11:38 a.m.
12 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e14f0956dfc9/
Changeset: e14f0956dfc9
Branch: next-stable
User: dannon
Date: 2014-05-28 15:47:22
Summary: Cleanup prior to tabular work.
Affected #: 3 files
diff -r eed45027e219df9c4fc87fcfc788380ecc500b1a -r
e14f0956dfc984a11d495eb59f77131596110ae4 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -633,9 +633,9 @@
};
return {
- Dataset: Dataset,
+ Dataset: Dataset,
TabularDataset: TabularDataset,
- DatasetCollection: DatasetCollection,
+ DatasetCollection: DatasetCollection,
TabularDatasetChunkedView: TabularDatasetChunkedView,
createTabularDatasetChunkedView: createTabularDatasetChunkedView
};
diff -r eed45027e219df9c4fc87fcfc788380ecc500b1a -r
e14f0956dfc984a11d495eb59f77131596110ae4 templates/webapps/galaxy/dataset/display.mako
--- a/templates/webapps/galaxy/dataset/display.mako
+++ b/templates/webapps/galaxy/dataset/display.mako
@@ -9,7 +9,7 @@
%if item.datatype.CHUNKABLE:
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -17,21 +17,21 @@
});
require(['mvc/data'], function(data) {
- //
+ //
// Use tabular data display progressively by deleting data from page body
// and then showing dataset view.
- //
+ //
$('.page-body').children().remove();
data.createTabularDatasetChunkedView({
// TODO: encode id.
- dataset_config:
- _.extend( ${h.to_json_string( item.to_dict() )},
+ dataset_config:
+ _.extend( ${h.to_json_string( item.to_dict() )},
{
- chunk_url: "${h.url_for(
controller='/dataset', action='display',
+ chunk_url: "${h.url_for(
controller='/dataset', action='display',
dataset_id=trans.security.encode_id(
item.id ))}",
first_data_chunk: ${first_chunk}
- }
+ }
),
parent_elt: $('.page-body')
});
@@ -58,9 +58,9 @@
<%def name="render_item_links( data )">
## Provide links to save data and import dataset.
<a href="${h.url_for( controller='/dataset',
action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext
)}" class="icon-button disk" title="Save dataset"></a>
- <a
+ <a
href="${h.url_for( controller='/dataset', action='imp',
dataset_id=trans.security.encode_id( data.id ) )}"
- class="icon-button import"
+ class="icon-button import"
title="Import dataset"></a></%def>
@@ -70,7 +70,7 @@
%if data_to_render:
%if truncated:
<div class="warningmessagelarge">
- This dataset is large and only the first megabyte is shown below. |
+ This dataset is large and only the first megabyte is shown below. |
<a href="${h.url_for( controller='dataset',
action='display_by_username_and_slug', username=data.history.user.username,
slug=trans.security.encode_id( data.id ), preview=False )}">Show
all</a></div>
%endif
@@ -100,9 +100,9 @@
| ${get_item_name( item ) | h}
</div></div>
-
+
<div class="unified-panel-body">
- <div style="overflow: auto; height: 100%;">
+ <div style="overflow: auto; height: 100%;"><div
class="page-body"><div style="float: right">
${self.render_item_links( item )}
@@ -110,7 +110,7 @@
<div>
${self.render_item_header( item )}
</div>
-
+
${self.render_item( item, item_data )}
</div></div>
@@ -123,20 +123,20 @@
About this ${get_class_display_name( item.__class__ )}
</div></div>
-
+
<div class="unified-panel-body"><div style="overflow: auto;
height: 100%;"><div style="padding:
10px;"><h4>Author</h4>
-
+
<p>${item.history.user.username | h}</p>
-
+
<div><img
src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.em...
- ## Page meta.
-
+ ## Page meta.
+
## No links for datasets right now.
-
+
## Tags.
<p><h4>Tags</h4>
@@ -155,8 +155,8 @@
Yours:
${render_individual_tagging_element( user=trans.get_user(),
tagged_item=item, elt_context='view.mako', use_toggle_link=False,
tag_click_fn='community_tag_click' )}
</div>
- </div>
+ </div></div></div>
-</%def>
\ No newline at end of file
+</%def>
diff -r eed45027e219df9c4fc87fcfc788380ecc500b1a -r
e14f0956dfc984a11d495eb59f77131596110ae4
templates/webapps/galaxy/dataset/tabular_chunked.mako
--- a/templates/webapps/galaxy/dataset/tabular_chunked.mako
+++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako
@@ -8,7 +8,7 @@
${h.js( "libs/require" )}
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -23,7 +23,7 @@
chunk_url: "${h.url_for( controller='/dataset',
action='display',
dataset_id=trans.security.encode_id(
dataset.id ))}",
first_data_chunk: ${chunk}
- }
+ }
),
parent_elt: $('body')
});
https://bitbucket.org/galaxy/galaxy-central/commits/e0470cb34e7a/
Changeset: e0470cb34e7a
Branch: next-stable
User: dannon
Date: 2014-05-29 14:22:47
Summary: Merge.
