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Extend charts with more visualizations, adjust interface #2875

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merged 86 commits into from
Oct 17, 2016
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8e0eaf2
Add biojs multiple sequence viewer
guerler Aug 25, 2016
9751923
Fix style
guerler Aug 25, 2016
6a450b9
Add basic options to configure msa viewer
guerler Aug 25, 2016
72ea2b0
Avoid parsing app to chart wrappers
guerler Aug 25, 2016
e02eb60
Decouple storage, parse parameters explicitly
guerler Aug 25, 2016
37c1e31
Move chart listener into storage
guerler Aug 25, 2016
48ff079
Fix save failed message
guerler Aug 25, 2016
3048b56
Remove unused container list
guerler Aug 25, 2016
a63b077
Fix scrolling behavior
guerler Aug 25, 2016
f2c1e23
Add description for biojs
guerler Aug 25, 2016
7107705
Remove unused menu div
guerler Aug 25, 2016
5f64211
Use shorter dom query command
guerler Aug 25, 2016
ebd0dab
Change draw label to indicate that the chart will be saved too
guerler Aug 25, 2016
30bd723
Fix tooltip
guerler Aug 25, 2016
9481939
Remove separated tabular input element
guerler Aug 25, 2016
70e68c2
Fix spacing
guerler Aug 25, 2016
77dddc3
Generalize internal use panels parameter option
guerler Aug 25, 2016
d6f174e
Filter exportable datatypes by chart type
guerler Aug 25, 2016
6d28721
Repack
guerler Aug 25, 2016
6c0df63
Fix tooltip
guerler Aug 25, 2016
004fbd6
Fix developer examples config
guerler Aug 25, 2016
9e2e0dc
Fix developer example
guerler Aug 25, 2016
e8eb48a
Remove unused app variable
guerler Aug 25, 2016
f98ade1
Add basic description for msa viewer
guerler Aug 25, 2016
c4e9ecf
Allow multiple datatype matching
guerler Aug 25, 2016
edfdef2
Enhance ui menu button view
guerler Aug 25, 2016
72f89a4
Fix requirements message
guerler Aug 26, 2016
59852d0
Use remote repo for chart plugins
guerler Aug 30, 2016
af45adb
Add error message if charts fails to retrieve plugin resources from i…
guerler Aug 30, 2016
3e7302f
Fix remote url
guerler Aug 30, 2016
42854e3
Bundle thumbnail view
guerler Aug 30, 2016
d4d403d
Show list instead
guerler Aug 30, 2016
6f444e5
Restore regular selection view
guerler Aug 30, 2016
ccd265e
Fix tab creation behavior
guerler Aug 30, 2016
d65bf1e
Fix sorting
guerler Aug 30, 2016
bee75fb
Fix order
guerler Aug 30, 2016
9601a0f
Revise thumbnail view
guerler Aug 31, 2016
ec038cb
Use original order
guerler Aug 31, 2016
5cae6f7
Fix spacing
guerler Aug 31, 2016
71fe20a
Identify links in visualizations plugins descriptions
guerler Aug 31, 2016
e0617bb
Add tooltip to thumbnail view?
guerler Aug 31, 2016
f03a064
Limit title length for thumbnails
guerler Aug 31, 2016
f2b26a6
Filter suitable visualization types on initialization
guerler Aug 31, 2016
8494258
Modify error message
guerler Aug 31, 2016
3e79da9
Fix error messages
guerler Aug 31, 2016
5d780d6
Revise exporting functions, increase png quality, remove unused libra…
guerler Aug 31, 2016
78bd9e8
Merge branch 'dev' into remote_chart_plugins
guerler Aug 31, 2016
a97b4ba
Rename types to registry to avoid confusion
guerler Sep 1, 2016
494141c
Use underscores for internal parameters to avoid conflicts
guerler Sep 1, 2016
6183963
Simplify storage handling
guerler Sep 1, 2016
7d20e90
Remove unused options variable
guerler Sep 1, 2016
30d4e33
Revise visualization config handling
guerler Sep 1, 2016
57b41b2
Fix chart saving
guerler Sep 1, 2016
22e79f7
Improve handling for cases with missing plugins
guerler Sep 1, 2016
76c9948
Enhance notification and handling when chart type is unavailable
guerler Sep 1, 2016
81dffca
Remove test case, replace change listeners
guerler Sep 1, 2016
fa7930d
Fix message persistence for missing column notification
guerler Sep 1, 2016
b3451ed
Fix message persistence for missing data groups
guerler Sep 1, 2016
4669d5e
Remove warning notification when leaving charts, data is saved upon d…
guerler Sep 1, 2016
00053b6
Fix spacing
guerler Sep 1, 2016
ffba835
Remove spacing
guerler Sep 1, 2016
7351d67
Remove unused listener
guerler Sep 1, 2016
05fa9b9
Rename remote to repository to avoid confusion
guerler Sep 1, 2016
3d9df64
Rename optional config attributes name accordingly
guerler Sep 1, 2016
ff301c5
Add debug log, fix config name, add comment for local repository
guerler Sep 2, 2016
36c1384
Use rawgit for proper MIME type handling
guerler Sep 2, 2016
819cb65
Add repository revision to url
guerler Sep 2, 2016
d5440f7
Upgrade repository version, allow pdb rendering type selection
guerler Sep 2, 2016
14ef3e3
Upgrade repository version
guerler Sep 2, 2016
d98a72d
Merge branch 'dev' into remote_chart_plugins
guerler Sep 2, 2016
14c0365
Upgrade repository revision
guerler Sep 5, 2016
5e8a2ce
Distinguish draw and save to avoid accumulation of saved visualizations
guerler Sep 9, 2016
cf9db96
Change label from draw to visualize
guerler Sep 9, 2016
a88942b
Unify labels and tooltips
guerler Sep 9, 2016
052b6e3
Fix tooltip
guerler Sep 9, 2016
8b13f63
Merge branch 'dev' into remote_chart_plugins
guerler Sep 14, 2016
46d05ba
Merge branch 'dev' into remote_chart_plugins
guerler Sep 30, 2016
494d50f
Repack client
guerler Sep 30, 2016
fdc81bd
Upgrade repository revision
guerler Oct 8, 2016
2316075
Merge branch 'dev' into remote_chart_plugins
guerler Oct 8, 2016
b7a25fc
Update repository revision to new drawrnajs logo
guerler Oct 8, 2016
bf5cc30
Remove tabular file from repo, fix comments
guerler Oct 11, 2016
1805ac8
Add chart plugins back to plugins directory of visualization framework
guerler Oct 12, 2016
f467384
Use fixed repository path
guerler Oct 12, 2016
fe73009
Fix default options for storing request
guerler Oct 12, 2016
f053f9b
Merge branch 'dev' into remote_chart_plugins
guerler Oct 14, 2016
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16 changes: 5 additions & 11 deletions client/galaxy/scripts/mvc/tool/tool-form-base.js
Original file line number Diff line number Diff line change
Expand Up @@ -255,19 +255,13 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
title : 'Requirements',
tooltip : 'Display tool requirements',
onclick : function() {
if (!this.visible || self.portlet.collapsed ) {
this.visible = true;
if ( !this.requirements_visible || self.portlet.collapsed ) {
this.requirements_visible = true;
self.portlet.expand();
self.message.update({
persistent : true,
message : self._templateRequirements(options),
status : 'info'
});
self.message.update( { persistent : true, message : self._templateRequirements( options ), status : 'info' } );
} else {
this.visible = false;
self.message.update({
message : ''
});
this.requirements_visible = false;
self.message.update( { message : '' } );
}
}
});
Expand Down
56 changes: 32 additions & 24 deletions client/galaxy/scripts/mvc/ui/ui-buttons.js
Original file line number Diff line number Diff line change
Expand Up @@ -223,9 +223,11 @@ define( [ 'utils/utils' ], function( Utils ) {
visible : true,
tag : ''
}).set( options );
this.collection = new Backbone.Collection();
this.setElement( $( '<div/>' ).append( this.$root = $( '<div/>' ).append( this.$icon = $( '<i/>' ) )
.append( this.$title = $( '<span/>' ) ) ) );
this.listenTo( this.model, 'change', this.render, this );
this.listenTo( this.collection, 'change add remove reset', this.render, this );
this.render();
},

