict )
+                new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list
+            else:
+                requirements_dict[ 'repository_name' ] = repository_name
+                requirements_dict[ 'repository_owner' ] = repository_owner
+                requirements_dict[ 'changeset_revision' ] = changeset_revision
+                new_tool_dependencies[ dependency_key ] = requirements_dict
+        tool_dependencies = new_tool_dependencies
     # Cast unicode to string.
     repo_info_dict[ str( repository.name ) ] = ( str( repository.description ),
                                                  str( repository_clone_url ),
@@ -1407,13 +1505,49 @@
                 if name == stripped_file_name:
                     return os.path.abspath( os.path.join( root, name ) )
     return file_path
+def get_categories( trans ):
+    """Get all categories from the database."""
+    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_category( trans, id ):
+    """Get a category from the database."""
+    return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) )
+def get_category_by_name( trans, name ):
+    """Get a category from the database via name."""
+    try:
+        return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one()
+    except sqlalchemy.orm.exc.NoResultFound:
+        return None
 def get_changectx_for_changeset( repo, changeset_revision, **kwd ):
-    """Retrieve a specified changectx from a repository"""
+    """Retrieve a specified changectx from a repository."""
     for changeset in repo.changelog:
         ctx = repo.changectx( changeset )
         if str( ctx ) == changeset_revision:
             return ctx
     return None
+def get_component( trans, id ):
+    """Get a component from the database."""
+    return trans.sa_session.query( trans.model.Component ).get( trans.security.decode_id( id ) )
+def get_component_by_name( trans, name ):
+    """Get a component from the database via a name."""
+    return trans.sa_session.query( trans.app.model.Component ) \
+                           .filter( trans.app.model.Component.table.c.name==name ) \
+                           .first()
+def get_component_review( trans, id ):
+    """Get a component_review from the database"""
+    return trans.sa_session.query( trans.model.ComponentReview ).get( trans.security.decode_id( id ) )
+def get_component_review_by_repository_review_id_component_id( trans, repository_review_id, component_id ):
+    """Get a component_review from the database via repository_review_id and component_id."""
+    return trans.sa_session.query( trans.model.ComponentReview ) \
+                           .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == trans.security.decode_id( repository_review_id ),
+                                          trans.model.ComponentReview.table.c.component_id == trans.security.decode_id( component_id ) ) ) \
+                           .first()
+def get_components( trans ):
+    return trans.sa_session.query( trans.app.model.Component ) \
+                           .order_by( trans.app.model.Component.name ) \
+                           .all()
 def get_config_from_disk( config_file, relative_install_dir ):
     for root, dirs, files in os.walk( relative_install_dir ):
         if root.find( '.hg' ) < 0:
@@ -1422,7 +1556,7 @@
                     return os.path.abspath( os.path.join( root, name ) )
     return None
 def get_configured_ui():
-    # Configure any desired ui settings.
+    """Configure any desired ui settings."""
     _ui = ui.ui()
     # The following will suppress all messages.  This is
     # the same as adding the following setting to the repo
@@ -1475,6 +1609,12 @@
 def get_installed_tool_shed_repository( trans, id ):
     """Get a repository on the Galaxy side from the database via id"""
     return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
+def get_latest_repository_metadata( trans, decoded_repository_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 == decoded_repository_id ) \
+                           .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \
+                           .first()
 def get_latest_tool_config_revision_from_repository_manifest( repo, filename, changeset_revision ):
     """
     Get the latest revision of a tool config file named filename from the repository manifest up to the value of changeset_revision.
@@ -1645,6 +1785,21 @@
                 return INITIAL_CHANGELOG_HASH
         else:
             previous_changeset_revision = changeset_revision
+def get_previous_repository_reviews( trans, repository, changeset_revision ):
+    """Return an ordered dictionary of repository reviews up to and including the received changeset revision."""
+    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
+    previous_reviews_dict = odict()
+    for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
+        previous_changeset_revision = str( repo.changectx( changeset ) )
+        if previous_changeset_revision in reviewed_revision_hashes:
+            previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision )
+            revision_reviews = get_reviews_by_repository_id_changeset_revision( trans,
+                                                                                trans.security.encode_id( repository.id ),
+                                                                                previous_changeset_revision )
+            previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label,
+                                                                         reviews=revision_reviews )
+    return previous_reviews_dict
 def get_readme_file_names( repository_name ):
     readme_files = [ 'readme', 'read_me', 'install' ]
     valid_filenames = [ r for r in readme_files ]
@@ -1660,6 +1815,9 @@
     elif len( repo_info_tuple ) == 7:
         description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
     return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies
+def get_repository_by_name( trans, name ):
+    """Get a repository from the database via name."""
+    return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one()
 def get_repository_by_name_and_owner( trans, name, owner ):
     """Get a repository from the database via name and owner"""
     if trans.webapp.name == 'galaxy':
@@ -1730,6 +1888,7 @@
             handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies )
     elif key_rd_dicts_to_be_processed:
         handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies )
+    all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies )
     return all_repository_dependencies
 def get_repository_dependency_as_key( repository_dependency ):
     return container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ],
@@ -1815,6 +1974,25 @@
                            .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ),
                                           trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \
                            .first()
+def get_repository_metadata_revisions_for_review( repository, reviewed=True ):
+    repository_metadata_revisions = []
+    metadata_changeset_revision_hashes = []
+    if reviewed:
+        for metadata_revision in repository.metadata_revisions:
+            metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision )
+        for review in repository.reviews:
+            if review.changeset_revision in metadata_changeset_revision_hashes:
+                rmcr_hashes = [ rmr.changeset_revision for rmr in repository_metadata_revisions ]
+                if review.changeset_revision not in rmcr_hashes:
+                    repository_metadata_revisions.append( review.repository_metadata )
+    else:
+        for review in repository.reviews:
+            if review.changeset_revision not in metadata_changeset_revision_hashes:
+                metadata_changeset_revision_hashes.append( review.changeset_revision )
+        for metadata_revision in repository.metadata_revisions:
+            if metadata_revision.changeset_revision not in metadata_changeset_revision_hashes:
+                repository_metadata_revisions.append( metadata_revision )
+    return repository_metadata_revisions
 def get_repository_tools_tups( app, metadata_dict ):
     repository_tools_tups = []
     index, shed_conf_dict = get_shed_tool_conf_dict( app, metadata_dict.get( 'shed_config_filename' ) )
@@ -1845,6 +2023,48 @@
             relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ):
             relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ]
     return relative_path_to_file
+def get_reversed_changelog_changesets( repo ):
+    reversed_changelog = []
+    for changeset in repo.changelog:
+        reversed_changelog.insert( 0, changeset )
+    return reversed_changelog
+def get_review( trans, id ):
+    """Get a repository_review from the database via id."""
+    return trans.sa_session.query( trans.model.RepositoryReview ).get( trans.security.decode_id( id ) )
+def get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ):
+    """Get all repository_reviews from the database via repository id and changeset_revision."""
+    return trans.sa_session.query( trans.model.RepositoryReview ) \
+                           .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ),
+                                          trans.model.RepositoryReview.changeset_revision == changeset_revision ) ) \
+                           .all()
+def get_review_by_repository_id_changeset_revision_user_id( trans, repository_id, changeset_revision, user_id ):
+    """Get a repository_review from the database via repository id, changeset_revision and user_id."""
+    return trans.sa_session.query( trans.model.RepositoryReview ) \
+                           .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ),
+                                          trans.model.RepositoryReview.changeset_revision == changeset_revision,
+                                          trans.model.RepositoryReview.user_id == trans.security.decode_id( user_id ) ) ) \
+                           .first()
+def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ):
+    if repository is None:
+        repository = repository_metadata.repository
+    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    changeset_revision = repository_metadata.changeset_revision
+    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    if ctx:
+        rev = '%04d' % ctx.rev()
+        label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
+    else:
+        rev = '-1'
+        label = "-1:%s" % changeset_revision
+    return rev, label, changeset_revision
+def get_revision_label( trans, repository, changeset_revision ):
+    """Return a string consisting of the human read-able changeset rev and the changeset revision string."""
+    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    if ctx:
+        return "%s:%s" % ( str( ctx.rev() ), changeset_revision )
+    else:
+        return "-1:%s" % changeset_revision
 def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, resetting_all_metadata_on_repository=False ):
     if resetting_all_metadata_on_repository:
         # Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata.
@@ -1873,6 +2093,15 @@
                                 relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :]
                         sample_file_metadata_paths.append( relative_path_to_sample_file )
     return sample_file_metadata_paths, sample_file_copy_paths
+def get_rev_label_from_changeset_revision( repo, changeset_revision ):
+    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    if ctx:
+        rev = '%04d' % ctx.rev()
+        label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
+    else:
+        rev = '-1'
+        label = "-1:%s" % changeset_revision
+    return rev, label
 def get_shed_tool_conf_dict( app, shed_tool_conf ):
     """
     Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry
@@ -1953,12 +2182,12 @@
     for key_rd_dict in key_rd_dicts:
         key = key_rd_dict.keys()[ 0 ]
         repository_dependency = key_rd_dict[ key ]
-        toolshed, name, owner, changeset_revision = repository_dependency
-        if tool_shed_is_this_tool_shed( toolshed ):
-            repository = get_repository_by_name_and_owner( trans, name, owner )
+        rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency
+        if tool_shed_is_this_tool_shed( rd_toolshed ):
+            repository = get_repository_by_name_and_owner( trans, rd_name, rd_owner )
             repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans,
                                                                                               trans.security.encode_id( repository.id ),
-                                                                                              changeset_revision )
+                                                                                              rd_changeset_revision )
             if repository_metadata:
                 # The repository changeset_revision is installable, so no updates are available.
                 new_key_rd_dict = {}
@@ -1968,15 +2197,20 @@
                 # The repository changeset_revision is no longer installable, so see if there's been an update.
                 repo_dir = repository.repo_path( trans.app )
                 repo = hg.repository( get_configured_ui(), repo_dir )
-                changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
+                changeset_revision = get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision )
                 repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans,
                                                                                                   trans.security.encode_id( repository.id ),
                                                                                                   changeset_revision )
                 if repository_metadata:
                     new_key_rd_dict = {}
-                    new_key_rd_dict[ key ] = [ toolshed, name, owner, repository_metadata.changeset_revision ]
+                    new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision ]
                     # We have the updated changset revision.
                     updated_key_rd_dicts.append( new_key_rd_dict )
+                else:
+                    toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key )
+                    message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \
+                        ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) )
+                    log.debug( message )
     return updated_key_rd_dicts
 def get_url_from_repository_tool_shed( app, repository ):
     """
@@ -2000,8 +2234,11 @@
             return shed_url
     # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml.
     return None
+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 ) )
 def get_user_by_username( trans, username ):
-    """Get a user from the database by username"""
+    """Get a user from the database by username."""
     return trans.sa_session.query( trans.model.User ) \
                            .filter( trans.model.User.table.c.username == username ) \
                            .one()
@@ -2040,6 +2277,94 @@
                                                                    all_repository_dependencies=all_repository_dependencies,
                                                                    handled_key_rd_dicts=handled_key_rd_dicts,
                                                                    circular_repository_dependencies=circular_repository_dependencies )
+def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ):
+    # There are 2 complementary features that enable a tool shed user to receive email notification:
+    # 1. Within User Preferences, they can elect to receive email when the first (or first valid)
+    #    change set is produced for a new repository.
+    # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts"
+    #    which caused them to receive email alerts when updates to the repository occur.  This same feature
+    #    is available on a per-repository basis on the repository grid within the tool shed.
+    #
+    # There are currently 4 scenarios for sending email notification when a change is made to a repository:
+    # 1. An admin user elects to receive email when the first change set is produced for a new repository
+    #    from User Preferences.  The change set does not have to include any valid content.  This allows for
+    #    the capture of inappropriate content being uploaded to new repositories.
+    # 2. A regular user elects to receive email when the first valid change set is produced for a new repository
+    #    from User Preferences.  This differs from 1 above in that the user will not receive email until a
+    #    change set tha tincludes valid content is produced.
+    # 3. An admin user checks the "Receive email alerts" check box on the manage repository page.  Since the
+    #    user is an admin user, the email will include information about both HTML and image content that was
+    #    included in the change set.
+    # 4. A regular user checks the "Receive email alerts" check box on the manage repository page.  Since the
+    #    user is not an admin user, the email will not include any information about both HTML and image content
+    #    that was included in the change set.
+    repo_dir = repository.repo_path( trans.app )
+    repo = hg.repository( get_configured_ui(), repo_dir )
+    smtp_server = trans.app.config.smtp_server
+    if smtp_server and ( new_repo_alert or repository.email_alerts ):
+        # Send email alert to users that want them.
+        if trans.app.config.email_from is not None:
+            email_from = trans.app.config.email_from
+        elif trans.request.host.split( ':' )[0] == 'localhost':
+            email_from = 'galaxy-no-reply@' + socket.getfqdn()
+        else:
+            email_from = 'galaxy-no-reply@' + trans.request.host.split( ':' )[0]
+        tip_changeset = repo.changelog.tip()
+        ctx = repo.changectx( tip_changeset )
+        t, tz = ctx.date()
+        date = datetime( *gmtime( float( t ) - tz )[:6] )
+        display_date = date.strftime( "%Y-%m-%d" )
+        try:
+            username = ctx.user().split()[0]
+        except:
+            username = ctx.user()
+        # We'll use 2 template bodies because we only want to send content
+        # alerts to tool shed admin users.
+        if new_repo_alert:
+            template = new_repo_email_alert_template
+        else:
+            template = email_alert_template
+        admin_body = string.Template( template ).safe_substitute( host=trans.request.host,
+                                                                  repository_name=repository.name,
+                                                                  revision='%s:%s' %( str( ctx.rev() ), ctx ),
+                                                                  display_date=display_date,
+                                                                  description=ctx.description(),
+                                                                  username=username,
+                                                                  content_alert_str=content_alert_str )
+        body = string.Template( template ).safe_substitute( host=trans.request.host,
+                                                            repository_name=repository.name,
+                                                            revision='%s:%s' %( str( ctx.rev() ), ctx ),
+                                                            display_date=display_date,
+                                                            description=ctx.description(),
+                                                            username=username,
+                                                            content_alert_str='' )
+        admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
+        frm = email_from
+        if new_repo_alert:
+            subject = "Galaxy tool shed alert for new repository named %s" % str( repository.name )
+            subject = subject[ :80 ]
+            email_alerts = []
+            for user in trans.sa_session.query( trans.model.User ) \
+                                        .filter( and_( trans.model.User.table.c.deleted == False,
+                                                       trans.model.User.table.c.new_repo_alert == True ) ):
+                if admin_only:
+                    if user.email in admin_users:
+                        email_alerts.append( user.email )
+                else:
+                    email_alerts.append( user.email )
+        else:
+            subject = "Galaxy tool shed update alert for repository named %s" % str( repository.name )
+            email_alerts = json.from_json_string( repository.email_alerts )
+        for email in email_alerts:
+            to = email.strip()
+            # Send it
+            try:
+                if to in admin_users:
+                    util.send_mail( frm, to, subject, admin_body, trans.app.config )
+                else:
+                    util.send_mail( frm, to, subject, body, trans.app.config )
+            except Exception, e:
+                log.exception( "An error occurred sending a tool shed repository update alert by email." )
 def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ):
     """
     This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an
@@ -2156,6 +2481,15 @@
         message = str( e )
         error = True
     return error, message
+def has_previous_repository_reviews( trans, repository, changeset_revision ):
+    """Determine if a repository has a changeset revision review prior to the received changeset revision."""
+    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
+    for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
+        previous_changeset_revision = str( repo.changectx( changeset ) )
+        if previous_changeset_revision in reviewed_revision_hashes:
+            return True
+    return False
 def in_all_repository_dependencies( repository_key, repository_dependency, all_repository_dependencies ):
     """Return True if { repository_key :repository_dependency } is in all_repository_dependencies."""
     for key, val in all_repository_dependencies.items():
@@ -2344,6 +2678,89 @@
             containers_dict[ 'tool_dependencies' ] = root_container
     containers_dict[ 'missing_tool_dependencies' ] = None
     return containers_dict
+def new_repository_dependency_metadata_required( trans, repository, metadata_dict ):
+    """
+    Compare the last saved metadata for each repository dependency in the repository with the new metadata in metadata_dict to determine if a new
+    repository_metadata table record is required or if the last saved metadata record can be updated instead.
+    """
+    if 'repository_dependencies' in metadata_dict:
+        repository_metadata = get_latest_repository_metadata( trans, repository.id )
+        if repository_metadata:
+            metadata = repository_metadata.metadata
+            if metadata:
+                if 'repository_dependencies' in metadata:
+                    saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ]
+                    new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ]
+                    # The saved metadata must be a subset of the new metadata.
+                    for new_repository_dependency_metadata in new_repository_dependencies:
+                        if new_repository_dependency_metadata not in saved_repository_dependencies:
+                            return True
+                    for saved_repository_dependency_metadata in saved_repository_dependencies:
+                        if saved_repository_dependency_metadata not in new_repository_dependencies:
+                            return True
+            else:
+                # We have repository metadata that does not include metadata for any repository dependencies in the
+                # repository, so we can update the existing repository metadata.
+                return False
+        else:
+            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
+            return True
+    # The received metadata_dict includes no metadata for repository dependencies, so a new repository_metadata table record is not needed.
+    return False
+def new_tool_metadata_required( trans, repository, metadata_dict ):
+    """
+    Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata
+    table record is required, or if the last saved metadata record can be updated instead.
+    """
+    if 'tools' in metadata_dict:
+        repository_metadata = get_latest_repository_metadata( trans, repository.id )
+        if repository_metadata:
+            metadata = repository_metadata.metadata
+            if metadata:
+                if 'tools' in metadata:
+                    saved_tool_ids = []
+                    # The metadata for one or more tools was successfully generated in the past
+                    # for this repository, so we first compare the version string for each tool id
+                    # in metadata_dict with what was previously saved to see if we need to create
+                    # a new table record or if we can simply update the existing record.
+                    for new_tool_metadata_dict in metadata_dict[ 'tools' ]:
+                        for saved_tool_metadata_dict in metadata[ 'tools' ]:
+                            if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids:
+                                saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] )
+                            if new_tool_metadata_dict[ 'id' ] == saved_tool_metadata_dict[ 'id' ]:
+                                if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]:
+                                    return True
+                    # So far, a new metadata record is not required, but we still have to check to see if
+                    # any new tool ids exist in metadata_dict that are not in the saved metadata.  We do
+                    # this because if a new tarball was uploaded to a repository that included tools, it
+                    # may have removed existing tool files if they were not included in the uploaded tarball.
+                    for new_tool_metadata_dict in metadata_dict[ 'tools' ]:
+                        if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids:
+                            return True
+            else:
+                # We have repository metadata that does not include metadata for any tools in the
+                # repository, so we can update the existing repository metadata.
+                return False
+        else:
+            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
+            return True
+    # The received metadata_dict includes no metadata for tools, so a new repository_metadata table record is not needed.
+    return False
+def new_workflow_metadata_required( trans, repository, metadata_dict ):
+    """
+    Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of
+    exported workflows.  If this changes at some future time, this method should be enhanced accordingly.
+    """
+    if 'workflows' in metadata_dict:
+        repository_metadata = get_latest_repository_metadata( trans, repository.id )
+        if repository_metadata:
+            # The repository has metadata, so update the workflows value - no new record is needed.
+            return False
+        else:
+            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
+            return True
+    # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed.
+    return False
 def open_repository_files_folder( trans, folder_path ):
     try:
         files_list = get_repository_files( trans, folder_path )
@@ -2368,6 +2785,7 @@
 def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed,
                                                            handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ):
     current_repository_key_rd_dicts = []
+    filtered_current_repository_key_rd_dicts = []
     for rd in repository_dependencies_dict[ 'repository_dependencies' ]:
         new_key_rd_dict = {}
         new_key_rd_dict[ current_repository_key ] = rd
@@ -2379,6 +2797,7 @@
     for key_rd_dict in current_repository_key_rd_dicts:
         is_circular = False
         if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ):
+            filtered_current_repository_key_rd_dicts.append( key_rd_dict )
             repository_dependency = key_rd_dict[ current_repository_key ]
             if current_repository_key in all_repository_dependencies:
                 # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies.
@@ -2402,7 +2821,26 @@
                 new_key_rd_dict = {}
                 new_key_rd_dict[ current_repository_key ] = repository_dependency
                 key_rd_dicts_to_be_processed.append( new_key_rd_dict )
-    return current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies
+    return filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies
+def prune_invalid_repository_dependencies( repository_dependencies ):
+    """
+    Eliminate all invalid entries in the received repository_dependencies dictionary.  An entry is invalid if if the value_list of the key/value pair is
+    empty.  This occurs when an invalid combination of tool shed, name , owner, changeset_revision is used and a repository_metadata reocrd is not found.
+    """
+    valid_repository_dependencies = {}
+    description = repository_dependencies.get( 'description', None )
+    root_key = repository_dependencies.get( 'root_key', None )
+    if root_key is None:
+        return valid_repository_dependencies
+    for key, value in repository_dependencies.items():
+        if key in [ 'description', 'root_key' ]:
+            continue
+        if value:
+            valid_repository_dependencies[ key ] = value
+    if valid_repository_dependencies:
+        valid_repository_dependencies[ 'description' ] = description
+        valid_repository_dependencies[ 'root_key' ] = root_key
+    return valid_repository_dependencies
 def remove_dir( dir ):
     if os.path.exists( dir ):
         try:
@@ -2697,6 +3135,77 @@
     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 set_repository_metadata( trans, repository, content_alert_str='', **kwd ):
+    """
+    Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset
+    has problems.
+    """
+    message = ''
+    status = 'done'
+    encoded_id = trans.security.encode_id( repository.id )
+    repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository )
+    repo_dir = repository.repo_path( trans.app )
+    repo = hg.repository( get_configured_ui(), repo_dir )
+    metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
+                                                                                 repository=repository,
+                                                                                 repository_clone_url=repository_clone_url,
+                                                                                 relative_install_dir=repo_dir,
+                                                                                 repository_files_dir=None,
+                                                                                 resetting_all_metadata_on_repository=False,
+                                                                                 updating_installed_repository=False,
+                                                                                 persist=False )
+    if metadata_dict:
+        downloadable = is_downloadable( metadata_dict )
+        repository_metadata = None
+        if new_repository_dependency_metadata_required( trans, repository, metadata_dict ) or \
+           new_tool_metadata_required( trans, repository, metadata_dict ) or \
+           new_workflow_metadata_required( trans, repository, metadata_dict ):
+            # Create a new repository_metadata table row.
+            repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, repository.tip( trans.app ), metadata_dict )
+            # If this is the first record stored for this repository, see if we need to send any email alerts.
+            if len( repository.downloadable_revisions ) == 1:
+                handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
+        else:
+            repository_metadata = get_latest_repository_metadata( trans, repository.id )
+            if repository_metadata:
+                downloadable = is_downloadable( metadata_dict )
+                # Update the last saved repository_metadata table row.
+                repository_metadata.changeset_revision = repository.tip( trans.app )
+                repository_metadata.metadata = metadata_dict
+                repository_metadata.downloadable = downloadable
+                trans.sa_session.add( repository_metadata )
+                trans.sa_session.flush()
+            else:
+                # There are no tools in the repository, and we're setting metadata on the repository tip.
+                repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, repository.tip( trans.app ), metadata_dict )
+        if 'tools' in metadata_dict and repository_metadata and status != 'error':
+            # Set tool versions on the new downloadable change set.  The order of the list of changesets is critical, so we use the repo's changelog.
+            changeset_revisions = []
+            for changeset in repo.changelog:
+                changeset_revision = str( repo.changectx( changeset ) )
+                if get_repository_metadata_by_changeset_revision( trans, encoded_id, changeset_revision ):
+                    changeset_revisions.append( changeset_revision )
+            add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions )
+    elif len( repo ) == 1 and not invalid_file_tups:
+        message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip( trans.app ) )
+        message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
+        status = "error"
+    if invalid_file_tups:
+        message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict )
+        status = 'error'
+    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
+    reset_tool_data_tables( trans.app )
+    return message, status
+def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ):
+    # Set metadata on the repository tip.
+    error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd )
+    if error_message:
+        # If there is an error, display it.
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action='manage_repository',
+                                                          id=trans.security.encode_id( repository.id ),
+                                                          message=error_message,
+                                                          status='error' ) )
 def strip_path( fpath ):
     if not fpath:
         return fpath
@@ -2858,10 +3367,8 @@
     # ? = not tracked
     # I = ignored
     # It would be nice if we could use mercurial's purge extension to remove untracked files.  The problem is that
-    # purging is not supported by the mercurial API.  See the deprecated update_for_browsing() method in common.py.
-    commands.update( get_configured_ui(),
-                     repo,
-                     rev=ctx_rev )
+    # purging is not supported by the mercurial API.
+    commands.update( get_configured_ui(), repo, rev=ctx_rev )
 def url_join( *args ):
     parts = []
     for arg in args:

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/web/base/controllers/admin.py
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -224,19 +224,20 @@
         role = get_role( trans, id )
         if params.get( 'role_members_edit_button', False ):
             in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ]
-            for ura in role.users:
-                user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id )
-                if user not in in_users:
-                    # Delete DefaultUserPermissions for previously associated users that have been removed from the role
-                    for dup in user.default_permissions:
-                        if role == dup.role:
-                            trans.sa_session.delete( dup )
-                    # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role
-                    for history in user.histories:
-                        for dhp in history.default_permissions:
-                            if role == dhp.role:
-                                trans.sa_session.delete( dhp )
-                    trans.sa_session.flush()
+            if trans.webapp.name == 'galaxy':
+                for ura in role.users:
+                    user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id )
+                    if user not in in_users:
+                        # Delete DefaultUserPermissions for previously associated users that have been removed from the role
+                        for dup in user.default_permissions:
+                            if role == dup.role:
+                                trans.sa_session.delete( dup )
+                        # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role
+                        for history in user.histories:
+                            for dhp in history.default_permissions:
+                                if role == dhp.role:
+                                    trans.sa_session.delete( dhp )
+                        trans.sa_session.flush()
             in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ]
             trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups )
             trans.sa_session.refresh( role )

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -274,7 +274,6 @@
         from galaxy.web.base.controller import ControllerUnavailable
         package = import_module( package_name )
         controller_dir = package.__path__[0]
-        print ">>>", controller_dir, package.__path__
         for fname in os.listdir( controller_dir ):
             if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ):
                 name = fname[:-3]

