Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002

Conflicts:
	client/galaxy/scripts/galaxy.workflows.js
	static/maps/galaxy.workflows.js.map
	static/scripts/galaxy.workflows.js

CONTRIBUTING.md

@@ -27,9 +27,8 @@ the [development mailing list](http://dev.list.galaxyproject.org/).
 ## How to Contribute
 
 * All changes to the [core galaxy project](https://github.com/galaxyproject/galaxy)
-  should be made through pull requests to this repository except when
-  serious security vulnerabilities must simulatenously be made to multiple
-  previously released versions of Galaxy.
+  should be made through pull requests to this repository (with just two
+  exceptions outlined below).
 
 * If you are new to Git - please check out the very useful tutorials on the [GitHub training hub](https://training.github.com/kit/)
 
@@ -102,3 +101,74 @@ developers.
 
   More information about tool development can be found [on the
   wiki](https://wiki.galaxyproject.org/Develop).
+
+## Handling Pull Requests
+
+Everyone is encouraged to express opinions and issue non-binding votes on pull
+requests, but only members of the *committers* group may issue binding votes
+on pull requests. Information on the *committers* group can be found in the
+[organization document](https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organization.rst)
+describing governance of the core Galaxy code base.
+
+Votes on pull requests should take the form of
+[+1, 0, -1, and fractions](http://www.apache.org/foundation/voting.html)
+as outlined by the Apache Foundation.
+
+Pull requests modifying pre-existing releases should be restricted to bug fixes
+and require at least 2 *+1* binding votes from someone other than the author of
+the pull request with no *-1* binding votes.
+
+Pull requests changing or clarifying the procedures governing this repository:
+
+- Must be made to the ``dev`` branch of this repository.
+- Must remain open for at least 192 hours (unless every qualified committer has
+  voted).
+- Require binding *+1* votes from at least 25% of qualified *committers* with no
+  *-1* binding votes.
+- Should be titled with the prefix *[PROCEDURES]* and tagged with
+  the *procedures* tag in Github.
+- Should not be modified once open. If changes are needed, the pull request
+  should be closed, re-opened with modifications, and votes reset.
+- Should be restricted to just modifying the procedures and generally should not
+  contain code modifications.
+- If the pull request adds or removes committers, there must be a separate
+  pull request for each person added or removed.
+
+Any other pull request requires at least 1 *+1* binding vote from someone other
+than the author of the pull request.
+
+### Timelines
+
+Except in the case of pull requests modifying governance procedures, there are
+generally no objective guidelines defining how long pull requests must remain
+open for comment. Subjectively speaking though - larger and more potentially
+controversial pull requests containing enhancements should remain open for a at
+least a few days to give everyone the opportunity to weigh in.
+
+### Vetos
+
+A note on vetos (*-1* votes) taken verbatim from the
+[Apache Foundation](http://www.apache.org/foundation/voting.html):
+
+>"A code-modification proposal may be stopped dead in its tracks by a -1 vote
+by a qualified voter. This constitutes a veto, and it cannot be overruled nor
+overridden by anyone. Vetos stand until and unless withdrawn by their casters.
+>
+>To prevent vetos from being used capriciously, they must be accompanied by a
+technical justification showing why the change is bad (opens a security
+exposure, negatively affects performance, etc. ). A veto without a
+justification is invalid and has no weight."
+
+For votes regarding non-coding issues such as procedure changes, the requirement
+that a veto is accompanied by a *technical* justification is relaxed somewhat,
+though a well reasoned justification must still be included.
+
+### Direct Commit Access
+
+The Galaxy *committers* group may only commit directly to Galaxy (i.e.  outside
+of a pull request and not following the procedures described here) the
+following two categories of patches:
+
+* Patches for serious security vulnerabilities.
+* Cherry-picking and/or merging of existing approved commits to other 
+branches.

client/GruntFile.js

@@ -1,6 +1,25 @@
 module.exports = function(grunt) {
     "use strict";
 
+    var GALAXY_PATHS = {
+            dist        : '../static/scripts',
+            maps        : '../static/maps',
+            // this symlink allows us to serve uncompressed scripts in DEV_PATH for use with sourcemaps
+            srcSymlink  : '../static/src',
+        },
+        TOOLSHED_PATHS = {
+            dist        : '../static/toolshed/scripts',
+            maps        : '../static/toolshed/maps',
+            srcSymlink  : '../static/toolshed/src',
+        };
+
+    grunt.config.set( 'app', 'galaxy' );
+    grunt.config.set( 'paths', GALAXY_PATHS );
+    if( grunt.option( 'app' ) === 'toolshed' ){
+	    grunt.config.set( 'app', grunt.option( 'app' ) );
+	    grunt.config.set( 'paths', TOOLSHED_PATHS );
+    }
+
     // see the sub directory grunt-tasks/ for individual task definitions
     grunt.loadTasks( 'grunt-tasks' );
     grunt.registerTask( 'default', [ 'uglify' ] );

client/README.md

@@ -69,3 +69,13 @@ version, you'll need to use the full, local path when calling it:
     ./node_modules/.bin/grunt
     # or
     ./node_modules/.bin/grunt watch
+
+
+The Toolshed Client Build
+=========================
+
+The commands mentioned above in 'Rebuilding' and 'Grunt watch' also can be applied to toolshed scripts by using the
+`--app=toolshed` option:
+
+	grunt watch --app=toolshed
+	grunt --app=toolshed

client/galaxy/scripts/mvc/groups/group-detail-view.js

@@ -0,0 +1,134 @@
+define([
+    "libs/toastr",
+    "mvc/groups/group-model"
+    ],
+function(
+    mod_toastr,
+    mod_group_model
+    ) {
+
+// toolshed group detail view
+var GroupDetailView = Backbone.View.extend({
+    el: "#groups_element",
+    options: {},
+    app: null,
+
+    initialize : function( options ){
+        this.options = _.extend( this.options, options );
+        this.app = window.globalTS.groups;
+
+        if ( this.app.collection !== null ){
+            this.model = this.app.collection.get( this.options.group_id );
+            this.render();
+        } else {
+            this.fetchGroup();
+        }
+
+    },
+
+    fetchGroup: function( options ){
+        var that = this;
+        this.options = _.extend( this.options, options );
+        this.model = new mod_group_model.Group( { id: this.options.group_id } );
+        this.model.fetch({
+          success: function( model ){
+            console.log( 'received data: ' );
+            console.log( model );
+            that.render();
+          },
+          error: function( model, response ){
+              if ( typeof response.responseJSON !== "undefined" ){
+                mod_toastr.error( response.responseJSON.err_msg );
+              } else {
+                mod_toastr.error( 'An error ocurred.' );
+              }
+          }
+        });
+    },
+
+    render: function(){
+        var template = this.templateRow();
+        this.$el.html( template( { group: this.model } ) );
+        $("#center [data-toggle]").tooltip();
+    },
+
+    templateRow: function() {
+        return _.template([
+                '<div>',
+                    '<h3><%= group.get("name") %></h3>',
+                    '<p class="" style="color:gray;">',
+                    'A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined tool downloads.</p>',
+
+                    '<h3>Members</h3>',
+                    '<table class="grid table table-condensed">',
+                        '<thead>',
+                            '<th>Name</th>',
+                            '<th>Repositories</th>',
+                            '<th>Registered</th>',
+                        '</thead>',
+                        '<tbody>',
+                            '<% _.each(group.get("members"), function(member) { %>',
+                            '<tr>',
+                                '<td>',
+                                    '<%= member.username %>',
+                                '</td>',
+                                '<td>',
+                                    '<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= member.username %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',
+                                '</td>',
+                                '<td>',
+                                    '<%= member.time_created %>',
+                                '</td>',
+                            '</tr>',
+                            '<% }); %>',
+                        '</tbody>',
+                    '</table>',
+
+                    '<h3>Repositories</h3>',
+                    '<table class="grid table table-condensed">',
+                        '<thead>',
+                            '<th>Name</th>',
+                            '<th>Description</th>',
+                            '<th>Downloads</th>',
+                            '<th>Owner</th>',
+                            '<th>Created</th>',
+                            '<th>Rating</th>',
+                            '<th>Verified</th>',
+                        '</thead>',
+                        '<tbody>',
+                            '<% _.each(group.get("repositories"), function(repo) { %>',
+                            '<tr>',
+                                '<td>',
+                                    '<a data-toggle="tooltip" data-placement="top" title="Details of <%= repo.name %>" href="/view/<%= repo.owner %>/<%= repo.name %>" id="<%= repo.id %>"><%= repo.name %></a>',
+                                '</td>',
+                                '<td>',
+                                    '<%= repo.description %>',
+                                '</td>',
+                                '<td>',
+                                    '<%= repo.times_downloaded %>',
+                                '</td>',
+                                '<td>',
+                                    '<%= repo.owner %>',
+                                '</td>',
+                                '<td>',
+                                    '<%= repo.time_created %>',
+                                '</td>',
+                                '<td>',
+                                    '<%= repo.ratings_mean %>',
+                                '</td>',
+                                '<td>',
+                                    '<%= repo.approved %>',
+                                '</td>',
+                            '</tr>',
+                            '<% }); %>',
+                        '</tbody>',
+                    '</table>',
+                '</div>'
+        ].join(''));
+  }
+});
+return {
+    GroupDetailView: GroupDetailView
+};
+
+});
+