Affected #: 1 file
diff -r e14f0956dfc984a11d495eb59f77131596110ae4 -r
e0470cb34e7a14198fa635055abd81def09bba06 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -204,6 +204,10 @@
using message queues (in the more traditional mode Galaxy sends
files to and pull files from the LWR - this is obviously less
appropriate when using a message queue).
+
+ The default_file_action currently requires pycurl be available
+ to Galaxy (presumably in its virtualenv). Making this dependency
+ optional is an open task.
--><param
id="default_file_action">remote_transfer</param></destination>
https://bitbucket.org/galaxy/galaxy-central/commits/b99e3eee6217/
Changeset: b99e3eee6217
User: dannon
Date: 2014-05-29 14:23:03
Summary: Merge next-stable.
Affected #: 3 files
diff -r 34d179b55c859f9c669c73733bde2684cf9d4a9f -r
b99e3eee6217db24efa3fad12bd5c00289522056 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -640,9 +640,9 @@
};
return {
- Dataset: Dataset,
+ Dataset: Dataset,
TabularDataset: TabularDataset,
- DatasetCollection: DatasetCollection,
+ DatasetCollection: DatasetCollection,
TabularDatasetChunkedView: TabularDatasetChunkedView,
createTabularDatasetChunkedView: createTabularDatasetChunkedView
};
diff -r 34d179b55c859f9c669c73733bde2684cf9d4a9f -r
b99e3eee6217db24efa3fad12bd5c00289522056 templates/webapps/galaxy/dataset/display.mako
--- a/templates/webapps/galaxy/dataset/display.mako
+++ b/templates/webapps/galaxy/dataset/display.mako
@@ -9,7 +9,7 @@
%if item.datatype.CHUNKABLE:
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -17,21 +17,21 @@
});
require(['mvc/data'], function(data) {
- //
+ //
// Use tabular data display progressively by deleting data from page body
// and then showing dataset view.
- //
+ //
$('.page-body').children().remove();
data.createTabularDatasetChunkedView({
// TODO: encode id.
- dataset_config:
- _.extend( ${h.to_json_string( item.to_dict() )},
+ dataset_config:
+ _.extend( ${h.to_json_string( item.to_dict() )},
{
- chunk_url: "${h.url_for(
controller='/dataset', action='display',
+ chunk_url: "${h.url_for(
controller='/dataset', action='display',
dataset_id=trans.security.encode_id(
item.id ))}",
first_data_chunk: ${first_chunk}
- }
+ }
),
parent_elt: $('.page-body')
});
@@ -58,9 +58,9 @@
<%def name="render_item_links( data )">
## Provide links to save data and import dataset.
<a href="${h.url_for( controller='/dataset',
action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext
)}" class="icon-button disk" title="Save dataset"></a>
- <a
+ <a
href="${h.url_for( controller='/dataset', action='imp',
dataset_id=trans.security.encode_id( data.id ) )}"
- class="icon-button import"
+ class="icon-button import"
title="Import dataset"></a></%def>
@@ -70,7 +70,7 @@
%if data_to_render:
%if truncated:
<div class="warningmessagelarge">
- This dataset is large and only the first megabyte is shown below. |
+ This dataset is large and only the first megabyte is shown below. |
<a href="${h.url_for( controller='dataset',
action='display_by_username_and_slug', username=data.history.user.username,
slug=trans.security.encode_id( data.id ), preview=False )}">Show
all</a></div>
%endif
@@ -100,9 +100,9 @@
| ${get_item_name( item ) | h}
</div></div>
-
+
<div class="unified-panel-body">
- <div style="overflow: auto; height: 100%;">
+ <div style="overflow: auto; height: 100%;"><div
class="page-body"><div style="float: right">
${self.render_item_links( item )}
@@ -110,7 +110,7 @@
<div>
${self.render_item_header( item )}
</div>
-
+
${self.render_item( item, item_data )}
</div></div>
@@ -123,20 +123,20 @@
About this ${get_class_display_name( item.__class__ )}
</div></div>
-
+
<div class="unified-panel-body"><div style="overflow: auto;
height: 100%;"><div style="padding:
10px;"><h4>Author</h4>
-
+
<p>${item.history.user.username | h}</p>
-
+
<div><img
src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.em...
