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Add genome selector to file upload

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This commit is contained in:
Aysam Guerler
2013-10-15 21:04:47 -04:00
parent d7eccdb0f2
commit 6a48a732ad
4 changed files with 60 additions and 31 deletions
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static/scripts/galaxy.modal.js
+13 -14
View File
@@ -15,7 +15,9 @@ var GalaxyModal = Backbone.View.extend(
optionsDefault: {
title : "galaxy-modal",
body : "",
backdrop : true
backdrop : true,
height : null,
width : null
},
// options
@@ -23,7 +25,6 @@ var GalaxyModal = Backbone.View.extend(
// initialize
initialize : function(options) {
// create
if (options)
this.create(options);
},
@@ -32,18 +33,18 @@ var GalaxyModal = Backbone.View.extend(
show: function(options) {
// create
this.initialize(options);
// fix height
var maxHeight = $(document).height() / 2;
this.$body.css('max-height', maxHeight);
// fix height if available
if (this.options.height)
this.$body.css('height', Math.min(this.options.height, maxHeight));
// remove scroll bar
if (this.options.height)
{
this.$body.css('height', this.options.height);
this.$body.css('overflow', 'hidden');
} else
this.$body.css('max-height', $(window).height() / 2);
// fix width
if (this.options.width)
this.$dialog.css('width', this.options.width);
// show
if (this.visible)
@@ -81,6 +82,7 @@ var GalaxyModal = Backbone.View.extend(
this.setElement(this.template(this.options.title));
// link elements
this.$dialog = (this.$el).find('.modal-dialog');
this.$body = (this.$el).find('.modal-body');
this.$footer = (this.$el).find('.modal-footer');
this.$buttons = (this.$el).find('.buttons');
@@ -89,9 +91,6 @@ var GalaxyModal = Backbone.View.extend(
// append body
this.$body.html(this.options.body);
// fix min-width so that modal cannot shrink considerably if new content is loaded.
this.$body.css('min-width', this.$body.width());
// configure background
if (!this.options.backdrop)
this.$backdrop.removeClass('in');
static/scripts/galaxy.upload.js
+41 -17
View File
@@ -22,6 +22,11 @@ var GalaxyUpload = Backbone.View.extend(
'auto' : 'Auto-detect'
},
// genomes
select_genome : {
'?' : 'Unspecified'
},
// states
state : {
init : 'fa-icon-trash',
@@ -82,10 +87,15 @@ var GalaxyUpload = Backbone.View.extend(
var self = this;
mod_util.jsonFromUrl(galaxy_config.root + "api/datatypes",
function(datatypes) {
for (key in datatypes) {
var filetype = datatypes[key];
self.select_extension[filetype] = filetype;
}
for (key in datatypes)
self.select_extension[datatypes[key]] = datatypes[key];
});
// load genomes
mod_util.jsonFromUrl(galaxy_config.root + "api/genomes",
function(genomes) {
for (key in genomes)
self.select_genome[genomes[key][1]] = genomes[key][0];
});
},
@@ -106,7 +116,7 @@ var GalaxyUpload = Backbone.View.extend(
var id = '#upload-' + index;
// add upload item
$(this.el).find('tbody:last').append(this.template_row(id, this.select_extension));
$(this.el).find('tbody:last').append(this.template_row(id));
// scroll to bottom
//$(this.el).scrollTop($(this.el).prop('scrollHeight'));
@@ -153,6 +163,7 @@ var GalaxyUpload = Backbone.View.extend(
// get configuration
var current_history = Galaxy.currHistoryPanel.model.get('id');
var file_type = it.find('#extension').val();
var genome = it.find('#genome').val();
var space_to_tabs = it.find('#space_to_tabs').is(':checked');
// configure uploadbox
@@ -160,7 +171,7 @@ var GalaxyUpload = Backbone.View.extend(
// configure tool
tool_input = {};
tool_input['dbkey'] = '?';
tool_input['dbkey'] = genome;
tool_input['file_type'] = file_type;
tool_input['files_0|NAME'] = file.name;
tool_input['files_0|type'] = 'upload_dataset';
@@ -285,6 +296,7 @@ var GalaxyUpload = Backbone.View.extend(
symbol.addClass(self.state.queued);
// disable options
$(this).find('#genome').attr('disabled', true);
$(this).find('#extension').attr('disabled', true);
$(this).find('#space_to_tabs').attr('disabled', true);
}
@@ -332,6 +344,7 @@ var GalaxyUpload = Backbone.View.extend(
symbol.addClass(self.state.init);
// disable options
$(this).find('#genome').attr('disabled', false);
$(this).find('#extension').attr('disabled', false);
$(this).find('#space_to_tabs').attr('disabled', false);
}
@@ -410,7 +423,8 @@ var GalaxyUpload = Backbone.View.extend(
'Reset' : function() {self.event_reset()},
'Close' : function() {self.modal.hide()}
},
height : '350'
height : '350',
width : '850'
});
// set element
@@ -528,6 +542,7 @@ var GalaxyUpload = Backbone.View.extend(
'<th>Name</th>' +
'<th>Size</th>' +
'<th>Type</th>' +
'<th>Genome</th>' +
'<th>Space&#8594;Tab</th>' +
'<th>Status</th>' +
'<th></th>' +
@@ -539,22 +554,31 @@ var GalaxyUpload = Backbone.View.extend(
'<h6 id="' + idInfo + '" class="upload-info"></h6>';
},
template_row: function(id, select_extension)
template_row: function(id)
{
// construct template
var tmpl = '<tr id="' + id.substr(1) + '" class="upload-item">' +
'<td><div id="title" class="title"></div></td>' +
'<td><div id="size" class="size"></div></td>' +
'<td>' +
'<select id="extension" class="extension">';
'<td><div id="size" class="size"></div></td>';
// add file types to selection
for (key in select_extension)
tmpl += '<option value="' + key + '">' + select_extension[key] + '</option>';
// add file type selectore
tmpl += '<td>' +
'<select id="extension" class="extension">';
for (key in this.select_extension)
tmpl += '<option value="' + key + '">' + this.select_extension[key] + '</option>';
tmpl += '</select>' +
'</td>' +
'<td><input id="space_to_tabs" type="checkbox"></input></td>' +
'</td>';
// add genome selector
tmpl += '<td>' +
'<select id="genome" class="genome">';
for (key in this.select_genome)
tmpl += '<option value="' + key + '">' + this.select_genome[key] + '</option>';
tmpl += '</select>' +
'</td>';
// add next row
tmpl += '<td><input id="space_to_tabs" type="checkbox"></input></td>' +
'<td>' +
'<div id="info" class="info">' +
'<div class="progress">' +
static/style/blue/base.css
+1
View File
@@ -1130,6 +1130,7 @@ ul.icons{list-style-type:none;text-indent:-0.75em}ul.icons li [class^="fa-icon-"
.upload-box .table td{margin:0px;paddign:0px}
.upload-box .title{width:130px;word-wrap:break-word;font-size:11px}
.upload-box .extension{width:100px;font-size:11px}
.upload-box .genome{width:150px;font-size:11px}
.upload-box .size{width:60px;white-space:nowrap}
.upload-box .info{width:130px;font-size:11px}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit}
.upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff}
static/style/src/less/upload.less
+5
View File
@@ -44,6 +44,11 @@
font-size : @font-size-small;
}
.genome {
width: 150px;
font-size : @font-size-small;
}
.size {
width: 60px;
white-space: nowrap;