client/galaxy/scripts/mvc/groups/group-list-view.js

@@ -0,0 +1,148 @@
+define([
+    "libs/toastr",
+    "mvc/groups/group-model",
+    "mvc/groups/group-listrow-view"
+
+], function(
+    mod_toastr,
+    mod_group_model,
+    mod_group_listrow_view
+){
+
+var GroupListView = Backbone.View.extend({
+    el: '#groups_element',
+    defaults: {},
+
+    /**
+     * Initialize and fetch the groups from server. 
+     * Async render afterwards.
+     * @param  {object} options an object with options
+     */
+    initialize : function( options ){
+        this.options = _.defaults( this.options || {}, this.defaults, options );
+        var that = this;
+        window.globalTS.groups.collection = new mod_group_model.Groups();
+        window.globalTS.groups.collection.fetch({
+          success: function( model ){
+            console.log( 'received data: ' );
+            console.log( model );
+            that.render();
+          },
+          error: function( model, response ){
+              if ( typeof response.responseJSON !== "undefined" ){
+                mod_toastr.error( response.responseJSON.err_msg );
+              } else {
+                mod_toastr.error( 'An error ocurred.' );
+              }
+          }
+        });
+        
+    },
+
+    fetch: function(){
+    },
+
+    /** 
+     * Render the groups table from the object's own collection. 
+     */
+    render: function ( options ) {
+        this.options = _.extend( this.options, options );
+        $( ".tooltip" ).hide();
+        var template = this.templateGroupsList();
+        this.$el.html( template( { length: 10, order: 'asc' } ) );
+        this.renderRows( window.globalTS.groups.collection.models );
+        $( "#center [data-toggle]" ).tooltip();
+        $( "#center" ).css( 'overflow','auto' );
+    },
+
+    /** 
+     * Render all given models as rows in the groups list
+     * @param  {array} groups_to_render array of group models to render
+     */
+    renderRows: function( groups_to_render ){
+        for ( var i = 0; i < groups_to_render.length; i++ ) {
+            var group = groups_to_render[i];
+            this.renderOne( { group: group } )
+        }
+    },
+
+    /**
+     * Create a view for the given model and add it to the groups view.
+     * @param {Group} model of the view that will be rendered
+     */
+    renderOne: function( options ){
+        var rowView = new mod_group_listrow_view.GroupListRowView( options );
+        this.$el.find( '#group_list_body' ).append( rowView.el );
+    },
+
+    /**
+     * Table heading was clicked, update sorting preferences and re-render.
+     * @return {[type]} [description]
+     */
+    // sort_clicked : function(){
+    //     if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
+    //         Galaxy.libraries.preferences.set({'sort_order': 'desc'});
+    //     } else {
+    //         Galaxy.libraries.preferences.set({'sort_order': 'asc'});
+    //     }
+    //     this.render();
+    // },
+
+    /**
+     * Sort the underlying collection according to the parameters received.
+     * Currently supports only sorting by name. 
+     */
+    // sortLibraries: function(){
+    //     if (Galaxy.libraries.preferences.get('sort_by') === 'name'){
+    //         if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
+    //             this.collection.sortByNameAsc();
+    //         } else if (Galaxy.libraries.preferences.get('sort_order') === 'desc'){
+    //             this.collection.sortByNameDesc();
+    //         }
+    //     }
+    // },
+
+    // redirectToHome: function(){
+    //     window.location = '../';
+    // },
+    // redirectToLogin: function(){
+    //     window.location = '/user/login';
+    // },
+
+// MMMMMMMMMMMMMMMMMM
+// === TEMPLATES ====
+// MMMMMMMMMMMMMMMMMM
+
+    templateGroupsList: function(){
+        tmpl_array = [];
+
+        tmpl_array.push('<div id="groups">');
+        tmpl_array.push('</div>');
+        tmpl_array.push('<div class="groups_container table-responsive">');
+        tmpl_array.push('<% if(length === 0) { %>');
+        tmpl_array.push('<div>There are no groups yet.</div>');
+        tmpl_array.push('<% } else{ %>');
+        tmpl_array.push('<table class="grid table table-condensed">');
+        tmpl_array.push('   <thead>');
+        tmpl_array.push('     <th style="width:30%;"><a class="sort-groups-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
+        tmpl_array.push('     <th style="width:22%;">description</th>');
+        tmpl_array.push('     <th style="width:22%;">members</th> ');
+        tmpl_array.push('     <th style="width:26%;">repositories</th>');
+        tmpl_array.push('   </thead>');
+        tmpl_array.push('   <tbody id="group_list_body">');
+        // group item views will attach here
+        tmpl_array.push('   </tbody>');
+        tmpl_array.push('</table>');
+        tmpl_array.push('<% }%>');
+        tmpl_array.push('</div>');
+
+        return _.template(tmpl_array.join(''));
+    },
+
+});
+
+return {
+    GroupListView: GroupListView
+};
+
+});

client/galaxy/scripts/mvc/groups/group-listrow-view.js

@@ -0,0 +1,36 @@
+define([],
+function() {
+
+// toolshed group row view
+var GroupListRowView = Backbone.View.extend({
+    events: {},
+
+    initialize : function( options ){
+        this.render( options.group );
+    },
+
+    render: function( group ){
+        var tmpl = this.templateRow();
+        this.setElement(tmpl( { group:group } ));
+        this.$el.show();
+        return this;
+    },
+
+    templateRow: function() {
+        return _.template([
+                '<tr class="" data-id="<%- group.get("id") %>">',
+                '<td><a href="groups#/<%= group.get("id") %>"><%= group.get("name") %></a></td>',
+                '<td>description</td>',
+                '<td><%= group.get("total_members") %></td>',
+                '<td><%= group.get("total_repos") %></td>',
+                '</tr>'
+        ].join(''));
+  }
+   
+});
+
+return {
+    GroupListRowView: GroupListRowView
+};
+
+});

client/galaxy/scripts/mvc/groups/group-model.js

@@ -0,0 +1,22 @@
+define([], function() {
+
+// ============================================================================
+// LIBRARY RELATED MODELS
+
+    var Group = Backbone.Model.extend({
+      urlRoot: '/api/groups',
+    });
+
+    var Groups = Backbone.Collection.extend({
+      url: '/api/groups',
+
+      model: Group,
+
+    });
+
+return {
+    Group: Group,
+    Groups: Groups
+};
+
+});

client/galaxy/scripts/toolshed.groups.js

@@ -0,0 +1,51 @@
+// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
+// === MAIN TOOLSHED GROUP MODULE ====
+// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
+
+define([
+        "mvc/groups/group-list-view",
+        "mvc/groups/group-detail-view",
+        "mvc/groups/group-model"
+    ],
+    function(
+        mod_group_list,
+        mod_group_detail,
+        mod_group_model
+    ) {
+
+// ============================================================================
+// ROUTER
+var ToolshedRouter = Backbone.Router.extend({
+    routes: {
+        ""                        : "groups",
+        ":group_id"               : "group_page"
+    }
+
+});
+
+var ToolshedGroups = Backbone.View.extend({
+    groupListView: null,
+    groupDetailView: null,
+    collection: null,
+
+    initialize : function(){
+        window.globalTS.groups = this;
+
+        this.ts_router = new ToolshedRouter();
+        this.ts_router.on( 'route:groups', function() {
+            window.globalTS.groups.groupListView = new mod_group_list.GroupListView();
+        });
+
+        this.ts_router.on( 'route:group_page', function( group_id ) {
+            window.globalTS.groups.groupDetailView = new mod_group_detail.GroupDetailView( { group_id: group_id } );
+        });
+        
+        Backbone.history.start({pushState: false});
+    }
+});
+
+return {
+    ToolshedGroups: ToolshedGroups
+};
+
+});

client/galaxy/style/less/base.less

@@ -134,6 +134,14 @@ body  {
 #left-border  {
     left: 250px;
 }
+.reports-panel-container {
+    position: absolute;
+    top: @panel_header_height;
+    bottom: 10px;
+    overflow: scroll;
+    width: 100%;
+    padding: 10px;
+}
 #center  {
     left:250 + @border-default-color_padding;
     right: 250 + @border-default-color_padding;

client/grunt-tasks/scripts.js

@@ -6,25 +6,22 @@
 module.exports = function( grunt ){
     "use strict";
 
-    var DIST_PATH = '../static/scripts',
-        MAPS_PATH = '../static/maps',
-        // this symlink allows us to serve uncompressed scripts in DEV_PATH for use with sourcemaps
-        SRC_SYMLINK = '../static/src';
+    var app = grunt.config.get( 'app' ),
+        paths = grunt.config.get( 'paths' );
 
-    // compress javascript
     grunt.config( 'uglify', {
         target : {
             files: [{
                 expand : true,
-                cwd : SRC_SYMLINK,
+                cwd : paths.srcSymlink,
                 src : '**/*.js',
-                dest : DIST_PATH
+                dest : paths.dist
             }],
             options : {
                 sourceMap : true,
                 sourceMapName : function( path ){
                     // rewrite name to have all source maps in 'static/maps'
-                    return path.replace( DIST_PATH, MAPS_PATH ) + '.map';
+                    return path.replace( paths.dist, paths.maps ) + '.map';
                 }
             }
         },
@@ -53,19 +50,6 @@ module.exports = function( grunt ){
         }
     });
 
