Merge branch 'dev' into grid_histories

client/galaxy/scripts/apps/analysis.js

@@ -9,7 +9,8 @@ var jQuery = require( 'jquery' ),
     UserPreferences = require( 'mvc/user/user-preferences' ),
     CustomBuilds = require( 'mvc/user/user-custom-builds' ),
     Tours = require( 'mvc/tours' ),
-    GridView = require( 'mvc/grid/grid-view' )
+    GridView = require( 'mvc/grid/grid-view' ),
+    PageList = require( 'mvc/page/page-list' ),
     Workflows = require( 'mvc/workflow/workflow' ),
     HistoryList = require( 'mvc/history/history-list' ),
     WorkflowsConfigureMenu = require( 'mvc/workflow/workflow-configure-menu' );
@@ -84,6 +85,7 @@ window.app = function app( options, bootstrapped ){
             '(/)workflow(/)' : 'show_workflows',
             '(/)pages(/)(:action_id)' : 'show_pages',
             '(/)histories(/)(:action_id)' : 'show_histories',
+            '(/)datasets(/)(:action_id)' : 'show_datasets',
             '(/)workflow/configure_menu(/)' : 'show_configure_menu',
             '(/)custom_builds' : 'show_custom_builds'
         },
@@ -123,8 +125,16 @@ window.app = function app( options, bootstrapped ){
             this.page.display( new HistoryList.View() );
         },
 
+        show_datasets : function() {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'dataset/list', dict_format: true } ) );
+        },
+
         show_pages : function( action_id ) {
-            this.page.display( new GridView( { url_base: Galaxy.root + 'page/list_published', dict_format: true } ) );
+            if ( action_id == 'list' ) {
+                this.page.display( new PageList.View() );
+            } else {
+                this.page.display( new GridView( { url_base: Galaxy.root + 'page/list_published', dict_format: true } ) );
+            }
         },
 
         show_workflows : function(){

client/galaxy/scripts/layout/menu.js

@@ -271,11 +271,11 @@ var Collection = Backbone.Collection.extend({
                         target  : '_top'
                     },{
                         title   : _l('Saved Datasets'),
-                        url     : 'dataset/list',
-                        target  : 'galaxy_main'
+                        url     : 'datasets/list',
+                        target  : '_top'
                     },{
                         title   : _l('Saved Pages'),
-                        url     : 'page/list',
+                        url     : 'pages/list',
                         target  : '_top'
                     }]
             };

client/galaxy/scripts/mvc/grid/grid-view.js

@@ -639,7 +639,7 @@ return Backbone.View.extend({
                 var insert = self.grid.get('insert');
 
                 // request new configuration
-                var json = self.dict_format ? response_text.embedded_grid || response_text : $.parseJSON(response_text);
+                var json = self.dict_format ? response_text : $.parseJSON(response_text);
 
                 // update
                 json.embedded = embedded;

client/galaxy/scripts/mvc/page/page-list.js

@@ -0,0 +1,56 @@
+/** This class renders the page list. */
+define( [ 'utils/utils', 'mvc/grid/grid-view' ], function( Utils, GridView ) {
+    var View = Backbone.View.extend({
+        initialize: function( options ) {
+            var self = this;
+            this.setElement( $( '<div/>' ) );
+            this.model = new Backbone.Model();
+            Utils.get({
+                url     : Galaxy.root + 'page/list',
+                success : function( response ) {
+                    response[ 'dict_format' ] = true;
+                    self.model.set( response );
+                    self.render();
+                }
+            });
+        },
+
+        render: function() {
+            var grid = new GridView( this.model.attributes );
+            this.$el.empty().append( grid.$el );
+            this.$el.append( this._templateShared() );
+        },
+
+        _templateShared: function() {
+            var $tmpl = $(  '<div>' +
+                                '<h2>Pages shared with you by others</h2>' +
+                            '</div>' );
+            var options = this.model.attributes;
+            if ( options.shared_by_others && options.shared_by_others.length > 0 ) {
+                var $table = $( '<table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">' +
+                                    '<tr class="header">' +
+                                        '<th>Title</th>' +
+                                        '<th>Owner</th>' +
+                                    '</tr>' +
+                                '</table>' );
+                _.each( options.shared_by_others, function( page, index ) {
+                    var display_url = Galaxy.root + 'page/display_by_username_and_slug?username=' + page.username + '&slug=' + page.slug;
+                    $table.append(  '<tr>' +
+                                        '<td>' +
+                                            '<a href="' + display_url + '">' + _.escape( page.title ) + '</a>' +
+                                        '</td>' +
+                                        '<td>' + _.escape( page.username ) + '</td>' +
+                                    '</tr>' );
+                });
+                $tmpl.append( $table );
+            } else {
+                $tmpl.append( 'No pages have been shared with you.' );
+            }
+            return $tmpl;
+        }
+    });
+
+    return {
+        View: View
+    }
+});