Expand All @@ -237,7 +239,7 @@ define( [ 'utils/utils' ], function( Utils ) {
.addClass( options.cls )
.attr( 'id', options.id )
.css( { float : options.floating,
display : options.visible ? 'block' : 'none' } );
display : options.visible && this.collection.where( { visible: true } ).length > 0 ? 'block' : 'none' } );
this.$root.addClass( 'root button dropdown-toggle' )
.attr( 'data-toggle', 'dropdown' )
.tooltip( { title: options.tooltip, placement: 'bottom' } )
Expand All @@ -249,40 +251,46 @@ define( [ 'utils/utils' ], function( Utils ) {
this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );
this.$title.removeClass().addClass( 'title' ).html( options.title );
options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );
this.$menu && this.$menu.remove();
if ( this.collection.length > 0 ) {
this.$menu = $( '<ul/>' ).addClass( 'menu dropdown-menu' )
.addClass( 'pull-' + self.model.get( 'pull' ) )
.attr( 'role', 'menu' );
this.$el.append( this.$menu );
}
this.collection.each( function( submodel ) {
var suboptions = submodel.attributes;
if ( suboptions.visible ) {
var $link = $( '<a/>' ).addClass( 'dropdown-item' )
.attr( { href : suboptions.href, target : suboptions.target } )
.append( $( '<i/>' ).addClass( 'fa' )
.addClass( suboptions.icon )
.css( 'display', suboptions.icon ? 'inline-block' : 'none' ) )
.append( suboptions.title )
.on( 'click', function( e ) {
if ( suboptions.onclick ) {
e.preventDefault();
suboptions.onclick();
}
} );
self.$menu.append( $( '<li/>' ).append( $link ) );
suboptions.divider && self.$menu.append( $( '<li/>' ).addClass( 'divider' ) );
}
});
},

/** Add a new menu item */
addMenu: function ( options ) {
var options = Utils.merge( options, {
this.collection.add( Utils.merge( options, {
title : '',
target : '',
href : '',
onclick : null,
divider : false,
visible : true,
icon : null,
cls : 'button-menu btn-group'
});
if ( !this.$menu ) {
this.$menu = $( '<ul/>' ).addClass( 'menu dropdown-menu' )
.addClass( 'pull-' + this.model.get( 'pull' ) )
.attr( 'role', 'menu' );
this.$el.append( this.$menu );
}
var $link = $( '<a/>' ).addClass( 'dropdown-item' )
.attr( { href : options.href,
target : options.target } )
.append( $( '<i/>' ).addClass( 'fa' )
.addClass( options.icon )
.css( 'display', options.icon ? 'inline-block' : 'none' ) )
.append( options.title )
.on( 'click', function( e ) {
if ( options.onclick ) {
e.preventDefault();
options.onclick();
}
} );
this.$menu.append( $( '<li/>' ).append( $link ) );
options.divider && this.$menu.append( $( '<li/>' ).addClass( 'divider' ) );
}));
}
});

Expand Down
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