-    // use 'grunt watch' (from a new tab in your terminal) to have grunt re-copy changed files automatically
-    grunt.config( 'watch', {
-        watch: {
-            // watch for changes in the src dir
-            files: [ SRC_SYMLINK + '/**' ],
-            tasks: [ 'uglify' ],
-            // tasks: [ 'copy', 'pack' ],
-            options: {
-                spawn: false
-            }
-        },
-    });
-
     // -------------------------------------------------------------------------- decompress for easier debugging
     grunt.registerTask( 'decompress', function(){
         grunt.log.writeln( "decompressing... (don't forget to call 'grunt' again before committing)" );
@@ -76,10 +60,18 @@ module.exports = function( grunt ){
     // alias for symmetry
     grunt.registerTask( 'compress', [ 'uglify' ] );
 
-    // -------------------------------------------------------------------------- copy,pack only those changed
-    // adapted from grunt-contrib-watch jslint example
-    //TODO: a bit hacky and there's prob. a better way
-    //NOTE: copy will fail silently if a file isn't found
+    // -------------------------------------------------------------------------- watch & copy,pack only those changed
+    // use 'grunt watch' (from a new tab in your terminal) to have grunt re-copy changed files automatically
+    grunt.config( 'watch', {
+        watch: {
+            // watch for changes in the src dir
+            files: [ paths.srcSymlink + '/**' ],
+            tasks: [ 'uglify' ],
+            options: {
+                spawn: false
+            }
+        }
+    });
 
     // outer scope variable for the event handler and onChange fn - begin with empty hash
     var changedFiles = Object.create(null);
@@ -89,23 +81,24 @@ module.exports = function( grunt ){
         grunt.log.writeln( 'onChange, changedFiles:', Object.keys( changedFiles ) );
         grunt.config( 'uglify.target.files', [{
             expand : true,
-            cwd : SRC_SYMLINK,
+            cwd : paths.srcSymlink,
             src : Object.keys( changedFiles ),
-            dest : DIST_PATH
+            dest : paths.dist
         }]);
         changedFiles = Object.create(null);
     }, 200);
 
-    grunt.event.on( 'watch', function( action, filepath ) {
+    var addChangedFile = function( action, filepath ) {
         // store each filepath in a Files obj, the debounced fn above will use it as an aggregate list for copying
         // we need to take galaxy/scripts out of the filepath or it will be copied to the wrong loc
-        filepath = filepath.replace( SRC_SYMLINK + '/', '' );
-        grunt.log.writeln( 'on.watch, filepath:', filepath );
-        changedFiles[filepath] = action;
+        filepath = filepath.replace( paths.srcSymlink + '/', '' );
+        // grunt.log.writeln( 'on.watch, filepath:', filepath );
+        changedFiles[ filepath ] = action;
         onChange();
-    });
-
+    };
+    grunt.event.on( 'watch', addChangedFile );
 
+    // --------------------------------------------------------------------------
     grunt.loadNpmTasks( 'grunt-contrib-watch' );
     grunt.loadNpmTasks( 'grunt-contrib-uglify' );
 };

client/toolshed/scripts/test-file.js

@@ -0,0 +1,3 @@
+define( [], function() {
+	return 'Remove this file';
+});

config/datatypes_conf.xml.sample

@@ -272,6 +272,102 @@
     <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/>
     <!-- Excel datatypes -->
     <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true" />
+    <datatype extension="btwisted" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cai" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="charge" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="checktrans" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="chips" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="codcmp" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="coderet" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="compseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cpgplot" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cpgreport" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cusp" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cut" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="dan" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="digest" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="dreg" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="einverted" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="epestfind" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="equicktandem" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="est2genome" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="etandem" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="freak" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="hmoment" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="isochore" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="match" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="nametable" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="needle" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="noreturn" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="palindrome" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pepcoil" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pepinfo" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pepstats" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="polydot" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="preg" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="prettyseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="primersearch" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="showfeat" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="showorf" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="sixpack" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="strider" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="supermatcher" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="syco" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="textsearch" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="wobble" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="wordcount" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <!-- Report formats http://emboss.sourceforge.net/docs/themes/ReportFormats.html -->
+    <datatype extension="dbmotif" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="diffseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="excel" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="feattable" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="motif" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="regions" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="seqtable" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="simple" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="table" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="tagseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <!-- Sequence formats http://emboss.sourceforge.net/docs/themes/SequenceFormats.html -->
+    <datatype extension="acedb" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="clustal" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="codata" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="mega" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="meganon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="ncbi" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="nexus" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="nexusnon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="phylip" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="phylipnon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pir" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="staden" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="swiss" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <!-- Alignment Formats http://emboss.sourceforge.net/docs/themes/AlignFormats.html -->
+    <datatype extension="markx0" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx1" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx10" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx2" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx3" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pair" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="score" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="srs" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="srspair" type="galaxy.datatypes.data:Text" subclass="True"/>
     <!-- MSA Datatypes -->
     <datatype extension="hmm2" type="galaxy.datatypes.msa:Hmmer2" display_in_upload="true" />
     <datatype extension="hmm3" type="galaxy.datatypes.msa:Hmmer3" display_in_upload="true" />

doc/source/project/organization.rst

@@ -0,0 +1,86 @@
+==================================
+Galaxy Core Governance
+==================================
+
+This document informally outlines the organizational structure governing the
+Galaxy core code base hosted at https://github.com/galaxyproject/galaxy. This
+governance extends to code-related activities of this repository such as
+releases and packaging. This governance does not include infrastructure such
+as Galaxy's Trello board, the Galaxy mailing lists, etc... or other Galaxy-
+related projects belonging to the ``galaxyproject`` organization on GitHub.
+
+Committers
+==========
+
+The `committers` group is the group of trusted developers and advocates who
+manage the core Galaxy code base. They assume many roles required to achieve
+the project's goals, especially those that require a high level of trust.
+
+Galaxy Project `committers` are the only individuals who may commit to the
+core Galaxy code base. All commits must be made in accordance with procedures
+outlined in Galaxy's CONTRIBUTING_ document. In particular, in most cases
+direct commit access is not allowed and this access is restricted to merging
+pull requests issued by others.
+
+Committers may participate in formal votes - these votes typically include
+votes to modify team membership, merge pull requests, and modify or clarify
+the procedures outlined in this document and CONTRIBUTING_.
+
+Members
+----------
+
+- Enis Afgan (@afgane)
+- Dannon Baker (@dannon)
+- Daniel Blankenberg (@blankenberg)
+- Dave Bouvier (@davebx)
+- Martin Čech (@martenson)
+- John Chilton (@jmchilton)
+- Dave Clements (@tnabtaf)
+- Nate Coraor (@natefoo)
+- Carl Eberhard (@carlfeberhard)
+- Jeremy Goecks (@jgoecks)
+- Björn Grüning (@bgruening)
+- Aysam Guerler (@guerler)
+- Jennifer Hillman Jackson (@jennaj)
+- Ross Lazarus (@fubar2)
+- Anton Nekrutenko (@nekrut)
+- Eric Rasche (@erasche)
+- Nicola Soranzo (@nsoranzo)
+- James Taylor (@jxtx)
+- Nitesh Turaga (@nitesh1989)
+
+Membership
+----------
+
+The `committers` group was seeded with the group of active developers and
+advocates with commit access to the repository as of May 2015. This group
+subsequently voted in new members.
+
+Any member of the `committers` group may nominate an individual for membership
+to the `committers` group. Such individuals must have demonstrated:
+
+- Good grasp of the design of Galaxy core project.
+- Solid track record of being constructive and helpful.
+- Significant contributions to the project.
+- Willingness to dedicate some time to improving Galaxy.
+
+The above list of `committers` is the canonical source used to determine
+membership to the `committers` group - as such new members may be added to
+this group by opening a pull request adding a qualified person to this list.
+Pull requests modifying the membership of this list are subject to the normal
+rules for pull requests that modify governance procedures outlined in Galaxy's
+CONTRIBUTING_ document - with one exception - a `commmitter` may not vote
+against their own removal from the group (for obvious reasons).
+
+Given the responsibilities and power invested in this group - it is important
+that individuals not actively working on Galaxy in some fashion are removed
+the group. If individuals in this group intend to change jobs or reallocate
+volunteer activities and will no longer be active in the Galaxy community,
+they should withdraw from membership of this group. Periodically, active
+members may review this group and request inactive members are removed - this
+should not be interpreted as a condemnation of these inactive members but
+merely as a reflection of a desire to keep this group focused enough to remain
+effective.
+
+.. _LICENSE: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt
+.. _CONTRIBUTING: https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md

lib/galaxy/datatypes/binary.py

@@ -114,6 +114,27 @@ class Ab1( Binary ):
 
 Binary.register_unsniffable_binary_ext("ab1")
 
+
+class Idat( Binary ):
+    """Binary data in idat format"""
+    file_ext = "idat"
+
+    def __init__( self, **kwd ):
+        Binary.__init__( self, **kwd )
+
+    def sniff( self, filename ):
+        try:
+            header = open( filename ).read(4)
+            if binascii.b2a_hex( header ) == binascii.hexlify( 'IDAT' ):
+                return True
+            return False
+        except:
+            return False
+
+Binary.register_sniffable_binary_format("idat", "idat", Idat)
+
+
+
 class CompressedArchive( Binary ):
     """
         Class describing an compressed binary file

lib/galaxy/datatypes/registry.py

@@ -208,7 +208,7 @@ class Registry( object ):
                                         for mod in fields:
                                             module = getattr( module, mod )
                                         datatype_class = getattr( module, datatype_class_name )
-                                        self.log.debug( 'Retrieved datatype module %s from the datatype registry.' % str( datatype_module ) )
+                                        self.log.debug( 'Retrieved datatype module %s:%s from the datatype registry.' % ( str( datatype_module ), datatype_class_name ) )
                                     except Exception, e:
                                         self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) )
                                         ok = False

lib/galaxy/model/__init__.py

@@ -2144,7 +2144,7 @@ class Library( object, Dictifiable, HasName ):
         """
         rval = super( Library, self ).to_dict( view=view, value_mapper=value_mapper )
         if 'root_folder_id' in rval:
-            rval[ 'root_folder_id' ] = 'F' + rval[ 'root_folder_id' ]
+            rval[ 'root_folder_id' ] = 'F' + str(rval[ 'root_folder_id' ])
         return rval
     def get_active_folders( self, folder, folders=None ):
         # TODO: should we make sure the library is not deleted?