- ## Page meta.
-
+ ## Page meta.
+
## No links for datasets right now.
-
+
## Tags.
<p><h4>Tags</h4>
@@ -155,8 +155,8 @@
Yours:
${render_individual_tagging_element( user=trans.get_user(),
tagged_item=item, elt_context='view.mako', use_toggle_link=False,
tag_click_fn='community_tag_click' )}
</div>
- </div>
+ </div></div></div>
-</%def>
\ No newline at end of file
+</%def>
diff -r 34d179b55c859f9c669c73733bde2684cf9d4a9f -r
b99e3eee6217db24efa3fad12bd5c00289522056
templates/webapps/galaxy/dataset/tabular_chunked.mako
--- a/templates/webapps/galaxy/dataset/tabular_chunked.mako
+++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako
@@ -8,7 +8,7 @@
${h.js( "libs/require" )}
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -23,7 +23,7 @@
chunk_url: "${h.url_for( controller='/dataset',
action='display',
dataset_id=trans.security.encode_id(
dataset.id ))}",
first_data_chunk: ${chunk}
- }
+ }
),
parent_elt: $('body')
});
https://bitbucket.org/galaxy/galaxy-central/commits/60aa2c0c0b21/
Changeset: 60aa2c0c0b21
User: dannon
Date: 2014-05-29 22:28:08
Summary: merge.
Affected #: 1 file
diff -r b99e3eee6217db24efa3fad12bd5c00289522056 -r
60aa2c0c0b21f4c52b1f83c7f19d0b148e198ee0 lib/galaxy/visualization/registry.py
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -243,10 +243,11 @@
datatype_class_name = test_result
test_result =
trans.app.datatypes_registry.get_datatype_class_by_name( datatype_class_name )
if not test_result:
- # warn if can't find class, but continue (with other tests)
- log.warn( 'visualizations_registry cannot find class
(%s)' +
- ' for applicability test on: %s, id: %s',
datatype_class_name,
- target_object, getattr( target_object, 'id',
'' ) )
+ # but continue (with other tests) if can't find class by that
name
+ #if self.debug:
+ # log.warn( 'visualizations_registry cannot find class
(%s)' +
+ # ' for applicability test on: %s, id: %s',
datatype_class_name,
+ # target_object, getattr( target_object,
'id', '' ) )
continue
#NOTE: tests are OR'd, if any test passes - the visualization can be
applied
https://bitbucket.org/galaxy/galaxy-central/commits/a37133f7364d/
Changeset: a37133f7364d
Branch: next-stable
User: dannon
Date: 2014-05-30 17:11:32
Summary: Add loading indicator back that disappeared (unintentionally?) in
b12b245510be
Affected #: 1 file
diff -r b8fef1dfa8e8eb5afdeaa96236a0a9990f7c532b -r
a37133f7364d75f3749e9eb72c0195b446dce781 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -133,6 +133,16 @@
},
render: function() {
+ // Add loading indicator.
+ var loading_indicator = $('<div/>').attr('id',
'loading_indicator');
+
+ loading_indicator.ajaxStart(function(){
+ $(this).show();
+ }).ajaxStop(function(){
+ $(this).hide();
+ });
+
+ this.$el.append(loading_indicator);
// Add data table and header.
var data_table = $('<table/>').attr({
id: 'content_table',
@@ -170,11 +180,6 @@
});
}
});
- $('#loading_indicator').ajaxStart(function(){
- $(this).show();
- }).ajaxStop(function(){
- $(this).hide();
- });
},
/**
https://bitbucket.org/galaxy/galaxy-central/commits/79a9d2b2c110/
Changeset: 79a9d2b2c110
User: dannon
Date: 2014-05-30 17:11:46
Summary: Merge.
Affected #: 1 file
diff -r 60aa2c0c0b21f4c52b1f83c7f19d0b148e198ee0 -r
79a9d2b2c11024b5cd3a67ef84f25d9c07029a85 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -133,6 +133,16 @@
},
render: function() {
+ // Add loading indicator.
