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commit/galaxy-central: dannon: Safe fix here, but we should follow up on the database migration to avoid having cruft.
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8ce690c0910c/
Changeset: 8ce690c0910c
User: dannon
Date: 2014-10-10 15:14:37+00:00
Summary: Safe fix here, but we should follow up on the database migration to avoid having cruft.
Merged in dan/galaxy-central-prs (pull request #511)
Allow Model objects to be loaded when they have bad JSON values. When bad JSON is encountered, substitute with None.
Affected #: 1 file
diff -r a40dc4c1f075938eac42fd428e5fc7697560d751 -r 8ce690c0910c1f6a11f90fe91b51ca964e879d1f lib/galaxy/model/custom_types.py
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -47,9 +47,12 @@
return json_encoder.encode( value )
def process_result_value( self, value, dialect ):
- if value is None:
- return None
- return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) )
+ if value is not None:
+ try:
+ return json_decoder.decode( str( _sniffnfix_pg9_hex( value ) ) )
+ except Exception, e:
+ log.error( 'Failed to decode JSON (%s): %s', value, e )
+ return None
def copy_value( self, value ):
# return json_decoder.decode( json_encoder.encode( value ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3807e1fc68f2/
Changeset: 3807e1fc68f2
User: dan
Date: 2014-06-27 19:24:23+00:00
Summary: merge stable
Affected #: 0 files
https://bitbucket.org/galaxy/galaxy-central/commits/6d91f897777d/
Changeset: 6d91f897777d
User: dan
Date: 2014-08-20 14:53:00+00:00
Summary: Merged galaxy/galaxy-central into default
Affected #: 606 files
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -11,8 +11,12 @@
scripts/scramble/lib
scripts/scramble/archives
+# Python virtualenv
+.venv
+
# Database stuff
database/beaker_sessions
+database/citations
database/community_files
database/compiled_templates
database/files
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -7,6 +7,15 @@
26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04
5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10
9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14
-68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14
7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02
-8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02
+7a4d321c0e38fa263ea83d29a35a608c3181fcba latest_2014.06.02
+9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14
+6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13
+3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08
+425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01
+9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03
+9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12
+81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
+2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
+ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
+7e4d21621ce12e13ebbdf9fd3259df58c3ef124c latest_2014.08.11
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b README.txt
--- a/README.txt
+++ b/README.txt
@@ -1,31 +1,34 @@
-GALAXY
-======
-http://galaxyproject.org/
-
-The latest information about Galaxy is always available via the Galaxy
-website above.
-
-HOW TO START
-============
-Galaxy requires Python 2.6 or 2.7. To check your python version, run:
-
-% python -V
-Python 2.7.3
-
-Start Galaxy:
-
-% sh run.sh
-
-Once Galaxy completes startup, you should be able to view Galaxy in your
-browser at:
-
-http://localhost:8080
-
-You may wish to make changes from the default configuration. This can be done
-in the universe_wsgi.ini file. Tools are configured in tool_conf.xml. Details
-on adding tools can be found on the Galaxy website (linked above).
-
-Not all dependencies are included for the tools provided in the sample
-tool_conf.xml. A full list of external dependencies is available at:
-
-https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
+GALAXY
+======
+http://galaxyproject.org/
+
+The latest information about Galaxy is always available via the Galaxy
+website above.
+
+HOW TO START
+============
+Galaxy requires Python 2.6 or 2.7. To check your python version, run:
+
+% python -V
+Python 2.7.3
+
+Start Galaxy:
+
+% sh run.sh
+
+Once Galaxy completes startup, you should be able to view Galaxy in your
+browser at:
+
+http://localhost:8080
+
+You may wish to make changes from the default configuration. This can be done
+in the universe_wsgi.ini file. Tools can be either installed from the Tool Shed
+or added manually. For details please see the Galaxy wiki:
+
+https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial.
+
+
+Not all dependencies are included for the tools provided in the sample
+tool_conf.xml. A full list of external dependencies is available at:
+
+https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
\ No newline at end of file
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b buildbot_setup.sh
--- a/buildbot_setup.sh
+++ b/buildbot_setup.sh
@@ -52,12 +52,9 @@
migrated_tools_conf.xml.sample
data_manager_conf.xml.sample
shed_data_manager_conf.xml.sample
-tool-data/shared/ensembl/builds.txt.sample
tool-data/shared/igv/igv_build_sites.txt.sample
-tool-data/shared/ncbi/builds.txt.sample
tool-data/shared/rviewer/rviewer_build_sites.txt.sample
tool-data/shared/ucsc/builds.txt.sample
-tool-data/shared/ucsc/publicbuilds.txt.sample
tool-data/shared/ucsc/ucsc_build_sites.txt.sample
"
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -1,26 +1,26 @@
// dependencies
-define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils',
- 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage',
+define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils',
+ 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage', 'plugin/library/deferred',
'plugin/views/viewer', 'plugin/views/editor',
'plugin/models/config', 'plugin/models/chart',
'plugin/charts/types'],
- function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage,
+ function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, Deferred,
ViewerView, EditorView,
Config, Chart, Types
) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * Main application class.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(options)
- {
+ initialize: function(options){
// deactivate all debugs outputs
//window.console.debug = function() {};
// link options
this.options = options;
-
+
// link galaxy modal or create one
if (Galaxy && Galaxy.modal) {
this.modal = Galaxy.modal;
@@ -41,6 +41,7 @@
this.jobs = new Jobs(this);
this.datasets = new Datasets(this);
this.storage = new Storage(this);
+ this.deferred = new Deferred();
//
// views
@@ -62,7 +63,7 @@
// draw chart
var self = this;
- this.chart.deferred.execute(function() {
+ this.deferred.execute(function() {
self.chart.trigger('redraw');
});
}
@@ -100,19 +101,6 @@
console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type);
}
return undefined;
- },
-
- // execute command
- execute: function(options) {
- },
-
- // unload
- onunload: function() {
- },
-
- // log
- log: function(location, message) {
- console.log(location + ' ' + message);
}
});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),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"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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'+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("mvc/ui/ui-checkbox",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="ui-checkbox">';for(key in e.data){var n=e.data[key];t+='<input type="checkbox" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"<br>"}return t+="</div>",t}});return{View:t}}),define("mvc/ui/ui-radiobutton",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{View:t}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r,Checkbox:n,Searchbox:p,Select:t,Textarea:v}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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$.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})});
\ No newline at end of file
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
@@ -1,9 +1,10 @@
// dependencies
define(['plugin/charts/jqplot/common/plot-config', 'plugin/charts/tools'], function(configmaker, Tools) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This is the common wrapper for jqplot based visualizations.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// get parameters
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
@@ -1,9 +1,10 @@
// dependencies
define(['plugin/charts/tools'], function(Tools) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This is the common wrapper for nvd3 based visualizations.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// get parameters
@@ -97,6 +98,7 @@
}
});
+ // return
return true;
},
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
@@ -28,7 +28,7 @@
chart.state('ok', 'Pie chart has been drawn.');
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
}
// request data
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/charts/tools.js
--- a/config/plugins/visualizations/charts/static/charts/tools.js
+++ b/config/plugins/visualizations/charts/static/charts/tools.js
@@ -2,8 +2,7 @@
define(['utils/utils'], function(Utils) {
// render
-function panelHelper (app, options)
-{
+function panelHelper (app, options) {
// link this
var self = this;
@@ -42,7 +41,7 @@
}
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
} catch (err) {
// log
console.debug('FAILED: Tools::panelHelper() - ' + err);
@@ -51,7 +50,7 @@
chart.state('failed', err);
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
}
};
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/datasets.js
--- a/config/plugins/visualizations/charts/static/library/datasets.js
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -1,7 +1,9 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// widget
+/**
+ * This class handles, formats and caches datasets.
+ */
return Backbone.Collection.extend(
{
// list of datasets
@@ -11,8 +13,7 @@
cache: {},
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link app
this.app = app;
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/deferred.js
--- a/config/plugins/visualizations/charts/static/library/deferred.js
+++ b/config/plugins/visualizations/charts/static/library/deferred.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// deferred process handler
-return Backbone.Model.extend(
-{
+/**
+ * This class handles deferred processes. It makes it easy to handle multiple and overlapping sets of deferred processes.
+ */
+return Backbone.Model.extend({
// queue
queue: [],
@@ -14,8 +15,7 @@
counter: 0,
// initialize
- initialize: function()
- {
+ initialize: function(){
// loop through queue and check states
this.on('refresh', function() {
for (var index in this.queue) {
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// widget
-return Backbone.Model.extend(
-{
+/**
+ * This class handles job submissions to the charts tool.
+ */
+return Backbone.Model.extend({
// initialize
initialize: function(app, options) {
// link app
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/screenshot.js
--- a/config/plugins/visualizations/charts/static/library/screenshot.js
+++ b/config/plugins/visualizations/charts/static/library/screenshot.js
@@ -1,4 +1,6 @@
-// dependencies
+/**
+ * This class enables users to export/download a chart as PNG, SVG or PDF.
+ */
define(["libs/underscore"], function(_) {
//
// PNG export
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/storage.js
--- a/config/plugins/visualizations/charts/static/library/storage.js
+++ b/config/plugins/visualizations/charts/static/library/storage.js
@@ -1,9 +1,10 @@
// dependencies
-define(['utils/utils', 'plugin/models/chart', 'plugin/models/group'], function(Utils, Chart, Group) {
+define(['utils/utils', 'plugin/models/chart', 'plugin/models/group', 'mvc/visualization/visualization-model'], function(Utils, Chart, Group) {
-// collection
-return Backbone.Model.extend(
-{
+/**
+ * This class saves and loads a chart through the api.
