Merging with dev

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' ),
     WorkflowsConfigureMenu = require( 'mvc/workflow/workflow-configure-menu' ),
     ToolFormComposite = require( 'mvc/tool/tool-form-composite' ),
@@ -122,7 +123,11 @@ window.app = function app( options, bootstrapped ){
         },
 
         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

@@ -275,7 +275,7 @@ var Collection = Backbone.Collection.extend({
                         target  : 'galaxy_main'
                     },{
                         title   : _l('Saved Pages'),
-                        url     : 'page/list',
+                        url     : 'pages/list',
                         target  : '_top'
                     }]
             };

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

@@ -656,7 +656,7 @@ 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 =
 

lib/galaxy/datatypes/data.py

@@ -367,7 +367,28 @@ class Data( object ):
             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:

lib/galaxy/datatypes/plant_tribes.py

@@ -0,0 +1,213 @@
+import logging
+import os
+import re
+
+from galaxy.datatypes.data import get_file_peek, Text
+from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
+from galaxy.datatypes.text import Html
+from galaxy.util import nice_size
+
+log = logging.getLogger(__name__)
+
+
+class Smat(Text):
+    file_ext = "smat"
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except:
+            return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            dataset.blurb = "ESTScan scores matrices"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disc'
+
+    def sniff(self, filename):
+        """
+        The use of ESTScan implies the creation of scores matrices which
+        reflect the codons preferences in the studied organisms.  The
+        ESTScan package includes scripts for generating these files.  The
+        output of these scripts consists of the matrices, one for each
+        isochor, and which look like this:
+
+        FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44
+        -1 0 2 -2
+        2 1 -8 0
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('test_space.txt')
+        >>> Smat().sniff(fname)
+        False
+        >>> fname = get_test_fname('test_tab.bed')
+        >>> Smat().sniff(fname)
+        False
+        >>> fname = get_test_fname('1.smat')
+        >>> Smat().sniff(fname)
+        True
+        """
+        line_no = 0
+        with open(filename, "r") as fh:
+            for line in fh:
+                line_no += 1
+                if line_no > 10000:
+                    return True
+                if line_no == 1 and not line.startswith('FORMAT'):
+                    # The first line is always the start of a format section.
+                    return False
+                if not line.startswith('FORMAT'):
+                    if line.find('\t') >= 0:
+                        # Smat files are not tabular.
+                        return False
+                    items = line.split()
+                    if len(items) != 4:
+                        return False
+                    for item in items:
+                        # Make sure each item is an integer.
+                        if re.match(r"[-+]?\d+$", item) is None:
+                            return False
+        return True
+
+
+class PlantTribes(Html):
+    """
+    PlantTribes abstract class.
+    """
+    composite_type = 'basic'
+    MetadataElement(name="num_files", default=0, desc="Number of files in files_path directory", param=MetadataParameter, readonly=True, visible=False, no_value=0)
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        try:
+            efp = dataset.extra_files_path
+            if os.path.exists(efp):
+                dataset.metadata.num_files = len(os.listdir(efp))
+        except Exception as e:
+            log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
+
+
+class PlantTribesOrtho(PlantTribes):
+    """
+    PlantTribes sequences classified into precomputed, orthologous gene family
+    clusters.
+    """
+    file_ext = "ptortho"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesOrthoCodingSequence(PlantTribes):
+    """
+    PlantTribes sequences classified into precomputed, orthologous gene family
+    clusters and corresponding coding sequences.
+    """
+    file_ext = "ptorthocs"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesTargetedGeneFamilies(PlantTribes):
+    """
+    PlantTribes targeted gene families.
+    """
+    file_ext = "pttgf"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Targeted gene families"
+
+
+class PlantTribesPhylogeneticTree(PlantTribes):
+    """
+    PlantTribes multiple sequence alignments and inferred maximum likelihood
+    phylogenies for orthogroups.
+    """
+    file_ext = "pttree"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesPhylip(PlantTribes):
+    """
+    PlantTribes orthogroup phylip multiple sequence alignments.
+    """
+    file_ext = "ptphylip"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesPhylip, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignment(PlantTribes):
+    """
+    PlantTribes multiple sequence alignments.
+    """
+    file_ext = "ptalign"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentCodonAlignment(PlantTribes):
+    """
+    PlantTribes multiple sequence alignments with codon alignments.
+    """
+    file_ext = "ptalignca"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentTrimmed(PlantTribes):
+    """
+    PlantTribes trimmed multiple sequence alignments.
+    """
+    file_ext = "ptaligntrimmed"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment(PlantTribes):
+    """
+    PlantTribes trimmed multiple sequence alignments with codon alignments.
+    """
+    file_ext = "ptaligntrimmedca"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentFiltered(PlantTribes):
+    """
+    PlantTribes filtered multiple sequence alignments.
+    """
+    file_ext = "ptalignfiltered"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment(PlantTribes):
+    """
+    PlantTribes filtered multiple sequence alignments with codon alignments.
+    """
+    file_ext = "ptalignfilteredca"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+        dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files

lib/galaxy/datatypes/text.py

@@ -546,113 +546,3 @@ class SnpSiftDbNSFP( Text ):
             else:
                 dataset.peek = 'file does not exist'
                 dataset.blurb = 'file purged from disc'
-
-
-class Smat(Text):
-    file_ext = "smat"
-
-    def display_peek(self, dataset):
-        try:
-            return dataset.peek
-        except:
-            return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        if not dataset.dataset.purged:
-            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
-            dataset.blurb = "ESTScan scores matrices"
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
-
-    def sniff(self, filename):
-        """
-        The use of ESTScan implies the creation of scores matrices which
-        reflect the codons preferences in the studied organisms.  The
-        ESTScan package includes scripts for generating these files.  The
-        output of these scripts consists of the matrices, one for each
-        isochor, and which look like this:
-
-        FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44
-        -1 0 2 -2
-        2 1 -8 0
-
-        >>> from galaxy.datatypes.sniff import get_test_fname
-        >>> fname = get_test_fname('test_space.txt')
-        >>> Smat().sniff(fname)
-        False
-        >>> fname = get_test_fname('test_tab.bed')
-        >>> Smat().sniff(fname)
-        False
-        >>> fname = get_test_fname('1.smat')
-        >>> Smat().sniff(fname)
-        True
-        """
-        line_no = 0
-        with open(filename, "r") as fh:
-            line_no += 1
-            if line_no > 10000:
-                return True
-            line = fh.readline(500)
-            if line_no == 1 and not line.startswith('FORMAT'):
-                # The first line is always the start of a format section.
-                return False
-            if not line.startswith('FORMAT'):
-                if line.find('\t') >= 0:
-                    # Smat files are not tabular.
-                    return False
-                items = line.split()
-                if len(items) != 4:
-                    return False
-                for item in items:
-                    # Make sure each item is an integer.
-                    if re.match(r"[-+]?\d+$", item) is None:
-                        return False
-        return True
-
-
-class PlantTribesOrtho(Html):
-    """
-    PlantTribes sequences classified into precomputed, orthologous gene family
-    clusters.
-    """
-    file_ext = "ptortho"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
-        dataset.blurb = "PlantTribes gene family clusters: %d files" % dataset.metadata.data_lines
-
-
-class PlantTribesOrthoCodingSequence(Html):
-    """
-    PlantTribes sequences classified into precomputed, orthologous gene family
-    clusters and corresponding coding sequences.
-    """
-    file_ext = "ptorthocs"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
-        dataset.blurb = "PlantTribes gene family clusters with corresponding coding sequences: %d files" % dataset.metadata.data_lines
-
-
-class PlantTribesPhylogeneticTree(Html):
-    """
-    PlantTribes multiple sequence alignments and inferred maximum likelihood
-    phylogenies for orthogroups.
-    """
-    file_ext = "pttree"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
-        dataset.blurb = "PlantTribes phylogenetic trees: %d files" % dataset.metadata.data_lines
-
-
-class PlantTribesMultipleSequenceAlignment(Html):
-    """
-    PlantTribes multiple sequence alignments for orthogroups.
-    """
-    file_ext = "ptalign"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
-        dataset.blurb = "PlantTribes multiple sequence alignments: %d files" % dataset.metadata.data_lines

lib/galaxy/webapps/galaxy/controllers/page.py

@@ -46,13 +46,13 @@ class PageListGrid( grids.Grid ):
                     key="free-text-search", visible=False, filterable="standard" )
                     )
     global_actions = [
-        grids.GridAction( "Add new page", dict( action='create' ) )
+        grids.GridAction( "Add new page", dict( action='create' ), target="inbound" )
     ]
     operations = [
         grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ),
-        grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ),
-        grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ),
-        grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
+        grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content' ) ),
+        grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit' ) ),
+        grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), url_args=dict( action='sharing' ) ),
         grids.GridOperation( "Delete", confirm="Are you sure you want to delete this page?" ),
     ]
 
@@ -308,6 +308,7 @@ class PageController( BaseUIController, SharableMixin,
         self.hda_manager = managers.hdas.HDAManager( app )
 
     @web.expose
+    @web.json
     @web.require_login()
     def list( self, trans, *args, **kwargs ):
         """ List user's pages. """
@@ -320,13 +321,10 @@ class PageController( BaseUIController, SharableMixin,
                 item = session.query( model.Page ).get( self.decode_id( id ) )
                 if operation == "delete":
                     item.deleted = True
-                if operation == "share or publish":
-                    return self.sharing( trans, **kwargs )
             session.flush()
 
-        # HACK: to prevent the insertion of an entire html document inside another
-        kwargs[ 'embedded' ] = True
-        # Build grid HTML.
+        # Build grid dictionary.
+        kwargs[ 'dict_format' ] = True
         grid = self._page_list( trans, *args, **kwargs )
 
         # Build list of pages shared with user.
@@ -339,7 +337,11 @@ class PageController( BaseUIController, SharableMixin,
             .all()
 
         # Render grid wrapped in panels
-        return trans.fill_template( "page/index.mako", embedded_grid=grid, shared_by_others=shared_by_others )
+        grid[ 'shared_by_others' ] = [ {
+            'username' : p.page.user.username,
+            'slug'     : p.page.slug,
+            'title'    : p.page.title } for p in shared_by_others ]
+        return grid
 
     @web.expose
     @web.json
@@ -384,7 +386,7 @@ class PageController( BaseUIController, SharableMixin,
                 session.flush()
                 # Display the management page
                 # trans.set_message( "Page '%s' created" % page.title )
-                return trans.response.send_redirect( web.url_for(controller='page', action='list' ) )
+                return trans.response.send_redirect( web.url_for(controller='pages', action='list' ) )
         return trans.show_form(
             web.FormBuilder( web.url_for(controller='page', action='create'), "Create new page", submit_text="Submit" )
             .add_text( "page_title", "Page title", value=page_title, error=page_title_err )
@@ -429,7 +431,7 @@ class PageController( BaseUIController, SharableMixin,
                 self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation )
                 session.flush()
                 # Redirect to page list.
-                return trans.response.send_redirect( web.url_for(controller='page', action='list' ) )
+                return trans.response.send_redirect( web.url_for(controller='pages', action='list' ) )
         else:
             page_title = page.title
             page_slug = page.slug
@@ -494,7 +496,7 @@ class PageController( BaseUIController, SharableMixin,
         session.flush()
 
         return trans.fill_template( "/sharing_base.mako",
-                                    item=page, use_panels=True )
+                                    item=page, controller_list='pages', use_panels=True )
 
     @web.expose
     @web.require_login( "use Galaxy pages" )

static/maps/mvc/page/page-list.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"page-list.js","sources":["../../../src/mvc/page/page-list.js"],"names":["define","Utils","GridView","View","Backbone","extend","initialize","self","this","setElement","$","model","Model","get","url","Galaxy","root","success","response","set","render","grid","attributes","$el","empty","append","_templateShared","$tmpl","options","shared_by_others","length","$table","_","each","page","display_url","username","slug","escape","title"],"mappings":"AACAA,QAAU,cAAe,sBAAwB,SAAUC,EAAOC,GAC9D,GAAIC,GAAOC,SAASD,KAAKE,QACrBC,WAAY,WACR,GAAIC,GAAOC,IACXA,MAAKC,WAAYC,EAAG,WACpBF,KAAKG,MAAQ,GAAIP,UAASQ,MAC1BX,EAAMY,KACFC,IAAUC,OAAOC,KAAO,YACxBC,QAAU,SAAUC,GAChBA,EAAwB,aAAI,EAC5BX,EAAKI,MAAMQ,IAAKD,GAChBX,EAAKa,aAKjBA,OAAQ,WACJ,GAAIC,GAAO,GAAInB,GAAUM,KAAKG,MAAMW,WACpCd,MAAKe,IAAIC,QAAQC,OAAQJ,EAAKE,KAC9Bf,KAAKe,IAAIE,OAAQjB,KAAKkB,oBAG1BA,gBAAiB,WACb,GAAIC,GAAQjB,EAAI,uDAGZkB,EAAUpB,KAAKG,MAAMW,UACzB,IAAKM,EAAQC,kBAAoBD,EAAQC,iBAAiBC,OAAS,EAAI,CACnE,GAAIC,GAASrB,EAAG,8IAMhBsB,GAAEC,KAAML,EAAQC,iBAAkB,SAAUK,GACxC,GAAIC,GAAcpB,OAAOC,KAAO,8CAAgDkB,EAAKE,SAAW,SAAWF,EAAKG,IAChHN,GAAON,OAAS,oBAEsBU,EAAc,KAAOH,EAAEM,OAAQJ,EAAKK,OAAU,gBAEvDP,EAAEM,OAAQJ,EAAKE,UAAa,gBAG7DT,EAAMF,OAAQM,OAEdJ,GAAMF,OAAQ,sCAElB,OAAOE,KAIf,QACIxB,KAAMA"}

static/scripts/bundled/admin.bundled.js

@@ -1,2 +1,2 @@
-webpackJsonp([4],{0:function(e,t,i){(function(e){var t=i(1),s=t,a=i(33).GalaxyApp,l=i(93),n=i(34);window.app=function(t,i){window.Galaxy=new a(t,i),Galaxy.debug("admin app"),Galaxy.params=Galaxy.config.params,s(function(){e.extend(t.config,{active_view:"admin"}),Galaxy.page=new n.View(e.extend(t,{Left:l}))})}}).call(t,i(2))},93:function(e,t,i){(function(t,s,a){var l=i(5),n=t.View.extend({initialize:function(e,i){var s=this;this.page=e,this.root=i.root,this.config=i.config,this.settings=i.settings,this.message=i.message,this.status=i.status,this.model=new t.Model({title:l("Administration")}),this.categories=new t.Collection([{title:"Server",items:[{title:"Data types registry",url:"admin/view_datatypes_registry"},{title:"Data tables registry",url:"admin/view_tool_data_tables"},{title:"Display applications",url:"admin/display_applications"},{title:"Manage jobs",url:"admin/jobs"}]},{title:"Tools and Tool Shed",items:[{title:"Search Tool Shed",url:"admin_toolshed/browse_tool_sheds",enabled:s.settings.is_tool_shed_installed},{title:"Search Tool Shed (Beta)",url:"admin_toolshed/browse_toolsheds",enabled:s.settings.is_tool_shed_installed&&s.config.enable_beta_ts_api_install},{title:"Monitor installing repositories",url:"admin_toolshed/monitor_repository_installation?installing_repository_ids="+s.settings.installing_repository_ids,enabled:s.settings.installing_repository_ids},{title:"Manage installed tools",url:"admin_toolshed/browse_repositories",enabled:s.settings.is_repo_installed},{title:"Reset metadata",url:"admin_toolshed/reset_metadata_on_selected_installed_repositories",enabled:s.settings.is_repo_installed},{title:"Download local tool",url:"admin/package_tool"},{title:"Tool lineage",url:"admin/tool_versions"},{title:"Reload a tool's configuration",url:"admin/reload_tool"},{title:"Review tool migration stages",url:"admin/review_tool_migration_stages"},{title:"View Tool Error Logs",url:"admin/tool_errors"},{title:"Manage Display Whitelist",url:"admin/sanitize_whitelist"},{title:"Manage Tool Dependencies",url:"admin/manage_tool_dependencies"}]},{title:"User Management",items:[{title:"Users",url:"admin/users"},{title:"Groups",url:"admin/groups"},{title:"Roles",url:"admin/roles"},{title:"API keys",url:"userskeys/all_users"},{title:"Impersonate a user",url:"admin/impersonate",enabled:s.config.allow_user_impersonation}]},{title:"Data",items:[{title:"Quotas",url:"admin/quotas",enabled:s.config.enable_quotas},{title:"Data libraries",url:"library_admin/browse_libraries"},{title:"Roles",url:"admin/roles"},{title:"Local data",url:"data_manager"}]},{title:"Form Definitions",items:[{title:"Form definitions",url:"forms/browse_form_definitions"}]},{title:"Sample Tracking",items:[{title:"Sequencers and external services",url:"external_service/browse_external_services"},{title:"Request types",url:"request_type/browse_request_types"},{title:"Sequencing requests",url:"requests_admin/browse_requests"},{title:"Find samples",url:"requests_common/find_samples?cntrller=requests_admin"}]}]),this.setElement(this._template())},render:function(){var e=this;this.$el.empty(),this.categories.each(function(t){var i=s(e._templateSection(t.attributes)),n=i.find(".ui-side-section-body");a.each(t.get("items"),function(t){(void 0===t.enabled||t.enabled)&&n.append(s("<div/>").addClass("ui-side-section-body-title").append(s("<a/>").attr({href:e.root+t.url,target:"galaxy_main"}).text(l(t.title))))}),e.$el.append(i)}),this.page.$("#galaxy_main").prop("src",this.root+"admin/center?message="+this.message+"&status="+this.status)},_templateSection:function(e){return["<div>",'<div class="ui-side-section-title">'+l(e.title)+"</div>",'<div class="ui-side-section-body"/>',"</div>"].join("")},_template:function(){return'<div class="ui-side-panel"/>'},toString:function(){return"adminPanel"}});e.exports=n}).call(t,i(3),i(1),i(2))}});
+webpackJsonp([4],{0:function(e,t,i){(function(e){var t=i(1),s=t,a=i(33).GalaxyApp,l=i(94),n=i(34);window.app=function(t,i){window.Galaxy=new a(t,i),Galaxy.debug("admin app"),Galaxy.params=Galaxy.config.params,s(function(){e.extend(t.config,{active_view:"admin"}),Galaxy.page=new n.View(e.extend(t,{Left:l}))})}}).call(t,i(2))},94:function(e,t,i){(function(t,s,a){var l=i(5),n=t.View.extend({initialize:function(e,i){var s=this;this.page=e,this.root=i.root,this.config=i.config,this.settings=i.settings,this.message=i.message,this.status=i.status,this.model=new t.Model({title:l("Administration")}),this.categories=new t.Collection([{title:"Server",items:[{title:"Data types registry",url:"admin/view_datatypes_registry"},{title:"Data tables registry",url:"admin/view_tool_data_tables"},{title:"Display applications",url:"admin/display_applications"},{title:"Manage jobs",url:"admin/jobs"}]},{title:"Tools and Tool Shed",items:[{title:"Search Tool Shed",url:"admin_toolshed/browse_tool_sheds",enabled:s.settings.is_tool_shed_installed},{title:"Search Tool Shed (Beta)",url:"admin_toolshed/browse_toolsheds",enabled:s.settings.is_tool_shed_installed&&s.config.enable_beta_ts_api_install},{title:"Monitor installing repositories",url:"admin_toolshed/monitor_repository_installation?installing_repository_ids="+s.settings.installing_repository_ids,enabled:s.settings.installing_repository_ids},{title:"Manage installed tools",url:"admin_toolshed/browse_repositories",enabled:s.settings.is_repo_installed},{title:"Reset metadata",url:"admin_toolshed/reset_metadata_on_selected_installed_repositories",enabled:s.settings.is_repo_installed},{title:"Download local tool",url:"admin/package_tool"},{title:"Tool lineage",url:"admin/tool_versions"},{title:"Reload a tool's configuration",url:"admin/reload_tool"},{title:"Review tool migration stages",url:"admin/review_tool_migration_stages"},{title:"View Tool Error Logs",url:"admin/tool_errors"},{title:"Manage Display Whitelist",url:"admin/sanitize_whitelist"},{title:"Manage Tool Dependencies",url:"admin/manage_tool_dependencies"}]},{title:"User Management",items:[{title:"Users",url:"admin/users"},{title:"Groups",url:"admin/groups"},{title:"Roles",url:"admin/roles"},{title:"API keys",url:"userskeys/all_users"},{title:"Impersonate a user",url:"admin/impersonate",enabled:s.config.allow_user_impersonation}]},{title:"Data",items:[{title:"Quotas",url:"admin/quotas",enabled:s.config.enable_quotas},{title:"Data libraries",url:"library_admin/browse_libraries"},{title:"Roles",url:"admin/roles"},{title:"Local data",url:"data_manager"}]},{title:"Form Definitions",items:[{title:"Form definitions",url:"forms/browse_form_definitions"}]},{title:"Sample Tracking",items:[{title:"Sequencers and external services",url:"external_service/browse_external_services"},{title:"Request types",url:"request_type/browse_request_types"},{title:"Sequencing requests",url:"requests_admin/browse_requests"},{title:"Find samples",url:"requests_common/find_samples?cntrller=requests_admin"}]}]),this.setElement(this._template())},render:function(){var e=this;this.$el.empty(),this.categories.each(function(t){var i=s(e._templateSection(t.attributes)),n=i.find(".ui-side-section-body");a.each(t.get("items"),function(t){(void 0===t.enabled||t.enabled)&&n.append(s("<div/>").addClass("ui-side-section-body-title").append(s("<a/>").attr({href:e.root+t.url,target:"galaxy_main"}).text(l(t.title))))}),e.$el.append(i)}),this.page.$("#galaxy_main").prop("src",this.root+"admin/center?message="+this.message+"&status="+this.status)},_templateSection:function(e){return["<div>",'<div class="ui-side-section-title">'+l(e.title)+"</div>",'<div class="ui-side-section-body"/>',"</div>"].join("")},_template:function(){return'<div class="ui-side-panel"/>'},toString:function(){return"adminPanel"}});e.exports=n}).call(t,i(3),i(1),i(2))}});
 //# sourceMappingURL=admin.bundled.js.map

static/scripts/mvc/page/page-list.js

@@ -0,0 +1,2 @@
+define(["utils/utils","mvc/grid/grid-view"],function(a,b){var c=Backbone.View.extend({initialize:function(){var b=this;this.setElement($("<div/>")),this.model=new Backbone.Model,a.get({url:Galaxy.root+"page/list",success:function(a){a.dict_format=!0,b.model.set(a),b.render()}})},render:function(){var a=new b(this.model.attributes);this.$el.empty().append(a.$el),this.$el.append(this._templateShared())},_templateShared:function(){var a=$("<div><h2>Pages shared with you by others</h2></div>"),b=this.model.attributes;if(b.shared_by_others&&b.shared_by_others.length>0){var c=$('<table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr class="header"><th>Title</th><th>Owner</th></tr></table>');_.each(b.shared_by_others,function(a){var b=Galaxy.root+"page/display_by_username_and_slug?username="+a.username+"&slug="+a.slug;c.append('<tr><td><a href="'+b+'">'+_.escape(a.title)+"</a></td><td>"+_.escape(a.username)+"</td></tr>")}),a.append(c)}else a.append("No pages have been shared with you.");return a}});return{View:c}});
+//# sourceMappingURL=../../../maps/mvc/page/page-list.js.map

templates/sharing_base.mako

@@ -73,6 +73,7 @@
     ## Set use_panels var for use in page's URLs.
     <% use_panels = context.get('use_panels', False)  %>
     <% controller_name = get_controller_name( item ) %>
+    <% controller_list = context.get('controller_list', controller_name)  %>
 