+ var loading_indicator = $('<div/>').attr('id',
'loading_indicator');
+
+ loading_indicator.ajaxStart(function(){
+ $(this).show();
+ }).ajaxStop(function(){
+ $(this).hide();
+ });
+
+ this.$el.append(loading_indicator);
// Add data table and header.
var data_table = $('<table/>').attr({
id: 'content_table',
@@ -177,11 +187,6 @@
});
}
});
- $('#loading_indicator').ajaxStart(function(){
- $(this).show();
- }).ajaxStop(function(){
- $(this).hide();
- });
},
/**
https://bitbucket.org/galaxy/galaxy-central/commits/afb293ca337b/
Changeset: afb293ca337b
Branch: next-stable
User: dannon
Date: 2014-05-30 17:33:08
Summary: Pack scripts.
Affected #: 1 file
diff -r a37133f7364d75f3749e9eb72c0195b446dce781 -r
afb293ca337be1e04a34f22a310367d99ff2a38f static/scripts/packed/mvc/data.js
--- a/static/scripts/packed/mvc/data.js
+++ b/static/scripts/packed/mvc/data.js
@@ -1,1 +1,1 @@
-define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var
g=Backbone.Model.extend({});var
b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var
m=new
g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var
o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete
this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return
this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var
h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return
null}var
m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var
p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return
n}});var e=Backbone.Collection.extend({model:b});var
a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new
d({model:m.model,$el:this.$el})},render:function(){var
q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var
m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var
o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var
n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return
false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var
o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return
n},_renderRow:function(m){var
n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return
p},_renderChunk:function(m){var
n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var
f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return
$(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var
l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return
this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var
d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var
r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var
n=o.model;var
q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster
: Bed-file metadata
incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var
s=0;s<u.length;s++){if(u[s].match(t)){return s}}return
-1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster
: VCF-file metadata
incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster
: Dataset identification is
missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster
: Url for visualization controller is
missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var
m=new IconButtonView({model:new
IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover
tr":"show",mouseleave:"hide"},show:function(r){function
q(w){return
!isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var
v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var
m=v.children().eq(this.col.start).html();var
o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var
u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var
p=v.offset();var n=p.left-10;var
t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var
n=this;return function(){var
q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something
went wrong!",body:"Unfortunately we could not add this dataset to the track
browser. Please try again or contact
us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View
Data in a New or Saved
Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved
visualization":function(){n.modal.show({title:"Add Data to Saved
Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to
visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var
s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View
in new
visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return
false}}});var k=function(p,n,q,m){var o=new n({model:new
p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new
h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete
o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new
f(o));m.render();if(n){n.append(m.$el)}return
m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
+define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var
g=Backbone.Model.extend({});var
b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var
m=new
g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var
o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete
this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return
this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var
h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return
null}var
m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var
p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return
n}});var e=Backbone.Collection.extend({model:b});var
a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new
d({model:m.model,$el:this.$el})},render:function(){var
s=$("<div/>").attr("id","loading_indicator");s.ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()});this.$el.append(s);var
q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var
m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var
o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var
n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(t){if(t){n._renderChunk(t);p=false}})}})},scrolled_to_bottom:function(){return
false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var
o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return
n},_renderRow:function(m){var
n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return
p},_renderChunk:function(m){var
n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var
f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return
$(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var
l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return
this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var
d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var
r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var
n=o.model;var
q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster
: Bed-file metadata
incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var
s=0;s<u.length;s++){if(u[s].match(t)){return s}}return
-1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster
: VCF-file metadata
incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster
: Dataset identification is
missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster
: Url for visualization controller is
missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var
m=new IconButtonView({model:new
IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover
tr":"show",mouseleave:"hide"},show:function(r){function
q(w){return
!isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var
v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var
m=v.children().eq(this.col.start).html();var
o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var
u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var
p=v.offset();var n=p.left-10;var
t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var
n=this;return function(){var
q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something
went wrong!",body:"Unfortunately we could not add this dataset to the track
browser. Please try again or contact
us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View
Data in a New or Saved
Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved
visualization":function(){n.modal.show({title:"Add Data to Saved
Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to
visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var
s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View
in new
visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return
false}}});var k=function(p,n,q,m){var o=new n({model:new
p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new
h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete
o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new
f(o));m.render();if(n){n.append(m.$el)}return
m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/47fbab3029e5/
Changeset: 47fbab3029e5
User: dannon
Date: 2014-05-30 17:33:18
Summary: Merge next-stable.