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/webapps/community/controllers/admin.py
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -1,12 +1,11 @@
-from galaxy.web.base.controller import *
+from galaxy.web.base.controller import BaseUIController
+from galaxy import web, util
 from galaxy.web.base.controllers.admin import Admin
 from galaxy.webapps.community import model
 from galaxy.model.orm import and_
-from galaxy.web.framework.helpers import time_ago, iff, grids
-from galaxy.web.form_builder import SelectField
+from galaxy.web.framework.helpers import time_ago, grids
 from galaxy.util import inflector
 import galaxy.util.shed_util_common as suc
-import common
 from repository import RepositoryGrid, CategoryGrid
 
 from galaxy import eggs
@@ -474,7 +473,7 @@
                     if k.startswith( 'f-' ):
                         del kwd[ k ]
                 if 'user_id' in kwd:
-                    user = common.get_user( trans, kwd[ 'user_id' ] )
+                    user = suc.get_user( trans, kwd[ 'user_id' ] )
                     kwd[ 'f-email' ] = user.email
                     del kwd[ 'user_id' ]
                 else:
@@ -489,7 +488,7 @@
                     if k.startswith( 'f-' ):
                         del kwd[ k ]
                 category_id = kwd.get( 'id', None )
-                category = common.get_category( trans, category_id )
+                category = suc.get_category( trans, category_id )
                 kwd[ 'f-Category.name' ] = category.name
             elif operation == "receive email alerts":
                 if kwd[ 'id' ]:
@@ -554,7 +553,7 @@
             if not name or not description:
                 message = 'Enter a valid name and a description'
                 status = 'error'
-            elif common.get_category_by_name( trans, name ):
+            elif suc.get_category_by_name( trans, name ):
                 message = 'A category with that name already exists'
                 status = 'error'
             else:
@@ -641,7 +640,7 @@
                                                        action='manage_categories',
                                                        message=message,
                                                        status='error' ) )
-        category = common.get_category( trans, id )
+        category = suc.get_category( trans, id )
         if params.get( 'edit_category_button', False ):
             new_name = util.restore_text( params.get( 'name', '' ) ).strip()
             new_description = util.restore_text( params.get( 'description', '' ) ).strip()
@@ -649,7 +648,7 @@
                 if not new_name:
                     message = 'Enter a valid name'
                     status = 'error'
-                elif category.name != new_name and common.get_category_by_name( trans, name ):
+                elif category.name != new_name and suc.get_category_by_name( trans, name ):
                     message = 'A category with that name already exists'
                     status = 'error'
                 else:
@@ -772,7 +771,7 @@
             ids = util.listify( id )
             message = "Deleted %d categories: " % len( ids )
             for category_id in ids:
-                category = common.get_category( trans, category_id )
+                category = suc.get_category( trans, category_id )
                 category.deleted = True
                 trans.sa_session.add( category )
                 trans.sa_session.flush()
@@ -800,7 +799,7 @@
             purged_categories = ""
             message = "Purged %d categories: " % len( ids )
             for category_id in ids:
-                category = common.get_category( trans, category_id )
+                category = suc.get_category( trans, category_id )
                 if category.deleted:
                     # Delete RepositoryCategoryAssociations
                     for rca in category.repositories:
@@ -827,7 +826,7 @@
             count = 0
             undeleted_categories = ""
             for category_id in ids:
-                category = common.get_category( trans, category_id )
+                category = suc.get_category( trans, category_id )
                 if category.deleted:
                     category.deleted = False
                     trans.sa_session.add( category )