config/datatypes_conf.xml.sample

@@ -602,11 +602,18 @@
     <datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" />
     <datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true" />
     <!-- PlantTribes datatypes -->
-    <datatype extension="ptalign" type="galaxy.datatypes.text:PlantTribesMultipleSequenceAlignment" />
-    <datatype extension="ptortho" type="galaxy.datatypes.text:PlantTribesOrtho" />
-    <datatype extension="ptorthocs" type="galaxy.datatypes.text:PlantTribesOrthoCodingSequence" />
-    <datatype extension="pttree" type="galaxy.datatypes.text:PlantTribesPhylogeneticTree" />
-    <datatype extension="smat" type="galaxy.datatypes.text:Smat" display_in_upload="true" />
+    <datatype extension="ptalign" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment" />
+    <datatype extension="ptalignca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment" />
+    <datatype extension="ptaligntrimmed" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed" />
+    <datatype extension="ptaligntrimmedca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment" />
+    <datatype extension="ptalignfiltered" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered" />
+    <datatype extension="ptalignfilteredca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment" />
+    <datatype extension="ptortho" type="galaxy.datatypes.plant_tribes:PlantTribesOrtho" />
+    <datatype extension="ptorthocs" type="galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence" />
+    <datatype extension="ptphylip" type="galaxy.datatypes.plant_tribes:PlantTribesPhylip" />
+    <datatype extension="pttgf" type="galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies" />
+    <datatype extension="pttree" type="galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree" />
+    <datatype extension="smat" type="galaxy.datatypes.plant_tribes:Smat" display_in_upload="true" />
   </registration>
   <sniffers>
     <!--
@@ -616,7 +623,7 @@
     defined format first, followed by next-most rigidly defined,
     and so on.
     -->
-    <sniffer type="galaxy.datatypes.text:Smat"/>
+    <sniffer type="galaxy.datatypes.plant_tribes:Smat"/>
     <sniffer type="galaxy.datatypes.mothur:Sabund"/>
     <sniffer type="galaxy.datatypes.mothur:Otu"/>
     <sniffer type="galaxy.datatypes.mothur:GroupAbund"/>

config/galaxy.ini.sample

@@ -349,10 +349,10 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 
 # Interactive environment plugins root directory: where to look for interactive
 # environment plugins.  By default none will be loaded.  Set to
-# config/plugins/interactive_environments to load Galaxy's stock plugins
-# (currently just Jupyter).  These will require Docker to be configured and
-# have security considerations, so proceed with caution. The path is relative to the
-# Galaxy root dir.  To use an absolute path begin the path with '/'.  This is a comma
+# config/plugins/interactive_environments to load Galaxy's stock plugins.
+# These will require Docker to be configured and have security considerations,
+# so proceed with caution. The path is relative to the Galaxy root dir.  To use
+# an absolute path begin the path with '/'.  This is a comma
 # separated list.
 #interactive_environment_plugins_directory =
 