Affected #: 1 file
diff -r 79a9d2b2c11024b5cd3a67ef84f25d9c07029a85 -r
47fbab3029e5fe1a1f3334bbcfa46c5856c63bc7 static/scripts/packed/mvc/data.js
--- a/static/scripts/packed/mvc/data.js
+++ b/static/scripts/packed/mvc/data.js
@@ -1,1 +1,1 @@
-define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var
g=Backbone.Model.extend({});var
b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var
m=new
g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var
o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete
this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return
this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var
h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return
null}var
m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var
p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return
n}});var e=Backbone.Collection.extend({model:b});var
a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new
d({model:m.model,$el:this.$el})},render:function(){var
q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var
m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var
o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var
n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return
false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var
o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return
n},_renderRow:function(m){var
n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return
p},_renderChunk:function(m){var
n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var
f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return
$(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var
l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return
this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var
d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var
r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var
n=o.model;var
q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster
: Bed-file metadata
incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var
s=0;s<u.length;s++){if(u[s].match(t)){return s}}return
-1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster
: VCF-file metadata
incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster
: Dataset identification is
missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster
: Url for visualization controller is
missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var
m=new IconButtonView({model:new
IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover
tr":"show",mouseleave:"hide"},show:function(r){function
q(w){return
!isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var
v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var
m=v.children().eq(this.col.start).html();var
o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var
u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var
p=v.offset();var n=p.left-10;var
t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var
n=this;return function(){var
q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something
went wrong!",body:"Unfortunately we could not add this dataset to the track
browser. Please try again or contact
us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View
Data in a New or Saved
Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved
visualization":function(){n.modal.show({title:"Add Data to Saved
Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to
visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var
s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View
in new
visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return
false}}});var k=function(p,n,q,m){var o=new n({model:new
p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new
h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete
o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new
f(o));m.render();if(n){n.append(m.$el)}return
m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
+define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var
g=Backbone.Model.extend({});var
b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var
m=new
g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var
o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete
this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return
this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var
h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return
null}var
m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var
p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return
n}});var e=Backbone.Collection.extend({model:b});var
a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new
d({model:m.model,$el:this.$el})},render:function(){var
s=$("<div/>").attr("id","loading_indicator");s.ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()});this.$el.append(s);var
q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var
m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var
o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var
n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(t){if(t){n._renderChunk(t);p=false}})}})},scrolled_to_bottom:function(){return
false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var
o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return
n},_renderRow:function(m){var
n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return
p},_renderChunk:function(m){var
n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var
f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return
$(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var
l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return
this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var
d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var
r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var
n=o.model;var
q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster
: Bed-file metadata
incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var
s=0;s<u.length;s++){if(u[s].match(t)){return s}}return
-1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster
: VCF-file metadata
incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster
: Dataset identification is
missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster
: Url for visualization controller is
missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var
m=new IconButtonView({model:new
IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover
tr":"show",mouseleave:"hide"},show:function(r){function
q(w){return
!isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var
v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var
m=v.children().eq(this.col.start).html();var
o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var
u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var
p=v.offset();var n=p.left-10;var
t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var
n=this;return function(){var
q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something
went wrong!",body:"Unfortunately we could not add this dataset to the track
browser. Please try again or contact
us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View
Data in a New or Saved
Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved
visualization":function(){n.modal.show({title:"Add Data to Saved
Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to
visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var
s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View
in new
visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return
false}}});var k=function(p,n,q,m){var o=new n({model:new
p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new
h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete
o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new
f(o));m.render();if(n){n.append(m.$el)}return
m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/cded8178bb48/
Changeset: cded8178bb48
Branch: next-stable
User: dannon
Date: 2014-05-30 17:34:15
Summary: Merge.
Affected #: 1 file
diff -r afb293ca337be1e04a34f22a310367d99ff2a38f -r
cded8178bb4834236d9ae6239c14b928ae2d282b lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -498,7 +498,7 @@
# Check that the file is in the right location
local_filename = os.path.abspath( value['path'] )
assert local_filename.startswith( upload_store ), \
- "Filename provided by nginx is not in correct directory"
+ "Filename provided by nginx (%s) is not in correct directory
(%s)" % (local_filename, upload_store)
value = dict(
filename=value["name"],
local_filename=local_filename
https://bitbucket.org/galaxy/galaxy-central/commits/f48fbe6866a5/
Changeset: f48fbe6866a5
User: dannon
Date: 2014-05-30 17:35:27
Summary: Merge
Affected #: 2 files
diff -r 3409e283965f58ec4bf96594f980a8e6ee2cb058 -r
f48fbe6866a56e0f05d36d84da8450d06bdac9c7 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -133,6 +133,16 @@
},
render: function() {
+ // Add loading indicator.
