Merge branch 'jbrowse_1.7' into add_files

plugins/WebApollo/css/main.css

@@ -1,8 +1,8 @@
+@import url("../jslib/jqueryui/themes/base/jquery.ui.all.css");
 @import url("genome.css");
 @import url("webapollo_track_styles.css");
 @import url("add_sequence_alteration.css");
 @import url("edit_dbxrefs.css");
 @import url("edit_comments.css");
 @import url("get_sequence.css");
 @import url("search_sequence.css");
-@import url("../jslib/jqueryui/themes/base/jquery.ui.all.css");

plugins/WebApollo/css/webapollo_track_styles.css

@@ -1209,6 +1209,7 @@ div.generic_parent-hist {
     -moz-box-sizing: border-box;
     -webkit-box-sizing: border-box;
     -ms-box-sizing: border-box;
+    background-color: transparent;
 }
 
 .ogsv3-CDS, 
@@ -2343,6 +2344,7 @@ div.generic_parent-hist {
     -moz-box-sizing: border-box;
     -webkit-box-sizing: border-box;
     -ms-box-sizing: border-box;
+    background-color: transparent;
 /* not needed?  residues overlay is on .annot, so that's where text selection needs to be disabled
   -moz-user-select: none;
   -khtml-user-select: none;
@@ -2420,7 +2422,8 @@ div.generic_parent-hist {
     position: absolute;
     height: 16px;
     z-index: 100;
-    background-image: url('img/exclamation_circle_orange.png'); 
+    background-image: url('../img/exclamation_circle_orange.png'); 
+/*    background-image: url('img/exclamation_circle_orange.png');  */
 /*    background-image: url('img/warning_exclamation_small.png'); */
 /*    background-image: url('img/warning_exclamation.png');  */
 /*    background-image: url('img/marker_rounded_red.png'); */

plugins/WebApollo/js/FeatureEdgeMatchManager.js

@@ -21,7 +21,7 @@ var FeatureEdgeMatchManager = declare( null,
     SHOW_EDGE_MATCHES: true,
 
     setBrowser: function( browser ) {
-        browser.subscribe('/jbrowse/v1/v/redraw', dojo.hitch( this, function() {
+        browser.subscribe('/jbrowse/v1/n/redraw', dojo.hitch( this, function() {
             var selected = this.featSelectionManager;
             var annot_selected = this.annotSelectionManager;
             this.selectionCleared();

plugins/WebApollo/js/Store/SeqFeature/ScratchPad.js

@@ -15,13 +15,19 @@ return declare( SeqFeatureStore,
         this._calculateStats();
     },
 
+/*
     delete: function( feature ) {
-        delete this.features[ feature.id() ];
+	this.deleteFeatureById[ feature.id() ];
+    },
+*/
+
+    deleteFeatureById: function( id ) {
+	delete  this.features[ id ];
         this._calculateStats();
     },
 
     /* if feature with given id is present in store, return it.  Otherwise return null */
-    contains: function( id )  {
+    getFeatureById: function( id )  {
 	return this.features[ id ];
     },
 

plugins/WebApollo/js/View/Track/AnnotTrack.js

@@ -3,6 +3,7 @@ define( [
             'jquery',
             'jqueryui/draggable',
             'jqueryui/droppable',
+            'jqueryui/resizable', 
             'dijit/Menu',
             'dijit/MenuItem',
             'dijit/Dialog',
@@ -14,7 +15,7 @@ define( [
             'JBrowse/Model/SimpleFeature',
             'JBrowse/Util'
         ],
-        function( declare, $, draggable, droppable, dijitMenu, dijitMenuItem, dijitDialog, DraggableFeatureTrack, FeatureSelectionManager, JSONUtils, BioFeatureUtils, Permission, SimpleFeature, Util ) {
+        function( declare, $, draggable, droppable, resizable, dijitMenu, dijitMenuItem, dijitDialog, DraggableFeatureTrack, FeatureSelectionManager, JSONUtils, BioFeatureUtils, Permission, SimpleFeature, Util ) {
 
 var listeners = [];
 
@@ -100,8 +101,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
         this.verbose_mouseleave = false;
         this.verbose_render = false;
 