lib/galaxy/tools/__init__.py

@@ -13,6 +13,8 @@ import threading
 import types
 import urllib
 import copy
+import traceback
+from datetime import datetime
 
 from galaxy import eggs, util
 
@@ -80,6 +82,24 @@ JOB_RESOURCE_CONDITIONAL_XML = """<conditional name="__job_resource">
 HELP_UNINITIALIZED = threading.Lock()
 
 
+class ToolErrorLog:
+    def __init__(self):
+        self.error_stack = []
+        self.max_errors = 100
+    
+    def add_error(self, file, phase, exception):
+        self.error_stack.insert(0, {
+            "file" : file,
+            "time" : str(datetime.now()),
+            "phase" : phase,
+            "error" :  str(exception)
+        } )
+        if len(self.error_stack) > self.max_errors:
+            self.error_stack.pop()
+        
+
+global_tool_errors = ToolErrorLog()
+
 class ToolNotFoundException( Exception ):
     pass
 
@@ -103,7 +123,12 @@ class ToolBox( AbstractToolBox ):
         return self._tools_by_id
 
     def create_tool( self, config_file, repository_id=None, guid=None, **kwds ):
-        tool_source = get_tool_source( config_file, getattr( self.app.config, "enable_beta_tool_formats", False ) )
+        try:
+            tool_source = get_tool_source( config_file, getattr( self.app.config, "enable_beta_tool_formats", False ) )
+        except Exception, e:
+            #capture and log parsing errors
+            global_tool_errors.add_error(config_file, "Tool XML parsing", e)
+            raise e
         # Allow specifying a different tool subclass to instantiate
         tool_module = tool_source.parse_tool_module()
         if tool_module is not None:
@@ -460,7 +485,11 @@ class Tool( object, Dictifiable ):
         #populate toolshed repository info, if available
         self.populate_tool_shed_info()
         # Parse XML element containing configuration
-        self.parse( tool_source, guid=guid )
+        try:
+            self.parse( tool_source, guid=guid )
+        except Exception, e:
+            global_tool_errors.add_error(config_file, "Tool Loading", e)
+            raise e
         self.external_runJob_script = app.config.drmaa_external_runjob_script
         self.history_manager = histories.HistoryManager( app )
 

lib/galaxy/tools/evaluation.py

@@ -21,6 +21,7 @@ from galaxy.tools.parameters.basic import (
     SelectToolParameter,
 )
 from galaxy.tools.parameters.grouping import Conditional, Repeat, Section
+from galaxy.tools import global_tool_errors
 from galaxy.jobs.datasets import dataset_path_rewrites
 
 import logging
@@ -400,10 +401,25 @@ class ToolEvaluator( object ):
         self.extra_filenames = []
         self.command_line = None
 
-        self.__build_config_files( )
-        self.__build_param_file( )
-        self.__build_command_line( )
-
+        try:
+            self.__build_config_files( )
+        except Exception, e:
+            #capture and log parsing errors
+            global_tool_errors.add_error(self.tool.config_file, "Building Config Files", e)
+            raise e        
+        try:
+            self.__build_param_file( )
+        except Exception, e:
+            #capture and log parsing errors
+            global_tool_errors.add_error(self.tool.config_file, "Building Param File", e)
+            raise e
+        try:
+            self.__build_command_line( )
+        except Exception, e:
+            #capture and log parsing errors
+            global_tool_errors.add_error(self.tool.config_file, "Building Command Line", e)
+            raise e
+            
         return self.command_line, self.extra_filenames
 
     def __build_command_line( self ):

lib/galaxy/tools/test.py

@@ -48,7 +48,7 @@ class ToolTestBuilder( object ):
         self.name = name
         self.maxseconds = maxseconds
         self.required_files = []
-        self.inputs = []
+        self.inputs = {}
         self.outputs = []
         # By default do not making assertions on number of outputs - but to
         # test filtering allow explicitly state number of outputs.
@@ -134,6 +134,7 @@ class ToolTestBuilder( object ):
             self.expect_failure = test_dict.get("expect_failure", False)
             self.md5 = test_dict.get("md5", None)
         except Exception, e:
+            self.inputs = {}
             self.error = True
             self.exception = e
 

lib/galaxy/web/framework/webapp.py

@@ -818,8 +818,7 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
         template = template_lookup.get_template( filename )
         template.output_encoding = 'utf-8'
 
-        data = dict( caller=self, t=self, trans=self, h=helpers, util=util,
-                     request=self.request, response=self.response, app=self.app )
+        data = dict( caller=self, t=self, trans=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app )
         data.update( self.template_context )
         data.update( kwargs )
         return template.render( **data )

lib/galaxy/webapps/galaxy/buildapp.py

@@ -2,11 +2,15 @@
 Provides factory methods to assemble the Galaxy web application
 """
 
-import atexit
+import os
 import sys
+import atexit
+
+try:
+    import configparser
+except:
+    import ConfigParser as configparser
 
-from paste import httpexceptions
-import pkg_resources
 
 import galaxy.app
 from galaxy.config import process_is_uwsgi
@@ -19,6 +23,10 @@ from galaxy import util
 from galaxy.util import asbool
 from galaxy.util.properties import load_app_properties
 
+from galaxy import eggs
+eggs.require('Paste')
+from paste import httpexceptions
+
 import logging
 log = logging.getLogger( __name__ )
 
@@ -37,6 +45,10 @@ class GalaxyWebApplication( galaxy.web.framework.webapp.WebApplication ):
 
 
 def app_factory( global_conf, **kwargs ):
+    return paste_app_factory( global_conf, **kwargs )
+
+
+def paste_app_factory( global_conf, **kwargs ):
     """
     Return a wsgi application serving the root object
     """
@@ -119,6 +131,22 @@ def app_factory( global_conf, **kwargs ):
     return webapp
 
 
+def uwsgi_app_factory():
+    import uwsgi
+    root = os.path.abspath(uwsgi.opt.get('galaxy_root', os.getcwd()))
+    config_file = uwsgi.opt.get('galaxy_config_file', os.path.join(root, 'config', 'galaxy.ini'))
+    global_conf = {
+        '__file__' : config_file if os.path.exists(__file__) else None,
+        'here' : root }
+    parser = configparser.ConfigParser()
+    parser.read(config_file)
+    try:
+        kwargs = dict(parser.items('app:main'))
+    except configparser.NoSectionError:
+        kwargs = {}
+    return app_factory(global_conf, **kwargs)
+
+
 @postfork
 def postfork_setup():
     from galaxy.app import app
@@ -635,7 +663,7 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
         # Interactive exception debugging, scary dangerous if publicly
         # accessible, if not enabled we'll use the regular error printing
         # middleware.
-        pkg_resources.require( "WebError" )
+        eggs.require( "WebError" )
         from weberror import evalexception
         app = evalexception.EvalException( app, conf,
                                            templating_formatters=build_template_error_formatters() )

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -18,6 +18,7 @@ from galaxy.web.base.controller import BaseUIController, UsesQuotaMixin
 from galaxy.web.base.controllers.admin import Admin
 from galaxy.web.framework.helpers import grids, time_ago
 from galaxy.web.params import QuotaParamParser
+from galaxy.tools import global_tool_errors
 from tool_shed.util import common_util
 from tool_shed.util import encoding_util
 from tool_shed.util.web_util import escape
@@ -824,6 +825,11 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
                                     message=message,
                                     status=status )
 
+    @web.expose
+    @web.require_admin
+    def tool_errors( self, trans, **kwd ):
+        return trans.fill_template('admin/tool_errors.mako', tool_errors=global_tool_errors.error_stack)
+
     @web.expose
     @web.require_admin
     def view_datatypes_registry( self, trans, **kwd ):