     ## Render message.
     %if message:
@@ -142,7 +143,7 @@
                         </blockquote>
 
                         %if item.published:
-                            This ${item_class_name_lc} is publicly listed and searchable in Galaxy's <a href='${h.url_for( controller=controller_name, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section.
+                            This ${item_class_name_lc} is publicly listed and searchable in Galaxy's <a href='${h.url_for( controller=controller_list, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section.
                         %endif
                     </div>
 
@@ -155,16 +156,16 @@
                             <div class="toolParamHelp">Disables ${item_class_name_lc}'s link so that it is not accessible.</div>
                             <br />
                             <input class="action-button" type="submit" name="publish" value="Publish ${item_class_name}" method="POST">
-                            <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( controller=controller_name, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div>
+                            <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( controller=controller_list, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div>
 
                         <br />
                         %else: ## item.published == True
                             ## Item is importable and published. User can unpublish or disable import and unpublish.
                             <input class="action-button" type="submit" name="unpublish" value="Unpublish ${item_class_name}">
-                            <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for(controller=controller_name, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div>
+                            <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for(controller=controller_list, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div>
                             <br />
                             <input class="action-button" type="submit" name="disable_link_access_and_unpublish" value="Disable Access to ${item_class_name} via Link and Unpublish">
-                            <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for(controller=controller_name, action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div>
+                            <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for(controller=controller_list, action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div>
                         %endif
                     </form>
                     </div>
@@ -179,7 +180,7 @@
 
                         <br />
                         <input class="action-button" type="submit" name="make_accessible_and_publish" value="Make ${item_class_name} Accessible and Publish" method="POST">
-                        <div class="toolParamHelp">Makes the ${item_class_name_lc} accessible via link (see above) and publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for(controller=controller_name, action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div>
+                        <div class="toolParamHelp">Makes the ${item_class_name_lc} accessible via link (see above) and publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for(controller=controller_list, action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div>
                     </form>
 
                 %endif
@@ -239,5 +240,5 @@
     %endif
 
     <br /><br />
-    <a href="${h.url_for(controller=controller_name, action="list" )}">Back to ${item_class_plural_name} List</a>
+    <a href="${h.url_for(controller=controller_list, action="list" )}">Back to ${item_class_plural_name} List</a>
 </%def>

templates/webapps/galaxy/page/editor.mako

@@ -14,7 +14,7 @@
     <script type="text/javascript">
         // Define variables needed by galaxy.pages script.
         var page_id = "${trans.security.encode_id(page.id)}",
-            page_list_url = '${h.url_for( controller='page', action='list' )}',
+            page_list_url = '${h.url_for( controller='pages', action='list' )}',
             list_objects_url = "${h.url_for(controller='page', action='LIST_ACTION' )}",
             set_accessible_url = "${h.url_for( controller='ITEM_CONTROLLER', action='set_accessible_async' )}",
             get_name_and_link_url = "${h.url_for( controller='ITEM_CONTROLLER', action='get_name_and_link_async' )}?id=",

templates/webapps/galaxy/page/index.mako

@@ -1,53 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.active_view="shared"
-    self.message_box_visible=False
-%>
-</%def>
-
-<%def name="center_panel()">
-
-    <div style="overflow: auto; height: 100%;">
-        <div class="page-container" style="padding: 10px;">
-            <!-- embedded grid -->
-            ${h.to_unicode( embedded_grid )}
-
-            <br><br>
-            <h2>Pages shared with you by others</h2>
-
-            %if shared_by_others:
-                <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-                    <tr class="header">
-                        <th>Title</th>
-                        <th>Owner</th>
-                        <th></th>
-                    </tr>
-                    %for i, association in enumerate( shared_by_others ):
-                        <% page = association.page %>
-                        <tr>
-                            <td>
-                                <a class="menubutton" id="shared-${i}-popup" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title | h}</a>
-                            </td>
-                            <td>${page.user.username}</td>
-                            <td>
-                                <div popupmenu="shared-${i}-popup">
-                                    <a class="action-button" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}" target="_top">View</a>
-                                </div>
-                            </td>
-                        </tr>    
-                    %endfor
-                </table>
-            %else:
-
-                No pages have been shared with you.
-
-            %endif
-
-        </div>
-    </div>
-
-</%def>