+ */
+return Backbone.Model.extend({
// viz model
vis: null,
@@ -44,7 +45,6 @@
// pack and save nested chart model
save: function() {
-
// link chart
var chart = this.app.chart;
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/ui-button-menu.js
--- a/config/plugins/visualizations/charts/static/library/ui-button-menu.js
+++ /dev/null
@@ -1,168 +0,0 @@
-// dependencies
-define(['utils/utils'],
- function(Utils) {
-
-// return button menu
-return Backbone.View.extend({
- // main options
- optionsDefault: {
- // same as Ui.ButtonIcon
- id : '',
- title : '',
- float : 'right',
- icon : null,
- onclick : null,
- cls : 'icon-btn',
- tooltip : '',
-
- // additional options
- target : '',
- href : '',
- onunload : null,
- visible : true,
- tag : ''
- },
-
- // optional sub menu
- $menu: null,
-
- // initialize
- initialize: function (options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // add template for tab
- this.setElement($(this._template(this.options)));
-
- // find root
- var $root = $(this.el).find('.root');
-
- // link head
- var self = this;
- $root.on('click', function(e) {
- // hide all tooltips
- $('.tooltip').hide();
-
- // prevent default
- e.preventDefault();
-
- // add click event
- if(self.options.onclick) {
- self.options.onclick();
- }
- });
-
- // visiblity
- if (!this.options.visible)
- this.hide();
-
- // add tooltip
- $root.tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // show
- show: function() {
- $(this.el).show();
- },
-
- // hide
- hide: function() {
- $(this.el).hide();
- },
-
- // add menu item
- addMenu: function (options) {
- // menu option defaults
- var menuOptions = {
- title : '',
- target : '',
- href : '',
- onclick : null,
- divider : false,
- icon : null,
- cls : 'button-menu btn-group'
- }
-
- // get options
- menuOptions = Utils.merge(options, menuOptions);
-
- // check if submenu element is available
- if (!this.$menu) {
- // insert submenu element into root
- $(this.el).append(this._templateMenu());
-
- // update element link
- this.$menu = $(this.el).find('.menu');
- }
-
- // create
- var $item = $(this._templateMenuItem(menuOptions));
-
- // add events
- $item.on('click', function(e) {
- // prevent default
- e.preventDefault();
-
- // add click event
- if(menuOptions.onclick) {
- menuOptions.onclick();
- }
- });
-
- // append menu
- this.$menu.append($item);
-
- // append divider
- if (menuOptions.divider)
- this.$menu.append($(this._templateDivider()));
- },
-
- // fill template header
- _templateMenuItem: function (options) {
- var tmpl = '<li>' +
- '<a href="' + options.href + '" target="' + options.target + '">';
-
- if (options.icon)
- tmpl += '<i class="fa ' + options.icon + '"></i>';
-
- tmpl += ' ' + options.title +
- '</a>' +
- '</li>';
- return tmpl;
- },
-
- // fill template header
- _templateMenu: function () {
- return '<ul class="menu dropdown-menu pull-right" role="menu"></ul>';
- },
-
- _templateDivider: function() {
- return '<li class="divider"></li>';
- },
-
- // element
- _template: function(options) {
- // width
- var width = '';
- if (options.title) {
- width = 'width: auto;';
- }
-
- // string
- var str = '<div id="' + options.id + '" style="float: ' + options.float + '; ' + width + '" class="ui-button-icon dropdown ' + options.cls + '">';
-
- // title
- if (options.title) {
- str += '<div class="root button dropdown-toggle" data-toggle="dropdown">' +
- '<i class="icon fa ' + options.icon + '"/> ' +
- '<span class="title">' + options.title + '</span>' +
- '</div>';
- } else {
- str += '<i class="icon fa ' + options.icon + '"/>';
- }
- str += '</div>';
- return str;
- }
-});
-
-});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/ui-select.js
--- a/config/plugins/visualizations/charts/static/library/ui-select.js
+++ /dev/null
@@ -1,240 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// plugin
-var View = Backbone.View.extend(
-{
- // options
- optionsDefault : {
- id : '',
- cls : '',
- empty : 'No data available',
- visible : true,
- wait : false
- },
-
- // value
- selected : null,
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // initial value
- this.selected = this.options.value;
-
- // create new element
- this.setElement(this._template(this.options));
-
- // link elements
- this.$select = this.$el.find('#select');
- this.$icon = this.$el.find('#icon');
-
- // add change event. fires only on user activity
- var self = this;
- this.$select.on('change', function() {
- self.value(self.$select.val());
- });
-
- // add change event. fires on trigger
- this.on('change', function() {
- if (self.options.onchange) {
- self.options.onchange(self.value());
- }
- });
-
- // refresh
- this._refresh();
-
- // show/hide
- if (!this.options.visible) {
- this.hide();
- }
-
- // wait
- if (this.options.wait) {
- this.wait();
- } else {
- this.show();
- }
- },
-
- // value
- value : function (new_value) {
-
- // get current id/value
- var before = this.selected;
-
- // check if new_value is defined
- if (new_value !== undefined) {
- this.selected = new_value;
- this.$select.val(new_value);
- }
-
- // get current id/value
- var after = this.selected;
- if (after) {
- // fire onchange
- if (after != before && this.options.onchange) {
- this.options.onchange(after);
- }
- }
-
- // return
- return after;
- },
-
- // first
- first: function() {
- var options = this.$select.find('option');
- if (options.length > 0) {
- return options.val();
- } else {
- return undefined;
- }
- },
-
- // label
- text : function () {
- return this.$select.find('option:selected').text();
- },
-
- // show
- show: function() {
- this.$icon.removeClass();
- this.$icon.addClass('fa fa-caret-down');
- this.$select.show();
- this.$el.show();
- },
-
- // hide
- hide: function() {
- this.$el.hide();
- },
-
- // wait
- wait: function() {
- this.$icon.removeClass();
- this.$icon.addClass('fa fa-spinner fa-spin');
- this.$select.hide();
- },
-
- // disabled
- disabled: function() {
- return this.$select.is(':disabled');
- },
-
- // enable
- enable: function() {
- this.$select.prop('disabled', false);
- },
-
- // disable
- disable: function() {
- this.$select.prop('disabled', true);
- },
-
- // add
- add: function(options) {
- // add options
- this.$select.append(this._templateOption(options));
-
- // refresh
- this._refresh();
- },
-
- // remove
- del: function(value) {
- // remove option
- this.$select.find('option[value=' + value + ']').remove();
- this.$select.trigger('change');
-
- // refresh
- this._refresh();
- },
-
- // render
- update: function(options) {
- // remove all options
- this.$select.find('option').remove();
-
- // add new options
- for (var key in options) {
- this.$select.append(this._templateOption(options[key]));
- }
-
- // refresh
- this._refresh();
- },
-
- // set on change event
- setOnChange: function(callback) {
- this.options.onchange = callback;
- },
-
- // check if selected value exists
- exists: function(value) {
- return this.$select.find('option[value=' + value + ']').length > 0;
- },
-
- // refresh
- _refresh: function() {
- // remove placeholder
- this.$select.find('option[value=null]').remove();
-
- // count remaining entries
- var remaining = this.$select.find('option').length;
- if (remaining == 0) {
- // disable select field
- this.disable();
-
- // append placeholder
- this.$select.append(this._templateOption({value : 'null', label : this.options.empty}));
- } else {
- // enable select field
- this.enable();
- }
-
- // update value
- if (this.selected) {
- this.$select.val(this.selected);
- }
- },
-
- // option
- _templateOption: function(options) {
- return '<option value="' + options.value + '">' + options.label + '</option>';
- },
-
- // element
- _template: function(options) {
- var tmpl = '<div id="' + options.id + '" class="ui-select">' +
- '<div class="button">' +
- '<i id="icon"/>' +
- '</div>' +
- '<select id="select" class="select ' + options.cls + ' ' + options.id + '">';
- for (key in options.data) {
- // options
- var item = options.data[key];
-
- // identify selected value
- var tag = '';
- if (item.value == options.value || item.value == '') {
- tag = 'selected';
- }
-
- // add template string
- tmpl += '<option value="' + item.value + '" ' + tag + '>' + item.label + '</option>';
- }
- tmpl += '</select>' +
- '</div>';
- return tmpl;
- }
-});
-
-return {
- View: View
-}
-
-});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/ui-table-form.js
--- a/config/plugins/visualizations/charts/static/library/ui-table-form.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js
@@ -1,10 +1,11 @@
// dependencies
-define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
+define(['mvc/ui/ui-table', 'mvc/ui/ui-misc', 'utils/utils'],
function(Table, Ui, Utils) {
-// widget
-var View = Backbone.View.extend(
-{
+/**
+ * This class takes a dictionary as input an creates an input form. It uses the Ui.Table element to organize and format the form elements.
+ */
+var View = Backbone.View.extend({
// options
optionsDefault: {
title : '',
@@ -87,7 +88,7 @@
break;
// radiobox field
case 'radiobutton' :
- field = new Ui.RadioButton({
+ field = new Ui.RadioButton.View({
id : 'field-' + id,
data : settings_def.data,
value : model.get(id),
@@ -229,10 +230,10 @@
// add to table
this.table.append(id);
- // show/hide
- if (settings_def.hide) {
- this.table.get(id).hide();
- }
+ // show/hide
+ if (settings_def.hide) {
+ this.table.get(id).hide();
+ }
}
});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/ui-table.js
--- a/config/plugins/visualizations/charts/static/library/ui-table.js
+++ /dev/null
@@ -1,214 +0,0 @@
-define(['utils/utils'], function(Utils) {
-
-var View = Backbone.View.extend(
-{
- // current row
- row: null,
-
- // count rows
- row_count: 0,
-
- // defaults options
- optionsDefault: {
- content : 'No content available.',
- onchange : null,
- ondblclick : null,
- onconfirm : null,
- cls : ''
- },
-
- // events
- events : {
- 'click' : '_onclick',
- 'dblclick' : '_ondblclick'
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- var $el = $(this._template(options));
-
- // link sub-elements
- this.$thead = $el.find('thead');
- this.$tbody = $el.find('tbody');
- this.$tmessage = $el.find('tmessage');
-
- // set element
- this.setElement($el);
-
- // initialize row
- this.row = $('<tr></tr>');
- },
-
- // add header cell
- addHeader: function($el) {
- var wrapper = $('<th></th>');
- wrapper.append($el);
- this.row.append(wrapper);
- },
-
- // header
- appendHeader: function() {
- // append header row
- this.$thead.append(this.row);
-
- // row
- this.row = $('<tr></tr>');
- },
-
- // add row cell
- add: function($el, width, align) {
- var wrapper = $('<td></td>');
- if (width) {
- wrapper.css('width', width);
- }
- if (align) {
- wrapper.css('text-align', align);
- }
- wrapper.append($el);
- this.row.append(wrapper);
- },
-
- // append
- append: function(id) {
- this._commit(id);
- },
-
- // prepend
- prepend: function(id) {
- this._commit(id, true);
- },
-
- // get element
- get: function(id) {
- return this.$el.find('#' + id);
- },
-
- // delete
- del: function(id) {
- var item = this.$tbody.find('#' + id);
- if (item.length > 0) {
- item.remove();
- this.row_count--;
- this._refresh();
- }
- },
-
- // delete all
- delAll: function() {
- this.$tbody.empty();
- this.row_count = 0;
- this._refresh();
- },
-
- // value
- value: function(new_value) {
- // get current id/value
- this.before = this.$tbody.find('.current').attr('id');
-
- // check if new_value is defined
- if (new_value !== undefined) {
- this.$tbody.find('tr').removeClass('current');
- if (new_value) {
- this.$tbody.find('#' + new_value).addClass('current');
- }
- }
-
- // get current id/value
- var after = this.$tbody.find('.current').attr('id');
- if(after === undefined) {
- return null;
- } else {
- // fire onchange
- if (after != this.before && this.options.onchange) {
- this.options.onchange(new_value);
- }
-
- // return current value
- return after;
- }
- },
-
- // size
- size: function() {
- return this.$tbody.find('tr').length;
- },
-
- // commit
- _commit: function(id, prepend) {
- // remove previous item with same id
- this.del(id);
-
- // add
- this.row.attr('id', id);
-
- // add row
- if (prepend) {
- this.$tbody.prepend(this.row);
- } else {
- this.$tbody.append(this.row);
- }
-
- // row
- this.row = $('<tr></tr>');
-
- // row count
- this.row_count++;
- this._refresh();
- },
-
- // onclick
- _onclick: function(e) {
- // get values
- var old_value = this.value();
- var new_value = $(e.target).closest('tr').attr('id');
- if (new_value != ''){
- // check equality
- if (new_value && old_value != new_value) {
- if (this.options.onconfirm) {
- this.options.onconfirm(new_value);
- } else {
- this.value(new_value);
- }
- }
- }
- },
-
- // ondblclick
- _ondblclick: function(e) {
- var value = this.value();
- if (value && this.options.ondblclick) {
- this.options.ondblclick(value);
- }
- },
-
- // refresh
- _refresh: function() {
- if (this.row_count == 0) {
- this.$tmessage.show();
- } else {
- this.$tmessage.hide();
- }
- },
-
- // load html template
- _template: function(options)
- {
- return '<div>' +
- '<table class="ui-table ' + options.cls + '">' +
- '<thead></thead>' +
- '<tbody style="cursor: pointer;"></tbody>' +
- '</table>' +
- '<tmessage>' + options.content + '</tmessage>' +
- '<div>';
- }
-});
-
-return {
- View: View
-}
-
-});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/library/ui.js
--- a/config/plugins/visualizations/charts/static/library/ui.js
+++ /dev/null
@@ -1,521 +0,0 @@
-// dependencies
-define(['utils/utils', 'plugin/library/ui-select', 'plugin/library/ui-button-menu', 'mvc/ui/ui-modal'],
- function(Utils, Select, ButtonMenu, Modal) {
-
-// plugin
-var Image = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- url : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
- },
-
- // template
- _template: function(options) {
- return '<img class="ui-image ' + options.cls + '" src="' + options.url + '"/>';
- }
-});
-
-// plugin
-var Label = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- title : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
- },
-
- // title
- title: function(new_title) {
- this.$el.html(new_title);
- },
-
- // template
- _template: function(options) {
- return '<label class="ui-label ' + options.cls + '">' + options.title + '</label>';
- },
-
- // value
- value: function() {
- return options.title;
- }
-});
-
-// plugin
-var Icon = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- float : 'right',
- icon : '',
- tooltip : '',
- placement : 'bottom',
- title : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add tooltip
- $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // element
- _template: function(options) {
- return '<div>' +
- '<span class="fa ' + options.icon + '" class="ui-icon"/> ' +
- options.title +
- '</div>';
- }
-});
-
-// plugin
-var Button = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- id : null,