-//        this.inherited( arguments );
-
         var track = this;
         // for AnnotTrack, features currently MUST be an NCList
     //    var features = this.features;
@@ -193,8 +192,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
 
     createAnnotationChangeListener: function() {
         var track = this;
-        var features = this.features;
-
         if (listeners[track.getUniqueTrackName()]) {
             if (listeners[track.getUniqueTrackName()].fired == -1) {
                     listeners[track.getUniqueTrackName()].cancel();
@@ -293,11 +290,9 @@ var AnnotTrack = declare( DraggableFeatureTrack,
 
     addFeatures: function(responseFeatures) {
             for (var i = 0; i < responseFeatures.length; ++i) {
-    //          var featureArray = JSONUtils.createJBrowseFeature(responseFeatures[i], this.fields, this.subFields);
                 var feat = JSONUtils.createJBrowseFeature( responseFeatures[i] );
                 var id = responseFeatures[i].uniquename;
-               // if (this.features.featIdMap[id] == null) {
-		if (! this.store.contains(id))  {
+		if (! this.store.getFeatureById(id))  {
                     // note that proper handling of subfeatures requires annotation trackData.json resource to
                     //    set sublistIndex one past last feature array index used by other fields
                     //    (currently Annotations always have 6 fields (0-5), so sublistIndex = 6
@@ -309,7 +304,7 @@ var AnnotTrack = declare( DraggableFeatureTrack,
     deleteFeatures: function(responseFeatures) {
         for (var i = 0; i < responseFeatures.length; ++i) {
             var id_to_delete = responseFeatures[i].uniquename;
-            this.store.delete(id_to_delete);
+            this.store.deleteFeatureById(id_to_delete);
         }
     },
 
@@ -436,7 +431,10 @@ var AnnotTrack = declare( DraggableFeatureTrack,
         if (verbose_resize || track.verbose_mousedown)  { console.log("AnnotTrack.onAnnotMouseDown called"); }
         event = event || window.event;
         var elem = (event.currentTarget || event.srcElement);
-        var featdiv = DraggableFeatureTrack.prototype.getLowestFeatureDiv(elem);
+        // need to redo getLowestFeatureDiv
+	// var featdiv = DraggableFeatureTrack.prototype.getLowestFeatureDiv(elem);
+	var featdiv = track.getLowestFeatureDiv(elem);
+
         if (featdiv && (featdiv != null))  {
             if (dojo.hasClass(featdiv, "ui-resizable"))  {
                 if (verbose_resize)  {
@@ -450,9 +448,14 @@ var AnnotTrack = declare( DraggableFeatureTrack,
                     console.log(featdiv);
                 }
                 var scale = track.gview.bpToPx(1);
+
+		var gridvals = false;
                 // if zoomed int to showing sequence residues, then make edge-dragging snap to interbase pixels
-                if (scale === track.browserParams.charWidth) { var gridvals = [track.browserParams.charWidth, 1]; }
-                else  { var gridvals = false; }
+
+		// GAH TODO JBrowse1.7 merge -- restore grid snap when resolve charWidth
+                // if (scale === track.browserParams.charWidth) { var gridvals = [track.browserParams.charWidth, 1]; }
+                // else  { var gridvals = false; }
+
                 $(featdiv).resizable( {
                     handles: "e, w",
                     helper: "ui-resizable-helper",
@@ -534,13 +537,15 @@ var AnnotTrack = declare( DraggableFeatureTrack,
         //   event.stopPropagation();
     },
 
-    addToAnnotation: function(annot, feats_to_add)  {
+    /* feature_records ==> { feature: the_feature, track: track_feature_is_from } */
+    addToAnnotation: function(annot, feature_records)  {
         var target_track = this;
 
                 var subfeats = new Array();
                 var allSameStrand = 1;
-                for (var i = 0; i < feats_to_add.length; ++i)  { 
-                        var feat = feats_to_add[i];
+                for (var i = 0; i < feature_records.length; ++i)  { 
+                    var feature_record = feature_records[i];
+		    var feat = feature_record.feature;
                         var isSubfeature = !! feat.parent();  // !! is shorthand for returning true if value is defined and non-null
                         var annotStrand = annot.get('strand');
                         if (isSubfeature)  {
@@ -555,7 +560,7 @@ var AnnotTrack = declare( DraggableFeatureTrack,
                                 subfeats.push(featToAdd);
                         }
                         else  {
-                                var source_track = feat.track;
+                            var source_track = feature_record.track;
                                 // if (source_track.fields["subfeatures"])  {
                                 if ( feat.get('subfeatures') ) {
                                     // var subs = feat[source_track.fields["subfeatures"]];
@@ -677,7 +682,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
 
     createAnnotations: function(selection_records)  {
             var target_track = this;
-            var features_nclist = target_track.features;
             var featuresToAdd = new Array();
             var parentFeatures = new Object();
             for (var i in selection_records)  {
@@ -730,33 +734,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
                     }
             }
 