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

@@ -0,0 +1,132 @@
+import logging
+from galaxy import util
+from galaxy import web
+from galaxy.util import pretty_print_time_interval
+from galaxy.exceptions import RequestParameterMissingException
+from galaxy.exceptions import AdminRequiredException
+from galaxy.exceptions import ObjectNotFound
+from galaxy.web import require_admin as require_admin
+from galaxy.web import _future_expose_api as expose_api
+from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
+from galaxy.web.base.controller import BaseAPIController
+from tool_shed.managers import groups
+
+log = logging.getLogger( __name__ )
+
+
+class GroupsController( BaseAPIController ):
+    """RESTful controller for interactions with groups in the Tool Shed."""
+
+    def __init__( self, app ):
+        super( GroupsController, self ).__init__( app )
+        self.group_manager = groups.GroupManager()
+
+    def __get_value_mapper( self, trans ):
+        value_mapper = { 'id' : trans.security.encode_id }
+        return value_mapper
+
+    @expose_api_anonymous_and_sessionless
+    def index( self, trans, deleted=False, **kwd ):
+        """
+        GET /api/groups
+        Return a list of dictionaries that contain information about each Group.
+
+        :param deleted: flag used to include deleted groups
+
+        Example: GET localhost:9009/api/groups
+        """
+        group_dicts = []
+        deleted = util.asbool( deleted )
+        if deleted and not trans.user_is_admin():
+            raise AdminRequiredException( 'Only administrators can query deleted groups.' )
+        for group in self.group_manager.list( trans, deleted ):
+            group_dicts.append( self._populate( trans, group ) )
+        return group_dicts
+
+    @expose_api
+    @require_admin
+    def create( self, trans, payload, **kwd ):
+        """
+        POST /api/groups
+        Return a dictionary of information about the created group.
+        The following parameters are included in the payload:
+
+        :param name (required): the name of the group
+        :param description (optional): the description of the group
+
+        Example: POST /api/groups/?key=XXXYYYXXXYYY
+        Content-Disposition: form-data; name="name" Group_Name
+        Content-Disposition: form-data; name="description" Group_Description
+        """
+        group_dict = dict( message='', status='ok' )
+        name = payload.get( 'name', '' )
+        if name:
+            description = payload.get( 'description', '' )
+            if not description:
+                description = ''
+            else:
+                # TODO add description field to the model
+                group_dict = self.group_manager.create( trans, name=name ).to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) )
+        else:
+            raise RequestParameterMissingException( 'Missing required parameter "name".' )
+        return group_dict
+
+    @expose_api_anonymous_and_sessionless
+    def show( self, trans, encoded_id, **kwd ):
+        """
+        GET /api/groups/{encoded_group_id}
+        Return a dictionary of information about a group.
+
+        :param id: the encoded id of the Group object
+
+        Example: GET localhost:9009/api/groups/f9cad7b01a472135
+        """
+        decoded_id = trans.security.decode_id( encoded_id )
+        group = self.group_manager.get( trans, decoded_id )
+        if group is None:
+            raise ObjectNotFound( 'Unable to locate group record for id %s.' % ( str( encoded_id ) ) )
+        return self._populate( trans, group )
+
+    def _populate( self, trans, group ):
+        """
+        Turn the given group information from DB into a dict
+        and add other characteristics like members and repositories.
+        """
+        model = trans.app.model
+        group_dict = group.to_dict( view='collection', value_mapper=self.__get_value_mapper( trans ) )
+        group_members = []
+        group_repos = []
+        total_downloads = 0
+        for uga in group.users:
+            user = trans.sa_session.query( model.User ).filter( model.User.table.c.id == uga.user_id ).one()
+            user_repos_count = 0
+            for repo in trans.sa_session.query( model.Repository ) \
+                    .filter( model.Repository.table.c.user_id == uga.user_id ) \
+                    .join( model.RepositoryMetadata.table ) \
+                    .join( model.User.table ) \
+                    .outerjoin( model.RepositoryCategoryAssociation.table ) \
+                    .outerjoin( model.Category.table ):
+                time_repo_created = pretty_print_time_interval( repo.create_time, True )
+                approved = ''
+                ratings = []
+                for review in repo.reviews:
+                    if review.rating:
+                        ratings.append( review.rating )
+                    if review.approved == 'yes':
+                        approved = 'yes'
+                # TODO add user ratings
+                ratings_mean = str( float( sum( ratings ) ) / len( ratings ) ) if len( ratings ) > 0 else ''
+                total_downloads += repo.times_downloaded
+                group_repos.append( { 'name': repo.name, 'times_downloaded': repo.times_downloaded, 'owner': repo.user.username, 'time_created': time_repo_created, 'description': repo.description, 'approved': approved, 'ratings_mean': ratings_mean, 'tools': 'unknown'  } )
+                user_repos_count += 1
+            encoded_user_id = trans.app.security.encode_id( repo.user.id )
+            user_repos_url = web.url_for( controller='repository', action='browse_repositories_by_user', user_id=encoded_user_id )
+            time_created = pretty_print_time_interval( user.create_time, True )
+            member_dict = { 'id': encoded_user_id, 'username': user.username, 'user_repos_url': user_repos_url, 'user_repos_count': user_repos_count, 'user_tools_count': 'unknown', 'time_created': time_created }
+            group_members.append( member_dict )
+        group_dict[ 'members' ] = group_members
+        group_dict[ 'total_members' ] = len( group_members )
+        group_dict[ 'repositories' ] = group_repos
+        group_dict[ 'total_repos' ] = len( group_repos )
+        group_dict[ 'total_downloads' ] = total_downloads
+        return group_dict

lib/galaxy/webapps/tool_shed/buildapp.py

@@ -86,6 +86,21 @@ def app_factory( global_conf, **kwargs ):
                            controller='authenticate',
                            action='get_tool_shed_api_key',
                            conditions=dict( method=[ "GET" ] ) )
+    webapp.mapper.connect( 'group',
+                           '/api/groups/',
+                           controller='groups',
+                           action='index',
+                           conditions=dict( method=[ "GET" ] ) )
+    webapp.mapper.connect( 'group',
+                           '/api/groups/',
+                           controller='groups',
+                           action='create',
+                           conditions=dict( method=[ "POST" ] ) )
+    webapp.mapper.connect( 'group',
+                           '/api/groups/:encoded_id',
+                           controller='groups',
+                           action='show',
+                           conditions=dict( method=[ "GET" ] ) )
     webapp.mapper.connect( 'repo_search',
                            '/api/search/',
                            controller='search',

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

@@ -0,0 +1,22 @@
+import logging
+from galaxy import model, util
+from galaxy import web
+from galaxy.model.orm import and_, not_, or_
+from galaxy.web.base.controller import BaseUIController
+from galaxy.web.framework.helpers import escape, grids
+
+log = logging.getLogger( __name__ )
+
+
+class Group( BaseUIController ):
+
+    @web.expose
+    def index( self, trans, **kwd ):
+        # define app configuration for generic mako template
+        app = {
+            'jscript'       : "toolshed.groups"
+        }
+        return trans.fill_template( '/webapps/tool_shed/group/index.mako',
+                                    config = { 
+                                    'title': 'Tool Shed Groups',
+                                    'app': app } )

lib/tool_shed/dependencies/tool/tag_attribute_handler.py

@@ -30,7 +30,7 @@ class TagAttributeHandler( object ):
                                                      elem_index=sub_index,
                                                      elem=sub_elem,
                                                      message=message )
-            if error_message:
+            if error_message and error_message not in message:
                 message += error_message
             if altered:
                 if not self.altered:
@@ -68,7 +68,7 @@ class TagAttributeHandler( object ):
                 altered, new_sub_elem, error_message = self.rdd.handle_sub_elem( parent_elem=elem,
                                                                                  elem_index=sub_index,
                                                                                  elem=sub_elem )
-            if error_message:
+            if error_message and error_message not in message:
                 message += error_message
             if altered:
                 if not self.altered:
@@ -98,7 +98,7 @@ class TagAttributeHandler( object ):
                 altered, new_sub_elem, error_message = \
                     self.process_actions_tag_set( elem=sub_elem,
                                                   message=message )
-            if error_message:
+            if error_message and error_message not in message:
                 message += error_message
             if altered:
                 if not self.altered:
@@ -150,7 +150,7 @@ class TagAttributeHandler( object ):
                     ( str( package_version ), str( package_name ) )
                 error_message += 'the recipe for installing the package is missing either an '
                 error_message += '<actions> tag set or an <actions_group> tag set.'
-            if error_message:
+            if error_message and error_message not in message:
                 message += error_message
             if altered:
                 if not self.altered:
@@ -176,7 +176,7 @@ class TagAttributeHandler( object ):
                                                      elem_index=sub_index,
                                                      elem=sub_elem,
                                                      message=message )
-            if error_message:
+            if error_message and error_message not in message:
                 message += error_message
             if altered:
                 if not self.altered:
@@ -191,7 +191,7 @@ class TagAttributeHandler( object ):
         altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem( parent_elem=parent_elem,
                                                                                     elem_index=elem_index,
                                                                                     elem=elem )
-        if error_message:
+        if error_message and error_message not in message:
             message += error_message
         if altered:
             if not self.altered:

lib/tool_shed/managers/groups.py

@@ -0,0 +1,120 @@
+"""
+Manager and Serializer for TS groups.
+"""
+from galaxy.exceptions import InconsistentDatabase
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import ObjectNotFound
+from galaxy.exceptions import InternalServerError
+from galaxy.exceptions import ItemAccessibilityException
+from galaxy.exceptions import Conflict
+from sqlalchemy.orm.exc import MultipleResultsFound
+from sqlalchemy.orm.exc import NoResultFound
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+# =============================================================================
+class GroupManager( object ):
+    """
+    Interface/service object for interacting with TS groups.
+    """
+
+    def __init__( self, *args, **kwargs ):
+        super( GroupManager, self ).__init__( *args, **kwargs )
+
+    def get( self, trans, decoded_group_id=None, name=None ):
+        """
+        Get the group from the DB based on its ID or name.
+
+        :param  decoded_group_id:       decoded group id
+        :type   decoded_group_id:       int
+
+        :returns:   the requested group
+        :rtype:     Group
+        """
+        if decoded_group_id is None and name is None:
+            raise RequestParameterInvalidException( 'You must supply either ID or a name of the group.' )
+
+        name_query = trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name == name )
+        id_query = trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.id == decoded_group_id )
+
+        try:
+            group = id_query.one() if decoded_group_id else name_query.one()
+        except MultipleResultsFound:
+            raise InconsistentDatabase( 'Multiple groups found with the same id.' )
+        except NoResultFound:
+            raise ObjectNotFound( 'No group found with the id provided.' )
+        except Exception:
+            raise InternalServerError( 'Error loading from the database.' )
+        return group
+
+    def create( self, trans, name, description=''):
+        """
+        Create a new group.
+        """
+        if not trans.user_is_admin:
+            raise ItemAccessibilityException( 'Only administrators can create groups.' )
+        else:
+            if self.get( trans, name=name ):
+                raise Conflict( 'Group with the given name already exists. Name: ' + str( name ) )
+            # TODO add description field to the model
+            group = trans.app.model.Group( name=name )
+            trans.sa_session.add( group )
+            trans.sa_session.flush()
+            return group
+
+    def update( self, trans, group, name=None, description=None ):
+        """
+        Update the given group
+        """
+        changed = False
+        if not trans.user_is_admin():
+            raise ItemAccessibilityException( 'Only administrators can update groups.' )
+        if group.deleted:
+            raise RequestParameterInvalidException( 'You cannot modify a deleted group. Undelete it first.' )
+        if name is not None:
+            group.name = name
+            changed = True
+        if description is not None:
+            group.description = description
+            changed = True
+        if changed:
+            trans.sa_session.add( group )
+            trans.sa_session.flush()
+        return group
+
+    def delete( self, trans, group, undelete=False ):
+        """
+        Mark given group deleted/undeleted based on the flag.
+        """
+        if not trans.user_is_admin():
+            raise ItemAccessibilityException( 'Only administrators can delete and undelete groups.' )
+        if undelete:
+            group.deleted = False
+        else:
+            group.deleted = True
+        trans.sa_session.add( group )
+        trans.sa_session.flush()
+        return group
+
+    def list( self, trans, deleted=False ):
+        """
+        Return a list of groups from the DB.
+
+        :returns: query that will emit all groups
+        :rtype:   sqlalchemy query
+        """
+        is_admin = trans.user_is_admin()
+        query = trans.sa_session.query( trans.app.model.Group )
+        if is_admin:
+            if deleted is None:
+                #  Flag is not specified, do not filter on it.
+                pass
+            elif deleted:
+                query = query.filter( trans.app.model.Group.table.c.deleted == True )
+            else:
+                query = query.filter( trans.app.model.Group.table.c.deleted == False )
+        else:
+            query = query.filter( trans.app.model.Group.table.c.deleted == False )
+        return query

lib/tool_shed/managers/repositories.py

@@ -0,0 +1,66 @@
+"""
+Manager and Serializer for TS repositories.
+"""
+from galaxy.exceptions import InconsistentDatabase
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import InternalServerError
+from sqlalchemy.orm.exc import MultipleResultsFound
+from sqlalchemy.orm.exc import NoResultFound
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+# =============================================================================
+class RepoManager( object ):
+    """
+    Interface/service object for interacting with TS repositories.
+    """
+
+    def __init__( self, *args, **kwargs ):
+        super( RepoManager, self ).__init__( *args, **kwargs )
+
+    def get( self, trans, decoded_repo_id ):
+        """
+        Get the repo from the DB.
+
+        :param  decoded_repo_id:       decoded repo id
+        :type   decoded_repo_id:       int
+
+        :returns:   the requested repo
+        :rtype:     Repository
+        """
+        try:
+            repo = trans.sa_session.query( trans.app.model.Repository ).filter( trans.app.model.Repository.table.c.id == decoded_repo_id ).one()
+        except MultipleResultsFound:
+            raise InconsistentDatabase( 'Multiple repositories found with the same id.' )
+        except NoResultFound:
+            raise RequestParameterInvalidException( 'No repository found with the id provided.' )
+        except Exception:
+            raise InternalServerError( 'Error loading from the database.' )
+        return repo
+
+    def list_by_owner( self, trans, user_id ):
+        """
+        Return a list of of repositories owned by a given TS user from the DB.
+
+        :returns: query that will emit repositories owned by given user
+        :rtype:   sqlalchemy query
+        """
+        query = trans.sa_session.query( trans.app.model.Repository ).filter( trans.app.model.Repository.table.c.user_id == user_id )
+        return query
+
+    def create( self, trans, name, description=''):
+        """
+        Create a new group.
+        """
+
+    def update( self, trans, group, name=None, description=None ):
+        """
+        Update the given group
+        """
+
+    def delete( self, trans, group, undelete=False ):
+        """
+        Mark given group deleted/undeleted based on the flag.
+        """

run_tests.sh

@@ -17,6 +17,7 @@ cat <<EOF
 '${0##*/} -api (test_path)'         for running all the test scripts in the ./test/api directory
 '${0##*/} -toolshed (test_path)'    for running all the test scripts in the ./test/tool_shed/functional directory
 '${0##*/} -workflow test.xml'       for running a workflow test case as defined by supplied workflow xml test file (experimental)
+'${0##*/} -installed'               for running tests of Tool Shed installed tools
 '${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
 '${0##*/} -framework -id toolid'    for testing one framework tool (in test/functional/tools/) with id 'toolid'
 '${0##*/} -data_managers -id data_manager_id'    for testing one Data Manager with id 'data_manager_id'

static/maps/mvc/groups/group-detail-view.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"group-detail-view.js","sources":["../../../src/mvc/groups/group-detail-view.js"],"names":["define","mod_toastr","mod_group_model","GroupDetailView","Backbone","View","extend","el","options","app","initialize","this","_","window","globalTS","groups","collection","model","get","group_id","render","fetchGroup","that","Group","id","fetch","success","console","log","error","response","responseJSON","err_msg","template","templateRow","$el","html","group","$","tooltip","join"],"mappings":"AAAAA,QACI,cACA,0BAEJ,SACIC,EACAC,GAIJ,GAAIC,GAAkBC,SAASC,KAAKC,QAChCC,GAAI,kBACJC,WACAC,IAAK,KAELC,WAAa,SAAUF,GACnBG,KAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKF,IAAMI,OAAOC,SAASC,OAEE,OAAxBJ,KAAKF,IAAIO,YACVL,KAAKM,MAAQN,KAAKF,IAAIO,WAAWE,IAAKP,KAAKH,QAAQW,UACnDR,KAAKS,UAELT,KAAKU,cAKbA,WAAY,SAAUb,GAClB,GAAIc,GAAOX,IACXA,MAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKM,MAAQ,GAAIf,GAAgBqB,OAASC,GAAIb,KAAKH,QAAQW,WAC3DR,KAAKM,MAAMQ,OACTC,QAAS,SAAUT,GACjBU,QAAQC,IAAK,mBACbD,QAAQC,IAAKX,GACbK,EAAKF,UAEPS,MAAO,SAAUZ,EAAOa,GAElB7B,EAAW4B,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAM9BZ,OAAQ,WACJ,GAAIa,GAAWtB,KAAKuB,aACpBvB,MAAKwB,IAAIC,KAAMH,GAAYI,MAAO1B,KAAKM,SACvCqB,EAAE,yBAAyBC,WAG/BL,YAAa,WACT,MAAOtB,GAAEqB,UACD,QACI,oCACA,mCACA,kMAEA,mBACA,6CACI,UACI,gBACA,wBACA,sBACJ,WACA,UACI,wDACA,OACI,OACI,yBACJ,QACA,OACI,gPACJ,QACA,OACI,6BACJ,QACJ,QACA,YACJ,WACJ,WAEA,wBACA,6CACI,UACI,gBACA,uBACA,qBACA,iBACA,mBACA,kBACA,oBACJ,WACA,UACI,2DACA,OACI,OACI,6KACJ,QACA,OACI,0BACJ,QACA,OACI,+BACJ,QACA,OACI,oBACJ,QACA,OACI,2BACJ,QACA,OACI,2BACJ,QACA,OACI,uBACJ,QACJ,QACA,YACJ,WACJ,WACJ,UACNO,KAAK,OAGf,QACIrC,gBAAiBA"}

static/maps/mvc/groups/group-groupdetail-view.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"group-groupdetail-view.js","sources":["../../../src/mvc/groups/group-groupdetail-view.js"],"names":["define","GroupDetailView","Backbone","View","extend","events","initialize","group","this","render","tmpl","templateRow","setElement","$el","show","_","template","join"],"mappings":"AAAAA,UACA,WAGA,GAAIC,GAAkBC,SAASC,KAAKC,QAChCC,UAGAC,WAAa,SAAUC,GACnBC,KAAKC,OAAQF,IAGjBE,OAAQ,SAAUF,GACd,GAAIG,GAAOF,KAAKG,aAGhB,OAFAH,MAAKI,WAAWF,GAAQH,MAAMA,KAC9BC,KAAKK,IAAIC,OACFN,MAGXG,YAAa,WACT,MAAOI,GAAEC,UACD,8BACNC,KAAK,OAKf,QACIhB,gBAAiBA"}