+ var loading_indicator = $('<div/>').attr('id',
'loading_indicator');
+
+ loading_indicator.ajaxStart(function(){
+ $(this).show();
+ }).ajaxStop(function(){
+ $(this).hide();
+ });
+
+ this.$el.append(loading_indicator);
// Add data table and header.
var data_table = $('<table/>').attr({
id: 'content_table',
@@ -177,11 +187,6 @@
});
}
});
- $('#loading_indicator').ajaxStart(function(){
- $(this).show();
- }).ajaxStop(function(){
- $(this).hide();
- });
},
/**
diff -r 3409e283965f58ec4bf96594f980a8e6ee2cb058 -r
f48fbe6866a56e0f05d36d84da8450d06bdac9c7 static/scripts/packed/mvc/data.js
--- a/static/scripts/packed/mvc/data.js
+++ b/static/scripts/packed/mvc/data.js
@@ -1,1 +1,1 @@
-define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var
g=Backbone.Model.extend({});var
b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var
m=new
g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var
o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete
this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return
this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var
h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return
null}var
m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var
p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return
n}});var e=Backbone.Collection.extend({model:b});var
a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new
d({model:m.model,$el:this.$el})},render:function(){var
q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var
m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var
o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var
n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return
false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var
o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return
n},_renderRow:function(m){var
n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return
p},_renderChunk:function(m){var
n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var
f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return
$(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var
l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return
this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var
d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var
r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var
n=o.model;var
q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster
: Bed-file metadata
incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var
s=0;s<u.length;s++){if(u[s].match(t)){return s}}return
-1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster
: VCF-file metadata
incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster
: Dataset identification is
missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster
: Url for visualization controller is
missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var
m=new IconButtonView({model:new
IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover
tr":"show",mouseleave:"hide"},show:function(r){function
q(w){return
!isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var
v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var
m=v.children().eq(this.col.start).html();var
o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var
u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var
p=v.offset();var n=p.left-10;var
t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var
n=this;return function(){var
q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something
went wrong!",body:"Unfortunately we could not add this dataset to the track
browser. Please try again or contact
us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View
Data in a New or Saved
Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved
visualization":function(){n.modal.show({title:"Add Data to Saved
Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to
visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var
s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View
in new
visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return
false}}});var k=function(p,n,q,m){var o=new n({model:new
p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new
h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete
o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new
f(o));m.render();if(n){n.append(m.$el)}return
m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
+define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var
g=Backbone.Model.extend({});var
b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var
m=new
g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var
o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete
this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return
this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var
h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return
null}var
m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var
p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return
n}});var e=Backbone.Collection.extend({model:b});var
a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new
d({model:m.model,$el:this.$el})},render:function(){var
s=$("<div/>").attr("id","loading_indicator");s.ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()});this.$el.append(s);var
q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var
m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var
o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var
n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(t){if(t){n._renderChunk(t);p=false}})}})},scrolled_to_bottom:function(){return
false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var
o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return
n},_renderRow:function(m){var
n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return
p},_renderChunk:function(m){var
n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var
f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return
$(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var
l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return
this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var
d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var
r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var
n=o.model;var
q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster
: Bed-file metadata
incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var
s=0;s<u.length;s++){if(u[s].match(t)){return s}}return
-1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster
: VCF-file metadata
incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster
: Dataset identification is
missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster
: Url for visualization controller is
missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var
m=new IconButtonView({model:new
IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover
tr":"show",mouseleave:"hide"},show:function(r){function
q(w){return
!isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var
v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var
m=v.children().eq(this.col.start).html();var
o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var
u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var
p=v.offset();var n=p.left-10;var
t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var
n=this;return function(){var
q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something
went wrong!",body:"Unfortunately we could not add this dataset to the track
browser. Please try again or contact
us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View
Data in a New or Saved
Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved
visualization":function(){n.modal.show({title:"Add Data to Saved
Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to
visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var
s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View
in new
visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return
false}}});var k=function(p,n,q,m){var o=new n({model:new
p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new
h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete
o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new
f(o));m.render();if(n){n.append(m.$el)}return
m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/cb1e86b187a3/
Changeset: cb1e86b187a3
Branch: next-stable
User: dannon
Date: 2014-05-30 17:37:13
Summary: Merge.