- title : '',
- float : 'right',
- cls : 'btn btn-default',
- icon : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add event
- $(this.el).on('click', options.onclick);
-
- // add tooltip
- $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // element
- _template: function(options) {
- var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.float + ';" type="button" class="ui-button ' + options.cls + '">';
- if (options.icon) {
- str += '<i class="icon fa ' + options.icon + '"></i> ' ;
- }
- str += options.title +
- '</button>';
- return str;
- }
-});
-
-// plugin
-var ButtonIcon = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- id : null,
- title : '',
- float : 'right',
- cls : 'icon-btn',
- icon : '',
- tooltip : '',
- onclick : null
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add event
- $(this.el).on('click', options.onclick);
-
- // add tooltip
- $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // element
- _template: function(options) {
- // width
- var width = '';
- if (options.title) {
- width = 'width: auto;';
- }
-
- // string
- var str = '<div id="' + options.id + '" style="float: ' + options.float + '; ' + width + '" class="ui-button-icon ' + options.cls + '">';
-
- // title
- if (options.title) {
- str += '<div class="button">' +
- '<i class="icon fa ' + options.icon + '"/> ' +
- '<span class="title">' + options.title + '</span>' +
- '</div>';
- } else {
- str += '<i class="icon fa ' + options.icon + '"/>';
- }
- str += '</div>';
- return str;
- }
-});
-
-// plugin
-var Anchor = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- title : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add event
- $(this.el).on('click', options.onclick);
- },
-
- // element
- _template: function(options) {
- return '<div><a href="javascript:void(0)" class="ui-anchor ' + options.cls + '">' + options.title + '</a></div>';
- }
-});
-
-// plugin
-var Message = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- message : '',
- status : 'info',
- persistent : false
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement('<div></div>');
- },
-
- // update
- update : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // show message
- if (options.message != '') {
- this.$el.html(this._template(this.options));
- this.$el.find('.alert').append(options.message);
- this.$el.fadeIn();
-
- // check if message is persistent
- if (!options.persistent) {
- // set timer
- var self = this;
- window.setTimeout(function() {
- if (self.$el.is(':visible')) {
- self.$el.fadeOut();
- } else {
- self.$el.hide();
- }
- }, 3000);
- }
- } else {
- this.$el.fadeOut();
- }
- },
-
- // element
- _template: function(options) {
- return '<div class="ui-message alert alert-' + options.status + '"/>';
- }
-});
-
-// plugin
-var Searchbox = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- onclick : null,
- searchword : ''
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add click event
- var self = this;
- if (this.options.onclick) {
- this.$el.on('submit', function(e) {
- var search_field = self.$el.find('#search');
- self.options.onclick(search_field.val());
- });
- }
- },
-
- // element
- _template: function(options) {
- return '<div class="ui-search">' +
- '<form onsubmit="return false;">' +
- '<input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="' + options.searchword + '">' +
- '<button type="submit" class="btn search-btn">' +
- '<i class="fa fa-search"></i>' +
- '</button>' +
- '</form>' +
- '</div>';
- }
-});
-
-// plugin
-var Input = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- value : '',
- type : 'text',
- placeholder : '',
- disabled : false,
- visible : true,
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // disable input field
- if (this.options.disabled) {
- this.$el.prop('disabled', true);
- }
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.on('input', function() {
- if (self.options.onchange) {
- self.options.onchange(self.$el.val());
- }
- });
- },
-
- // value
- value : function (new_val) {
- if (new_val !== undefined) {
- this.$el.val(new_val);
- }
- return this.$el.val();
- },
-
- // element
- _template: function(options) {
- return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="ui-input ' + options.cls + '">';
- }
-});
-
-// plugin
-var Textarea = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- value : '',
- type : 'text',
- placeholder : '',
- disabled : false,
- visible : true,
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // disable input field
- if (this.options.disabled) {
- this.$el.prop('disabled', true);
- }
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.on('input', function() {
- if (self.options.onchange) {
- self.options.onchange(self.$el.val());
- }
- });
- },
-
- // value
- value : function (new_val) {
- if (new_val !== undefined) {
- this.$el.val(new_val);
- }
- return this.$el.val();
- },
-
- // element
- _template: function(options) {
- return '<textarea id="' + options.id + '" class="ui-textarea ' + options.cls + '" rows="5"></textarea>';
- }
-});
-
-// plugin
-var RadioButton = Backbone.View.extend(
-{
- // options
- optionsDefault: {
- value : '',
- visible : true,
- cls : '',
- data : [],
- id : Utils.uuid()
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // set initial value
- if (this.options.value) {
- this.value(this.options.value);
- }
-
- // current value
- this.current = this.options.value;
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.find('input').on('change', function() {
- self.value(self._getValue());
- });
- },
-
- // value
- value : function (new_val) {
- // get current value
- var before = this.current;
-
- // set new value
- if (new_val !== undefined) {
- this.$el.find('label').removeClass('active');
- this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
- this.current = new_val;
- }
-
- // check value
- var after = this.current;
- if (after != before && this.options.onchange) {
- this.options.onchange(this.current);
- }
-
- // get and return value
- return this.current;
- },
-
- // get value
- _getValue: function() {
- var selected = this.$el.find(':checked');
- var value = null;
- if (selected.length > 0) {
- value = selected.val();
- }
- return value;
- },
-
- // element
- _template: function(options) {
- var tmpl = '<div class="btn-group ui-radiobutton" data-toggle="buttons">';
- for (key in options.data) {
- var pair = options.data[key];
- tmpl += '<label class="btn btn-default">' +
- '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label +
- '</label>';
- }
- tmpl += '</div>';
- return tmpl;
- }
-});
-
-// return
-return {
- Label : Label,
- Button : Button,
- Icon : Icon,
- ButtonIcon : ButtonIcon,
- Input : Input,
- Anchor : Anchor,
- Message : Message,
- Searchbox : Searchbox,
- Select : Select,
- ButtonMenu : ButtonMenu,
- Modal: Modal,
- Textarea: Textarea,
- Image: Image,
- RadioButton: RadioButton
-}
-});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/models/chart.js
--- a/config/plugins/visualizations/charts/static/models/chart.js
+++ b/config/plugins/visualizations/charts/static/models/chart.js
@@ -1,11 +1,8 @@
// dependencies
-define(['plugin/models/groups', 'plugin/library/deferred', 'mvc/visualization/visualization-model'],
- function(Groups, Deferred) {
-
+define(['plugin/models/groups'], function(Groups) {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// defaults
defaults : {
id : null,
@@ -23,7 +20,6 @@
initialize: function(options) {
this.groups = new Groups();
this.settings = new Backbone.Model();
- this.deferred = new Deferred();
},
// reset
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -2,8 +2,7 @@
define([], function() {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// options
defaults : {
query_limit : 500,
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/models/group.js
--- a/config/plugins/visualizations/charts/static/models/group.js
+++ b/config/plugins/visualizations/charts/static/models/group.js
@@ -2,8 +2,7 @@
define([], function() {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// options
defaults : {
key : 'Data label',
@@ -11,8 +10,7 @@
},
// reset
- reset: function()
- {
+ reset: function(){
this.clear({silent: true}).set(this.defaults);
this.trigger('reset', this);
}
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/models/groups.js
--- a/config/plugins/visualizations/charts/static/models/groups.js
+++ b/config/plugins/visualizations/charts/static/models/groups.js
@@ -2,8 +2,7 @@
define(['plugin/models/group'], function(Group) {
// collection
-return Backbone.Collection.extend(
-{
+return Backbone.Collection.extend({
model: Group
});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
@@ -0,0 +1,1 @@
+!function(r){function n(r){return r}function t(r,n){for(var t=0,e=n.length,u=Array(e);e>t;++t)u[t]=r[n[t]];return u}function e(r){function n(n,t,e,u){for(;u>e;){var f=e+u>>>1;r(n[f])<t?e=f+1:u=f}return e}function t(n,t,e,u){for(;u>e;){var f=e+u>>>1;t<r(n[f])?u=f:e=f+1}return e}return t.right=t,t.left=n,t}function u(r){function n(r,n,t){for(var u=t-n,f=(u>>>1)+1;--f>0;)e(r,f,u,n);return r}function t(r,n,t){for(var u,f=t-n;--f>0;)u=r[n],r[n]=r[n+f],r[n+f]=u,e(r,1,f,n);return r}function e(n,t,e,u){for(var f,o=n[--u+t],i=r(o);(f=t<<1)<=e&&(e>f&&r(n[u+f])>r(n[u+f+1])&&f++,!(i<=r(n[u+f])));)n[u+t]=n[u+f],t=f;n[u+t]=o}return n.sort=t,n}function f(r){function n(n,e,u,f){var o,i,a,c,l=Array(f=Math.min(u-e,f));for(i=0;f>i;++i)l[i]=n[e++];if(t(l,0,f),u>e){o=r(l[0]);do(a=r(c=n[e])>o)&&(l[0]=c,o=r(t(l,0,f)[0]));while(++e<u)}return l}var t=u(r);return n}function o(r){function n(n,t,e){for(var u=t+1;e>u;++u){for(var f=u,o=n[u],i=r(o);f>t&&r(n[f-1])>i;--f)n[f]=n[f-1];n[f]=o}return n}return n}function i(r){function n(r,n,u){return(N>u-n?e:t)(r,n,u)}function t(t,e,u){var f,o=0|(u-e)/6,i=e+o,a=u-1-o,c=e+u-1>>1,l=c-o,v=c+o,s=t[i],h=r(s),d=t[l],p=r(d),g=t[c],y=r(g),m=t[v],x=r(m),b=t[a],A=r(b);h>p&&(f=s,s=d,d=f,f=h,h=p,p=f),x>A&&(f=m,m=b,b=f,f=x,x=A,A=f),h>y&&(f=s,s=g,g=f,f=h,h=y,y=f),p>y&&(f=d,d=g,g=f,f=p,p=y,y=f),h>x&&(f=s,s=m,m=f,f=h,h=x,x=f),y>x&&(f=g,g=m,m=f,f=y,y=x,x=f),p>A&&(f=d,d=b,b=f,f=p,p=A,A=f),p>y&&(f=d,d=g,g=f,f=p,p=y,y=f),x>A&&(f=m,m=b,b=f,f=x,x=A,A=f);var k=d,O=p,w=m,E=x;t[i]=s,t[l]=t[e],t[c]=g,t[v]=t[u-1],t[a]=b;var M=e+1,U=u-2,z=E>=O&&O>=E;if(z)for(var N=M;U>=N;++N){var C=t[N],S=r(C);if(O>S)N!==M&&(t[N]=t[M],t[M]=C),++M;else if(S>O)for(;;){var q=r(t[U]);{if(!(q>O)){if(O>q){t[N]=t[M],t[M++]=t[U],t[U--]=C;break}t[N]=t[U],t[U--]=C;break}U--}}}else for(var N=M;U>=N;N++){var C=t[N],S=r(C);if(O>S)N!==M&&(t[N]=t[M],t[M]=C),++M;else if(S>E)for(;;){var 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\ No newline at end of file
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/views/editor.js
--- a/config/plugins/visualizations/charts/static/views/editor.js
+++ b/config/plugins/visualizations/charts/static/views/editor.js
@@ -1,21 +1,16 @@
// dependencies
-define(['mvc/ui/ui-tabs', 'plugin/library/ui', 'mvc/ui/ui-portlet', 'utils/utils',
+define(['mvc/ui/ui-tabs', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'utils/utils',
'plugin/models/chart', 'plugin/models/group',
'plugin/views/group', 'plugin/views/settings', 'plugin/views/types'],
function(Tabs, Ui, Portlet, Utils, Chart, Group, GroupView, SettingsView, TypesView) {
-// widget
-return Backbone.View.extend(
-{
- // defaults options
- optionsDefault: {
- header : true,
- content : 'No content available.'
- },
-
+/**
+ * The charts editor holds the tabs for selecting chart types, chart configuration
+ * and data group selections.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link this
var self = this;
@@ -25,9 +20,6 @@
// get current chart object
this.chart = this.app.chart;
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
// message element
this.message = new Ui.Message();
@@ -49,7 +41,7 @@
tooltip : 'Return to Viewer',
title : 'Cancel',
onclick : function() {
- // show viewport
+ // show viewer/viewport
self.app.go('viewer');
// reset chart
@@ -200,7 +192,7 @@
this.title.value(title);
},
- // update
+ // refresh group
_refreshGroupKey: function() {
var self = this;
var counter = 0;
@@ -213,7 +205,7 @@
});
},
- // new group
+ // add group model
_addGroupModel: function() {
var group = new Group({
id : Utils.uuid()
@@ -222,7 +214,7 @@
return group;
},
- // add group
+ // add group tab
_addGroup: function(group) {
// link this
var self = this;
@@ -319,7 +311,7 @@
// wait until chart is ready
var self = this;
- this.chart.deferred.execute(function() {
+ this.app.deferred.execute(function() {
// save
self.app.storage.save();
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -1,10 +1,11 @@
// dependencies
-define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
+define(['mvc/ui/ui-table', 'mvc/ui/ui-misc', 'utils/utils'],
function(Table, Ui, Utils) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the data group selection fields.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// link app
@@ -59,7 +60,7 @@
this._refreshGroup();
},
- // update dataset
+ // update group selection table
_refreshTable: function() {
// identify datasets
var dataset_id = this.chart.get('dataset_id');
@@ -116,7 +117,7 @@
this.chart.state('wait', 'Loading metadata...');
// register process
- var process_id = this.chart.deferred.register();
+ var process_id = this.app.deferred.register();
// request dictionary
var request_dictionary = {
@@ -131,7 +132,7 @@
self.chart.state('ok', 'Metadata initialized...');
// unregister
- self.chart.deferred.done(process_id);
+ self.app.deferred.done(process_id);
}
};
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/views/settings.js
--- a/config/plugins/visualizations/charts/static/views/settings.js
+++ b/config/plugins/visualizations/charts/static/views/settings.js
@@ -1,10 +1,11 @@
// dependencies
-define(['plugin/library/ui', 'plugin/library/ui-table-form', 'utils/utils'],
+define(['mvc/ui/ui-misc', 'plugin/library/ui-table-form', 'utils/utils'],
function(Ui, TableForm, Utils) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart configuration form.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// link app
@@ -18,6 +19,7 @@
// create settings
this.form = new TableForm.View(app, {
+ title : 'Configuration',
content : 'This chart type does not provide any options.'
});
@@ -36,7 +38,7 @@
// get settings
var chart_definition = this.chart.definition;
- // check if dataset is available
+ // check if chart definition is available
if (!chart_definition) {
return;
}
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/views/types.js
--- a/config/plugins/visualizations/charts/static/views/types.js
+++ b/config/plugins/visualizations/charts/static/views/types.js
@@ -1,7 +1,10 @@
-define(['utils/utils', 'plugin/library/ui'], function(Utils, Ui) {
+// dependencies
+define(['utils/utils', 'mvc/ui/ui-misc'], function(Utils, Ui) {
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart type selection grid.