static/maps/mvc/groups/group-grouprow-view.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"group-grouprow-view.js","sources":["../../../src/mvc/groups/group-grouprow-view.js"],"names":["define","GroupRowView","Backbone","View","extend","events","initialize","group","this","render","tmpl","templateRow","setElement","$el","show","_","template","join"],"mappings":"AAAAA,UACA,WAGA,GAAIC,GAAeC,SAASC,KAAKC,QAC7BC,UAGAC,WAAa,SAAUC,GACnBC,KAAKC,OAAOF,IAGhBE,OAAQ,SAAUF,GACd,GAAIG,GAAOF,KAAKG,aAIhB,OAFAH,MAAKI,WAAWF,GAAQH,MAAMA,KAC9BC,KAAKK,IAAIC,OACFN,MAaXG,YAAa,WACT,MAAOI,GAAEC,UACD,iDACA,iFACA,uBACA,6CACA,2CACA,SACNC,KAAK,OAKf,QACIhB,aAAcA"}

static/maps/mvc/groups/group-list-view.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"group-list-view.js","sources":["../../../src/mvc/groups/group-list-view.js"],"names":["define","mod_toastr","mod_group_model","mod_group_listrow_view","GroupListView","Backbone","View","extend","el","defaults","initialize","options","this","_","that","window","globalTS","groups","collection","Groups","fetch","success","model","console","log","render","error","response","responseJSON","err_msg","$","hide","template","templateGroupsList","$el","html","length","order","renderRows","models","tooltip","css","groups_to_render","i","group","renderOne","rowView","GroupListRowView","find","append","tmpl_array","push","join"],"mappings":"AAAAA,QACI,cACA,yBACA,iCAED,SACCC,EACAC,EACAC,GAGJ,GAAIC,GAAgBC,SAASC,KAAKC,QAC9BC,GAAI,kBACJC,YAOAC,WAAa,SAAUC,GACnBC,KAAKD,QAAUE,EAAEJ,SAAUG,KAAKD,YAAeC,KAAKH,SAAUE,EAC9D,IAAIG,GAAOF,IACXG,QAAOC,SAASC,OAAOC,WAAa,GAAIhB,GAAgBiB,OACxDJ,OAAOC,SAASC,OAAOC,WAAWE,OAChCC,QAAS,SAAUC,GACjBC,QAAQC,IAAK,mBACbD,QAAQC,IAAKF,GACbR,EAAKW,UAEPC,MAAO,SAAUJ,EAAOK,GAElB1B,EAAWyB,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAO9BT,MAAO,aAMPK,OAAQ,SAAWd,GACfC,KAAKD,QAAUE,EAAEN,OAAQK,KAAKD,QAASA,GACvCmB,EAAG,YAAaC,MAChB,IAAIC,GAAWpB,KAAKqB,oBACpBrB,MAAKsB,IAAIC,KAAMH,GAAYI,OAAQ,GAAIC,MAAO,SAC9CzB,KAAK0B,WAAYvB,OAAOC,SAASC,OAAOC,WAAWqB,QACnDT,EAAG,yBAA0BU,UAC7BV,EAAG,WAAYW,IAAK,WAAW,SAOnCH,WAAY,SAAUI,GAClB,IAAM,GAAIC,GAAI,EAAGA,EAAID,EAAiBN,OAAQO,IAAM,CAChD,GAAIC,GAAQF,EAAiBC,EAC7B/B,MAAKiC,WAAaD,MAAOA,MAQjCC,UAAW,SAAUlC,GACjB,GAAImC,GAAU,GAAI3C,GAAuB4C,iBAAkBpC,EAC3DC,MAAKsB,IAAIc,KAAM,oBAAqBC,OAAQH,EAAQtC,KAyCxDyB,mBAAoB,WAuBhB,MAtBAiB,eAEAA,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,mDAChBD,WAAWC,KAAK,4BAChBD,WAAWC,KAAK,uCAChBD,WAAWC,KAAK,iBAChBD,WAAWC,KAAK,8CAChBD,WAAWC,KAAK,cAChBD,WAAWC,KAAK,mMAChBD,WAAWC,KAAK,gDAChBD,WAAWC,KAAK,6CAChBD,WAAWC,KAAK,iDAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,mCAEhBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,YAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,UAETtC,EAAEmB,SAASkB,WAAWE,KAAK,OAK1C,QACIhD,cAAeA"}

static/maps/mvc/groups/group-listrow-view.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"group-listrow-view.js","sources":["../../../src/mvc/groups/group-listrow-view.js"],"names":["define","GroupListRowView","Backbone","View","extend","events","initialize","options","this","render","group","tmpl","templateRow","setElement","$el","show","_","template","join"],"mappings":"AAAAA,UACA,WAGA,GAAIC,GAAmBC,SAASC,KAAKC,QACjCC,UAEAC,WAAa,SAAUC,GACnBC,KAAKC,OAAQF,EAAQG,QAGzBD,OAAQ,SAAUC,GACd,GAAIC,GAAOH,KAAKI,aAGhB,OAFAJ,MAAKK,WAAWF,GAAQD,MAAMA,KAC9BF,KAAKM,IAAIC,OACFP,MAGXI,YAAa,WACT,MAAOI,GAAEC,UACD,iDACA,iFACA,uBACA,6CACA,2CACA,SACNC,KAAK,OAKf,QACIjB,iBAAkBA"}

static/maps/mvc/groups/group-model.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"group-model.js","sources":["../../../src/mvc/groups/group-model.js"],"names":["define","Group","Backbone","Model","extend","urlRoot","Groups","Collection","url","model"],"mappings":"AAAAA,UAAW,WAKP,GAAIC,GAAQC,SAASC,MAAMC,QACzBC,QAAS,gBAGPC,EAASJ,SAASK,WAAWH,QAC/BI,IAAK,cAELC,MAAOR,GAIb,QACIA,MAAOA,EACPK,OAAQA"}

static/maps/mvc/groups/group.model.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"group.model.js","sources":["../../../src/mvc/groups/group.model.js"],"names":["define","Group","Backbone","Model","extend","urlRoot","Groups","Collection","url","model"],"mappings":"AAAAA,UAAW,WAKP,GAAIC,GAAQC,SAASC,MAAMC,QACzBC,QAAS,iBAGPC,EAASJ,SAASK,WAAWH,QAC/BI,IAAK,cAELC,MAAOR,GAIb,QACIA,MAAOA,EACPK,OAAQA"}

static/maps/toolshed.groups.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"toolshed.groups.js","sources":["../src/toolshed.groups.js"],"names":["define","mod_group_list","mod_group_detail","ToolshedRouter","Backbone","Router","extend","routes",":group_id","ToolshedGroups","View","groupListView","groupDetailView","collection","initialize","window","globalTS","groups","this","ts_router","on","GroupListView","group_id","GroupDetailView","history","start","pushState"],"mappings":"AAIAA,QACQ,6BACA,+BACA,0BAEJ,SACIC,EACAC,GAMR,GAAIC,GAAiBC,SAASC,OAAOC,QACjCC,QACI,GAA4B,SAC5BC,YAA4B,gBAKhCC,EAAiBL,SAASM,KAAKJ,QAC/BK,cAAe,KACfC,gBAAiB,KACjBC,WAAY,KAEZC,WAAa,WACTC,OAAOC,SAASC,OAASC,KAEzBA,KAAKC,UAAY,GAAIhB,GACrBe,KAAKC,UAAUC,GAAI,eAAgB,WAC/BL,OAAOC,SAASC,OAAON,cAAgB,GAAIV,GAAeoB,gBAG9DH,KAAKC,UAAUC,GAAI,mBAAoB,SAAUE,GAC7CP,OAAOC,SAASC,OAAOL,gBAAkB,GAAIV,GAAiBqB,iBAAmBD,SAAUA,MAG/FlB,SAASoB,QAAQC,OAAOC,WAAW,MAI3C,QACIjB,eAAgBA"}

static/scripts/mvc/groups/group-detail-view.js

@@ -0,0 +1,2 @@
+define(["libs/toastr","mvc/groups/group-model"],function(a,b){var c=Backbone.View.extend({el:"#groups_element",options:{},app:null,initialize:function(a){this.options=_.extend(this.options,a),this.app=window.globalTS.groups,null!==this.app.collection?(this.model=this.app.collection.get(this.options.group_id),this.render()):this.fetchGroup()},fetchGroup:function(c){var d=this;this.options=_.extend(this.options,c),this.model=new b.Group({id:this.options.group_id}),this.model.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},render:function(){var a=this.templateRow();this.$el.html(a({group:this.model})),$("#center [data-toggle]").tooltip()},templateRow:function(){return _.template(["<div>",'<h3><%= group.get("name") %></h3>','<p class="" style="color:gray;">','A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined tool downloads.</p>',"<h3>Members</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Repositories</th>","<th>Registered</th>","</thead>","<tbody>",'<% _.each(group.get("members"), function(member) { %>',"<tr>","<td>","<%= member.username %>","</td>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= member.username %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',"</td>","<td>","<%= member.time_created %>","</td>","</tr>","<% }); %>","</tbody>","</table>","<h3>Repositories</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Description</th>","<th>Downloads</th>","<th>Owner</th>","<th>Created</th>","<th>Rating</th>","<th>Verified</th>","</thead>","<tbody>",'<% _.each(group.get("repositories"), function(repo) { %>',"<tr>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Details of <%= repo.name %>" href="/view/<%= repo.owner %>/<%= repo.name %>" id="<%= repo.id %>"><%= repo.name %></a>',"</td>","<td>","<%= repo.description %>","</td>","<td>","<%= repo.times_downloaded %>","</td>","<td>","<%= repo.owner %>","</td>","<td>","<%= repo.time_created %>","</td>","<td>","<%= repo.ratings_mean %>","</td>","<td>","<%= repo.approved %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>"].join(""))}});return{GroupDetailView:c}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-detail-view.js.map

