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kandaj
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extjs 5.1.0 version added and varian widget panel height altered
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549 files changed

+65
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‎eva-web/Gruntfile.js‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -163,7 +163,8 @@ module.exports = function (grunt) {
163163
// 'build/<%= meta.version.eva %>/lib/jsorolla/build/*/lib.min.js'
164164
],
165165
'vendor': [
166-
'build/<%= meta.version.eva %>/vendor/ext-5.0.1/js/ext-all.js',
166+
// 'build/<%= meta.version.eva %>/vendor/ext-5.0.1/js/ext-all.js',
167+
'build/<%= meta.version.eva %>/vendor/ext-5.1.0/js/ext-all.js',
167168
'build/<%= meta.version.eva %>/lib/jsorolla/vendor/underscore-min.js',
168169
'build/<%= meta.version.eva %>/lib/jsorolla/vendor/backbone-min.js',
169170
'build/<%= meta.version.eva %>/lib/jsorolla/vendor/jquery.min.js',
@@ -192,7 +193,8 @@ module.exports = function (grunt) {
192193
'build/<%= meta.version.eva %>/css/eva.css'
193194
],
194195
'vendor': [
195-
'build/<%= meta.version.eva %>/vendor/ext-5.0.1/theme/theme-eva-ebi-all.css',
196+
// 'build/<%= meta.version.eva %>/vendor/ext-5.0.1/theme/theme-eva-ebi-all.css',
197+
'build/<%= meta.version.eva %>/vendor/ext-5.1.0/theme/theme-ebi-embl-all.css',
196198
'build/<%= meta.version.eva %>/lib/jsorolla/vendor/jquery.qtip.min.css',
197199
'build/<%= meta.version.eva %>/vendor/bootstrap-3.2.0/css/bootstrap.min.css',
198200
'build/<%= meta.version.eva %>/lib/jsorolla/vendor/font-awesome/css/font-awesome.min.css'

‎eva-web/src/index.html‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,8 @@
1111
<!-- /build -->
1212

1313
<!-- build:style vendor -->
14-
<link type="text/css" rel="stylesheet" href="../vendor/ext-5.0.1/theme/theme-eva-ebi-all.css"/>
14+
<!--<link type="text/css" rel="stylesheet" href="../vendor/ext-5.0.1/theme/theme-eva-ebi-all.css"/>-->
15+
<link type="text/css" rel="stylesheet" href="../vendor/ext-5.1.0/theme/theme-ebi-embl-all.css"/>
1516
<link type="text/css" rel="stylesheet" href="../lib/jsorolla/vendor/jquery.qtip.min.css"/>
1617
<link rel="stylesheet" href="../vendor/bootstrap-3.2.0/css/bootstrap.min.css">
1718
<link rel="stylesheet" href="../lib/jsorolla/vendor/font-awesome/css/font-awesome.min.css">
@@ -483,7 +484,8 @@ <h3 class="about"><a href="//www.ebi.ac.uk/about">About us</a></h3>
483484

484485
<!-- JavaScript at the bottom for fast page loading -->
485486
<!-- build:script vendor -->
486-
<script type="text/javascript" src="../vendor/ext-5.0.1/js/ext-all.js"></script>
487+
<!--<script type="text/javascript" src="../vendor/ext-5.0.1/js/ext-all.js"></script>-->
488+
<script type="text/javascript" src="../vendor/ext-5.1.0/js/ext-all.js"></script>
487489
<script type="text/javascript" src="../lib/jsorolla/vendor/underscore-min.js"></script>
488490
<script type="text/javascript" src="../lib/jsorolla/vendor/backbone-min.js"></script>
489491
<script type="text/javascript" src="../lib/jsorolla/vendor/jquery.min.js"></script>

‎eva-web/src/js/eva.js‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -186,6 +186,7 @@ Eva.prototype = {
186186
this.variantWidgetPanel.show();
187187
}else{
188188
this.variantWidgetPanel = this._createVariantWidgetPanel(this.contentDiv);
189+
this.select('Variant Browser');
189190
// this.variantWidgetPanel.formPanelVariantFilter.trigger('submit', {values: this.variantWidgetPanel.formPanelVariantFilter.getValues(), sender: _this});
190191
}
191192

‎eva-web/src/js/variant-widget/eva-variant-browser-grid.js‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -131,6 +131,7 @@ EvaVariantBrowserGrid.prototype = {
131131
animCollapse: false,
132132
height: this.height,
133133
overflowX:true,
134+
overflowY: true,
134135
collapsible:true,
135136
features: [
136137
{ftype: 'summary'}
@@ -145,6 +146,7 @@ EvaVariantBrowserGrid.prototype = {
145146
);
146147

147148
grid.getSelectionModel().on('selectionchange', function (sm, selectedRecord) {
149+
console.log(selectedRecord.length)
148150
if (selectedRecord.length) {
149151
var row = selectedRecord[0].data;
150152
_this.trigger("variant:change", {sender: _this, args: row});