+ */
+return Backbone.View.extend({
// defaults options
optionsDefault: {
onchange : null,
@@ -16,7 +19,6 @@
// initialize
initialize : function(app, options) {
-
// link this
var self = this;
@@ -33,7 +35,7 @@
$el.append(Utils.wrap((new Ui.Label({ title : 'How many data points would you like to analyze?'})).$el));
// construct chart type subset selection buttons
- this.library = new Ui.RadioButton({
+ this.library = new Ui.RadioButton.View({
data : [ { label: 'Few (<500)', value: 'small' },
{ label: 'Some (<10k)', value: 'medium' },
{ label: 'Many (>10k)', value: 'large' }],
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/views/viewer.js
--- a/config/plugins/visualizations/charts/static/views/viewer.js
+++ b/config/plugins/visualizations/charts/static/views/viewer.js
@@ -1,14 +1,14 @@
// dependencies
-define(['utils/utils', 'plugin/library/ui', 'mvc/ui/ui-portlet',
- 'plugin/models/group', 'plugin/views/viewport', 'plugin/library/screenshot'],
- function(Utils, Ui, Portlet, Group, ViewportView, Screenshot) {
+define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet',
+ 'plugin/views/viewport', 'plugin/library/screenshot'],
+ function(Utils, Ui, Portlet, ViewportView, Screenshot) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart viewer which encapsulates the chart viewport.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link app
this.app = app;
@@ -152,7 +152,7 @@
// wait for chart to be ready
_wait: function(chart, callback) {
// get chart
- if (chart.deferred.ready()) {
+ if (this.app.deferred.ready()) {
callback();
} else {
this.message.update({message: 'Your chart is currently being processed. Please wait and try again.'});
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -1,8 +1,12 @@
// dependencies
-define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils'],
+define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils'],
function(Portlet, Ui, Utils) {
-// widget
+/**
+ * The viewport creates and manages the dom elements used by the visualization plugins to draw the chart.
+ * Additionally, this class creates default request strings and request dictionaries parsed to the visualization plugins.
+ * This is the last class of the charts core classes before handing control over to the visualization plugins.
+ */
return Backbone.View.extend({
// list of canvas elements
@@ -26,7 +30,7 @@
// use full screen for viewer
this._fullscreen(this.$el, 100);
- // create canvas element
+ // create container element
this._createContainer('div');
// events
@@ -126,7 +130,7 @@
var self = this;
// register process
- var process_id = chart.deferred.register();
+ var process_id = this.app.deferred.register();
// identify chart type
var chart_type = chart.get('type');
@@ -171,7 +175,7 @@
});
},
function() {
- chart.deferred.done(process_id);
+ this.app.deferred.done(process_id);
}
);
} else {
diff -r 3807e1fc68f24d47bedc9bdd9014e1114468c2b0 -r 6d91f897777df812ce68fe8597cbdd38fab3da0b config/plugins/visualizations/charts/templates/charts.mako
--- a/config/plugins/visualizations/charts/templates/charts.mako
+++ b/config/plugins/visualizations/charts/templates/charts.mako
@@ -21,6 +21,9 @@
## shared css
${h.css( 'base' )}
+ ## crossfilter
+ ${h.javascript_link( app_root + "plugins/crossfilter/crossfilter.js" )}
+
## canvg
${h.javascript_link( app_root + "plugins/canvg/rgbcolor.js" )}
${h.javascript_link( app_root + "plugins/canvg/canvg.js" )}
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/f1ee1bcbc990/
Changeset: f1ee1bcbc990
User: dan
Date: 2014-08-20 14:56:19+00:00
Summary: merge stable
Affected #: 0 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 0f70d302b85e
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ee1521d29ebf/
Changeset: ee1521d29ebf
Branch: stable
User: natefoo
Date: 2014-10-10 14:00:19+00:00
Summary: Update tag latest_2014.10.06 for changeset 0f70d302b85e
Affected #: 1 file
diff -r 0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac -r ee1521d29ebf54cf16e44ae4f1d46e25a32fc297 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-a4f8476d787e254f11735896d0a3d2dced86e10b latest_2014.10.06
+0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Merged in BjoernGruening/galaxy-central-5 (pull request #519)
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a40dc4c1f075/
Changeset: a40dc4c1f075
User: dannon
Date: 2014-10-10 13:58:18+00:00
Summary: Merged in BjoernGruening/galaxy-central-5 (pull request #519)
Include cbx as new datatype, used by recent versions of cufftools.
Affected #: 1 file
diff -r 934dc228aeeed80e4973af32a3686ffb8ab5d624 -r a40dc4c1f075938eac42fd428e5fc7697560d751 config/datatypes_conf.xml.sample
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -43,6 +43,7 @@
<display file="ucsc/bigwig.xml" /><display file="igb/bigwig.xml" /></datatype>
+ <datatype extension="cxb" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" display_in_upload="true" description="Cuffquant output format" /><datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"><converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6f7356018ed9/
Changeset: 6f7356018ed9
User: BjoernGruening
Date: 2014-10-08 13:58:34+00:00
Summary: Include cbx as new datatype used by recent versions of cufftools.
Affected #: 1 file
diff -r 0e99c30878af56e23f447854a7ae70b412a9d627 -r 6f7356018ed9311250c9a6c1a616e27e814ef954 config/datatypes_conf.xml.sample
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -43,6 +43,7 @@
<display file="ucsc/bigwig.xml" /><display file="igb/bigwig.xml" /></datatype>
+ <datatype extension="cxb" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" display_in_upload="true" description="Cuffquant output format" /><datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"><converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
https://bitbucket.org/galaxy/galaxy-central/commits/a40dc4c1f075/
Changeset: a40dc4c1f075
User: dannon
Date: 2014-10-10 13:58:18+00:00
Summary: Merged in BjoernGruening/galaxy-central-5 (pull request #519)
Include cbx as new datatype, used by recent versions of cufftools.
Affected #: 1 file
diff -r 934dc228aeeed80e4973af32a3686ffb8ab5d624 -r a40dc4c1f075938eac42fd428e5fc7697560d751 config/datatypes_conf.xml.sample
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -43,6 +43,7 @@
<display file="ucsc/bigwig.xml" /><display file="igb/bigwig.xml" /></datatype>
+ <datatype extension="cxb" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" display_in_upload="true" description="Cuffquant output format" /><datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"><converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/934dc228aeee/
Changeset: 934dc228aeee
User: dannon
Date: 2014-10-10 13:13:32+00:00
Summary: Merge stable changes.
Affected #: 1 file
diff -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 -r 934dc228aeeed80e4973af32a3686ffb8ab5d624 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 latest_2014.10.06
+a4f8476d787e254f11735896d0a3d2dced86e10b latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: More flexibility for tool data table configuration in the install and test framework.
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0f70d302b85e/
Changeset: 0f70d302b85e
Branch: stable
User: davebgx
Date: 2014-10-09 18:17:33+00:00
Summary: More flexibility for tool data table configuration in the install and test framework.
Affected #: 1 file
diff -r 9bb2f032a455f0e63f407b396027102679d619ee -r 0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac test/install_and_test_tool_shed_repositories/base/util.py
--- a/test/install_and_test_tool_shed_repositories/base/util.py
+++ b/test/install_and_test_tool_shed_repositories/base/util.py
@@ -115,13 +115,16 @@
additional_tool_data_tables = None
additional_tool_data_path = None
-# Set up default tool data tables.
-if os.path.exists( 'tool_data_table_conf.xml' ):
- tool_data_table_conf = 'tool_data_table_conf.xml'
-elif os.path.exists( 'tool_data_table_conf.xml.sample' ):
- tool_data_table_conf = 'tool_data_table_conf.xml.sample'
-else:
- tool_data_table_conf = None
+tool_data_table_conf = None
+# Set up default tool data tables. If a non-sample version is in config/, use that. Otherwise iterate through lower
+# priority versions.
+for conf in [ 'config/tool_data_table_conf.xml',
+ 'config/tool_data_table_conf.xml.sample',
+ 'tool_data_table_conf.xml',
+ 'tool_data_table_conf.xml.sample' ]:
+ if os.path.exists( conf ):
+ tool_data_table_conf = conf
+ break
# The GALAXY_INSTALL_TEST_TOOL_SHED_URL and GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variables must be
# set for this script to work correctly. If the value of GALAXY_INSTALL_TEST_TOOL_SHED_URL does not refer to one
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset a4f8476d787e
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9bb2f032a455/
Changeset: 9bb2f032a455
Branch: stable
User: natefoo
Date: 2014-10-10 13:00:38+00:00
Summary: Update tag latest_2014.10.06 for changeset a4f8476d787e
Affected #: 1 file
diff -r a4f8476d787e254f11735896d0a3d2dced86e10b -r 9bb2f032a455f0e63f407b396027102679d619ee .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 latest_2014.10.06
+a4f8476d787e254f11735896d0a3d2dced86e10b latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/060d5e65f5c5/
Changeset: 060d5e65f5c5
User: dannon
Date: 2014-10-10 11:24:02+00:00
Summary: Merge from stable.
Affected #: 3 files
diff -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -19,3 +19,5 @@
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
+2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
+bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 latest_2014.10.06
diff -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -39,7 +39,7 @@
.. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys`
"""
- deleted = kwd.get( 'deleted', None )
+ deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) )
query = self.library_manager.list( trans, deleted )
libraries = []
for library in query:
diff -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 lib/tool_shed/metadata/repository_metadata_manager.py
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -5,6 +5,7 @@
from galaxy import util
from galaxy.util import inflector
from galaxy.web.form_builder import SelectField
+from galaxy.model.orm import or_
from tool_shed.metadata import metadata_generator
from tool_shed.repository_types.metadata import TipOnly
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: fix a bug with parsing params in data libraries API introduced recently with refactoring into managers
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a4f8476d787e/
Changeset: a4f8476d787e
Branch: stable
User: martenson
Date: 2014-10-10 00:36:54+00:00
Summary: fix a bug with parsing params in data libraries API introduced recently with refactoring into managers
Affected #: 1 file
diff -r ff30da7a2873416a332b7700eb15e26a1bf3c46e -r a4f8476d787e254f11735896d0a3d2dced86e10b lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -39,7 +39,7 @@
.. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys`
"""
- deleted = kwd.get( 'deleted', None )
+ deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) )
query = self.library_manager.list( trans, deleted )
libraries = []
for library in query:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fix link shown for tool sharing
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5321b19715b1/
Changeset: 5321b19715b1
User: guerler
Date: 2014-10-10 04:11:21+00:00
Summary: ToolForm: Fix link shown for tool sharing
Affected #: 3 files
diff -r 10b4f2107e90f3821f94be4286f320628c518034 -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -158,7 +158,7 @@
title : 'Share',
tooltip : 'Share this tool',
onclick : function() {
- prompt('Copy to clipboard: Ctrl+C, Enter', galaxy_config.root + 'root?tool_id=' + self.options.id);
+ prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + galaxy_config.root + 'root?tool_id=' + self.options.id);
}
});
diff -r 10b4f2107e90f3821f94be4286f320628c518034 -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -158,7 +158,7 @@
title : 'Share',
tooltip : 'Share this tool',
onclick : function() {
- prompt('Copy to clipboard: Ctrl+C, Enter', galaxy_config.root + 'root?tool_id=' + self.options.id);
+ prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + galaxy_config.root + 'root?tool_id=' + self.options.id);
}
});
diff -r 10b4f2107e90f3821f94be4286f320628c518034 -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(j,i,m,k,a,f,d,g,l,c,h){var e=Backbone.Model.extend({initialize:function(n){this.url=galaxy_config.root+"api/tools/"+n.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(o){var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:o.id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){n._initializeToolForm()}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},refresh:function(){this.tree.refresh();for(var n in this.field_list){this.field_list[n].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;this.model.fetch({error:function(o){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");if(n.options.job_id){j.get({url:galaxy_config.root+"api/jobs/"+n.options.job_id,success:function(o){n._buildForm()}})}else{n._buildForm()}}})},_buildForm:function(){var p=this;var r=new m.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/p/new/post/")}});var s=new m.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/t/"+p.options.id+"/")}});var n=new m.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+p.options.id)}});var q={button_question:r,button_search:s,button_share:n};if(Galaxy.currUser.get("is_admin")){q.button_download=new m.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+p.options.id+"/download"}})}this.section=new l.View(p,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new i.View({icon:"fa-wrench",title:"<b>"+this.model.get("name")+"</b> "+this.model.get("description"),operations:q,buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){p.job_handler.submit()}})}});if(!this.options.biostar_url){r.$el.hide();s.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var o=new k.ToolCitationCollection();o.tool_id=this.options.id;var t=new a.CitationListView({collection:o});t.render();o.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(j,i,m,k,a,f,d,g,l,c,h){var e=Backbone.Model.extend({initialize:function(n){this.url=galaxy_config.root+"api/tools/"+n.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(o){var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:o.id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){n._initializeToolForm()}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},refresh:function(){this.tree.refresh();for(var n in this.field_list){this.field_list[n].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;this.model.fetch({error:function(o){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");if(n.options.job_id){j.get({url:galaxy_config.root+"api/jobs/"+n.options.job_id,success:function(o){n._buildForm()}})}else{n._buildForm()}}})},_buildForm:function(){var p=this;var r=new m.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/p/new/post/")}});var s=new m.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/t/"+p.options.id+"/")}});var n=new m.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+p.options.id)}});var q={button_question:r,button_search:s,button_share:n};if(Galaxy.currUser.get("is_admin")){q.button_download=new m.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+p.options.id+"/download"}})}this.section=new l.View(p,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new i.View({icon:"fa-wrench",title:"<b>"+this.model.get("name")+"</b> "+this.model.get("description"),operations:q,buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){p.job_handler.submit()}})}});if(!this.options.biostar_url){r.$el.hide();s.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var o=new k.ToolCitationCollection();o.tool_id=this.options.id;var t=new a.CitationListView({collection:o});t.render();o.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fix optional label, add file