static/scripts/mvc/groups/group-groupdetail-view.js

@@ -0,0 +1,2 @@
+define([],function(){var a=Backbone.View.extend({events:{},initialize:function(a){this.render(a)},render:function(a){var b=this.templateRow();return this.setElement(b({group:a})),this.$el.show(),this},templateRow:function(){return _.template(["<div>TEST GROUP PAGE</div>"].join(""))}});return{GroupDetailView:a}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-groupdetail-view.js.map

static/scripts/mvc/groups/group-grouprow-view.js

@@ -0,0 +1,2 @@
+define([],function(){var a=Backbone.View.extend({events:{},initialize:function(a){this.render(a)},render:function(a){var b=this.templateRow();return this.setElement(b({group:a})),this.$el.show(),this},templateRow:function(){return _.template(['<tr class="" data-id="<%- group.get("id") %>">','<td><a href="/groups/<%= group.get("id") %>"><%= group.get("name") %></a></td>',"<td>description</td>",'<td><%= group.get("total_members") %></td>','<td><%= group.get("total_repos") %></td>',"</tr>"].join(""))}});return{GroupRowView:a}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-grouprow-view.js.map

static/scripts/mvc/groups/group-list-view.js

@@ -0,0 +1,2 @@
+define(["libs/toastr","mvc/groups/group-model","mvc/groups/group-listrow-view"],function(a,b,c){var d=Backbone.View.extend({el:"#groups_element",defaults:{},initialize:function(c){this.options=_.defaults(this.options||{},this.defaults,c);var d=this;window.globalTS.groups.collection=new b.Groups,window.globalTS.groups.collection.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},fetch:function(){},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").hide();var b=this.templateGroupsList();this.$el.html(b({length:10,order:"asc"})),this.renderRows(window.globalTS.groups.collection.models),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({group:c})}},renderOne:function(a){var b=new c.GroupListRowView(a);this.$el.find("#group_list_body").append(b.el)},templateGroupsList:function(){return tmpl_array=[],tmpl_array.push('<div id="groups">'),tmpl_array.push("</div>"),tmpl_array.push('<div class="groups_container table-responsive">'),tmpl_array.push("<% if(length === 0) { %>"),tmpl_array.push("<div>There are no groups yet.</div>"),tmpl_array.push("<% } else{ %>"),tmpl_array.push('<table class="grid table table-condensed">'),tmpl_array.push("   <thead>"),tmpl_array.push('     <th style="width:30%;"><a class="sort-groups-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'),tmpl_array.push('     <th style="width:22%;">description</th>'),tmpl_array.push('     <th style="width:22%;">members</th> '),tmpl_array.push('     <th style="width:26%;">repositories</th>'),tmpl_array.push("   </thead>"),tmpl_array.push('   <tbody id="group_list_body">'),tmpl_array.push("   </tbody>"),tmpl_array.push("</table>"),tmpl_array.push("<% }%>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))}});return{GroupListView:d}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-list-view.js.map

static/scripts/mvc/groups/group-listrow-view.js

@@ -0,0 +1,2 @@
+define([],function(){var a=Backbone.View.extend({events:{},initialize:function(a){this.render(a.group)},render:function(a){var b=this.templateRow();return this.setElement(b({group:a})),this.$el.show(),this},templateRow:function(){return _.template(['<tr class="" data-id="<%- group.get("id") %>">','<td><a href="groups#/<%= group.get("id") %>"><%= group.get("name") %></a></td>',"<td>description</td>",'<td><%= group.get("total_members") %></td>','<td><%= group.get("total_repos") %></td>',"</tr>"].join(""))}});return{GroupListRowView:a}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-listrow-view.js.map

static/scripts/mvc/groups/group-model.js

@@ -0,0 +1,2 @@
+define([],function(){var a=Backbone.Model.extend({urlRoot:"/api/groups"}),b=Backbone.Collection.extend({url:"/api/groups",model:a});return{Group:a,Groups:b}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-model.js.map

static/scripts/mvc/groups/group.model.js

@@ -0,0 +1,2 @@
+define([],function(){var a=Backbone.Model.extend({urlRoot:"/api/groups/"}),b=Backbone.Collection.extend({url:"/api/groups",model:a});return{Group:a,Groups:b}});
+//# sourceMappingURL=../../../maps/mvc/groups/group.model.js.map

static/scripts/toolshed.groups.js

@@ -0,0 +1,2 @@
+define(["mvc/groups/group-list-view","mvc/groups/group-detail-view","mvc/groups/group-model"],function(a,b){var c=Backbone.Router.extend({routes:{"":"groups",":group_id":"group_page"}}),d=Backbone.View.extend({groupListView:null,groupDetailView:null,collection:null,initialize:function(){window.globalTS.groups=this,this.ts_router=new c,this.ts_router.on("route:groups",function(){window.globalTS.groups.groupListView=new a.GroupListView}),this.ts_router.on("route:group_page",function(a){window.globalTS.groups.groupDetailView=new b.GroupDetailView({group_id:a})}),Backbone.history.start({pushState:!1})}});return{ToolshedGroups:d}});
+//# sourceMappingURL=../maps/toolshed.groups.js.map

static/style/blue/base.css

@@ -1761,6 +1761,7 @@ body{background:#fff;color:#000;margin:10px}body.full-content{overflow:hidden;ma
 #left,#left-border,#center,#right-border,#right{position:absolute;top:34px;bottom:0px;overflow:hidden;background:#fff}
 #left{left:0px;width:250px;z-index:200;border-right:solid #999 1px}
 #left-border{left:250px}
+.reports-panel-container{position:absolute;top:30px;bottom:10px;overflow:scroll;width:100%;padding:10px}
 #center{left:250px;right:250px;overflow:hidden;z-index:1}
 #right-border{right:250px}
 #right{width:250px;right:0px;z-index:200;border-left:solid #999 1px}

static/toolshed/src

@@ -0,0 +1 @@
+../../client/toolshed/scripts/

templates/admin/tool_errors.mako

@@ -0,0 +1,27 @@
+<%inherit file="/base.mako"/>
+
+<%def name="title()">Tool Errors</%def>
+
+<h2>Tool Errors</h2>
+
+<p>
+Internal Tool Error log
+</p>
+
+<table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
+<tr class="header">
+<td>Time</td>
+<td>Phase</td>
+<td>File</td>
+<td>Error</td>
+</tr>
+%for error in tool_errors:
+<tr>
+    <td>${error['time']}</td>
+    <td>${error['phase']}</td>
+    <td>${error['file']}</td>
+    <td>${error['error']}</td>
+</tr>
+%endfor
+</table>
+

templates/grid_base.mako

@@ -6,7 +6,6 @@
         if kwargs.get( 'embedded', False ):
             # No inheritance - using only embeddable content (self.body)
             return None
-
         if context.get('use_panels'):
             if context.get('webapp'):
                 app_name = context.get('webapp')

templates/webapps/galaxy/admin/index.mako

@@ -73,6 +73,7 @@
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_versions' )}" target="galaxy_main">Tool lineage</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='reload_tool' )}" target="galaxy_main">Reload a tool's configuration</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='review_tool_migration_stages' )}" target="galaxy_main">Review tool migration stages</a></div>
+                        <div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_errors' )}" target="galaxy_main">View Tool Error Logs</a></div>
                     </div>
                 </div>
                 <div class="toolSectionPad"></div>

templates/webapps/reports/index.mako

@@ -36,7 +36,7 @@
     <div class="unified-panel-header" unselectable="on">
         <div class='unified-panel-header-inner'>Reports</div>
     </div>
-    <div class="page-container" style="padding: 10px;">
+    <div class="page-container reports-panel-container">
         <div class="toolMenu">
             <div class="toolSectionList">
                 <div class="toolSectionPad"></div>

templates/webapps/tool_shed/base_panels.mako

@@ -80,6 +80,9 @@
                 ## Repositories tab.
                 ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index' ) )}
                 
+                ## Groups tab.
+                ${tab( "groups", "Groups", h.url_for( controller='/groups', action='index' ) )}
+
                 ## Admin tab.
                 ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )}
 

templates/webapps/tool_shed/group/index.mako

@@ -0,0 +1,50 @@
+<%inherit file="/webapps/tool_shed/base_panels.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="stylesheets()">
+    ## Include "base.css" for styling tool menu and forms (details)
+    ${h.css( "base", "autocomplete_tagging", "tool_menu" )}
+
+    ## But make sure styles for the layout take precedence
+    ${parent.stylesheets()}
+
+    <style type="text/css">
+        body { margin: 0; padding: 0; overflow: hidden; }
+        #left {
+            background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x;
+        }
+        .unified-panel-body {
+            overflow: auto;
+        }
+        .toolMenu {
+            margin-left: 10px;
+        }
+    </style>
+</%def>
+
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+</%def>
+
+<%def name="init()">
+    %if trans.app.config.require_login and not trans.user:
+        <script type="text/javascript">
+            if ( window != top ) {
+                top.location.href = location.href;
+            }
+        </script>
+    %endif
+</%def>
+
+<%def name="center_panel()">
+    <script type="text/javascript">
+        window.globalTS = new Object();
+        $( function(){
+            require([ '${config.get( "app" ).get( "jscript" )}' ], function( groups ){
+                app = new groups.ToolshedGroups();
+            });
+        });
+    </script>
+    <div id="groups_element" style="width: 95%; margin:auto; margin-top:2em; "></div>
+</%def>