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ /dev/null
@@ -1,597 +0,0 @@
-import os, string, socket, logging, simplejson, binascii, tempfile
-from time import gmtime, strftime
-from datetime import *
-from galaxy.tools import *
-from galaxy.util.odict import odict
-from galaxy.util.json import from_json_string, to_json_string
-import galaxy.util.shed_util_common as suc
-from galaxy.web.base.controllers.admin import *
-from galaxy.webapps.community import model
-from galaxy.model.orm import and_
-from galaxy.model.item_attrs import UsesItemRatings
-
-from galaxy import eggs
-eggs.require('mercurial')
-from mercurial import hg, ui, commands
-
-log = logging.getLogger( __name__ )
-
-new_repo_email_alert_template = """
-Repository name:       ${repository_name}
-Revision:              ${revision}
-Change description:
-${description}
-
-Uploaded by:           ${username}
-Date content uploaded: ${display_date}
-
-${content_alert_str}
-
------------------------------------------------------------------------------
-This change alert was sent from the Galaxy tool shed hosted on the server
-"${host}"
------------------------------------------------------------------------------
-You received this alert because you registered to receive email when
-new repositories were created in the Galaxy tool shed named "${host}".
------------------------------------------------------------------------------
-"""
-
-email_alert_template = """
-Repository name:       ${repository_name}
-Revision: ${revision}
-Change description:
-${description}
-
-Changed by:     ${username}
-Date of change: ${display_date}
-
-${content_alert_str}
-
------------------------------------------------------------------------------
-This change alert was sent from the Galaxy tool shed hosted on the server
-"${host}"
------------------------------------------------------------------------------
-You received this alert because you registered to receive email whenever
-changes were made to the repository named "${repository_name}".
------------------------------------------------------------------------------
-"""
-
-contact_owner_template = """
-GALAXY TOOL SHED REPOSITORY MESSAGE
-------------------------
-
-The user '${username}' sent you the following message regarding your tool shed
-repository named '${repository_name}'.  You can respond by sending a reply to
-the user's email address: ${email}.
------------------------------------------------------------------------------
-${message}
------------------------------------------------------------------------------
-This message was sent from the Galaxy Tool Shed instance hosted on the server
-'${host}'
-"""
-
-malicious_error = "  This changeset cannot be downloaded because it potentially produces malicious behavior or contains inappropriate content."
-malicious_error_can_push = "  Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content."
-
-class ItemRatings( UsesItemRatings ):
-    """Overrides rate_item method since we also allow for comments"""
-    def rate_item( self, trans, user, item, rating, comment='' ):
-        """ Rate an item. Return type is <item_class>RatingAssociation. """
-        item_rating = self.get_user_item_rating( trans.sa_session, user, item, webapp_model=trans.model )
-        if not item_rating:
-            # User has not yet rated item; create rating.
-            item_rating_assoc_class = self._get_item_rating_assoc_class( item, webapp_model=trans.model )
-            item_rating = item_rating_assoc_class()
-            item_rating.user = trans.user
-            item_rating.set_item( item )
-            item_rating.rating = rating
-            item_rating.comment = comment
-            trans.sa_session.add( item_rating )
-            trans.sa_session.flush()
-        elif item_rating.rating != rating or item_rating.comment != comment:
-            # User has previously rated item; update rating.
-            item_rating.rating = rating
-            item_rating.comment = comment
-            trans.sa_session.add( item_rating )
-            trans.sa_session.flush()
-        return item_rating
-
-def add_tool_versions( trans, id, repository_metadata, changeset_revisions ):
-    # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata.
-    metadata = repository_metadata.metadata
-    tool_versions_dict = {}
-    for tool_dict in metadata.get( 'tools', [] ):
-        # We have at least 2 changeset revisions to compare tool guids and tool ids.
-        parent_id = suc.get_parent_id( trans,
-                                       id,
-                                       tool_dict[ 'id' ],
-                                       tool_dict[ 'version' ],
-                                       tool_dict[ 'guid' ],
-                                       changeset_revisions )
-        tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id
-    if tool_versions_dict:
-        repository_metadata.tool_versions = tool_versions_dict
-        trans.sa_session.add( repository_metadata )
-        trans.sa_session.flush()
-def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
-    """Check the malicious flag in repository metadata for a specified change set"""
-    repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
-    if repository_metadata:
-        return repository_metadata.malicious
-    return False
-def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ):
-    """Determine if the current changeset revision has been reviewed by the current user."""
-    for review in repository.reviews:
-        if review.changeset_revision == changeset_revision and review.user == user:
-            return True
-    return False
-def check_file_contents( trans ):
-    # See if any admin users have chosen to receive email alerts when a repository is updated.
-    # If so, the file contents of the update must be checked for inappropriate content.
-    admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
-    for repository in trans.sa_session.query( trans.model.Repository ) \
-                                      .filter( trans.model.Repository.table.c.email_alerts != None ):
-        email_alerts = from_json_string( repository.email_alerts )
-        for user_email in email_alerts:
-            if user_email in admin_users:
-                return True
-    return False
-def get_category( trans, id ):
-    """Get a category from the database"""
-    return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) )
-def get_category_by_name( trans, name ):
-    """Get a category from the database via name"""
-    try:
-        return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one()
-    except sqlalchemy.orm.exc.NoResultFound:
-        return None
-def get_categories( trans ):
-    """Get all categories from the database"""
-    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_component( trans, id ):
-    """Get a component from the database"""
-    return trans.sa_session.query( trans.model.Component ).get( trans.security.decode_id( id ) )
-def get_component_by_name( trans, name ):
-    return trans.sa_session.query( trans.app.model.Component ) \
-                           .filter( trans.app.model.Component.table.c.name==name ) \
-                           .first()
-def get_component_review( trans, id ):
-    """Get a component_review from the database"""
-    return trans.sa_session.query( trans.model.ComponentReview ).get( trans.security.decode_id( id ) )
-def get_component_review_by_repository_review_id_component_id( trans, repository_review_id, component_id ):
-    """Get a component_review from the database via repository_review_id and component_id"""
-    return trans.sa_session.query( trans.model.ComponentReview ) \
-                           .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == trans.security.decode_id( repository_review_id ),
-                                          trans.model.ComponentReview.table.c.component_id == trans.security.decode_id( component_id ) ) ) \
-                           .first()
-def get_components( trans ):
-    return trans.sa_session.query( trans.app.model.Component ) \
-                           .order_by( trans.app.model.Component.name ) \
-                           .all()
-def get_latest_repository_metadata( trans, decoded_repository_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 == decoded_repository_id ) \
-                           .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \
-                           .first()
-def get_previous_repository_reviews( trans, repository, changeset_revision ):
-    """Return an ordered dictionary of repository reviews up to and including the received changeset revision."""
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-    reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
-    previous_reviews_dict = odict()
-    for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ):
-        previous_changeset_revision = str( repo.changectx( changeset ) )
-        if previous_changeset_revision in reviewed_revision_hashes:
-            previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision )
-            revision_reviews = get_reviews_by_repository_id_changeset_revision( trans,
-                                                                                trans.security.encode_id( repository.id ),
-                                                                                previous_changeset_revision )
-            previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label,
-                                                                         reviews=revision_reviews )
-    return previous_reviews_dict
-def get_repository_by_name( trans, name ):
-    """Get a repository from the database via name"""
-    return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one()
-def get_repository_metadata_revisions_for_review( repository, reviewed=True ):
-    repository_metadata_revisions = []
-    metadata_changeset_revision_hashes = []
-    if reviewed:
-        for metadata_revision in repository.metadata_revisions:
-            metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision )
-        for review in repository.reviews:
-            if review.changeset_revision in metadata_changeset_revision_hashes:
-                rmcr_hashes = [ rmr.changeset_revision for rmr in repository_metadata_revisions ]
-                if review.changeset_revision not in rmcr_hashes:
-                    repository_metadata_revisions.append( review.repository_metadata )
-    else:
-        for review in repository.reviews:
-            if review.changeset_revision not in metadata_changeset_revision_hashes:
-                metadata_changeset_revision_hashes.append( review.changeset_revision )
-        for metadata_revision in repository.metadata_revisions:
-            if metadata_revision.changeset_revision not in metadata_changeset_revision_hashes:
-                repository_metadata_revisions.append( metadata_revision )
-    return repository_metadata_revisions
-def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ):
-    if repository is None:
-        repository = repository_metadata.repository
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-    changeset_revision = repository_metadata.changeset_revision
-    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
-    if ctx:
-        rev = '%04d' % ctx.rev()
-        label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
-    else:
-        rev = '-1'
-        label = "-1:%s" % changeset_revision
-    return rev, label, changeset_revision
-def get_rev_label_from_changeset_revision( repo, changeset_revision ):
-    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
-    if ctx:
-        rev = '%04d' % ctx.rev()
-        label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
-    else:
-        rev = '-1'
-        label = "-1:%s" % changeset_revision
-    return rev, label
-def get_reversed_changelog_changesets( repo ):
-    reversed_changelog = []
-    for changeset in repo.changelog:
-        reversed_changelog.insert( 0, changeset )
-    return reversed_changelog
-def get_review( trans, id ):
-    """Get a repository_review from the database via id"""
-    return trans.sa_session.query( trans.model.RepositoryReview ).get( trans.security.decode_id( id ) )
-def get_review_by_repository_id_changeset_revision_user_id( trans, repository_id, changeset_revision, user_id ):
-    """Get a repository_review from the database via repository id, changeset_revision and user_id"""
-    return trans.sa_session.query( trans.model.RepositoryReview ) \
-                           .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ),
-                                          trans.model.RepositoryReview.changeset_revision == changeset_revision,
-                                          trans.model.RepositoryReview.user_id == trans.security.decode_id( user_id ) ) ) \
-                           .first()
-def get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ):
-    """Get all repository_reviews from the database via repository id and changeset_revision"""
-    return trans.sa_session.query( trans.model.RepositoryReview ) \
-                           .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ),
-                                          trans.model.RepositoryReview.changeset_revision == changeset_revision ) ) \
-                           .all()
-def get_revision_label( trans, repository, changeset_revision ):
-    """
-    Return a string consisting of the human read-able 
-    changeset rev and the changeset revision string.
-    """
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
-    if ctx:
-        return "%s:%s" % ( str( ctx.rev() ), changeset_revision )
-    else:
-        return "-1:%s" % changeset_revision
-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 ) )
-def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ):
-    # There are 2 complementary features that enable a tool shed user to receive email notification:
-    # 1. Within User Preferences, they can elect to receive email when the first (or first valid)
-    #    change set is produced for a new repository.
-    # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts"
-    #    which caused them to receive email alerts when updates to the repository occur.  This same feature
-    #    is available on a per-repository basis on the repository grid within the tool shed.
-    #
-    # There are currently 4 scenarios for sending email notification when a change is made to a repository:
-    # 1. An admin user elects to receive email when the first change set is produced for a new repository
-    #    from User Preferences.  The change set does not have to include any valid content.  This allows for
-    #    the capture of inappropriate content being uploaded to new repositories.
-    # 2. A regular user elects to receive email when the first valid change set is produced for a new repository
-    #    from User Preferences.  This differs from 1 above in that the user will not receive email until a
-    #    change set tha tincludes valid content is produced.
-    # 3. An admin user checks the "Receive email alerts" check box on the manage repository page.  Since the
-    #    user is an admin user, the email will include information about both HTML and image content that was
-    #    included in the change set.
-    # 4. A regular user checks the "Receive email alerts" check box on the manage repository page.  Since the
-    #    user is not an admin user, the email will not include any information about both HTML and image content
-    #    that was included in the change set.
-    repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
-    smtp_server = trans.app.config.smtp_server
-    if smtp_server and ( new_repo_alert or repository.email_alerts ):
-        # Send email alert to users that want them.
-        if trans.app.config.email_from is not None:
-            email_from = trans.app.config.email_from
-        elif trans.request.host.split( ':' )[0] == 'localhost':
-            email_from = 'galaxy-no-reply@' + socket.getfqdn()
-        else:
-            email_from = 'galaxy-no-reply@' + trans.request.host.split( ':' )[0]
-        tip_changeset = repo.changelog.tip()
-        ctx = repo.changectx( tip_changeset )
-        t, tz = ctx.date()
-        date = datetime( *gmtime( float( t ) - tz )[:6] )
-        display_date = date.strftime( "%Y-%m-%d" )
-        try:
-            username = ctx.user().split()[0]
-        except:
-            username = ctx.user()
-        # We'll use 2 template bodies because we only want to send content
-        # alerts to tool shed admin users.
-        if new_repo_alert:
-            template = new_repo_email_alert_template
-        else:
-            template = email_alert_template