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/10b4f2107e90/
Changeset: 10b4f2107e90
User: guerler
Date: 2014-10-10 04:03:59+00:00
Summary: ToolForm: Fix optional label, add file
Affected #: 3 files
diff -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 -r 10b4f2107e90f3821f94be4286f320628c518034 client/galaxy/scripts/mvc/tools/tools-input.js
--- /dev/null
+++ b/client/galaxy/scripts/mvc/tools/tools-input.js
@@ -0,0 +1,108 @@
+/**
+ This class creates a tool form input element wrapper
+*/
+define([], function() {
+
+ // input field element wrapper
+ return Backbone.View.extend({
+ // initialize input wrapper
+ initialize: function(options) {
+ // link field
+ this.field = options.field;
+
+ // set element
+ this.setElement(this._template(options));
+
+ // link elements
+ this.$field = this.$el.find('.ui-table-form-field');
+ this.$title_optional = this.$el.find('.ui-table-form-title-optional');
+ this.$error_text = this.$el.find('.ui-table-form-error-text');
+ this.$error = this.$el.find('.ui-table-form-error');
+
+ // add field element
+ this.$field.prepend(this.field.$el);
+
+ // hide optional field on initialization
+ if (options.optional) {
+ this.field.skip = true;
+ } else {
+ this.field.skip = false;
+ }
+
+ // refresh view
+ this._refresh();
+
+ // add optional hide/show
+ var self = this;
+ this.$title_optional.on('click', function() {
+ // flip flag
+ self.field.skip = !self.field.skip;
+
+ // refresh view
+ self._refresh();
+ });
+ },
+
+ /** Set error text
+ */
+ error: function(text) {
+ this.$error_text.html(text);
+ this.$error.fadeIn();
+ this.$el.addClass('ui-error');
+ },
+
+ /** Reset this view
+ */
+ reset: function() {
+ this.$error.hide();
+ this.$el.removeClass('ui-error');
+ },
+
+ /** Refresh element
+ */
+ _refresh: function() {
+ // show/hide field element
+ if (!this.field.skip) {
+ this.$field.fadeIn('fast');
+ this.$title_optional.html('Disable');
+ } else {
+ this.$field.hide();
+ this.$title_optional.html('Enable');
+ }
+ },
+
+ /** Main Template
+ */
+ _template: function(options) {
+ // create table element
+ var tmp = '<div class="ui-table-form-element">' +
+ '<div class="ui-table-form-error ui-error">' +
+ '<span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/>' +
+ '</div>' +
+ '<div class="ui-table-form-title-strong">';
+
+ // is optional
+ if (options.optional) {
+ tmp += 'Optional: ' + options.label +
+ '<span> [<span class="ui-table-form-title-optional"/>]</span>';
+ } else {
+ tmp += options.label;
+ }
+
+ // finalize title
+ tmp += '</div>' +
+ '<div class="ui-table-form-field">';
+ // add help
+ if (options.help) {
+ tmp += '<div class="ui-table-form-info">' + options.help + '</div>';
+ }
+
+ // finalize
+ tmp += '</div>' +
+ '</div>';
+
+ // return input element
+ return tmp;
+ }
+ });
+});
diff -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 -r 10b4f2107e90f3821f94be4286f320628c518034 static/scripts/mvc/tools/tools-input.js
--- a/static/scripts/mvc/tools/tools-input.js
+++ b/static/scripts/mvc/tools/tools-input.js
@@ -83,7 +83,7 @@
// is optional
if (options.optional) {
- tmp += '*Optional: ' + options.label +
+ tmp += 'Optional: ' + options.label +
'<span> [<span class="ui-table-form-title-optional"/>]</span>';
} else {
tmp += options.label;
diff -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 -r 10b4f2107e90f3821f94be4286f320628c518034 static/scripts/packed/mvc/tools/tools-input.js
--- a/static/scripts/packed/mvc/tools/tools-input.js
+++ b/static/scripts/packed/mvc/tools/tools-input.js
@@ -1,1 +1,1 @@
-define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="*Optional: "+a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
\ No newline at end of file
+define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fix optional parameters
by commits-noreply@bitbucket.org 10 Oct '14
by commits-noreply@bitbucket.org 10 Oct '14
10 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/34e643839cda/
Changeset: 34e643839cda
User: guerler
Date: 2014-10-10 03:48:59+00:00
Summary: ToolForm: Fix optional parameters
Affected #: 17 files
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -1,10 +1,10 @@
/**
This is the main class of the tool form plugin. It is referenced as 'app' in all lower level modules.
*/
-define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
+define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
'mvc/citation/citation-model', 'mvc/citation/citation-view',
'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-content', 'mvc/tools/tools-section', 'mvc/tools/tools-tree', 'mvc/tools/tools-jobs'],
- function(Portlet, Ui, CitationModel, CitationView,
+ function(Utils, Portlet, Ui, CitationModel, CitationView,
Tools, ToolTemplate, ToolContent, ToolSection, ToolTree, ToolJobs) {
// create tool model
@@ -42,8 +42,7 @@
// load tool model
this.model = new Model({
- id : options.id,
- job_id : options.job_id
+ id : options.id
});
// creates a tree/json structure from the input form
@@ -102,6 +101,37 @@
// link this
var self = this;
+ // fetch model and render form
+ this.model.fetch({
+ error: function(response) {
+ console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.');
+ },
+ success: function() {
+ // backup inputs
+ self.inputs = self.model.get('inputs');
+
+ // update inputs with job parameters
+ if (self.options.job_id) {
+ Utils.get({
+ url: galaxy_config.root + 'api/jobs/' + self.options.job_id,
+ success: function(parameters) {
+ // TODO: Update input parameters
+ //self._updateInputs(self.inputs, parameters);
+ self._buildForm();
+ }
+ });
+ } else {
+ self._buildForm();
+ }
+ }
+ });
+ },
+
+ // builds the tool form
+ _buildForm: function() {
+ // link this
+ var self = this;
+
// create question button
var button_question = new Ui.ButtonIcon({
icon : 'fa-question-circle',
@@ -152,79 +182,70 @@
});
}
- // fetch model and render form
- this.model.fetch({
- error: function(response) {
- console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.');
- },
- success: function() {
- // create tool form section
- self.section = new ToolSection.View(self, {
- inputs : self.model.get('inputs'),
- cls : 'ui-table-plain'
- });
-
- // TEMPORARY SWITCH
- // switch to classic tool form mako if the form definition is incompatible
- if (self.incompatible) {
- self.$el.hide();
- $('#tool-form-classic').show();
- return;
- }
-
- // create portlet
- self.portlet = new Portlet.View({
- icon : 'fa-wrench',
- title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'),
- operations: operations,
- buttons: {
- execute: new Ui.Button({
- icon : 'fa-check',
- tooltip : 'Execute the tool',
- title : 'Execute',
- cls : 'btn btn-primary',
- floating : 'clear',
- onclick : function() {
- self.job_handler.submit();
- }
- })
+ // create tool form section
+ this.section = new ToolSection.View(self, {
+ inputs : this.inputs,
+ cls : 'ui-table-plain'
+ });
+
+ // switch to classic tool form mako if the form definition is incompatible
+ if (this.incompatible) {
+ this.$el.hide();
+ $('#tool-form-classic').show();
+ return;
+ }
+
+ // create portlet
+ this.portlet = new Portlet.View({
+ icon : 'fa-wrench',
+ title: '<b>' + this.model.get('name') + '</b> ' + this.model.get('description'),
+ operations: operations,
+ buttons: {
+ execute: new Ui.Button({
+ icon : 'fa-check',
+ tooltip : 'Execute the tool',
+ title : 'Execute',
+ cls : 'btn btn-primary',
+ floating : 'clear',
+ onclick : function() {
+ self.job_handler.submit();
}
- });
-
- // configure button selection
- if(!self.options.biostar_url) {
- button_question.$el.hide();
- button_search.$el.hide();
- }
-
- // append form
- self.$el.append(self.portlet.$el);
-
- // append help
- if (self.options.help != '') {
- self.$el.append(ToolTemplate.help(self.options.help));
- }
-
- // append citations
- if (self.options.citations) {
- // append html
- self.$el.append(ToolTemplate.citations());
-
- // fetch citations
- var citations = new CitationModel.ToolCitationCollection();
- citations.tool_id = self.options.id;
- var citation_list_view = new CitationView.CitationListView({ collection: citations } );
- citation_list_view.render();
- citations.fetch();
- }
-
- // append tool section
- self.portlet.append(self.section.$el);
-
- // trigger refresh
- self.refresh();
+ })
}
});
+
+ // configure button selection
+ if(!this.options.biostar_url) {
+ button_question.$el.hide();
+ button_search.$el.hide();
+ }
+
+ // append form
+ this.$el.append(this.portlet.$el);
+
+ // append help
+ if (this.options.help != '') {
+ this.$el.append(ToolTemplate.help(this.options.help));
+ }
+
+ // append citations
+ if (this.options.citations) {
+ // append html
+ this.$el.append(ToolTemplate.citations());
+
+ // fetch citations
+ var citations = new CitationModel.ToolCitationCollection();
+ citations.tool_id = this.options.id;
+ var citation_list_view = new CitationView.CitationListView({ collection: citations } );
+ citation_list_view.render();
+ citations.fetch();
+ }
+
+ // append tool section
+ this.portlet.append(this.section.$el);
+
+ // trigger refresh
+ this.refresh();
}
});
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -98,9 +98,9 @@
var input_id = this.app.tree.match(job_input_id);
var input_field = this.app.field_list[input_id];
var input_def = this.app.input_list[input_id];
-
+
// check basic field validation
- if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) {
+ if (input_def && input_field && input_field.validate && !input_field.validate()) {
this._foundError(input_id);
return false;
}
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -1,58 +1,8 @@
/**
This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _addRow() function.
*/
-define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content'],
- function(Utils, Table, Ui, Repeat, SelectContent) {
-
- // input field element wrapper
- var InputElement = Backbone.View.extend({
- // initialize input wrapper
- initialize: function(options) {
- this.setElement(this._template(options));
- },
-
- /** Set error text
- */
- error: function(text) {
- // set text
- this.$el.find('.ui-table-form-error-text').html(text);
- this.$el.find('.ui-table-form-error').fadeIn();
- this.$el.addClass('ui-error');
- },
-
- /** Reset this view
- */
- reset: function() {
- this.$el.find('.ui-table-form-error').hide();
- this.$el.removeClass('ui-error');
- },
-
- /** Main Template
- */
- _template: function(options) {
- // create table element
- var $input = $('<div class="ui-table-element"/>');
-
- // add error
- $input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');
-
- // add label
- if (options.label) {
- $input.append('<div class="ui-table-form-title-strong">' + options.label + '</div>');
- }
-
- // add input element
- $input.append(options.$el);
-
- // add help
- if (options.help) {
- $input.append('<div class="ui-table-form-info">' + options.help + '</div>');
- }
-
- // return input element
- return $input;
- }
- });
+define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'],
+ function(Utils, Table, Ui, Repeat, SelectContent, InputElement) {
// create form view
var View = Backbone.View.extend({
@@ -234,7 +184,7 @@
var input_element = new InputElement({
label : input_def.title,
help : input_def.help,
- $el : repeat.$el
+ field : repeat
});
// displays as grouped subsection
@@ -337,9 +287,10 @@
// create input field wrapper
var input_element = new InputElement({
- label : input_def.label,
- help : input_def.help,
- $el : field.$el
+ label : input_def.label,
+ optional : input_def.optional,
+ help : input_def.help,
+ field : field
});
// add to element list
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 client/galaxy/scripts/mvc/tools/tools-tree.js
--- a/client/galaxy/scripts/mvc/tools/tools-tree.js
+++ b/client/galaxy/scripts/mvc/tools/tools-tree.js
@@ -110,8 +110,13 @@
}
break;
default:
+ // get conditional value
+ var field = self.app.field_list[input.id];
+
// handle default value
- add (job_input_id, input.id, self.app.field_list[input.id].value());
+ if (!field.skip) {
+ add (job_input_id, input.id, field.value());
+ }
}
}
}
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -200,6 +200,7 @@
pass #HACK for assert trans.history, 'requires a history'
tool_dict[ 'model_class' ] = self.__class__.__name__
+ tool_dict[ 'optional' ] = self.optional
if hasattr( self, 'value' ):
tool_dict[ 'value' ] = self.value
return tool_dict
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -1,10 +1,10 @@
/**
This is the main class of the tool form plugin. It is referenced as 'app' in all lower level modules.