Affected #: 3 files
diff -r cded8178bb4834236d9ae6239c14b928ae2d282b -r
cb1e86b187a38fce1b9601115fc1a51809f3b292 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -638,9 +638,9 @@
};
return {
- Dataset: Dataset,
+ Dataset: Dataset,
TabularDataset: TabularDataset,
- DatasetCollection: DatasetCollection,
+ DatasetCollection: DatasetCollection,
TabularDatasetChunkedView: TabularDatasetChunkedView,
createTabularDatasetChunkedView: createTabularDatasetChunkedView
};
diff -r cded8178bb4834236d9ae6239c14b928ae2d282b -r
cb1e86b187a38fce1b9601115fc1a51809f3b292 templates/webapps/galaxy/dataset/display.mako
--- a/templates/webapps/galaxy/dataset/display.mako
+++ b/templates/webapps/galaxy/dataset/display.mako
@@ -9,7 +9,7 @@
%if item.datatype.CHUNKABLE:
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -17,21 +17,21 @@
});
require(['mvc/data'], function(data) {
- //
+ //
// Use tabular data display progressively by deleting data from page body
// and then showing dataset view.
- //
+ //
$('.page-body').children().remove();
data.createTabularDatasetChunkedView({
// TODO: encode id.
- dataset_config:
- _.extend( ${h.to_json_string( item.to_dict() )},
+ dataset_config:
+ _.extend( ${h.to_json_string( item.to_dict() )},
{
- chunk_url: "${h.url_for(
controller='/dataset', action='display',
+ chunk_url: "${h.url_for(
controller='/dataset', action='display',
dataset_id=trans.security.encode_id(
item.id ))}",
first_data_chunk: ${first_chunk}
- }
+ }
),
parent_elt: $('.page-body')
});
@@ -58,9 +58,9 @@
<%def name="render_item_links( data )">
## Provide links to save data and import dataset.
<a href="${h.url_for( controller='/dataset',
action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext
)}" class="icon-button disk" title="Save dataset"></a>
- <a
+ <a
href="${h.url_for( controller='/dataset', action='imp',
dataset_id=trans.security.encode_id( data.id ) )}"
- class="icon-button import"
+ class="icon-button import"
title="Import dataset"></a></%def>
@@ -70,7 +70,7 @@
%if data_to_render:
%if truncated:
<div class="warningmessagelarge">
- This dataset is large and only the first megabyte is shown below. |
+ This dataset is large and only the first megabyte is shown below. |
<a href="${h.url_for( controller='dataset',
action='display_by_username_and_slug', username=data.history.user.username,
slug=trans.security.encode_id( data.id ), preview=False )}">Show
all</a></div>
%endif
@@ -100,9 +100,9 @@
| ${get_item_name( item ) | h}
</div></div>
-
+
<div class="unified-panel-body">
- <div style="overflow: auto; height: 100%;">
+ <div style="overflow: auto; height: 100%;"><div
class="page-body"><div style="float: right">
${self.render_item_links( item )}
@@ -110,7 +110,7 @@
<div>
${self.render_item_header( item )}
</div>
-
+
${self.render_item( item, item_data )}
</div></div>
@@ -123,20 +123,20 @@
About this ${get_class_display_name( item.__class__ )}
</div></div>
-
+
<div class="unified-panel-body"><div style="overflow: auto;
height: 100%;"><div style="padding:
10px;"><h4>Author</h4>
-
+
<p>${item.history.user.username | h}</p>
-
+
<div><img
src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.em...
- ## Page meta.
-
+ ## Page meta.
+
## No links for datasets right now.
-
+
## Tags.
<p><h4>Tags</h4>
@@ -155,8 +155,8 @@
Yours:
${render_individual_tagging_element( user=trans.get_user(),
tagged_item=item, elt_context='view.mako', use_toggle_link=False,
tag_click_fn='community_tag_click' )}
</div>
- </div>
+ </div></div></div>
-</%def>
\ No newline at end of file
+</%def>
diff -r cded8178bb4834236d9ae6239c14b928ae2d282b -r
cb1e86b187a38fce1b9601115fc1a51809f3b292
templates/webapps/galaxy/dataset/tabular_chunked.mako
--- a/templates/webapps/galaxy/dataset/tabular_chunked.mako
+++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako
@@ -8,7 +8,7 @@
${h.js( "libs/require" )}
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -23,7 +23,7 @@
chunk_url: "${h.url_for( controller='/dataset',
action='display',
dataset_id=trans.security.encode_id(
dataset.id ))}",
first_data_chunk: ${chunk}
- }
+ }
),
parent_elt: $('body')
});
https://bitbucket.org/galaxy/galaxy-central/commits/25ab1fe9dbc7/
Changeset: 25ab1fe9dbc7
User: dannon
Date: 2014-05-30 17:38:13
Summary: Merge.
Affected #: 3 files
diff -r f48fbe6866a56e0f05d36d84da8450d06bdac9c7 -r
25ab1fe9dbc7659fbf3cdfea26d5f03e4c521701 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -645,9 +645,9 @@
};
return {
- Dataset: Dataset,
+ Dataset: Dataset,
TabularDataset: TabularDataset,
- DatasetCollection: DatasetCollection,
+ DatasetCollection: DatasetCollection,
TabularDatasetChunkedView: TabularDatasetChunkedView,
createTabularDatasetChunkedView: createTabularDatasetChunkedView
};
diff -r f48fbe6866a56e0f05d36d84da8450d06bdac9c7 -r
25ab1fe9dbc7659fbf3cdfea26d5f03e4c521701 templates/webapps/galaxy/dataset/display.mako
--- a/templates/webapps/galaxy/dataset/display.mako
+++ b/templates/webapps/galaxy/dataset/display.mako
@@ -9,7 +9,7 @@
%if item.datatype.CHUNKABLE:
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -17,21 +17,21 @@
});
require(['mvc/data'], function(data) {
- //
+ //
// Use tabular data display progressively by deleting data from page body
// and then showing dataset view.
- //
+ //
$('.page-body').children().remove();
data.createTabularDatasetChunkedView({
// TODO: encode id.
- dataset_config:
- _.extend( ${h.to_json_string( item.to_dict() )},
+ dataset_config:
+ _.extend( ${h.to_json_string( item.to_dict() )},
{
- chunk_url: "${h.url_for(
controller='/dataset', action='display',
+ chunk_url: "${h.url_for(
controller='/dataset', action='display',
dataset_id=trans.security.encode_id(
item.id ))}",
first_data_chunk: ${first_chunk}
- }
+ }
),
parent_elt: $('.page-body')
});
@@ -58,9 +58,9 @@
<%def name="render_item_links( data )">
## Provide links to save data and import dataset.
<a href="${h.url_for( controller='/dataset',
action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext
)}" class="icon-button disk" title="Save dataset"></a>
- <a
+ <a
href="${h.url_for( controller='/dataset', action='imp',
dataset_id=trans.security.encode_id( data.id ) )}"
- class="icon-button import"
+ class="icon-button import"
title="Import dataset"></a></%def>
@@ -70,7 +70,7 @@
%if data_to_render:
%if truncated:
<div class="warningmessagelarge">
- This dataset is large and only the first megabyte is shown below. |
+ This dataset is large and only the first megabyte is shown below. |
<a href="${h.url_for( controller='dataset',
action='display_by_username_and_slug', username=data.history.user.username,
slug=trans.security.encode_id( data.id ), preview=False )}">Show
all</a></div>
%endif
@@ -100,9 +100,9 @@
| ${get_item_name( item ) | h}
</div></div>
-
+
<div class="unified-panel-body">
- <div style="overflow: auto; height: 100%;">
+ <div style="overflow: auto; height: 100%;"><div
class="page-body"><div style="float: right">
${self.render_item_links( item )}
@@ -110,7 +110,7 @@
<div>
${self.render_item_header( item )}
</div>
-
+
${self.render_item( item, item_data )}
</div></div>
@@ -123,20 +123,20 @@
About this ${get_class_display_name( item.__class__ )}
</div></div>
-
+
<div class="unified-panel-body"><div style="overflow: auto;
height: 100%;"><div style="padding:
10px;"><h4>Author</h4>
-
+
<p>${item.history.user.username | h}</p>
-
+
<div><img
src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.em...
- ## Page meta.
-
+ ## Page meta.
+
## No links for datasets right now.
-
+
## Tags.
<p><h4>Tags</h4>
@@ -155,8 +155,8 @@
Yours:
${render_individual_tagging_element( user=trans.get_user(),
tagged_item=item, elt_context='view.mako', use_toggle_link=False,
tag_click_fn='community_tag_click' )}
</div>
- </div>
+ </div></div></div>
-</%def>
\ No newline at end of file
+</%def>
diff -r f48fbe6866a56e0f05d36d84da8450d06bdac9c7 -r
25ab1fe9dbc7659fbf3cdfea26d5f03e4c521701
templates/webapps/galaxy/dataset/tabular_chunked.mako
--- a/templates/webapps/galaxy/dataset/tabular_chunked.mako
+++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako
@@ -8,7 +8,7 @@
${h.js( "libs/require" )}
<script type="text/javascript">
- require.config({
+ require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/backbone/backbone": { exports: "Backbone" },
@@ -23,7 +23,7 @@
chunk_url: "${h.url_for( controller='/dataset',
action='display',
dataset_id=trans.security.encode_id(
dataset.id ))}",
first_data_chunk: ${chunk}
- }
+ }
),
parent_elt: $('body')
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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