-        admin_body = string.Template( template ).safe_substitute( host=trans.request.host,
-                                                                  repository_name=repository.name,
-                                                                  revision='%s:%s' %( str( ctx.rev() ), ctx ),
-                                                                  display_date=display_date,
-                                                                  description=ctx.description(),
-                                                                  username=username,
-                                                                  content_alert_str=content_alert_str )
-        body = string.Template( template ).safe_substitute( host=trans.request.host,
-                                                            repository_name=repository.name,
-                                                            revision='%s:%s' %( str( ctx.rev() ), ctx ),
-                                                            display_date=display_date,
-                                                            description=ctx.description(),
-                                                            username=username,
-                                                            content_alert_str='' )
-        admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
-        frm = email_from
-        if new_repo_alert:
-            subject = "Galaxy tool shed alert for new repository named %s" % str( repository.name )
-            subject = subject[ :80 ]
-            email_alerts = []
-            for user in trans.sa_session.query( trans.model.User ) \
-                                        .filter( and_( trans.model.User.table.c.deleted == False,
-                                                       trans.model.User.table.c.new_repo_alert == True ) ):
-                if admin_only:
-                    if user.email in admin_users:
-                        email_alerts.append( user.email )
-                else:
-                    email_alerts.append( user.email )
-        else:
-            subject = "Galaxy tool shed update alert for repository named %s" % str( repository.name )
-            email_alerts = from_json_string( repository.email_alerts )
-        for email in email_alerts:
-            to = email.strip()
-            # Send it
-            try:
-                if to in admin_users:
-                    util.send_mail( frm, to, subject, admin_body, trans.app.config )
-                else:
-                    util.send_mail( frm, to, subject, body, trans.app.config )
-            except Exception, e:
-                log.exception( "An error occurred sending a tool shed repository update alert by email." )
-def has_previous_repository_reviews( trans, repository, changeset_revision ):
-    """Determine if a repository has a changeset revision review prior to the received changeset revision."""
-    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
-    reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
-    for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ):
-        previous_changeset_revision = str( repo.changectx( changeset ) )
-        if previous_changeset_revision in reviewed_revision_hashes:
-            return True
-    return False
-def new_repository_dependency_metadata_required( trans, repository, metadata_dict ):
-    """
-    Compare the last saved metadata for each repository dependency in the repository with the new 
-    metadata in metadata_dict to determine if a new repository_metadata table record is required, 
-    or if the last saved metadata record can be updated instead.
-    """
-    if 'repository_dependencies' in metadata_dict:
-        repository_metadata = get_latest_repository_metadata( trans, repository.id )
-        if repository_metadata:
-            metadata = repository_metadata.metadata
-            if metadata:
-                if 'repository_dependencies' in metadata:
-                    saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ]
-                    new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ]
-                    # The saved metadata must be a subset of the new metadata.
-                    for new_repository_dependency_metadata in new_repository_dependencies:
-                        if new_repository_dependency_metadata not in saved_repository_dependencies:
-                            return True
-                    for saved_repository_dependency_metadata in saved_repository_dependencies:
-                        if saved_repository_dependency_metadata not in new_repository_dependencies:
-                            return True
-            else:
-                # We have repository metadata that does not include metadata for any repository dependencies in the
-                # repository, so we can update the existing repository metadata.
-                return False
-        else:
-            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
-            return True
-    # The received metadata_dict includes no metadata for repository dependencies, so a new repository_metadata table record is not needed.
-    return False
-def new_tool_metadata_required( trans, repository, metadata_dict ):
-    """
-    Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata
-    table record is required, or if the last saved metadata record can be updated instead.
-    """
-    if 'tools' in metadata_dict:
-        repository_metadata = get_latest_repository_metadata( trans, repository.id )
-        if repository_metadata:
-            metadata = repository_metadata.metadata
-            if metadata:
-                if 'tools' in metadata:
-                    saved_tool_ids = []
-                    # The metadata for one or more tools was successfully generated in the past
-                    # for this repository, so we first compare the version string for each tool id
-                    # in metadata_dict with what was previously saved to see if we need to create
-                    # a new table record or if we can simply update the existing record.
-                    for new_tool_metadata_dict in metadata_dict[ 'tools' ]:
-                        for saved_tool_metadata_dict in metadata[ 'tools' ]:
-                            if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids:
-                                saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] )
-                            if new_tool_metadata_dict[ 'id' ] == saved_tool_metadata_dict[ 'id' ]:
-                                if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]:
-                                    return True
-                    # So far, a new metadata record is not required, but we still have to check to see if
-                    # any new tool ids exist in metadata_dict that are not in the saved metadata.  We do
-                    # this because if a new tarball was uploaded to a repository that included tools, it
-                    # may have removed existing tool files if they were not included in the uploaded tarball.
-                    for new_tool_metadata_dict in metadata_dict[ 'tools' ]:
-                        if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids:
-                            return True
-            else:
-                # We have repository metadata that does not include metadata for any tools in the
-                # repository, so we can update the existing repository metadata.
-                return False
-        else:
-            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
-            return True
-    # The received metadata_dict includes no metadata for tools, so a new repository_metadata table record is not needed.
-    return False
-def new_workflow_metadata_required( trans, repository, metadata_dict ):
-    """
-    Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of
-    exported workflows.  If this changes at some future time, this method should be enhanced accordingly.
-    """
-    if 'workflows' in metadata_dict:
-        repository_metadata = get_latest_repository_metadata( trans, repository.id )
-        if repository_metadata:
-            # The repository has metadata, so update the workflows value - no new record is needed.
-            return False
-        else:
-            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
-            return True
-    # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed.
-    return False
-def set_repository_metadata( trans, repository, content_alert_str='', **kwd ):
-    """
-    Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset
-    has problems.
-    """
-    message = ''
-    status = 'done'
-    encoded_id = trans.security.encode_id( repository.id )
-    repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
-    repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
-    metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app,
-                                                                                     repository=repository,
-                                                                                     repository_clone_url=repository_clone_url,
-                                                                                     relative_install_dir=repo_dir,
-                                                                                     repository_files_dir=None,
-                                                                                     resetting_all_metadata_on_repository=False,
-                                                                                     updating_installed_repository=False,
-                                                                                     persist=False )
-    if metadata_dict:
-        downloadable = suc.is_downloadable( metadata_dict )
-        repository_metadata = None
-        if new_repository_dependency_metadata_required( trans, repository, metadata_dict ) or \
-           new_tool_metadata_required( trans, repository, metadata_dict ) or \
-           new_workflow_metadata_required( trans, repository, metadata_dict ):
-            # Create a new repository_metadata table row.
-            repository_metadata = suc.create_or_update_repository_metadata( trans,
-                                                                            encoded_id,
-                                                                            repository,
-                                                                            repository.tip( trans.app ),
-                                                                            metadata_dict )
-            # If this is the first record stored for this repository, see if we need to send any email alerts.
-            if len( repository.downloadable_revisions ) == 1:
-                handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
-        else:
-            repository_metadata = get_latest_repository_metadata( trans, repository.id )
-            if repository_metadata:
-                downloadable = suc.is_downloadable( metadata_dict )
-                # Update the last saved repository_metadata table row.
-                repository_metadata.changeset_revision = repository.tip( trans.app )
-                repository_metadata.metadata = metadata_dict
-                repository_metadata.downloadable = downloadable
-                trans.sa_session.add( repository_metadata )
-                trans.sa_session.flush()
-            else:
-                # There are no tools in the repository, and we're setting metadata on the repository tip.
-                repository_metadata = suc.create_or_update_repository_metadata( trans,
-                                                                                encoded_id,
-                                                                                repository,
-                                                                                repository.tip( trans.app ),
-                                                                                metadata_dict )
-        if 'tools' in metadata_dict and repository_metadata and status != 'error':
-            # Set tool versions on the new downloadable change set.  The order of the list of changesets is critical, so we use the repo's changelog.
-            changeset_revisions = []
-            for changeset in repo.changelog:
-                changeset_revision = str( repo.changectx( changeset ) )
-                if suc.get_repository_metadata_by_changeset_revision( trans, encoded_id, changeset_revision ):
-                    changeset_revisions.append( changeset_revision )
-            add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions )
-    elif len( repo ) == 1 and not invalid_file_tups:
-        message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip( trans.app ) )
-        message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
-        status = "error"
-    if invalid_file_tups:
-        message = suc.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict )
-        status = 'error'
-    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-    suc.reset_tool_data_tables( trans.app )
-    return message, status
-def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ):
-    # Set metadata on the repository tip.
-    error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd )
-    if error_message:
-        # If there is an error, display it.
-        return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action='manage_repository',
-                                                          id=trans.security.encode_id( repository.id ),
-                                                          message=error_message,
-                                                          status='error' ) )
-def update_for_browsing( trans, repository, current_working_dir, commit_message='' ):
-    # This method id deprecated, but we'll keep it around for a while in case we need it.  The problem is that hg purge
-    # is not supported by the mercurial API.
-    # Make a copy of a repository's files for browsing, remove from disk all files that are not tracked, and commit all
-    # added, modified or removed files that have not yet been committed.
-    repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_dir )
-    # The following will delete the disk copy of only the files in the repository.
-    #os.system( 'hg update -r null > /dev/null 2>&1' )
-    files_to_remove_from_disk = []
-    files_to_commit = []
-    # We may have files on disk in the repo directory that aren't being tracked, so they must be removed.
-    # The codes used to show the status of files are as follows.
-    # M = modified
-    # A = added
-    # R = removed
-    # C = clean
-    # ! = deleted, but still tracked
-    # ? = not tracked
-    # I = ignored
-    # We'll use mercurial's purge extension to remove untracked file.  Using this extension requires the
-    # following entry in the repository's hgrc file which was not required for some time, so we'll add it
-    # if it's missing.
-    # [extensions]
-    # hgext.purge=
-    lines = repo.opener( 'hgrc', 'rb' ).readlines()
-    if not '[extensions]\n' in lines:
-        # No extensions have been added at all, so just append to the file.
-        fp = repo.opener( 'hgrc', 'a' )
-        fp.write( '[extensions]\n' )
-        fp.write( 'hgext.purge=\n' )
-        fp.close()
-    elif not 'hgext.purge=\n' in lines:
-        # The file includes and [extensions] section, but we need to add the
-        # purge extension.
-        fp = repo.opener( 'hgrc', 'wb' )
-        for line in lines:
-            if line.startswith( '[extensions]' ):
-                fp.write( line )
-                fp.write( 'hgext.purge=\n' )
-            else:
-                fp.write( line )
-        fp.close()
-    cmd = 'hg purge'
-    os.chdir( repo_dir )
-    proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
-    return_code = proc.wait()
-    os.chdir( current_working_dir )
-    if return_code != 0:
-        output = proc.stdout.read( 32768 )
-        log.debug( 'hg purge failed in repository directory %s, reason: %s' % ( repo_dir, output ) )
-    if files_to_commit:
-        if not commit_message:
-            commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit )
-        repo.dirstate.write()
-        repo.commit( user=trans.user.username, text=commit_message )
-    cmd = 'hg update > /dev/null 2>&1'
-    os.chdir( repo_dir )
-    proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
-    return_code = proc.wait()
-    os.chdir( current_working_dir )
-    if return_code != 0:
-        output = proc.stdout.read( 32768 )
-        log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) )