*/
-define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
+define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
'mvc/citation/citation-model', 'mvc/citation/citation-view',
'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-content', 'mvc/tools/tools-section', 'mvc/tools/tools-tree', 'mvc/tools/tools-jobs'],
- function(Portlet, Ui, CitationModel, CitationView,
+ function(Utils, Portlet, Ui, CitationModel, CitationView,
Tools, ToolTemplate, ToolContent, ToolSection, ToolTree, ToolJobs) {
// create tool model
@@ -42,8 +42,7 @@
// load tool model
this.model = new Model({
- id : options.id,
- job_id : options.job_id
+ id : options.id
});
// creates a tree/json structure from the input form
@@ -102,6 +101,37 @@
// link this
var self = this;
+ // fetch model and render form
+ this.model.fetch({
+ error: function(response) {
+ console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.');
+ },
+ success: function() {
+ // backup inputs
+ self.inputs = self.model.get('inputs');
+
+ // update inputs with job parameters
+ if (self.options.job_id) {
+ Utils.get({
+ url: galaxy_config.root + 'api/jobs/' + self.options.job_id,
+ success: function(parameters) {
+ // TODO: Update input parameters
+ //self._updateInputs(self.inputs, parameters);
+ self._buildForm();
+ }
+ });
+ } else {
+ self._buildForm();
+ }
+ }
+ });
+ },
+
+ // builds the tool form
+ _buildForm: function() {
+ // link this
+ var self = this;
+
// create question button
var button_question = new Ui.ButtonIcon({
icon : 'fa-question-circle',
@@ -152,79 +182,70 @@
});
}
- // fetch model and render form
- this.model.fetch({
- error: function(response) {
- console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.');
- },
- success: function() {
- // create tool form section
- self.section = new ToolSection.View(self, {
- inputs : self.model.get('inputs'),
- cls : 'ui-table-plain'
- });
-
- // TEMPORARY SWITCH
- // switch to classic tool form mako if the form definition is incompatible
- if (self.incompatible) {
- self.$el.hide();
- $('#tool-form-classic').show();
- return;
- }
-
- // create portlet
- self.portlet = new Portlet.View({
- icon : 'fa-wrench',
- title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'),
- operations: operations,
- buttons: {
- execute: new Ui.Button({
- icon : 'fa-check',
- tooltip : 'Execute the tool',
- title : 'Execute',
- cls : 'btn btn-primary',
- floating : 'clear',
- onclick : function() {
- self.job_handler.submit();
- }
- })
+ // create tool form section
+ this.section = new ToolSection.View(self, {
+ inputs : this.inputs,
+ cls : 'ui-table-plain'
+ });
+
+ // switch to classic tool form mako if the form definition is incompatible
+ if (this.incompatible) {
+ this.$el.hide();
+ $('#tool-form-classic').show();
+ return;
+ }
+
+ // create portlet
+ this.portlet = new Portlet.View({
+ icon : 'fa-wrench',
+ title: '<b>' + this.model.get('name') + '</b> ' + this.model.get('description'),
+ operations: operations,
+ buttons: {
+ execute: new Ui.Button({
+ icon : 'fa-check',
+ tooltip : 'Execute the tool',
+ title : 'Execute',
+ cls : 'btn btn-primary',
+ floating : 'clear',
+ onclick : function() {
+ self.job_handler.submit();
}
- });
-
- // configure button selection
- if(!self.options.biostar_url) {
- button_question.$el.hide();
- button_search.$el.hide();
- }
-
- // append form
- self.$el.append(self.portlet.$el);
-
- // append help
- if (self.options.help != '') {
- self.$el.append(ToolTemplate.help(self.options.help));
- }
-
- // append citations
- if (self.options.citations) {
- // append html
- self.$el.append(ToolTemplate.citations());
-
- // fetch citations
- var citations = new CitationModel.ToolCitationCollection();
- citations.tool_id = self.options.id;
- var citation_list_view = new CitationView.CitationListView({ collection: citations } );
- citation_list_view.render();
- citations.fetch();
- }
-
- // append tool section
- self.portlet.append(self.section.$el);
-
- // trigger refresh
- self.refresh();
+ })
}
});
+
+ // configure button selection
+ if(!this.options.biostar_url) {
+ button_question.$el.hide();
+ button_search.$el.hide();
+ }
+
+ // append form
+ this.$el.append(this.portlet.$el);
+
+ // append help
+ if (this.options.help != '') {
+ this.$el.append(ToolTemplate.help(this.options.help));
+ }
+
+ // append citations
+ if (this.options.citations) {
+ // append html
+ this.$el.append(ToolTemplate.citations());
+
+ // fetch citations
+ var citations = new CitationModel.ToolCitationCollection();
+ citations.tool_id = this.options.id;
+ var citation_list_view = new CitationView.CitationListView({ collection: citations } );
+ citation_list_view.render();
+ citations.fetch();
+ }
+
+ // append tool section
+ this.portlet.append(this.section.$el);
+
+ // trigger refresh
+ this.refresh();
}
});
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-input.js
--- /dev/null
+++ b/static/scripts/mvc/tools/tools-input.js
@@ -0,0 +1,108 @@
+/**
+ This class creates a tool form input element wrapper
+*/
+define([], function() {
+
+ // input field element wrapper
+ return Backbone.View.extend({
+ // initialize input wrapper
+ initialize: function(options) {
+ // link field
+ this.field = options.field;
+
+ // set element
+ this.setElement(this._template(options));
+
+ // link elements
+ this.$field = this.$el.find('.ui-table-form-field');
+ this.$title_optional = this.$el.find('.ui-table-form-title-optional');
+ this.$error_text = this.$el.find('.ui-table-form-error-text');
+ this.$error = this.$el.find('.ui-table-form-error');
+
+ // add field element
+ this.$field.prepend(this.field.$el);
+
+ // hide optional field on initialization
+ if (options.optional) {
+ this.field.skip = true;
+ } else {
+ this.field.skip = false;
+ }
+
+ // refresh view
+ this._refresh();
+
+ // add optional hide/show
+ var self = this;
+ this.$title_optional.on('click', function() {
+ // flip flag
+ self.field.skip = !self.field.skip;
+
+ // refresh view
+ self._refresh();
+ });
+ },
+
+ /** Set error text
+ */
+ error: function(text) {
+ this.$error_text.html(text);
+ this.$error.fadeIn();
+ this.$el.addClass('ui-error');
+ },
+
+ /** Reset this view
+ */
+ reset: function() {
+ this.$error.hide();
+ this.$el.removeClass('ui-error');
+ },
+
+ /** Refresh element
+ */
+ _refresh: function() {
+ // show/hide field element
+ if (!this.field.skip) {
+ this.$field.fadeIn('fast');
+ this.$title_optional.html('Disable');
+ } else {
+ this.$field.hide();
+ this.$title_optional.html('Enable');
+ }
+ },
+
+ /** Main Template
+ */
+ _template: function(options) {
+ // create table element
+ var tmp = '<div class="ui-table-form-element">' +
+ '<div class="ui-table-form-error ui-error">' +
+ '<span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/>' +
+ '</div>' +
+ '<div class="ui-table-form-title-strong">';
+
+ // is optional
+ if (options.optional) {
+ tmp += '*Optional: ' + options.label +
+ '<span> [<span class="ui-table-form-title-optional"/>]</span>';
+ } else {
+ tmp += options.label;
+ }
+
+ // finalize title
+ tmp += '</div>' +
+ '<div class="ui-table-form-field">';
+ // add help
+ if (options.help) {
+ tmp += '<div class="ui-table-form-info">' + options.help + '</div>';
+ }
+
+ // finalize
+ tmp += '</div>' +
+ '</div>';
+
+ // return input element
+ return tmp;
+ }
+ });
+});
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -98,9 +98,9 @@
var input_id = this.app.tree.match(job_input_id);
var input_field = this.app.field_list[input_id];
var input_def = this.app.input_list[input_id];
-
+
// check basic field validation
- if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) {
+ if (input_def && input_field && input_field.validate && !input_field.validate()) {
this._foundError(input_id);
return false;
}
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -1,58 +1,8 @@
/**
This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _addRow() function.
*/
-define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content'],
- function(Utils, Table, Ui, Repeat, SelectContent) {
-
- // input field element wrapper
- var InputElement = Backbone.View.extend({
- // initialize input wrapper
- initialize: function(options) {
- this.setElement(this._template(options));
- },
-
- /** Set error text
- */
- error: function(text) {
- // set text
- this.$el.find('.ui-table-form-error-text').html(text);
- this.$el.find('.ui-table-form-error').fadeIn();
- this.$el.addClass('ui-error');
- },
-
- /** Reset this view
- */
- reset: function() {
- this.$el.find('.ui-table-form-error').hide();
- this.$el.removeClass('ui-error');
- },
-
- /** Main Template
- */
- _template: function(options) {
- // create table element
- var $input = $('<div class="ui-table-element"/>');
-
- // add error
- $input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');
-
- // add label
- if (options.label) {
- $input.append('<div class="ui-table-form-title-strong">' + options.label + '</div>');
- }
-
- // add input element
- $input.append(options.$el);
-
- // add help
- if (options.help) {
- $input.append('<div class="ui-table-form-info">' + options.help + '</div>');
- }
-
- // return input element
- return $input;
- }
- });
+define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'],
+ function(Utils, Table, Ui, Repeat, SelectContent, InputElement) {
// create form view
var View = Backbone.View.extend({
@@ -234,7 +184,7 @@
var input_element = new InputElement({
label : input_def.title,
help : input_def.help,
- $el : repeat.$el
+ field : repeat
});
// displays as grouped subsection
@@ -337,9 +287,10 @@
// create input field wrapper
var input_element = new InputElement({
- label : input_def.label,
- help : input_def.help,
- $el : field.$el
+ label : input_def.label,
+ optional : input_def.optional,
+ help : input_def.help,
+ field : field
});
// add to element list
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-tree.js
--- a/static/scripts/mvc/tools/tools-tree.js
+++ b/static/scripts/mvc/tools/tools-tree.js
@@ -110,8 +110,13 @@
}
break;
default:
+ // get conditional value
+ var field = self.app.field_list[input.id];
+
// handle default value
- add (job_input_id, input.id, self.app.field_list[input.id].value());
+ if (!field.skip) {
+ add (job_input_id, input.id, field.value());
+ }
}
}
}
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,l,j,a,f,d,g,k,c,h){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id,job_id:n.job_id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;var p=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var q=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});var o={button_question:p,button_search:q,button_share:m};if(Galaxy.currUser.get("is_admin")){o.button_download=new l.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.model.fetch({error:function(r){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});if(n.incompatible){n.$el.hide();$("#tool-form-classic").show();return}n.portlet=new i.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),operations:o,buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!n.options.biostar_url){p.$el.hide();q.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var r=new j.ToolCitationCollection();r.tool_id=n.options.id;var s=new a.CitationListView({collection:r});s.render();r.fetch()}n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(j,i,m,k,a,f,d,g,l,c,h){var e=Backbone.Model.extend({initialize:function(n){this.url=galaxy_config.root+"api/tools/"+n.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(o){var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:o.id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){n._initializeToolForm()}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},refresh:function(){this.tree.refresh();for(var n in this.field_list){this.field_list[n].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;this.model.fetch({error:function(o){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");if(n.options.job_id){j.get({url:galaxy_config.root+"api/jobs/"+n.options.job_id,success:function(o){n._buildForm()}})}else{n._buildForm()}}})},_buildForm:function(){var p=this;var r=new m.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/p/new/post/")}});var s=new m.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/t/"+p.options.id+"/")}});var n=new m.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+p.options.id)}});var q={button_question:r,button_search:s,button_share:n};if(Galaxy.currUser.get("is_admin")){q.button_download=new m.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+p.options.id+"/download"}})}this.section=new l.View(p,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new i.View({icon:"fa-wrench",title:"<b>"+this.model.get("name")+"</b> "+this.model.get("description"),operations:q,buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){p.job_handler.submit()}})}});if(!this.options.biostar_url){r.$el.hide();s.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var o=new k.ToolCitationCollection();o.tool_id=this.options.id;var t=new a.CitationListView({collection:o});t.render();o.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}});
\ No newline at end of file
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-input.js
--- /dev/null
+++ b/static/scripts/packed/mvc/tools/tools-input.js
@@ -0,0 +1,1 @@
+define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="*Optional: "+a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
\ No newline at end of file
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content"],function(d,b,g,c,a){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,field:m});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-tree.js
--- a/static/scripts/packed/mvc/tools/tools-tree.js
+++ b/static/scripts/packed/mvc/tools/tools-tree.js
@@ -1,1 +1,1 @@
-define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var n=e.input;var h=j;if(j!=""){h+="|"}h+=n.name;switch(n.type){case"repeat":var d="section-";var q=[];var l=null;for(var p in e){var k=p.indexOf(d);if(k!=-1){k+=d.length;q.push(parseInt(p.substr(k)));if(!l){l=p.substr(0,k)}}}q.sort(function(r,i){return r-i});var g=0;for(var f in q){b(h+"_"+g++,e[l+q[f]])}break;case"conditional":var o=a.app.field_list[n.id].value();c(h+"|"+n.test_param.name,n.id,o);for(var f in n.cases){if(n.cases[f].value==o){b(h,m[n.id+"-section-"+f]);break}}break;default:c(h,n.id,a.app.field_list[n.id].value())}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})});
\ No newline at end of file
+define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var o=e.input;var h=j;if(j!=""){h+="|"}h+=o.name;switch(o.type){case"repeat":var d="section-";var r=[];var l=null;for(var q in e){var k=q.indexOf(d);if(k!=-1){k+=d.length;r.push(parseInt(q.substr(k)));if(!l){l=q.substr(0,k)}}}r.sort(function(s,i){return s-i});var g=0;for(var f in r){b(h+"_"+g++,e[l+r[f]])}break;case"conditional":var p=a.app.field_list[o.id].value();c(h+"|"+o.test_param.name,o.id,p);for(var f in o.cases){if(o.cases[f].value==p){b(h,m[o.id+"-section-"+f]);break}}break;default:var n=a.app.field_list[o.id];if(!n.skip){c(h,o.id,n.value())}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})});
\ No newline at end of file
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1284,8 +1284,10 @@
.ui-table tbody{cursor:pointer}
.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important}
.ui-table-plain tbody{cursor:auto !important}
+.ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer}
+.ui-table-form-element .ui-table-form-field{margin-top:5px}
.ui-table-form-section{border-left:solid 3px #ebd9b2;border-radius:5px !important;padding-left:10px}
-.ui-table-form-title-strong{font-weight:bold;padding-bottom:5px}
+.ui-table-form-title-strong{font-weight:bold}
.ui-table-form-info{clear:both !important}
.ui-table-form-separator{font-weight:bold;font-size:0.9em}
.ui-label{font-weight:bold}
diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -44,6 +44,17 @@
}
}
+.ui-table-form-element {
+ .ui-table-form-title-optional {
+ font-weight: bold;
+ text-decoration: underline;
+ cursor: pointer;
+ }
+ .ui-table-form-field {
+ margin-top: 5px;
+ }
+}
+
.ui-table-form-section {
border-left: solid 3px @form-heading-bg;
border-radius: 5px !important;
@@ -52,7 +63,6 @@
.ui-table-form-title-strong {
font-weight: bold;
- padding-bottom: 5px;
}
.ui-table-form-info {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1
0
09 Oct '14
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 6f878bbac19e180d9417e8445695269edbebdc1c
https://github.com/galaxyproject/usegalaxy-playbook/commit/6f878bbac19e180d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2014-10-09 (Thu, 09 Oct 2014)
Changed paths:
M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml
A files/galaxy/test.galaxyproject.org/dynamic_rules/multi_dynamic_walltime.py
M files/galaxy/test.galaxyproject.org/dynamic_rules/reserved.py
R files/galaxy/test.galaxyproject.org/dynamic_rules/roundup_multi_walltime.py
A files/galaxy/test.galaxyproject.org/dynamic_rules/stampede_select.py
M stage/group_vars/galaxyservers.yml
M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
Log Message:
-----------
Overhaul job running on Test.
