diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 30792835d2d..a909699ab69 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -363,14 +363,18 @@ class RawBedDataProvider( BedDataProvider ):
for large datasets.
"""
- def get_iterator( self, chrom, start, end ):
+ def get_iterator( self, chrom=None, start=None, end=None ):
def line_filter_iter():
for line in open( self.original_dataset.file_name ):
+ if line.startswith( "track" ) or line.startswith( "browser" ):
+ continue
feature = line.split()
feature_chrom = feature[0]
feature_start = int( feature[1] )
feature_end = int( feature[2] )
- if feature_chrom != chrom or feature_start > int( end ) or feature_end < int( start ):
+ if ( chrom is not None and feature_chrom != chrom ) \
+ or ( start is not None and feature_start > int( end ) ) \
+ or ( end is not None and feature_end < int( start ) ):
continue
yield line
return line_filter_iter()
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 3ae6cea5063..8dd0d3fa22f 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -13,7 +13,7 @@ from galaxy.web.controllers.library import LibraryListGrid
from galaxy.web.framework import simplejson
from galaxy.web.framework.helpers import time_ago, grids
from galaxy.util.bunch import Bunch
-from galaxy.datatypes.interval import Gff
+from galaxy.datatypes.interval import Gff, Bed
from galaxy.model import NoConverterException, ConverterDependencyException
from galaxy.visualization.tracks.data_providers import *
from galaxy.visualization.tracks.visual_analytics import get_tool_def, get_dataset_job
@@ -246,6 +246,27 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
"tool": get_tool_def( trans, dataset )
}
return track
+
+ @web.json
+ def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ):
+ if hda_id:
+ hda_ldda = "hda"
+ dataset = self.get_dataset( trans, hda_id, check_ownership=False, check_accessible=True )
+ elif ldda_id:
+ hda_ldda = "ldda"
+ dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
+ rows = []
+ if isinstance( dataset.datatype, Bed ):
+ data = RawBedDataProvider( original_dataset=dataset ).get_iterator()
+ for i, line in enumerate( data ):
+ if ( i > 500 ): break
+ fields = line.split()
+ location = name = "%s:%s-%s" % ( fields[0], fields[1], fields[2] )
+ if len( fields ) > 3:
+ name = fields[4]
+ rows.append( [location, name] )
+ return { 'data': rows }
+
@web.expose
@web.require_login()
diff --git a/static/june_2007_style/base.css.tmpl b/static/june_2007_style/base.css.tmpl
index d53be3086af..2e2f1e4c4d9 100644
--- a/static/june_2007_style/base.css.tmpl
+++ b/static/june_2007_style/base.css.tmpl
@@ -909,6 +909,14 @@ div.permissionContainer {
-sprite-group: fugue;
-sprite-image: fugue/plus-circle.png;
}
+.icon-button.plus-button {
+ -sprite-group: fugue;
+ -sprite-image: fugue/plus-button.png;
+}
+.icon-button.gear {
+ -sprite-group: fugue;
+ -sprite-image: fugue/gear.png;
+}
.tipsy {
padding: 5px;
diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css
index 70bc7fede74..432582606d5 100644
--- a/static/june_2007_style/blue/base.css
+++ b/static/june_2007_style/blue/base.css
@@ -163,6 +163,8 @@ div.permissionContainer{padding-left:20px;}
.icon-button.vis-chart{background:url(fugue.png) no-repeat 0px -286px;}
.icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -312px;}
.icon-button.import{background:url(fugue.png) no-repeat 0px -338px;}
+.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -364px;}
+.icon-button.gear{background:url(fugue.png) no-repeat 0px -390px;}
.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);}
.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;}
.tipsy-north{background-position:top center;}
@@ -171,7 +173,7 @@ div.permissionContainer{padding-left:20px;}
.tipsy-west{background-position:left center;}
.editable-text{cursor:pointer;}
.editable-text:hover{cursor:text;border:dotted #999999 1px;}
-.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;}
+.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -416px;}
.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;}
.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;}
.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;}
diff --git a/static/june_2007_style/blue/fugue.png b/static/june_2007_style/blue/fugue.png
index d6212bec398..393ca9daedb 100644
Binary files a/static/june_2007_style/blue/fugue.png and b/static/june_2007_style/blue/fugue.png differ
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index b0874d450b9..40bae40def9 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3313,7 +3313,6 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
};
extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
set_painter_from_config: function() {
- console.log( this, this.config );
if ( this.config.values['connector_style'] == 'arcs' ) {
this.painter = painters.ArcLinkedFeaturePainter;
} else {
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 8b9b7069714..113bc5e1129 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -110,6 +110,52 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
}
});
};
+
+ /**
+ * Use a popup grid to bookmarks from a dataset.
+ */
+ var add_bookmarks = function() {
+ show_modal( "Select dataset for new bookmarks", "progress" );
+ $.ajax({
+ url: "${h.url_for( action='list_histories' )}",
+ data: { "f-dbkey": view.dbkey },
+ error: function() { alert( "Grid failed" ); },
+ success: function(table_html) {
+ show_modal(
+ "Select dataset for new bookmarks",
+ table_html, {
+ "Cancel": function() {
+ hide_modal();
+ },
+ "Insert": function() {
+ // Just use the first selected
+ $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){
+ var data, id = $(this).val();
+ if ($(this).attr("name") === "id") {
+ data = { hda_id: id };
+ } else {
+ data = { ldda_id: id};
+ }
+
+ $.ajax({
+ url: "${h.url_for( action='bookmarks_from_dataset' )}",
+ data: data,
+ dataType: "json",
+ }).then( function(data) {
+ for( i = 0; i < data.data.length; i++ ) {
+ var row = data.data[i];
+ console.log( row[0], row[1] );
+ add_bookmark( row[0], row[1] );
+ }
+ });
+ });
+ hide_modal();
+ }
+ }
+ );
+ }
+ });
+ };
$(function() {
// Manual tipsy config because default gravity is S and cannot be changed.
@@ -240,7 +286,13 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
annotation = "Bookmark description";
return add_bookmark(position, annotation);
});
-
+
+ // make_popupmenu( $("#bookmarks-more-button"), {
+ // "Add from BED dataset": function() {
+ // add_bookmarks();
+ // }
+ // });
+
init_keyboard_nav(view);
};
@@ -271,14 +323,15 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e