-            /*
-            {
-             
-       
-                    var source_track = dragfeat.track;
-                    if (this.verbose_create)  {
-                            console.log("creating annotation based on feature: ");
-                            console.log(dragfeat);
-                    }
-                    var dragdiv = source_track.getFeatDiv(dragfeat);
-
-
-                    var newfeat = JSONUtils.convertToTrack(dragfeat, source_track, target_track);
-                    var source_fields = source_track.fields;
-                    var source_subFields = source_track.subFields;
-                    var target_fields = target_track.fields;
-                    var target_subFields = target_track.subFields;
-                    if (this.verbose_create)  {
-                            console.log("local feat conversion: " );
-                            console.log(newfeat);
-                    }
-                    var afeat = JSONUtils.createApolloFeature(source_track.attrs, dragfeat, "transcript");
-                    featuresToAdd.push(afeat);
-
-            }
-            */
-
             dojo.xhrPost( {
                     postData: '{ "track": "' + target_track.getUniqueTrackName() + '", "features": ' + JSON.stringify(featuresToAdd) + ', "operation": "add_transcript" }',
                     url: context_path + "/AnnotationEditorService",
@@ -861,7 +838,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
 
     deleteAnnotations: function(selection_records) {
         var track = this;
-//        var features_nclist = track.features;
         var features = '"features": [';
         var uniqueNames = [];
         for (var i in selection_records)  {
@@ -1683,7 +1659,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
 
     undoSelectedFeatures: function(annots) {
         var track = this;
-        var features_nclist = track.features;
         var features = '"features": [';
         for (var i in annots)  {
             var annot = AnnotTrack.getTopLevelAnnotation(annots[i]);
@@ -1744,7 +1719,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
 
     redoSelectedFeatures: function(annots) {
         var track = this;
-        var features_nclist = track.features;
         var features = '"features": [';
         for (var i in annots)  {
             var annot = AnnotTrack.getTopLevelAnnotation(annots[i]);

plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js

@@ -337,6 +337,7 @@ var draggableTrack = declare( HTMLFeatureTrack,
             }
         }
 
+/*
         // try to make a wholeCDS if we don't have one
         if( ! wholeCDS ) {
             wholeCDS = (function() {
@@ -361,6 +362,7 @@ var draggableTrack = declare( HTMLFeatureTrack,
                 }
             }).call(this);
         }
+*/
 
         if (wholeCDS) {
             var cdsStart = wholeCDS.get('start');

plugins/WebApollo/tests/selenium_tests/lib/WebApolloTest.py

@@ -0,0 +1,35 @@
+import os
+import sys
+import time
+sys.path.append( 'tests/selenium_tests' ) # relative to JBrowse root
+
+from jbrowse_selenium import JBrowseTest
+
+class WebApolloTest (JBrowseTest):
+
+    wa_url = None
+
+    def setUp( self ):
+        super( WebApolloTest, self ).setUp()
+        self.login( os.environ['WA_USER'], os.environ['WA_PASS'] )
+        self.browser.get( self.baseURL() )
+
+    def baseURL( self ):
+        return self.waURL()+'/jbrowse/index.html'
+
+    def waURL( self ):
+        if not self.wa_url:
+            self.wa_url = os.environ['WA_URL']
+        return self.wa_url
+
+    def login( self, username, password ):
+        self.browser.get( self.waURL() + '/Login' );
+        username_input = self.assert_element('//input[@id="username"]')
+        password_input = self.assert_element('//input[@id="password"]')
+        username_input.send_keys(username)
+        password_input.send_keys(password)
+        login_button = self.assert_element('//button[@id="login_button"]')
+        login_button.click()
+        time.sleep( 0.4 )
+        pass
+