1
0
commit/galaxy-central: jmchilton: More informative exceptions for startup failure due to job config XML errors.
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/46523237518b/
Changeset: 46523237518b
User: jmchilton
Date: 2014-10-09 19:04:38+00:00
Summary: More informative exceptions for startup failure due to job config XML errors.
Describe that this is an XML formatting issue that is causing the problem and include the full path of the file when to the user starting Galaxy.
Inspired by problems described here: https://biostar.usegalaxy.org/p/9245/.
Affected #: 1 file
diff -r dd0d4fa44feb1d620a288093cb72e1b83811ce0f -r 46523237518bb9ec8ed9fa4cf30453c800580c24 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -91,6 +91,15 @@
return self.get( "resources", None )
+def config_exception(e, file):
+ abs_path = os.path.abspath(file)
+ message = 'Problem parsing the XML in file %s, ' % abs_path
+ message += 'please correct the indicated portion of the file and restart Galaxy.'
+ message += str(e)
+ log.exception(message)
+ return Exception(message)
+
+
class JobConfiguration( object ):
"""A parser and interface to advanced job management features.
@@ -118,12 +127,15 @@
self.__parse_resource_parameters()
# Initialize the config
+ job_config_file = self.app.config.job_config_file
try:
- tree = util.parse_xml(self.app.config.job_config_file)
+ tree = util.parse_xml(job_config_file)
self.__parse_job_conf_xml(tree)
except IOError:
log.warning( 'Job configuration "%s" does not exist, using legacy job configuration from Galaxy config file "%s" instead' % ( self.app.config.job_config_file, self.app.config.config_file ) )
self.__parse_job_conf_legacy()
+ except Exception as e:
+ raise config_exception(e, job_config_file)
def __parse_job_conf_xml(self, tree):
"""Loads the new-style job configuration from options in the job config file (by default, job_conf.xml).
@@ -358,7 +370,12 @@
if not os.path.exists( self.app.config.job_resource_params_file ):
return
- resource_definitions = util.parse_xml( self.app.config.job_resource_params_file )
+ resource_param_file = self.app.config.job_resource_params_file
+ try:
+ resource_definitions = util.parse_xml( resource_param_file )
+ except Exception as e:
+ raise config_exception(e, resource_param_file)
+
resource_definitions_root = resource_definitions.getroot()
# TODO: Also handling conditionals would be awesome!
for parameter_elem in resource_definitions_root.findall( "param" ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxyproject/usegalaxy-playbook] ec8b9e: Return to running jobs on rodeo now that slurm-drm...
by GitHub 09 Oct '14
by GitHub 09 Oct '14
09 Oct '14
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: ec8b9e45188359bac081e151c2a4c8b5734d5c54
https://github.com/galaxyproject/usegalaxy-playbook/commit/ec8b9e45188359ba…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2014-10-09 (Thu, 09 Oct 2014)
Changed paths:
M files/galaxy/test.galaxyproject.org/dynamic_rules/reserved.py
M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
Log Message:
-----------
Return to running jobs on rodeo now that slurm-drmaa supports it.
1
0
commit/galaxy-central: davebgx: More flexibility for tool data table configuration in the install and test framework.
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dd0d4fa44feb/
Changeset: dd0d4fa44feb
User: davebgx
Date: 2014-10-09 18:17:33+00:00
Summary: More flexibility for tool data table configuration in the install and test framework.
Affected #: 1 file
diff -r 1ae6886199e5277ff822cc14c52bf9215b3593d4 -r dd0d4fa44feb1d620a288093cb72e1b83811ce0f test/install_and_test_tool_shed_repositories/base/util.py
--- a/test/install_and_test_tool_shed_repositories/base/util.py
+++ b/test/install_and_test_tool_shed_repositories/base/util.py
@@ -115,13 +115,16 @@
additional_tool_data_tables = None
additional_tool_data_path = None
-# Set up default tool data tables.
-if os.path.exists( 'tool_data_table_conf.xml' ):
- tool_data_table_conf = 'tool_data_table_conf.xml'
-elif os.path.exists( 'tool_data_table_conf.xml.sample' ):
- tool_data_table_conf = 'tool_data_table_conf.xml.sample'
-else:
- tool_data_table_conf = None
+tool_data_table_conf = None
+# Set up default tool data tables. If a non-sample version is in config/, use that. Otherwise iterate through lower
+# priority versions.
+for conf in [ 'config/tool_data_table_conf.xml',
+ 'config/tool_data_table_conf.xml.sample',
+ 'tool_data_table_conf.xml',
+ 'tool_data_table_conf.xml.sample' ]:
+ if os.path.exists( conf ):
+ tool_data_table_conf = conf
+ break
# The GALAXY_INSTALL_TEST_TOOL_SHED_URL and GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variables must be
# set for this script to work correctly. If the value of GALAXY_INSTALL_TEST_TOOL_SHED_URL does not refer to one
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fix compatibility check
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1ae6886199e5/
Changeset: 1ae6886199e5
User: guerler
Date: 2014-10-09 16:50:35+00:00
Summary: ToolForm: Fix compatibility check
Affected #: 4 files
diff -r d7fb2045f0c5e31cb18b45799ace9bc4cfd15efe -r 1ae6886199e5277ff822cc14c52bf9215b3593d4 client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -275,6 +275,7 @@
// data column
case 'data_column':
+ input_def.is_dynamic = false;
field = this._fieldSelect(input_def);
break;
@@ -308,7 +309,7 @@
field = this._fieldSelect(input_def);
break;
- // flag as incompatible
+ // field not found
default:
// flag
this.app.incompatible = true;
@@ -525,6 +526,11 @@
/** Select/Checkbox/Radio options field
*/
_fieldSelect : function (input_def) {
+ // check compatibility
+ if (input_def.is_dynamic) {
+ this.app.incompatible = true;
+ }
+
// configure options fields
var options = [];
for (var i in input_def.options) {
diff -r d7fb2045f0c5e31cb18b45799ace9bc4cfd15efe -r 1ae6886199e5277ff822cc14c52bf9215b3593d4 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1007,6 +1007,7 @@
d['display'] = self.display
d['multiple'] = self.multiple
+ d['is_dynamic'] = self.is_dynamic
return d
diff -r d7fb2045f0c5e31cb18b45799ace9bc4cfd15efe -r 1ae6886199e5277ff822cc14c52bf9215b3593d4 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -275,6 +275,7 @@
// data column
case 'data_column':
+ input_def.is_dynamic = false;
field = this._fieldSelect(input_def);
break;
@@ -308,7 +309,7 @@
field = this._fieldSelect(input_def);
break;
- // flag as incompatible
+ // field not found
default:
// flag
this.app.incompatible = true;
@@ -525,6 +526,11 @@
/** Select/Checkbox/Radio options field
*/
_fieldSelect : function (input_def) {
+ // check compatibility
+ if (input_def.is_dynamic) {
+ this.app.incompatible = true;
+ }
+
// configure options fields
var options = [];
for (var i in input_def.options) {
diff -r d7fb2045f0c5e31cb18b45799ace9bc4cfd15efe -r 1ae6886199e5277ff822cc14c52bf9215b3593d4 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content"],function(d,b,g,c,a){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content"],function(d,b,g,c,a){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Remove stray print statements.
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d7fb2045f0c5/
Changeset: d7fb2045f0c5
User: jmchilton
Date: 2014-10-09 16:08:15+00:00
Summary: Remove stray print statements.
This should maybe be backported to -stable? If anyone feels strongly that it should I will open a PR.