‎eva-web/src/js/variant-widget/eva-variant-widget-panel.js‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -95,7 +95,7 @@ EvaVariantWidgetPanel.prototype = {
9595
align: 'left'
9696
},
9797
items: [view],
98-
height:1200,
98+
// height:1200,
9999
cls: 'variant-widget-panel'
100100
});
101101

‎eva-web/src/js/variant-widget/eva-variant-widget.js‎

Lines changed: 19 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -267,7 +267,7 @@ EvaVariantWidget.prototype = {
267267
{
268268
text: "Chr",
269269
dataIndex: 'chromosome',
270-
flex: 0.
270+
flex: 0.5
271271
},
272272
{
273273
text: 'Position',
@@ -326,14 +326,19 @@ EvaVariantWidget.prototype = {
326326
renderer: function(value, meta, rec, rowIndex, colIndex, store){
327327
var tempArray = [];
328328
var consequenceTypes = rec.data.consequenceTypes;
329-
for (i = 0; i < consequenceTypes.length; i++) {
330-
tempArray.push(consequenceTypes[i].soTerms[0].soName)
329+
if(consequenceTypes){
330+
for (i = 0; i < consequenceTypes.length; i++) {
331+
tempArray.push(consequenceTypes[i].soTerms[0].soName)
332+
}
333+
meta.tdAttr = 'data-qtip="'+tempArray.join('\n')+'"';
334+
return value ? Ext.String.format(
335+
'<tpl>'+tempArray.join()+'</tpl>',
336+
value
337+
) : '';
338+
}else{
339+
return '';
331340
}
332-
meta.tdAttr = 'data-qtip="'+tempArray.join('\n')+'"';
333-
return value ? Ext.String.format(
334-
'<tpl>'+tempArray.join()+'</tpl>',
335-
value
336-
) : '';
341+
337342
// return tempArray.join();
338343
},
339344
flex: 1
@@ -495,7 +500,8 @@ EvaVariantWidget.prototype = {
495500
var _this = this;
496501
var url = variantBrowserGrid.store.proxy.url;
497502
var params = variantBrowserGrid.store.proxy.extraParams;
498-
variantBrowserGrid.pageSize = record[0].id;
503+
// variantBrowserGrid.pageSize = record[0].id;
504+
variantBrowserGrid.pageSize = record.id;
499505
_this.retrieveData(url,params);
500506
}, this);
501507

@@ -571,11 +577,11 @@ EvaVariantWidget.prototype = {
571577
});
572578

573579
this.on("variant:change", function (e) {
574-
575580
if(_.isUndefined(e.variant)){
576581
variantStatsPanel.clear(true);
577582
}else{
578-
if (target === _this.selectedToolDiv) {
583+
// if (target === _this.selectedToolDiv) {
584+
if (target.id === _this.selectedToolDiv.id) {
579585
var variant = e.variant;
580586
var region = variant.chromosome+':'+variant.start+'-'+variant.end;
581587
var proxy = _.clone(this.variantBrowserGrid.store.proxy);
@@ -694,7 +700,8 @@ EvaVariantWidget.prototype = {
694700
if(_.isUndefined(e.variant)){
695701
variantGenotypeGrid.clear(true);
696702
}else{
697-
if (target === _this.selectedToolDiv) {
703+
// if (target === _this.selectedToolDiv) {
704+
if (target.id === _this.selectedToolDiv.id) {
698705
var variant = e.variant;
699706
var query = e.variant.chromosome+':'+e.variant.start+'-'+e.variant.end;
700707
var params = _.omit(this.variantBrowserGrid.store.proxy.extraParams, 'region','studies');

‎eva-web/src/js/variant-widget/filters/eva-species-filter-form-panel.js‎

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -78,14 +78,21 @@ SpeciesFilterFormPanel.prototype = {
7878
name: 'displayName',
7979
type: 'string',
8080
convert: function( v, record ) {
81-
return record.get( 'taxonomyEvaName').substr(0,1).toUpperCase()+record.get( 'taxonomyEvaName').substr(1) + ' / ' + record.get( 'assemblyName' )
81+
82+
if( record.get( 'taxonomyEvaName')){
83+
return record.get( 'taxonomyEvaName').substr(0,1).toUpperCase()+record.get( 'taxonomyEvaName').substr(1) + ' / ' + record.get( 'assemblyName' )
84+
}
85+
86+
8287
}
8388
},
8489
{
8590
name: 'value',
8691
type: 'string',
8792
convert: function( v, record ) {
88-
return record.get( 'taxonomyCode' ) + '_' + record.get( 'assemblyCode' )
93+
if( record.get( 'taxonomyCode')){
94+
return record.get( 'taxonomyCode' ) + '_' + record.get( 'assemblyCode' )
95+
}
8996
}
9097
}
9198
]

‎eva-web/vendor/ext-5.1.0/js/ext-all.js‎

Lines changed: 22 additions & 0 deletions
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‎eva-web/vendor/ext-5.1.0/theme/images/breadcrumb/default-arrow-open-rtl.png‎

205 Bytes

‎eva-web/vendor/ext-5.1.0/theme/images/breadcrumb/default-arrow-open.png‎

206 Bytes

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