plugins/WebApollo/tests/selenium_tests/lib/__init__.py

@@ -0,0 +1,2 @@
+from WebApolloTest import WebApolloTest
+

plugins/WebApollo/tests/selenium_tests/pythium_test.py

@@ -0,0 +1,29 @@
+import unittest
+from lib import WebApolloTest;
+
+class PythiumTest(WebApolloTest, unittest.TestCase):
+
+    data_dir = 'sample_data/json/volvox'
+
+    def setUp( self ):
+        # call( "rm -rf sample_data/json/volvox/", shell=True )
+        # call( "bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox/", shell=True )
+        # call( "bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox/", shell=True )
+        # call( "bin/wig-to-json.pl --out sample_data/json/volvox/ --wig docs/tutorial/data_files/volvox_microarray.wig", shell=True )
+        # call( "bin/add-track-json.pl sample_data/raw/volvox/volvox_microarray.bw.conf sample_data/json/volvox/trackList.json", shell=True )
+        # call( "bin/add-track-json.pl sample_data/raw/volvox/volvox-sorted.bam.conf sample_data/json/volvox/trackList.json", shell=True )
+        # call( "bin/add-track-json.pl sample_data/raw/volvox/volvox-sorted.bam.coverage.conf sample_data/json/volvox/trackList.json", shell=True )
+        # call( "bin/generate-names.pl --dir sample_data/json/volvox/", shell=True )
+        super( PythiumTest, self ).setUp()
+
+
+    def test_pythium( self ):
+        test_ref = 'scf1117875582023';
+        # select "ctgA from the dropdown
+        self.select_refseq( test_ref )
+
+        # check a good browser title
+        assert test_ref in self.browser.title, "browser title is actually %s" % self.browser.title
+
+        self.browser.close()
+

src/JBrowse/Browser.js

@@ -389,8 +389,8 @@ Browser.prototype.initView = function() {
 
     // hook up GenomeView
     this.view = this.viewElem.view =
-        new GenomeView(this, this.viewElem, 250, this.refSeq, 1/200,
-                       this.config.browserRoot);
+        new GenomeView(this, this.viewElem, 250, this.refSeq, 1/200 );
+
     dojo.connect( this.view, "onFineMove",   this, "onFineMove"   );
     dojo.connect( this.view, "onCoarseMove", this, "onCoarseMove" );
 
@@ -625,6 +625,7 @@ Browser.prototype._calculateClientStats = function() {
                 '+'
             ),
         'tracks-count': this.config.tracks.length,
+        'plugins': dojof.keys( this.plugins ).sort().join(','),
 
         // screen geometry
         'scn-h': scn ? scn.height : null,

src/JBrowse/GenomeView.js

@@ -43,7 +43,7 @@ var locationThumbMover = declare( dndMove.constrainedMoveable, {
  * @class
  * @constructor
  */
-var GenomeView = function( browser, elem, stripeWidth, refseq, zoomLevel, browserRoot) {
+var GenomeView = function( browser, elem, stripeWidth, refseq, zoomLevel ) {
 
     // keep a reference to the main browser object
     this.browser = browser;
@@ -60,8 +60,7 @@ var GenomeView = function( browser, elem, stripeWidth, refseq, zoomLevel, browse
     this.ref = refseq;
     //current scale, in pixels per bp
     this.pxPerBp = zoomLevel;
-    //path prefix for static assets (e.g., cursors)
-    this.browserRoot = browserRoot ? browserRoot : "";
+
     //width, in pixels, of the vertical stripes
     this.stripeWidth = stripeWidth;
     //the page element that the GenomeView lives in
@@ -1100,7 +1099,7 @@ GenomeView.prototype.scaleMouseOut = function( evt ) {
  * Draws the red line across the work area, or updates it if it already exists.
  */
 GenomeView.prototype.drawVerticalPositionLine = function( parent, evt){
-    var numX = evt.pageX;
+    var numX = evt.pageX + 2;
 
     if( ! this.verticalPositionLine ){
         // if line does not exist, create it
@@ -1111,7 +1110,7 @@ GenomeView.prototype.drawVerticalPositionLine = function( parent, evt){
 
     var line = this.verticalPositionLine;
     line.style.display = 'block';      //make line visible
-    line.style.left = numX+2+'px'; //set location on screen
+    line.style.left = numX+'px'; //set location on screen
 
     this.drawBasePairLabel({ name: 'single', offset: 0, x: numX, parent: parent });
 };
@@ -1690,7 +1689,7 @@ GenomeView.prototype.showVisibleBlocks = function(updateHeight, pos, startX, end
                                           containerStart, containerEnd);
                       });
 
-    this.browser.publish( '/jbrowse/v1/v/redraw' );
+    this.browser.publish( '/jbrowse/v1/n/redraw' );
 };
 
 /**