Affected #: 1 file
diff -r bda732e549b775718e31423c175a2f415f18a7b7 -r d7fb2045f0c5e31cb18b45799ace9bc4cfd15efe lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -482,10 +482,8 @@
#process change_format tags
if output.change_format:
for change_elem in output.change_format:
- print change_elem
for when_elem in change_elem.findall( 'when' ):
check = when_elem.get( 'input', None )
- print check
if check is not None:
try:
if '$' not in check:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset bde1c35ef8e5
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ff30da7a2873/
Changeset: ff30da7a2873
Branch: stable
User: natefoo
Date: 2014-10-09 13:00:13+00:00
Summary: Update tag latest_2014.10.06 for changeset bde1c35ef8e5
Affected #: 1 file
diff -r bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 -r ff30da7a2873416a332b7700eb15e26a1bf3c46e .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-2092948937ac30ef82f71463a235c66d34987088 latest_2014.10.06
+bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Highlight first error only
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/
Changeset: bda732e549b7
User: guerler
Date: 2014-10-09 03:01:37+00:00
Summary: ToolForm: Highlight first error only
Affected #: 3 files
diff -r 386258341ae7da120bc5421bb62ece96e7c32624 -r bda732e549b775718e31423c175a2f415f18a7b7 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -73,17 +73,11 @@
// mark error
input_element.error(message || 'Please verify this parameter.');
-
- // set flag
- if (this.valid) {
- // scroll to first input element
- $(this.app.container).animate({
- scrollTop: input_element.$el.offset().top - 20
- }, 500);
-
- // set error flag
- this.valid = false;
- }
+
+ // scroll to first input element
+ $(this.app.container).animate({
+ scrollTop: input_element.$el.offset().top - 20
+ }, 500);
},
/** Validate job definition
@@ -92,9 +86,6 @@
// get input parameters
var job_inputs = job_def.inputs;
- // validation flag
- this.valid = true;
-
// counter for values declared in batch mode
var n_values = -1;
@@ -111,6 +102,7 @@
// check basic field validation
if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) {
this._foundError(input_id);
+ return false;
}
// check if input field is in batch mode
@@ -121,6 +113,7 @@
} else {
if (n_values !== n) {
this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.');
+ return false;
}
}
}
@@ -128,7 +121,7 @@
}
// return validation result
- return this.valid;
+ return true;
},
/** Refreshes the history panel
diff -r 386258341ae7da120bc5421bb62ece96e7c32624 -r bda732e549b775718e31423c175a2f415f18a7b7 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -73,17 +73,11 @@
// mark error
input_element.error(message || 'Please verify this parameter.');
-
- // set flag
- if (this.valid) {
- // scroll to first input element
- $(this.app.container).animate({
- scrollTop: input_element.$el.offset().top - 20
- }, 500);
-
- // set error flag
- this.valid = false;
- }
+
+ // scroll to first input element
+ $(this.app.container).animate({
+ scrollTop: input_element.$el.offset().top - 20
+ }, 500);
},
/** Validate job definition
@@ -92,9 +86,6 @@
// get input parameters
var job_inputs = job_def.inputs;
- // validation flag
- this.valid = true;
-
// counter for values declared in batch mode
var n_values = -1;
@@ -111,6 +102,7 @@
// check basic field validation
if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) {
this._foundError(input_id);
+ return false;
}
// check if input field is in batch mode
@@ -121,6 +113,7 @@
} else {
if (n_values !== n) {
this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.');
+ return false;
}
}
}
@@ -128,7 +121,7 @@
}
// return validation result
- return this.valid;
+ return true;
},
/** Refreshes the history panel
diff -r 386258341ae7da120bc5421bb62ece96e7c32624 -r bda732e549b775718e31423c175a2f415f18a7b7 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fix execute button style
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/386258341ae7/
Changeset: 386258341ae7
User: guerler
Date: 2014-10-09 02:49:39+00:00
Summary: ToolForm: Fix execute button style
Affected #: 6 files
diff -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 -r 386258341ae7da120bc5421bb62ece96e7c32624 client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -178,10 +178,11 @@
title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'),
operations: operations,
buttons: {
- execute: new Ui.ButtonIcon({
+ execute: new Ui.Button({
icon : 'fa-check',
tooltip : 'Execute the tool',
title : 'Execute',
+ cls : 'btn btn-primary',
floating : 'clear',
onclick : function() {
self.job_handler.submit();
diff -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 -r 386258341ae7da120bc5421bb62ece96e7c32624 client/galaxy/scripts/mvc/ui/ui-misc.js
--- a/client/galaxy/scripts/mvc/ui/ui-misc.js
+++ b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -102,7 +102,7 @@
id : null,
title : '',
floating : 'right',
- cls : 'btn btn-default',
+ cls : 'ui-button btn btn-default',
icon : ''
},
@@ -131,7 +131,7 @@
// element
_template: function(options) {
- var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.floating + ';" type="button" class="ui-button ' + options.cls + '">';
+ var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.floating + ';" type="button" class="' + options.cls + '">';
if (options.icon) {
str += '<i class="icon fa ' + options.icon + '"></i> ' ;
}
diff -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 -r 386258341ae7da120bc5421bb62ece96e7c32624 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -178,10 +178,11 @@
title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'),
operations: operations,
buttons: {
- execute: new Ui.ButtonIcon({
+ execute: new Ui.Button({
icon : 'fa-check',
tooltip : 'Execute the tool',
title : 'Execute',
+ cls : 'btn btn-primary',
floating : 'clear',
onclick : function() {
self.job_handler.submit();
diff -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 -r 386258341ae7da120bc5421bb62ece96e7c32624 static/scripts/mvc/ui/ui-misc.js
--- a/static/scripts/mvc/ui/ui-misc.js
+++ b/static/scripts/mvc/ui/ui-misc.js
@@ -102,7 +102,7 @@
id : null,
title : '',
floating : 'right',
- cls : 'btn btn-default',
+ cls : 'ui-button btn btn-default',
icon : ''
},
@@ -131,7 +131,7 @@
// element
_template: function(options) {
- var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.floating + ';" type="button" class="ui-button ' + options.cls + '">';
+ var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.floating + ';" type="button" class="' + options.cls + '">';
if (options.icon) {
str += '<i class="icon fa ' + options.icon + '"></i> ' ;
}
diff -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 -r 386258341ae7da120bc5421bb62ece96e7c32624 static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,l,j,a,f,d,g,k,c,h){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id,job_id:n.job_id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;var p=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var q=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});var o={button_question:p,button_search:q,button_share:m};if(Galaxy.currUser.get("is_admin")){o.button_download=new l.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.model.fetch({error:function(r){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});if(n.incompatible){n.$el.hide();$("#tool-form-classic").show();return}n.portlet=new i.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),operations:o,buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!n.options.biostar_url){p.$el.hide();q.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var r=new j.ToolCitationCollection();r.tool_id=n.options.id;var s=new a.CitationListView({collection:r});s.render();r.fetch()}n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}});
\ No newline at end of file
+define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,l,j,a,f,d,g,k,c,h){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id,job_id:n.job_id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;var p=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var q=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});var o={button_question:p,button_search:q,button_share:m};if(Galaxy.currUser.get("is_admin")){o.button_download=new l.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.model.fetch({error:function(r){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});if(n.incompatible){n.$el.hide();$("#tool-form-classic").show();return}n.portlet=new i.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),operations:o,buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!n.options.biostar_url){p.$el.hide();q.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var r=new j.ToolCitationCollection();r.tool_id=n.options.id;var s=new a.CitationListView({collection:r});s.render();r.fetch()}n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}});
\ No newline at end of file
diff -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 -r 386258341ae7da120bc5421bb62ece96e7c32624 static/scripts/packed/mvc/ui/ui-misc.js
--- a/static/scripts/packed/mvc/ui/ui-misc.js
+++ b/static/scripts/packed/mvc/ui/ui-misc.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(q.onclick){q.onclick()}});$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="ui-button '+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var q=this;$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick&&!q.disabled){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="'+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Searchbox:a,Select:b,Hidden:o,Slider:e}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(q.onclick){q.onclick()}});$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="'+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var q=this;$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick&&!q.disabled){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="'+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Searchbox:a,Select:b,Hidden:o,Slider:e}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Replace error modal
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f08384fff770/
Changeset: f08384fff770
User: guerler
Date: 2014-10-09 02:38:36+00:00
Summary: ToolForm: Replace error modal
Affected #: 3 files
diff -r 40742ec31f5cdbcf337df5ee1c47637e78168501 -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -57,17 +57,9 @@
self._foundError(input_id, error_messages[input_id]);
}
} else {
- // show modal with error message
- self.app.modal.show({
- title: response_full.statusText,
- body: ToolTemplate.error(job_def),
- closing_events: true,
- buttons: {
- 'Close': function() {
- self.app.modal.hide();
- }
- }
- });
+ // show error message with details
+ console.debug(job_def);
+ console.debug(response);
}
}
});
diff -r 40742ec31f5cdbcf337df5ee1c47637e78168501 -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -57,17 +57,9 @@
self._foundError(input_id, error_messages[input_id]);
}
} else {
- // show modal with error message
- self.app.modal.show({
- title: response_full.statusText,
- body: ToolTemplate.error(job_def),
- closing_events: true,
- buttons: {
- 'Close': function() {
- self.app.modal.hide();
- }
- }
- });
+ // show error message with details
+ console.debug(job_def);
+ console.debug(response);
}
}
});
diff -r 40742ec31f5cdbcf337df5ee1c47637e78168501 -r f08384fff7709c7edb3a3f8b6883bc398f3e78d8 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{c.app.modal.show({title:g.statusText,body:a.error(d),closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Add close button to modal
by commits-noreply@bitbucket.org 09 Oct '14
by commits-noreply@bitbucket.org 09 Oct '14
09 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/40742ec31f5c/
Changeset: 40742ec31f5c
User: guerler
Date: 2014-10-09 02:31:32+00:00
Summary: ToolForm: Add close button to modal
Affected #: 3 files
diff -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 -r 40742ec31f5cdbcf337df5ee1c47637e78168501 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -37,7 +37,7 @@
console.debug(job_def);
// show progress modal
- this.app.modal.show({title: 'Please wait...', body: 'progress'});
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: { 'Close' : function () {self.app.modal.hide();} }});
// post job
Utils.request({
diff -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 -r 40742ec31f5cdbcf337df5ee1c47637e78168501 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -37,7 +37,7 @@
console.debug(job_def);
// show progress modal
- this.app.modal.show({title: 'Please wait...', body: 'progress'});
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: { 'Close' : function () {self.app.modal.hide();} }});
// post job
Utils.request({
diff -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 -r 40742ec31f5cdbcf337df5ee1c47637e78168501 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress"});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{c.app.modal.show({title:g.statusText,body:a.error(d),closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{c.app.modal.show({title:g.statusText,body:a.error(d),closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fix empty collection
by commits-noreply@bitbucket.org 08 Oct '14
by commits-noreply@bitbucket.org 08 Oct '14
08 Oct '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/86825b18e71f/
Changeset: 86825b18e71f
User: guerler
Date: 2014-10-08 20:31:22+00:00
Summary: ToolForm: Fix empty collection
Affected #: 7 files
diff -r 05f112a611b683c82acd6f5c4918cff299daf2c5 -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 client/galaxy/scripts/mvc/tools/tools-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-content.js
@@ -86,16 +86,26 @@
/** Get details of a content by id.
*/
getDetails: function(options) {
+ // check id
+ if (!options.id || options.id === 'null') {
+ options.success && options.success();
+ return;
+ }
+
+ // create url
var api_url = this.base_url + '/datasets/' + options.id;
if (options.src == 'hdca') {
api_url = this.base_url + '/dataset_collections/' + options.id;
}
+
+ // request details
Utils.get({
url : api_url,
success : function(response) {
options.success && options.success(response);
},
error : function(response) {
+ options.success && options.success();
console.debug('tools-content::getDetails() - Ajax request for content failed.');
console.debug(response);
}
diff -r 05f112a611b683c82acd6f5c4918cff299daf2c5 -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -447,11 +447,6 @@
id : content_id,
src : content_src,
success : function(content) {
- // select the first dataset to represent collections
- if (content_src == 'hdca' && content.elements && content.elements.length > 0) {
- content = content.elements[0].object;
- }
-
// meta data
var meta = null;
@@ -460,6 +455,11 @@
// log selection
console.debug('tool-form::field_data() - Selected content ' + content_id + '.');
+ // select the first dataset to represent collections
+ if (content_src == 'hdca' && content.elements && content.elements.length > 0) {
+ content = content.elements[0].object;
+ }
+
// get meta data
meta = content.metadata_column_types;
diff -r 05f112a611b683c82acd6f5c4918cff299daf2c5 -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -204,7 +204,7 @@
except Exception, e:
log.exception( "Error in history API at listing dataset collection: %s", e )
trans.response.status = 500
- return msg
+ return { 'error': str( e ) }
def __show_dataset( self, trans, id, **kwd ):
hda = self.mgrs.hdas.get( trans, self._decode_id( trans, id ), check_ownership=False, check_accessible=True )
diff -r 05f112a611b683c82acd6f5c4918cff299daf2c5 -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 static/scripts/mvc/tools/tools-content.js
--- a/static/scripts/mvc/tools/tools-content.js
+++ b/static/scripts/mvc/tools/tools-content.js
@@ -86,16 +86,26 @@
/** Get details of a content by id.
*/
getDetails: function(options) {
+ // check id
+ if (!options.id || options.id === 'null') {
+ options.success && options.success();
+ return;
+ }
+
+ // create url
var api_url = this.base_url + '/datasets/' + options.id;
if (options.src == 'hdca') {
api_url = this.base_url + '/dataset_collections/' + options.id;
}
+
+ // request details
Utils.get({
url : api_url,
success : function(response) {
options.success && options.success(response);
},
error : function(response) {
+ options.success && options.success();
console.debug('tools-content::getDetails() - Ajax request for content failed.');
console.debug(response);
}
diff -r 05f112a611b683c82acd6f5c4918cff299daf2c5 -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -447,11 +447,6 @@
id : content_id,
src : content_src,
success : function(content) {
- // select the first dataset to represent collections
- if (content_src == 'hdca' && content.elements && content.elements.length > 0) {
- content = content.elements[0].object;
- }
-
// meta data
var meta = null;
@@ -460,6 +455,11 @@
// log selection
console.debug('tool-form::field_data() - Selected content ' + content_id + '.');
+ // select the first dataset to represent collections
+ if (content_src == 'hdca' && content.elements && content.elements.length > 0) {
+ content = content.elements[0].object;
+ }
+
// get meta data
meta = content.metadata_column_types;
diff -r 05f112a611b683c82acd6f5c4918cff299daf2c5 -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 static/scripts/packed/mvc/tools/tools-content.js
--- a/static/scripts/packed/mvc/tools/tools-content.js
+++ b/static/scripts/packed/mvc/tools/tools-content.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},getDetails:function(b){var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})});
\ No newline at end of file
+define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})});
\ No newline at end of file
diff -r 05f112a611b683c82acd6f5c4918cff299daf2c5 -r 86825b18e71f05e6eec2904edf9d9ba7b0490698 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content"],function(d,b,g,c,a){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content"],function(d,b,g,c,a){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
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