diff -r be5107c0321d1a7e7ab0221e7feb711932488bb0 -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 lib/galaxy/webapps/community/controllers/hg.py
--- a/lib/galaxy/webapps/community/controllers/hg.py
+++ b/lib/galaxy/webapps/community/controllers/hg.py
@@ -1,7 +1,7 @@
 import os, logging
-from galaxy.web.base.controller import *
-from galaxy.util.shed_util_common import get_repository_by_name_and_owner
-from galaxy.webapps.community.controllers.common import set_repository_metadata
+from galaxy import web
+from galaxy.web.base.controller import BaseUIController
+from galaxy.util.shed_util_common import get_repository_by_name_and_owner, set_repository_metadata
 
 from galaxy import eggs
 eggs.require('mercurial')

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

https://bitbucket.org/galaxy/galaxy-central/commits/8517df5bb78d/
Changeset:   8517df5bb78d
Branch:      search
User:        Kyle Ellrott
Date:        2013-01-25 01:49:10
Summary:     Getting more of the search engine to work
Affected #:  2 files

diff -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 -r 8517df5bb78d36a68fea8e9670299ef075e17b0f lib/galaxy/model/search.py
--- a/lib/galaxy/model/search.py
+++ b/lib/galaxy/model/search.py
@@ -51,6 +51,7 @@
             print self.query
             for row in self.query.distinct().all():
                 out = {}
+                out['domain'] = self.DOMAIN
                 for col in self.OUTPUT_COLUMNS:
                     out[col] = getattr(row, col)
                 yield out
@@ -76,9 +77,11 @@
 #Library Searching
 ##################
 
-class LibraryQuery(QueryBaseClass):
+class LibraryDatasetQuery(QueryBaseClass):
+    DOMAIN = "library_dataset"
     OUTPUT_COLUMNS = [ 'extended_metadata', 'name', 'id' ]
     def filter(self, arg):
+        print "Library", arg
         if arg.name == 'extended_metadata':
             self.do_query = True
             self.query = self.query.join( ExtendedMetadata )
@@ -92,9 +95,16 @@
                         alias.value == str(ex_meta[f]) 
                     )
                 )
+        if arg.name == "name":
+            self.do_query = True
+            if arg.mode == "==":
+                self.query = self.query.filter( LibraryDatasetDatasetAssociation.name == arg.other )
+            if arg.mode == "like":
+                self.query = self.query.filter( LibraryDatasetDatasetAssociation.name.like(arg.other) )
 
 
-class LibrarySearch(SearchBaseClass):
+
+class LibraryDatasetSearch(SearchBaseClass):
     FIELDS = [
         SearchField("name"),
         SearchField("id"),
@@ -104,7 +114,7 @@
     @staticmethod
     def search(trans):
         query = trans.sa_session.query( LibraryDatasetDatasetAssociation )
-        return LibraryQuery(query)
+        return LibraryDatasetQuery(query)
 
 ##################
 #History Dataset Searching
@@ -112,6 +122,7 @@
 
 
 class HistoryDatasetQuery(QueryBaseClass):
+    DOMAIN = "history_dataset"
     OUTPUT_COLUMNS = ['name', 'id']
 
     def filter(self, arg):
@@ -139,6 +150,7 @@
 
 
 class HistoryQuery(QueryBaseClass):
+    DOMAIN = "history"
     OUTPUT_COLUMNS = ['name', 'id']
 
     def filter(self, arg):
@@ -197,6 +209,7 @@
 
 
 class WorkflowQuery(QueryBaseClass):
+    DOMAIN = "workflow"
     OUTPUT_COLUMNS = ['name', 'id']
 
     def filter(self, arg):
@@ -233,7 +246,7 @@
 
 
 search_mapping = {
-    'library' : LibrarySearch,
+    'library_dataset' : LibraryDatasetSearch,
     'history_dataset' : HistoryDatasetSearch,
     'history' : HistorySearch,
     'workflow' : WorkflowSearch

diff -r bd6d97447ef8736fdeb1ff8d7ea8aa5412468f16 -r 8517df5bb78d36a68fea8e9670299ef075e17b0f lib/galaxy/webapps/galaxy/api/search.py
--- a/lib/galaxy/webapps/galaxy/api/search.py
+++ b/lib/galaxy/webapps/galaxy/api/search.py
@@ -50,6 +50,7 @@
 
     FIELD_NAME = "name"
     FIELD_ID = "id"
+    FIELD_DOMAIN = "domain"
     FIELD_EXTENDED_METADATA = "extended_metadata"
     FIELD_ANNOTATION = "annotation"
     FIELD_TAGS = "tags"
@@ -86,8 +87,9 @@
             o = {}
             o[ self.FIELD_ID ] =  trans.security.encode_id(row['id'])
             o[ self.FIELD_NAME ] = row['name']
+            o[ self.FIELD_DOMAIN ] = row['domain']
 
-            if self.FIELD_EXTENDED_METADATA in result_fields and 'extended_metadata' in row:
+            if self.FIELD_EXTENDED_METADATA in result_fields and 'extended_metadata.data' in row:
                 o[ self.FIELD_EXTENDED_METADATA ] = row['extended_metadata.data']
 
             if self.FIELD_ANNOTATION in result_fields:


https://bitbucket.org/galaxy/galaxy-central/commits/288c79b3b694/
Changeset:   288c79b3b694
Branch:      search
User:        Kyle Ellrott
Date:        2013-02-05 20:04:26
Summary:     Default merge
Affected #:  410 files
Diff not available.

https://bitbucket.org/galaxy/galaxy-central/commits/87a206380c4b/
Changeset:   87a206380c4b
Branch:      search
User:        Kyle Ellrott
Date:        2013-02-05 21:34:07
Summary:     Using methods from model to produce json api output
Affected #:  3 files
Diff not available.

https://bitbucket.org/galaxy/galaxy-central/commits/dc7e1310ed83/
Changeset:   dc7e1310ed83
Branch:      search
User:        Kyle Ellrott
Date:        2013-02-06 01:29:23
Summary:     Working on the HTML output of the search page
Affected #:  2 files
Diff not available.

https://bitbucket.org/galaxy/galaxy-central/commits/e790dfa809d3/
Changeset:   e790dfa809d3
Branch:      search
User:        Kyle Ellrott
Date:        2013-02-06 19:40:57
Summary:     Adding peek to search page
Affected #:  2 files
Diff not available.

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

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