config/job_conf.xml.sample_advanced

@@ -440,6 +440,53 @@
                the deployer. -->
           <!-- <param id="require_container">true</param> -->
         </destination>
+        <destination id="singularity_local" runner="local">
+          <param id="singularity_enabled">true</param>
+          <!-- See the above documentation for docker_volumes, singularity_volumes works
+               almost the same way. The only difference is that $default will expand with
+               rw directories that in Docker would expand as ro if any of subdirectories are rw.
+
+               As an example consider that Docker mounts the parent of the working directory
+               (this is known as the job directory) as ro and the working directory itself as rw.
+               This doesn't work in Singularity because if any parent directory is mounted as ro
+               none of its children will be rw. So the job directory will be mounted rw for
+               Singularity.
+          -->
+          <!--
+          <param id="singularity_volumes">$defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro</param>
+          -->
+          <!-- You can configure singularity to run using sudo - this probably should not
+               be set and may be removed in the future.
+          -->
+          <!-- <param id="singularity_sudo">false</param> -->
+          <!-- Following option can be used to tweak sudo command used by
+               default. -->
+          <!-- <param id="singularity_sudo_cmd">/usr/bin/sudo -extra_param</param> -->
+          <!-- Pass extra arguments to the singularity exec command not covered by the
+               above options. -->
+          <!-- <param id="singularity_run_extra_arguments"></param> -->
+          <!-- Following command can be used to tweak singularity command. -->
+          <!-- <param id="singularity_cmd">/usr/local/custom_docker/docker</param> -->
+
+          <!-- If deployer wants to use singularity for isolation, but does not
+               trust tool's specified container - a destination wide override
+               can be set. This will cause all jobs on this destination to use
+               that singularity image. -->
+          <!-- <param id="singularity_container_id_override">/path/to/singularity/image</param> -->
+
+          <!-- Likewise, if deployer wants to use singularity for isolation and
+               does trust tool's specified container - but also wants tool's not
+               configured to run in a container the following option can provide
+               a fallback. -->
+          <!-- <param id="singularity_default_container_id">/path/to/singularity/image</param> -->
+
+          <!-- If the destination should be secured to only allow containerized jobs
+               the following parameter may be set for the job destination. Not all,
+               or even most, tools available in Galaxy core or in the Tool Shed
+               support Docker yet so this option may require a lot of extra work for
+               the deployer. -->
+          <!-- <param id="require_container">true</param> -->
+        </destination>
         <destination id="pbs" runner="pbs" tags="mycluster"/>
         <destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs">
             <!-- Define parameters that are native to the job runner plugin. -->

lib/galaxy/config.py

@@ -247,7 +247,11 @@ def __init__( self, **kwargs ):
             log.warn("preserve_python_environment set to unknown value [%s], defaulting to legacy_only")
             preserve_python_environment = "legacy_only"
         self.preserve_python_environment = preserve_python_environment
+        # Older default container cache path, I don't think anyone is using it anymore and it wasn't documented - we
+        # should probably drop the backward compatiblity to save the path check.
         self.container_image_cache_path = self.resolve_path( kwargs.get( "container_image_cache_path", "database/container_images" ) )
+        if not os.path.exists( self.container_image_cache_path ):
+            self.container_image_cache_path = self.resolve_path( kwargs.get( "container_image_cache_path", "database/container_cache" ) )
         self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) )
         self.output_size_limit = int( kwargs.get( 'output_size_limit', 0 ) )
         self.retry_job_output_collection = int( kwargs.get( 'retry_job_output_collection', 0 ) )

lib/galaxy/datatypes/data.py

@@ -367,7 +367,28 @@ def display_data(self, trans, data, preview=False, filename=None, to_ext=None, *
             file_path = trans.app.object_store.get_filename(data.dataset, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename)
             if os.path.exists( file_path ):
                 if os.path.isdir( file_path ):
-                    return trans.show_error_message( "Directory listing is not allowed." )  # TODO: Reconsider allowing listing of directories?
+                    tmp_fh = tempfile.NamedTemporaryFile(delete=False)
+                    tmp_file_name = tmp_fh.name
+                    dir_items = sorted(os.listdir(file_path))
+                    base_path, item_name = os.path.split(file_path)
+                    tmp_fh.write('<html><head><h3>Directory %s contents: %d items</h3></head>\n' % (item_name, len(dir_items)))
+                    tmp_fh.write('<body><p/><table cellpadding="2">\n')
+                    for index, fname in enumerate(dir_items):
+                        if index % 2 == 0:
+                            bgcolor = '#D8D8D8'
+                        else:
+                            bgcolor = '#FFFFFF'
+                        # Can't have an href link here because there is no route
+                        # defined for files contained within multiple subdirectory
+                        # levels of the primary dataset.  Something like this is
+                        # close, but not quite correct:
+                        # href = url_for(controller='dataset', action='display',
+                        # dataset_id=trans.security.encode_id(data.dataset.id),
+                        # preview=preview, filename=fname, to_ext=to_ext)
+                        tmp_fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, fname))
+                    tmp_fh.write('</table></body></html>\n')
+                    tmp_fh.close()
+                    return open(tmp_file_name)
                 mime = mimetypes.guess_type( file_path )[0]
                 if not mime:
                     try: