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July 2014
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commit/galaxy-central: jmchilton: Small style fix in run_tests.sh.
by commits-noreply＠bitbucket.org 25 Jul '14
by commits-noreply＠bitbucket.org 25 Jul '14
25 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e359c370aeac/
Changeset: e359c370aeac
User: jmchilton
Date: 2014-07-25 17:40:53
Summary: Small style fix in run_tests.sh.
Affected #: 1 file
diff -r 92546e4b743fd876067a6bf68daffde9c6eca231 -r e359c370aeac38cafa61c01112c09c1560153523 run_tests.sh
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -88,7 +88,7 @@
shift 1
fi
;;
- -with_framework_test_tools|--with_framework_test_tools)
+ -with_framework_test_tools|--with_framework_test_tools)
with_framework_test_tools_arg="-with_framework_test_tools"
shift
;;
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/64e429d43a0e/
Changeset: 64e429d43a0e
User: jmchilton
Date: 2014-07-25 17:28:50
Summary: Implement optional collection params.
Was already parsing optional attribute but I put exactly zero thought into the implementation so these didn't work at all I don't think. This fills out the implementation, adds a test tool, and some cheetah helpers to facilitate this: "#if $collect_param" will fail if input not supplied or collection is empty and "#if $collect_param.is_input_supplied" will fail is input not supplied (i.e. empty collections will pass this check).
Affected #: 4 files
diff -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 -r 64e429d43a0e81ca684e51c51a7f07e38962e0da lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -114,6 +114,8 @@
#allow explicit conversion to be stored in job_parameter table
target_dict[ conversion_name ] = conversion_data.id # a more robust way to determine JSONable value is desired
elif isinstance( input, DataCollectionToolParameter ):
+ if not value:
+ return
for i, v in enumerate( value.collection.dataset_instances ):
data = v
current_user_roles = trans.get_current_user_roles()
diff -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 -r 64e429d43a0e81ca684e51c51a7f07e38962e0da lib/galaxy/tools/wrappers.py
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -269,6 +269,12 @@
def __init__( self, has_collection, dataset_paths=[], **kwargs ):
super(DatasetCollectionWrapper, self).__init__()
+ if has_collection is None:
+ self.__input_supplied = False
+ return
+ else:
+ self.__input_supplied = True
+
if hasattr( has_collection, "name" ):
# It is a HistoryDatasetCollectionAssociation
collection = has_collection.collection
@@ -298,20 +304,37 @@
self.element_instance_list = element_instance_list
def keys( self ):
+ if not self.__input_supplied:
+ return []
return self.element_instances.keys()
@property
def is_collection( self ):
return True
+ @property
+ def is_input_supplied( self ):
+ return self.__input_supplied
+
def __getitem__( self, key ):
+ if not self.__input_supplied:
+ return None
if isinstance( key, int ):
return self.element_instance_list[ key ]
else:
return self.element_instances[ key ]
def __getattr__( self, key ):
+ if not self.__input_supplied:
+ return None
return self.element_instances[ key ]
def __iter__( self ):
+ if not self.__input_supplied:
+ return [].__iter__()
return self.element_instance_list.__iter__()
+
+ def __nonzero__( self ):
+ # Fail `#if $param` checks in cheetah is optional input
+ # not specified or if resulting collection is empty.
+ return self.__input_supplied and bool( self.element_instance_list )
diff -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 -r 64e429d43a0e81ca684e51c51a7f07e38962e0da test/functional/tools/collection_optional_param.xml
--- /dev/null
+++ b/test/functional/tools/collection_optional_param.xml
@@ -0,0 +1,38 @@
+<tool id="collection_optional_param" name="collection_optional_param" version="0.1.0">
+ <command>
+ #if $f1
+ cat $f1.forward $f1['reverse'] >> $out1;
+ #else
+ echo "No input specified." >> $out1;
+ #end if
+ </command>
+ <inputs>
+ <param name="f1" type="data_collection" collection_type="paired" optional="true" />
+ </inputs>
+ <outputs>
+ <data format="txt" name="out1" />
+ </outputs>
+ <tests>
+ <test>
+ <param name="f1">
+ <collection type="paired">
+ <element name="forward" value="simple_line.txt" />
+ <element name="reverse" value="simple_line_alternative.txt" />
+ </collection>
+ </param>
+ <output name="out1">
+ <assert_contents>
+ <has_line line="This is a line of text." />
+ <has_line line="This is a different line of text." />
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <output name="out1">
+ <assert_contents>
+ <has_line line="No input specified." />
+ </assert_contents>
+ </output>
+ </test>
+ </tests>
+</tool>
diff -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 -r 64e429d43a0e81ca684e51c51a7f07e38962e0da test/functional/tools/samples_tool_conf.xml
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -22,4 +22,5 @@
<tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" /><tool file="collection_two_paired.xml" />
+ <tool file="collection_optional_param.xml" /></toolbox>
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/92546e4b743f/
Changeset: 92546e4b743f
User: jmchilton
Date: 2014-07-25 17:28:50
Summary: Improved object attribute naming DatasetCollectionWrapper.
To try to limit potential ambibuity introduced by (probably mistakenly) allowing syntax such $param.<element_identifier> (e.g. $pair.forward).
Affected #: 1 file
diff -r 64e429d43a0e81ca684e51c51a7f07e38962e0da -r 92546e4b743fd876067a6bf68daffde9c6eca231 lib/galaxy/tools/wrappers.py
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -300,13 +300,13 @@
element_instances[element_identifier] = element_wrapper
element_instance_list.append( element_wrapper )
- self.element_instances = element_instances
- self.element_instance_list = element_instance_list
+ self.__element_instances = element_instances
+ self.__element_instance_list = element_instance_list
def keys( self ):
if not self.__input_supplied:
return []
- return self.element_instances.keys()
+ return self.__element_instances.keys()
@property
def is_collection( self ):
@@ -320,21 +320,21 @@
if not self.__input_supplied:
return None
if isinstance( key, int ):
- return self.element_instance_list[ key ]
+ return self.__element_instance_list[ key ]
else:
- return self.element_instances[ key ]
+ return self.__element_instances[ key ]
def __getattr__( self, key ):
if not self.__input_supplied:
return None
- return self.element_instances[ key ]
+ return self.__element_instances[ key ]
def __iter__( self ):
if not self.__input_supplied:
return [].__iter__()
- return self.element_instance_list.__iter__()
+ return self.__element_instance_list.__iter__()
def __nonzero__( self ):
# Fail `#if $param` checks in cheetah is optional input
# not specified or if resulting collection is empty.
- return self.__input_supplied and bool( self.element_instance_list )
+ return self.__input_supplied and bool( self.__element_instance_list )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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25 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a2e4a980cdde/
Changeset: a2e4a980cdde
User: guerler
Date: 2014-07-25 17:22:43
Summary: Charts: Add crossfilter
Affected #: 4 files
diff -r 31aeeefd6020bfd61fa6587cce9e03cf670f62d6 -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$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.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),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","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=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","plugin/library/ui","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("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.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<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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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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$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.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$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{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),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","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=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=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(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.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",["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,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$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","plugin/library/ui","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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\ No newline at end of file
diff -r 31aeeefd6020bfd61fa6587cce9e03cf670f62d6 -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 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 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\ No newline at end of file
diff -r 31aeeefd6020bfd61fa6587cce9e03cf670f62d6 -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 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
@@ -19,6 +19,7 @@
// create settings
this.form = new TableForm.View(app, {
+ title : 'Configuration',
content : 'This chart type does not provide any options.'
});
diff -r 31aeeefd6020bfd61fa6587cce9e03cf670f62d6 -r a2e4a980cdde2494e14f6eb17a3a518321ca65d1 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" )}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Don't allow tool form to submit with missing collection inputs if param non-optional.
by commits-noreply＠bitbucket.org 25 Jul '14
by commits-noreply＠bitbucket.org 25 Jul '14
25 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/31aeeefd6020/
Changeset: 31aeeefd6020
User: jmchilton
Date: 2014-07-25 16:17:38
Summary: Don't allow tool form to submit with missing collection inputs if param non-optional.
Affected #: 2 files
diff -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 -r 31aeeefd6020bfd61fa6587cce9e03cf670f62d6 lib/galaxy/tools/parameters/__init__.py
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -53,7 +53,7 @@
value = incoming_value
error = None
try:
- if value is not None or isinstance( param, DataToolParameter ):
+ if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ):
# Convert value from HTML representation
if source == 'html':
value = param.from_html( value, trans, param_values )
diff -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 -r 31aeeefd6020bfd61fa6587cce9e03cf670f62d6 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2078,7 +2078,7 @@
def from_html( self, value, trans, other_values={} ):
if not value and not self.optional:
- raise ValueError( "History does not include a dataset of the required format / build" )
+ raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" )
if value in [None, "None"]:
return None
if isinstance( value, str ) and value.find( "," ) > 0:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
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1
0
6 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/aed2268f79d1/
Changeset: aed2268f79d1
User: jgoecks
Date: 2014-07-24 19:54:50
Summary: Trackster: variable clean up for read track painter, preventing features from being cutoff at the bottom.
Affected #: 1 file
diff -r 9d8967752787556b3d814e086fe2bd9eb1992170 -r aed2268f79d13f5604d69db109c20374cf311511 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -783,7 +783,9 @@
char_width_px = ctx.canvas.manager.char_width_px,
block_color = (strand === "+" ? this.prefs.detail_block_color : this.prefs.reverse_strand_color),
pack_mode = (mode === 'Pack'),
- paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale, mode),
+ draw_height = (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT),
+ rect_y = y_start + 1,
+ paint_utils = new ReadPainterUtils(ctx, draw_height, w_scale, mode),
drawing_blocks = [];
// Keep list of items that need to be drawn on top of initial drawing layer.
@@ -813,10 +815,7 @@
// Draw read base as rectangle.
ctx.fillStyle = block_color;
- ctx.fillRect(s_start,
- y_start + (pack_mode ? 1 : 4 ),
- s_end - s_start,
- (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
+ ctx.fillRect(s_start, rect_y, s_end - s_start, draw_height);
}
}
@@ -893,10 +892,7 @@
}
// Require a minimum w_scale so that variants are only drawn when somewhat zoomed in.
else if (w_scale > 0.05) {
- ctx.fillRect(c_start - gap,
- y_start + (pack_mode ? 1 : 4),
- Math.max( 1, Math.round(w_scale) ),
- (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
+ ctx.fillRect(c_start - gap, rect_y, Math.max( 1, Math.round(w_scale) ), draw_height);
}
}
}
@@ -913,7 +909,7 @@
base_offset += cig_len;
break;
case "D": // Deletion.
- paint_utils.draw_deletion(s_start, y_start + (pack_mode ? 1 : 4), cig_len);
+ paint_utils.draw_deletion(s_start, rect_y, cig_len);
base_offset += cig_len;
break;
case "I": // Insertion.
https://bitbucket.org/galaxy/galaxy-central/commits/9f94c75733e9/
Changeset: 9f94c75733e9
User: jgoecks
Date: 2014-07-24 20:34:53
Summary: Client-side visualization framework: remove extend aliasing.
Affected #: 1 file
diff -r aed2268f79d13f5604d69db109c20374cf311511 -r 9f94c75733e9e61f94658ecdf436d57f70eec9a6 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -1,7 +1,5 @@
define( ["libs/underscore"], function( _ ) {
-var extend = _.extend;
-
/**
* Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig.
* The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first
@@ -128,7 +126,7 @@
this.view_start = view_start;
this.view_end = view_end;
// Drawing prefs
- this.prefs = extend({}, this.default_prefs, prefs);
+ this.prefs = _.extend({}, this.default_prefs, prefs);
this.mode = mode;
};
@@ -354,7 +352,7 @@
FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" };
-extend(FeaturePainter.prototype, {
+_.extend(FeaturePainter.prototype, {
get_required_height: function(rows_required, width) {
// y_scale is the height per row
var required_height = this.get_row_height(),
@@ -451,7 +449,7 @@
this.draw_individual_connectors = false;
};
-extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
+_.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
/**
* Height of a single row, depends on mode
@@ -692,7 +690,7 @@
this.base_color_fn = base_color_fn;
};
-extend(ReadPainter.prototype, FeaturePainter.prototype, {
+_.extend(ReadPainter.prototype, FeaturePainter.prototype, {
/**
* Returns height based on mode.
*/
@@ -1077,7 +1075,7 @@
this.draw_individual_connectors = true;
};
-extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeaturePainter.prototype, {
+_.extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeaturePainter.prototype, {
calculate_longest_feature_length: function () {
var longest_feature_length = 0;
@@ -1336,7 +1334,7 @@
this.delete_details_thickness = 0.2;
};
-extend(ReadPainterUtils.prototype, {
+_.extend(ReadPainterUtils.prototype, {
/**
* Draw deletion of base(s).
* @param draw_detail if true, drawing in detail and deletion is drawn more subtly
@@ -1358,7 +1356,7 @@
this.divider_height = 1;
};
-extend(VariantPainter.prototype, Painter.prototype, {
+_.extend(VariantPainter.prototype, Painter.prototype, {
/**
* Height of a single row, depends on mode
*/
https://bitbucket.org/galaxy/galaxy-central/commits/537e1c3b80ee/
Changeset: 537e1c3b80ee
User: jgoecks
Date: 2014-07-25 15:38:05
Summary: Trackster: better handling for drawing features across tiles.
Affected #: 2 files
diff -r 9f94c75733e9e61f94658ecdf436d57f70eec9a6 -r 537e1c3b80eec65f83871272f49f6de6393523c9 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -1055,10 +1055,10 @@
ctx.fillStyle = this.prefs.label_color;
if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
- ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8, this.max_label_length);
+ ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 9, this.max_label_length);
} else {
ctx.textAlign = "right";
- ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8, this.max_label_length);
+ ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 9, this.max_label_length);
}
}
diff -r 9f94c75733e9e61f94658ecdf436d57f70eec9a6 -r 537e1c3b80eec65f83871272f49f6de6393523c9 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1968,6 +1968,7 @@
* Sets up support for popups.
*/
FeatureTrackTile.prototype.predisplay_actions = function() {
+ /*
//
// Add support for popups.
//
@@ -2062,6 +2063,7 @@
.mouseleave(function() {
$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove();
});
+*/
};
/**
@@ -3722,11 +3724,22 @@
});
});
- // Draw features on each tile.
+ // Draw incomplete features on each tile.
var self = this;
_.each(tiles, function(tile) {
- self.draw_tile({ 'data': _.values(all_incomplete_features) }, tile.canvas.getContext('2d'),
- tile.mode, tile.region, w_scale, tile.seq_data, true);
+ // To draw incomplete features, copy original canvas and then draw incomplete features
+ // on the canvas.
+ var features = { data: _.values( all_incomplete_features ) },
+ canvas = self.view.canvas_manager.new_canvas();
+ canvas.height = self.get_canvas_height(features, tile.mode, tile.w_scale, 100);
+ canvas.width = tile.canvas.width;
+ canvas.getContext('2d').drawImage(tile.canvas, 0, 0);
+ canvas.getContext('2d').translate(track.left_offset, 0);
+ var new_tile = self.draw_tile(features, canvas.getContext('2d'),
+ tile.mode, tile.region, tile.w_scale, tile.seq_data);
+ $(new_tile.canvas).addClass('incomplete_features');
+ $(tile.canvas).replaceWith($(new_tile.canvas));
+ tile.canvas = canvas;
});
}
https://bitbucket.org/galaxy/galaxy-central/commits/4ca83b9de85f/
Changeset: 4ca83b9de85f
User: jgoecks
Date: 2014-07-25 15:45:28
Summary: Trackster: disable track popups because they are slow and don't work well.
Affected #: 1 file
diff -r 537e1c3b80eec65f83871272f49f6de6393523c9 -r 4ca83b9de85f10b371c457fff1e06470f1a1944c static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1969,6 +1969,7 @@
*/
FeatureTrackTile.prototype.predisplay_actions = function() {
/*
+ FIXME: use a canvas library to handle popups.
//
// Add support for popups.
//
@@ -2063,7 +2064,7 @@
.mouseleave(function() {
$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove();
});
-*/
+ */
};
/**
https://bitbucket.org/galaxy/galaxy-central/commits/b2613d9978a4/
Changeset: b2613d9978a4
User: jgoecks
Date: 2014-07-25 15:48:31
Summary: Trackster: better variable naming.
Affected #: 1 file
diff -r 4ca83b9de85f10b371c457fff1e06470f1a1944c -r b2613d9978a499db6e905ba8f4e452029b1aff61 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -3731,16 +3731,16 @@
// To draw incomplete features, copy original canvas and then draw incomplete features
// on the canvas.
var features = { data: _.values( all_incomplete_features ) },
- canvas = self.view.canvas_manager.new_canvas();
- canvas.height = self.get_canvas_height(features, tile.mode, tile.w_scale, 100);
- canvas.width = tile.canvas.width;
- canvas.getContext('2d').drawImage(tile.canvas, 0, 0);
- canvas.getContext('2d').translate(track.left_offset, 0);
- var new_tile = self.draw_tile(features, canvas.getContext('2d'),
+ new_canvas = self.view.canvas_manager.new_canvas();
+ new_canvas.height = self.get_canvas_height(features, tile.mode, tile.w_scale, 100);
+ new_canvas.width = tile.canvas.width;
+ new_canvas.getContext('2d').drawImage(tile.canvas, 0, 0);
+ new_canvas.getContext('2d').translate(track.left_offset, 0);
+ var new_tile = self.draw_tile(features, new_canvas.getContext('2d'),
tile.mode, tile.region, tile.w_scale, tile.seq_data);
$(new_tile.canvas).addClass('incomplete_features');
$(tile.canvas).replaceWith($(new_tile.canvas));
- tile.canvas = canvas;
+ tile.canvas = new_canvas;
});
}
https://bitbucket.org/galaxy/galaxy-central/commits/8b98752f4fbc/
Changeset: 8b98752f4fbc
User: jgoecks
Date: 2014-07-25 15:48:56
Summary: Automated merge
Affected #: 13 files
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -177,6 +177,7 @@
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
+ <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
@@ -262,6 +263,7 @@
--><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/>
+ <sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/>
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -12,6 +12,7 @@
import subprocess
import tempfile
import zipfile
+import sqlite3
from urllib import urlencode, quote_plus
from galaxy import eggs
@@ -545,3 +546,45 @@
return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size()))
Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit)
+
+
+(a)dataproviders.decorators.has_dataproviders
+class SQlite ( Binary ):
+ file_ext = "sqlite"
+
+ # Connects and runs a query that should work on any real database
+ # If the file is not sqlite, an exception will be thrown and the sniffer will return false
+ def sniff( self, filename ):
+ try:
+ conn = sqlite3.connect(filename)
+ schema_version=conn.cursor().execute("pragma schema_version").fetchone()
+ conn.close()
+ if schema_version is not None:
+ return True
+ return False
+ except:
+ return False
+
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ dataset.peek = "SQLite Database"
+ dataset.blurb = data.nice_size( dataset.get_size() )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def display_peek( self, dataset ):
+ try:
+ return dataset.peek
+ except:
+ return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+
+ @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
+ def sqlite_dataprovider( self, dataset, **settings ):
+ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
+ return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings )
+
+
+Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite)
+
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 lib/galaxy/datatypes/dataproviders/dataset.py
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -11,6 +11,8 @@
import line
import column
import external
+import sqlite3
+import re
from galaxy import eggs
eggs.require( 'bx-python' )
@@ -700,3 +702,39 @@
#TODO: as samtools - need more info on output format
raise NotImplementedError()
super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs )
+
+
+
+class SQliteDataProvider ( base.DataProvider ):
+ """
+ Data provider that uses a sqlite database file as its source.
+
+ Allows any query to be run and returns the resulting rows as sqlite3 row objects
+ """
+ settings = {
+ 'query' : 'str'
+ }
+
+ def __init__( self, source, query=None, **kwargs ):
+ self.query=query
+ self.connection = sqlite3.connect(source.dataset.file_name);
+ self.connection.row_factory = sqlite3.Row
+ super( SQliteDataProvider, self ).__init__( source, **kwargs )
+
+ def query_matches_whitelist(self,query):
+ if re.match("select ",query,re.IGNORECASE):
+ if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query):
+ return False
+ else:
+ return True
+ return False
+
+
+
+ def __iter__( self ):
+ if (self.query is not None) and self.query_matches_whitelist(self.query):
+ for row in self.connection.cursor().execute(self.query):
+ yield row
+ else:
+ yield
+
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -34,6 +34,7 @@
from galaxy.util.bunch import Bunch
from galaxy.util.hash_util import new_secure_hash
from galaxy.util.directory_hash import directory_hash_id
+from galaxy.util.sanitize_html import sanitize_html
from galaxy.web.framework.helpers import to_unicode
from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField,
PasswordField, SelectField, TextArea, TextField, WorkflowField,
@@ -2589,8 +2590,8 @@
class DatasetCollection( object, Dictifiable, UsesAnnotations ):
"""
"""
- dict_collection_visible_keys = ( 'id', 'name', 'collection_type' )
- dict_element_visible_keys = ( 'id', 'name', 'collection_type' )
+ dict_collection_visible_keys = ( 'id', 'collection_type' )
+ dict_element_visible_keys = ( 'id', 'collection_type' )
def __init__(
self,
@@ -3703,23 +3704,27 @@
self.country = country
self.phone = phone
def get_html(self):
+ # This should probably be deprecated eventually. It should currently
+ # sanitize.
+ # TODO Find out where else uses this and replace with
+ # templates
html = ''
if self.name:
- html = html + self.name
+ html = html + sanitize_html(self.name)
if self.institution:
- html = html + '<br/>' + self.institution
+ html = html + '<br/>' + sanitize_html(self.institution)
if self.address:
- html = html + '<br/>' + self.address
+ html = html + '<br/>' + sanitize_html(self.address)
if self.city:
- html = html + '<br/>' + self.city
+ html = html + '<br/>' + sanitize_html(self.city)
if self.state:
- html = html + ' ' + self.state
+ html = html + ' ' + sanitize_html(self.state)
if self.postal_code:
- html = html + ' ' + self.postal_code
+ html = html + ' ' + sanitize_html(self.postal_code)
if self.country:
- html = html + '<br/>' + self.country
+ html = html + '<br/>' + sanitize_html(self.country)
if self.phone:
- html = html + '<br/>' + 'Phone: ' + self.phone
+ html = html + '<br/>' + 'phone: ' + sanitize_html(self.phone)
return html
class UserOpenID( object ):
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1391,7 +1391,7 @@
# Load parameters (optional)
input_elem = root.find("inputs")
enctypes = set()
- if input_elem:
+ if input_elem is not None:
# Handle properties of the input form
self.check_values = string_as_bool( input_elem.get("check_values", self.check_values ) )
self.nginx_upload = string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) )
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1712,10 +1712,15 @@
if self.__display_multirun_option():
# Select multiple datasets, run multiple jobs.
multirun_key = "%s|__multirun__" % self.name
+ collection_multirun_key = "%s|__collection_multirun__" % self.name
if multirun_key in (other_values or {}):
multirun_value = listify( other_values[ multirun_key ] )
if multirun_value and len( multirun_value ) > 1:
default_field = "select_multiple"
+ elif collection_multirun_key in (other_values or {}):
+ multirun_value = listify( other_values[ collection_multirun_key ] )
+ if multirun_value:
+ default_field = "select_collection"
else:
multirun_value = value
multi_dataset_matcher = DatasetMatcher( trans, self, multirun_value, other_values )
@@ -2014,9 +2019,17 @@
default_field = "select_single_collection"
fields = odict()
+ collection_multirun_key = "%s|__collection_multirun__" % self.name
+ if collection_multirun_key in (other_values or {}):
+ multirun_value = other_values[ collection_multirun_key ]
+ if multirun_value:
+ default_field = "select_map_over_collections"
+ else:
+ multirun_value = value
+
history = self._get_history( trans )
fields[ "select_single_collection" ] = self._get_single_collection_field( trans=trans, history=history, value=value, other_values=other_values )
- fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=value, other_values=other_values )
+ fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=multirun_value, other_values=other_values )
return self._switch_fields( fields, default_field=default_field )
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -48,10 +48,10 @@
from .inflection import Inflector, English
inflector = Inflector(English)
-log = logging.getLogger(__name__)
+log = logging.getLogger(__name__)
_lock = threading.RLock()
-CHUNK_SIZE = 65536 #64k
+CHUNK_SIZE = 65536 # 64k
DATABASE_MAX_STRING_SIZE = 32768
DATABASE_MAX_STRING_SIZE_PRETTY = '32K'
@@ -62,6 +62,7 @@
NULL_CHAR = '\000'
BINARY_CHARS = [ NULL_CHAR ]
+
def is_multi_byte( chars ):
for char in chars:
try:
@@ -69,18 +70,15 @@
except UnicodeDecodeError:
# Probably binary
return False
- if wchartype.is_asian( char ) or \
- wchartype.is_full_width( char ) or \
- wchartype.is_kanji( char ) or \
- wchartype.is_hiragana( char ) or \
- wchartype.is_katakana( char ) or \
- wchartype.is_half_katakana( char ) or \
- wchartype.is_hangul( char ) or \
- wchartype.is_full_digit( char ) or \
- wchartype.is_full_letter( char ):
+ if ( wchartype.is_asian( char ) or wchartype.is_full_width( char ) or
+ wchartype.is_kanji( char ) or wchartype.is_hiragana( char ) or
+ wchartype.is_katakana( char ) or wchartype.is_half_katakana( char )
+ or wchartype.is_hangul( char ) or wchartype.is_full_digit( char )
+ or wchartype.is_full_letter( char )):
return True
return False
+
def is_binary( value, binary_chars=None ):
"""
File is binary if it contains a null-byte by default (e.g. behavior of grep, etc.).
@@ -99,6 +97,7 @@
return True
return False
+
def get_charset_from_http_headers( headers, default=None ):
rval = headers.get('content-type', None )
if rval and 'charset=' in rval:
@@ -107,16 +106,18 @@
return rval
return default
+
def synchronized(func):
"""This wrapper will serialize access to 'func' to a single thread. Use it as a decorator."""
def caller(*params, **kparams):
- _lock.acquire(True) # Wait
+ _lock.acquire(True) # Wait
try:
return func(*params, **kparams)
finally:
_lock.release()
return caller
+
def file_iter(fname, sep=None):
"""
This generator iterates over a file and yields its lines
@@ -131,6 +132,7 @@
if line and line[0] != '#':
yield line.split(sep)
+
def file_reader( fp, chunk_size=CHUNK_SIZE ):
"""This generator yields the open fileobject in chunks (default 64k). Closes the file at the end"""
while 1:
@@ -140,6 +142,7 @@
yield data
fp.close()
+
def unique_id(KEY_SIZE=128):
"""
Generates an unique id
@@ -148,8 +151,8 @@
>>> len(set(ids))
1000
"""
- id = str( random.getrandbits( KEY_SIZE ) )
- return md5(id).hexdigest()
+ return md5(str( random.getrandbits( KEY_SIZE ) )).hexdigest()
+
def parse_xml(fname):
"""Returns a parsed xml tree"""
@@ -163,6 +166,7 @@
tree = ElementTree.fromstring(xml_string)
return tree
+
def xml_to_string( elem, pretty=False ):
"""Returns a string from an xml tree"""
if pretty:
@@ -170,12 +174,13 @@
try:
return ElementTree.tostring( elem )
except TypeError, e:
- #assume this is a comment
+ # we assume this is a comment
if hasattr( elem, 'text' ):
return "<!-- %s -->\n" % ( elem.text )
else:
raise e
+
def xml_element_compare( elem1, elem2 ):
if not isinstance( elem1, dict ):
elem1 = xml_element_to_dict( elem1 )
@@ -183,9 +188,11 @@
elem2 = xml_element_to_dict( elem2 )
return elem1 == elem2
+
def xml_element_list_compare( elem_list1, elem_list2 ):
return [ xml_element_to_dict( elem ) for elem in elem_list1 ] == [ xml_element_to_dict( elem ) for elem in elem_list2 ]
+
def xml_element_to_dict( elem ):
rval = {}
if elem.attrib:
@@ -220,7 +227,6 @@
return rval
-
def pretty_print_xml( elem, level=0 ):
pad = ' '
i = "\n" + level * pad
@@ -238,26 +244,28 @@
elem.tail = i + pad
return elem
+
def get_file_size( value, default=None ):
try:
- #try built-in
+ # try built-in
return os.path.getsize( value )
except:
try:
- #try built-in one name attribute
+ # try built-in one name attribute
return os.path.getsize( value.name )
except:
try:
- #try tell() of end of object
+ # try tell() of end of object
offset = value.tell()
value.seek( 0, 2 )
rval = value.tell()
value.seek( offset )
return rval
except:
- #return default value
+ # return default value
return default
+
def shrink_stream_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ):
rval = ''
if get_file_size( value ) > size:
@@ -292,6 +300,7 @@
rval += data
return rval
+
def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ):
if len( value ) > size:
len_join_by = len( join_by )
@@ -311,29 +320,30 @@
value = "%s%s%s" % ( value[:left_index], join_by, value[-right_index:] )
return value
+
def pretty_print_json(json_data, is_json_string=False):
if is_json_string:
json_data = json.from_json_string(json_data)
return json.to_json_string(json_data, sort_keys=True, indent=4)
# characters that are valid
-valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")
+valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")
# characters that are allowed but need to be escaped
-mapped_chars = { '>' :'__gt__',
- '<' :'__lt__',
- "'" :'__sq__',
- '"' :'__dq__',
- '[' :'__ob__',
- ']' :'__cb__',
- '{' :'__oc__',
- '}' :'__cc__',
- '@' : '__at__',
- '\n' : '__cn__',
- '\r' : '__cr__',
- '\t' : '__tc__',
- '#' : '__pd__'
- }
+mapped_chars = { '>': '__gt__',
+ '<': '__lt__',
+ "'": '__sq__',
+ '"': '__dq__',
+ '[': '__ob__',
+ ']': '__cb__',
+ '{': '__oc__',
+ '}': '__cc__',
+ '@': '__at__',
+ '\n': '__cn__',
+ '\r': '__cr__',
+ '\t': '__tc__',
+ '#': '__pd__'}
+
def restore_text(text):
"""Restores sanitized text"""
@@ -343,6 +353,7 @@
text = text.replace(value, key)
return text
+
def sanitize_text(text):
"""
Restricts the characters that are allowed in text; accepts both strings
@@ -353,6 +364,7 @@
elif isinstance( text, list ):
return [ _sanitize_text_helper(t) for t in text ]
+
def _sanitize_text_helper(text):
"""Restricts the characters that are allowed in a string"""
@@ -363,9 +375,10 @@
elif c in mapped_chars:
out.append(mapped_chars[c])
else:
- out.append('X') # makes debugging easier
+ out.append('X') # makes debugging easier
return ''.join(out)
+
def sanitize_param(value):
"""Clean incoming parameters (strings or lists)"""
if isinstance( value, basestring ):
@@ -373,10 +386,12 @@
elif isinstance( value, list ):
return map(sanitize_text, value)
else:
- raise Exception, 'Unknown parameter type (%s)' % ( type( value ) )
+ raise Exception('Unknown parameter type (%s)' % ( type( value ) ))
valid_filename_chars = set( string.ascii_letters + string.digits + '_.' )
invalid_filenames = [ '', '.', '..' ]
+
+
def sanitize_for_filename( text, default=None ):
"""
Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name.
@@ -512,7 +527,7 @@
def __init__( self, params, sanitize=True ):
if sanitize:
for key, value in params.items():
- if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: #sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed.
+ if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: # sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed.
self.__dict__[ key ] = sanitize_param( value )
else:
self.__dict__[ key ] = value
@@ -525,7 +540,7 @@
"""
flat = []
for key, value in self.__dict__.items():
- if type(value) == type([]):
+ if isinstance(value, list):
for v in value:
flat.append( (key, v) )
else:
@@ -551,16 +566,19 @@
def update(self, values):
self.__dict__.update(values)
+
def rst_to_html( s ):
"""Convert a blob of reStructuredText to HTML"""
log = logging.getLogger( "docutils" )
+
class FakeStream( object ):
def write( self, str ):
if len( str ) > 0 and not str.isspace():
log.warn( str )
return unicodify( docutils.core.publish_string( s,
- writer=docutils.writers.html4css1.Writer(),
- settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) )
+ writer=docutils.writers.html4css1.Writer(),
+ settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) )
+
def xml_text(root, name=None):
"""Returns the text inside an element"""
@@ -582,6 +600,8 @@
# asbool implementation pulled from PasteDeploy
truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
+
+
def asbool(obj):
if isinstance(obj, basestring):
obj = obj.strip().lower()
@@ -600,6 +620,7 @@
else:
return False
+
def string_as_bool_or_none( string ):
"""
Returns True, None or False based on the argument:
@@ -618,6 +639,7 @@
else:
return False
+
def listify( item, do_strip=False ):
"""
Make a single item a single item list, or return a list if passed a
@@ -635,6 +657,7 @@
else:
return [ item ]
+
def commaify(amount):
orig = amount
new = re.sub("^(-?\d+)(\d{3})", '\g<1>,\g<2>', amount)
@@ -643,7 +666,8 @@
else:
return commaify(new)
-def roundify(amount, sfs = 2):
+
+def roundify(amount, sfs=2):
"""
Take a number in string form and truncate to 'sfs' significant figures.
"""
@@ -652,6 +676,7 @@
else:
return amount[0:sfs] + '0'*(len(amount) - sfs)
+
def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None ):
"""
Returns a unicode string or None
@@ -691,6 +716,7 @@
def object_to_string( obj ):
return binascii.hexlify( pickle.dumps( obj, 2 ) )
+
def string_to_object( s ):
return pickle.loads( binascii.unhexlify( s ) )
@@ -743,19 +769,23 @@
return False
return True
+
def get_ucsc_by_build(build):
sites = []
for site in ucsc_build_sites:
if build in site['builds']:
- sites.append((site['name'],site['url']))
+ sites.append((site['name'], site['url']))
return sites
+
+
def get_gbrowse_sites_by_build(build):
sites = []
for site in gbrowse_build_sites:
if build in site['builds']:
- sites.append((site['name'],site['url']))
+ sites.append((site['name'], site['url']))
return sites
+
def read_dbnames(filename):
""" Read build names from file """
class DBNames( list ):
@@ -764,48 +794,54 @@
db_names = DBNames()
try:
ucsc_builds = {}
- man_builds = [] #assume these are integers
+ man_builds = [] # assume these are integers
name_to_db_base = {}
for line in open(filename):
try:
- if line[0:1] == "#": continue
- fields = line.replace("\r","").replace("\n","").split("\t")
- #Special case of unspecified build is at top of list
+ if line[0:1] == "#":
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
+ # Special case of unspecified build is at top of list
if fields[0] == "?":
- db_names.insert(0,(fields[0],fields[1]))
+ db_names.insert(0, (fields[0], fields[1]))
continue
- try: #manual build (i.e. microbes)
+ try: # manual build (i.e. microbes)
int(fields[0])
man_builds.append((fields[1], fields[0]))
- except: #UCSC build
+ except: # UCSC build
db_base = fields[0].rstrip('0123456789')
if db_base not in ucsc_builds:
ucsc_builds[db_base] = []
name_to_db_base[fields[1]] = db_base
- #we want to sort within a species numerically by revision number
+ # we want to sort within a species numerically by revision number
build_rev = re.compile(r'\d+$')
- try: build_rev = int(build_rev.findall(fields[0])[0])
- except: build_rev = 0
- ucsc_builds[db_base].append((build_rev, fields[0],fields[1]))
- except: continue
+ try:
+ build_rev = int(build_rev.findall(fields[0])[0])
+ except:
+ build_rev = 0
+ ucsc_builds[db_base].append((build_rev, fields[0], fields[1]))
+ except:
+ continue
sort_names = name_to_db_base.keys()
sort_names.sort()
for name in sort_names:
db_base = name_to_db_base[name]
ucsc_builds[db_base].sort()
ucsc_builds[db_base].reverse()
- ucsc_builds[db_base] = [(build, name) for build_rev, build, name in ucsc_builds[db_base]]
+ ucsc_builds[db_base] = [(build, name) for _, build, name in ucsc_builds[db_base]]
db_names = DBNames( db_names + ucsc_builds[db_base] )
- if len( db_names ) > 1 and len( man_builds ) > 0: db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) )
+ if len( db_names ) > 1 and len( man_builds ) > 0:
+ db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) )
man_builds.sort()
- man_builds = [(build, name) for name, build in man_builds]
+ man_builds = [(build, name) for name, build in man_builds]
db_names = DBNames( db_names + man_builds )
except Exception, e:
print "ERROR: Unable to read builds file:", e
- if len(db_names)<1:
+ if len(db_names) < 1:
db_names = DBNames( [( db_names.default_value, db_names.default_name )] )
return db_names
+
def read_ensembl( filename, ucsc ):
""" Read Ensembl build names from file """
ucsc_builds = []
@@ -814,47 +850,55 @@
ensembl_builds = list()
try:
for line in open( filename ):
- if line[0:1] in [ '#', '\t' ]: continue
- fields = line.replace("\r","").replace("\n","").split("\t")
- if fields[0] in ucsc_builds: continue
+ if line[0:1] in [ '#', '\t' ]:
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
+ if fields[0] in ucsc_builds:
+ continue
ensembl_builds.append( dict( dbkey=fields[0], release=fields[1], name=fields[2].replace( '_', ' ' ) ) )
except Exception, e:
print "ERROR: Unable to read builds file:", e
return ensembl_builds
+
def read_ncbi( filename ):
""" Read NCBI build names from file """
ncbi_builds = list()
try:
for line in open( filename ):
- if line[0:1] in [ '#', '\t' ]: continue
- fields = line.replace("\r","").replace("\n","").split("\t")
+ if line[0:1] in [ '#', '\t' ]:
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
ncbi_builds.append( dict( dbkey=fields[0], name=fields[1] ) )
except Exception, e:
print "ERROR: Unable to read builds file:", e
return ncbi_builds
+
def read_build_sites( filename, check_builds=True ):
""" read db names to ucsc mappings from file, this file should probably be merged with the one above """
build_sites = []
try:
for line in open(filename):
try:
- if line[0:1] == "#": continue
- fields = line.replace("\r","").replace("\n","").split("\t")
+ if line[0:1] == "#":
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
site_name = fields[0]
site = fields[1]
if check_builds:
site_builds = fields[2].split(",")
- site_dict = {'name':site_name, 'url':site, 'builds':site_builds}
+ site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
else:
- site_dict = {'name':site_name, 'url':site}
+ site_dict = {'name': site_name, 'url': site}
build_sites.append( site_dict )
- except: continue
+ except:
+ continue
except:
- print "ERROR: Unable to read builds for site file %s" %filename
+ print "ERROR: Unable to read builds for site file %s" % filename
return build_sites
+
def relativize_symlinks( path, start=None, followlinks=False):
for root, dirs, files in os.walk( path, followlinks=followlinks ):
rel_start = None
@@ -871,23 +915,26 @@
os.remove( symlink_file_name )
os.symlink( rel_path, symlink_file_name )
+
def stringify_dictionary_keys( in_dict ):
- #returns a new dictionary
- #changes unicode keys into strings, only works on top level (does not recurse)
- #unicode keys are not valid for expansion into keyword arguments on method calls
+ # returns a new dictionary
+ # changes unicode keys into strings, only works on top level (does not recurse)
+ # unicode keys are not valid for expansion into keyword arguments on method calls
out_dict = {}
for key, value in in_dict.iteritems():
out_dict[ str( key ) ] = value
return out_dict
+
def recursively_stringify_dictionary_keys( d ):
if isinstance(d, dict):
- return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k,v in d.iteritems()])
+ return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k, v in d.iteritems()])
elif isinstance(d, list):
return [recursively_stringify_dictionary_keys(x) for x in d]
else:
return d
+
def mkstemp_ln( src, prefix='mkstemp_ln_' ):
"""
From tempfile._mkstemp_inner, generate a hard link in the same dir with a
@@ -904,9 +951,10 @@
return (os.path.abspath(file))
except OSError, e:
if e.errno == errno.EEXIST:
- continue # try again
+ continue # try again
raise
- raise IOError, (errno.EEXIST, "No usable temporary file name found")
+ raise IOError(errno.EEXIST, "No usable temporary file name found")
+
def umask_fix_perms( path, umask, unmasked_perms, gid=None ):
"""
@@ -923,7 +971,7 @@
try:
os.chmod( path, perms )
except Exception, e:
- log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ), \
+ log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ),
path,
oct( perms ),
oct( stat.S_IMODE( st.st_mode ) ),
@@ -939,11 +987,12 @@
except:
desired_group = gid
current_group = st.st_gid
- log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group, \
+ log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group,
path,
current_group,
e ) )
+
def docstring_trim(docstring):
"""Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/"""
if not docstring:
@@ -970,6 +1019,7 @@
# Return a single string:
return '\n'.join(trimmed)
+
def nice_size(size):
"""
Returns a readably formatted string with the size
@@ -989,14 +1039,15 @@
except:
return '??? bytes'
for ind, word in enumerate(words):
- step = 1024 ** (ind + 1)
+ step = 1024 ** (ind + 1)
if step > size:
size = size / float(1024 ** ind)
- if word == 'bytes': # No decimals for bytes
+ if word == 'bytes': # No decimals for bytes
return "%d bytes" % size
return "%.1f %s" % (size, word)
return '??? bytes'
+
def size_to_bytes( size ):
"""
Returns a number of bytes if given a reasonably formatted string with the size
@@ -1023,6 +1074,7 @@
elif multiple.startswith( 'b' ):
return int( size )
+
def send_mail( frm, to, subject, body, config ):
"""
Sends an email.
@@ -1072,6 +1124,7 @@
s.sendmail( frm, to, msg.as_string() )
s.quit()
+
def force_symlink( source, link_name ):
try:
os.symlink( source, link_name )
@@ -1082,12 +1135,13 @@
else:
raise e
+
def move_merge( source, target ):
- #when using shutil and moving a directory, if the target exists,
- #then the directory is placed inside of it
- #if the target doesn't exist, then the target is made into the directory
- #this makes it so that the target is always the target, and if it exists,
- #the source contents are moved into the target
+ # when using shutil and moving a directory, if the target exists,
+ # then the directory is placed inside of it
+ # if the target doesn't exist, then the target is made into the directory
+ # this makes it so that the target is always the target, and if it exists,
+ # the source contents are moved into the target
if os.path.isdir( source ) and os.path.exists( target ) and os.path.isdir( target ):
for name in os.listdir( source ):
move_merge( os.path.join( source, name ), os.path.join( target, name ) )
@@ -1103,7 +1157,7 @@
rv |= ord(x) ^ ord(y)
return rv == 0
-galaxy_root_path = os.path.join(__path__[0], "..","..","..")
+galaxy_root_path = os.path.join(__path__[0], "..", "..", "..")
# The dbnames list is used in edit attributes and the upload tool
dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) )
@@ -1114,6 +1168,7 @@
gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) )
dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names)
+
def galaxy_directory():
return os.path.abspath(galaxy_root_path)
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 static/scripts/galaxy.tools.js
--- a/static/scripts/galaxy.tools.js
+++ b/static/scripts/galaxy.tools.js
@@ -86,7 +86,7 @@
}).attr(
'title',
selectionType['select_by']
- );
+ ).data( "index", iIndex );
view.formRow().find( "label" ).append( button );
}
});
@@ -114,11 +114,13 @@
} else {
$("div#remap-row").css("display", "none");
}
- this.formRow().find( "i" ).each(function(index, iElement) {
+ this.formRow().find( "i" ).each(function(_, iElement) {
+ var $iElement = $(iElement);
+ var index = $iElement.data("index");
if(index == enableIndex) {
- $(iElement).css('color', 'black');
+ $iElement.css('color', 'black');
} else {
- $(iElement).css('color', 'Gray');
+ $iElement.css('color', 'Gray');
}
});
var $select = this.$( "select" );
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 templates/webapps/galaxy/user/manage_info.mako
--- a/templates/webapps/galaxy/user/manage_info.mako
+++ b/templates/webapps/galaxy/user/manage_info.mako
@@ -49,7 +49,7 @@
<div class="form-row"><div class="grid-header">
%for i, filter in enumerate( ['Active', 'Deleted', 'All'] ):
- %if i > 0:
+ %if i > 0:
<span>|</span>
%endif
%if show_filter == filter:
@@ -62,11 +62,11 @@
</div><table class="grid"><tbody>
- %for index, address in enumerate(addresses):
+ %for index, address in enumerate(addresses):
<tr class="libraryRow libraryOrFolderRow" id="libraryRow"><td>
- <div class="form-row">
- <label>${address.desc}:</label>
+ <div class="form-row">
+ <label>${address.desc | h}:</label>
${address.get_html()}
</div><div class="form-row">
@@ -82,7 +82,7 @@
</ul></div></td>
- </tr>
+ </tr>
%endfor
</tbody></table>
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -1,4 +1,5 @@
import os
+import re
from StringIO import StringIO
from galaxy.tools.parameters import grouping
from galaxy.tools import test
@@ -330,10 +331,11 @@
try:
test_user = [ user for user in all_users if user["email"] == email ][0]
except IndexError:
+ username = re.sub('[^a-z-]', '--', email.lower())
data = dict(
email=email,
password='testuser',
- username='admin-user',
+ username=username,
)
test_user = self._post( 'users', data, key=admin_key ).json()
return test_user
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 test/functional/tools/collection_two_paired.xml
--- /dev/null
+++ b/test/functional/tools/collection_two_paired.xml
@@ -0,0 +1,69 @@
+<tool id="collection_two_paired" name="collection_two_paired" version="0.1.0">
+ <command>
+ #if $kind.collection_type == "paired"
+ cat $kind.f1.forward $kind.f1['reverse'] >> $out1;
+ cat $kind.f2.forward $kind.f2['reverse'] >> $out1;
+ #else
+ #for $i, $_ in enumerate($kind.f1):
+ cat $kind.f1[$i] $kind.f2[$i] >> $out1;
+ #end for
+ #end if
+ </command>
+ <inputs>
+ <conditional name="kind">
+ <param type="select" name="collection_type">
+ <option value="paired">Paired Datasets</option>
+ <option value="list">List of Datasets</option>
+ </param>
+ <when value="paired">
+ <param name="f1" type="data_collection" collection_type="paired" />
+ <param name="f2" type="data_collection" collection_type="paired" />
+ </when>
+ <when value="list">
+ <param name="f1" type="data_collection" collection_type="list" />
+ <param name="f2" type="data_collection" collection_type="list" />
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <data format="txt" name="out1" />
+ </outputs>
+ <tests>
+ <test>
+ <conditional name="kind">
+ <param name="collection_type" value="paired" />
+ <param name="f1">
+ <collection type="paired">
+ <element name="forward" value="simple_line.txt" />
+ <element name="reverse" value="simple_line_alternative.txt" />
+ </collection>
+ </param>
+ <param name="f2">
+ <collection type="paired">
+ <element name="forward" value="simple_line.txt" />
+ <element name="reverse" value="simple_line_alternative.txt" />
+ </collection>
+ </param>
+ </conditional>
+ <output name="out1" file="simple_lines_interleaved.txt"/>
+ </test>
+ <test>
+ <conditional name="kind">
+ <param name="collection_type" value="list" />
+ <param name="f1">
+ <collection type="list">
+ <element name="l11" value="simple_line.txt" />
+ <element name="l12" value="simple_line.txt" />
+ </collection>
+ </param>
+ <param name="f2">
+ <collection type="list">
+ <element name="l21" value="simple_line_alternative.txt" />
+ <element name="l22" value="simple_line_alternative.txt" />
+ </collection>
+ </param>
+ </conditional>
+ <output name="out1" file="simple_lines_interleaved.txt"/>
+ </test>
+ </tests>
+</tool>
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 test/functional/tools/samples_tool_conf.xml
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -21,4 +21,5 @@
<tool file="collection_paired_test.xml" /><tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" />
+ <tool file="collection_two_paired.xml" /></toolbox>
\ No newline at end of file
diff -r b2613d9978a499db6e905ba8f4e452029b1aff61 -r 8b98752f4fbc11fb50f23b219f9037e7afa9a234 test/unit/tools/test_execution.py
--- a/test/unit/tools/test_execution.py
+++ b/test/unit/tools/test_execution.py
@@ -16,13 +16,12 @@
eggs.require( "Paste" )
from paste import httpexceptions
-# Tool with a repeat parameter, to test state update.
-REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
+BASE_REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"><command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command><inputs><param type="text" name="param1" value="" /><repeat name="repeat1" label="Repeat 1">
- <param type="text" name="param2" value="" />
+ %s
</repeat></inputs><outputs>
@@ -31,6 +30,10 @@
</tool>
'''
+# Tool with a repeat parameter, to test state update.
+REPEAT_TOOL_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="text" name="param2" value="" />'''
+REPEAT_COLLECTION_PARAM_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="data_collection" name="param2" collection_type="paired" />'''
+
class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.UsesTools ):
@@ -287,13 +290,48 @@
} )
self.__assert_exeuted( template, template_vars )
- def __history_dataset_collection_for( self, hdas, id=1234 ):
- collection = galaxy.model.DatasetCollection()
+ def test_subcollection_multirun_with_state_updates( self ):
+ self._init_tool( REPEAT_COLLECTION_PARAM_CONTENTS )
+ hda1, hda2 = self.__add_dataset( 1 ), self.__add_dataset( 2 )
+ collection = self.__history_dataset_collection_for( [ hda1, hda2 ], collection_type="list:paired" )
+ collection_id = self.app.security.encode_id( collection.id )
+ self.app.dataset_collections_service = Bunch(
+ match_collections=lambda collections: None
+ )
+ template, template_vars = self.__handle_with_incoming(
+ repeat1_add="dummy",
+ )
+ state = self.__assert_rerenders_tool_without_errors( template, template_vars )
+ assert len( state.inputs[ "repeat1" ] ) == 1
+ template, template_vars = self.__handle_with_incoming( state, **{
+ "repeat1_0|param2|__collection_multirun__": "%s|paired" % collection_id,
+ "repeat1_add": "dummy",
+ } )
+ state = self.__assert_rerenders_tool_without_errors( template, template_vars )
+ assert state.inputs[ "repeat1" ][ 0 ][ "param2|__collection_multirun__" ] == "%s|paired" % collection_id
+
+ def __history_dataset_collection_for( self, hdas, collection_type="list", id=1234 ):
+ collection = galaxy.model.DatasetCollection(
+ collection_type=collection_type,
+ )
to_element = lambda hda: galaxy.model.DatasetCollectionElement(
collection=collection,
element=hda,
)
- collection.datasets = map(to_element, hdas)
+ elements = map(to_element, hdas)
+ if collection_type == "list:paired":
+ paired_collection = galaxy.model.DatasetCollection(
+ collection_type="paired",
+ )
+ paired_collection.elements = elements
+ list_dce = galaxy.model.DatasetCollectionElement(
+ collection=collection,
+ element=paired_collection,
+ )
+ elements = [ list_dce ]
+
+ collection.elements = elements
+
history_dataset_collection_association = galaxy.model.HistoryDatasetCollectionAssociation(
id=id,
collection=collection,
@@ -349,13 +387,13 @@
self.history.datasets.append( hda )
return hda
- def __add_collection_dataset( self, id, *hdas ):
+ def __add_collection_dataset( self, id, collection_type="paired", *hdas ):
hdca = galaxy.model.HistoryDatasetCollectionAssociation()
hdca.id = id
collection = galaxy.model.DatasetCollection()
hdca.collection = collection
collection.elements = [ galaxy.model.DatasetCollectionElement(element=self.__add_dataset( 1 )) ]
-
+ collection.type = collection_type
self.trans.sa_session.model_objects[ galaxy.model.HistoryDatasetCollectionAssociation ][ id ] = hdca
self.history.dataset_collections.append( hdca )
return hdca
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Fix API test interactor to use unique usernames.
by commits-noreply＠bitbucket.org 25 Jul '14
by commits-noreply＠bitbucket.org 25 Jul '14
25 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/15ca9a679522/
Changeset: 15ca9a679522
User: jmchilton
Date: 2014-07-25 15:42:36
Summary: Fix API test interactor to use unique usernames.
Should fixes API tests broken when validation of these changed recently.
Affected #: 1 file
diff -r 646c414e90515d78d99461e090815f1a01f18c72 -r 15ca9a6795225c9777b5f12f858e9a87754d8301 test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -1,4 +1,5 @@
import os
+import re
from StringIO import StringIO
from galaxy.tools.parameters import grouping
from galaxy.tools import test
@@ -330,10 +331,11 @@
try:
test_user = [ user for user in all_users if user["email"] == email ][0]
except IndexError:
+ username = re.sub('[^a-z-]', '--', email.lower())
data = dict(
email=email,
password='testuser',
- username='admin-user',
+ username=username,
)
test_user = self._post( 'users', data, key=admin_key ).json()
return test_user
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Remove invalid attribute name from DatasetCollection's to_dict.
by commits-noreply＠bitbucket.org 24 Jul '14
by commits-noreply＠bitbucket.org 24 Jul '14
24 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/646c414e9051/
Changeset: 646c414e9051
User: jmchilton
Date: 2014-07-25 03:01:14
Summary: Remove invalid attribute name from DatasetCollection's to_dict.
This wasn't breaking anything per se, but was always adding a null 'name' attribute to collections dictified representation.
This is a remnant from an earlier version of this code that had the name attribute on the DatasetCollection instead of DatasetCollectionInstance.
Affected #: 1 file
diff -r 56a7b27577dec0dac17ef94d4c131e7f1f61cb15 -r 646c414e90515d78d99461e090815f1a01f18c72 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2590,8 +2590,8 @@
class DatasetCollection( object, Dictifiable, UsesAnnotations ):
"""
"""
- dict_collection_visible_keys = ( 'id', 'name', 'collection_type' )
- dict_element_visible_keys = ( 'id', 'name', 'collection_type' )
+ dict_collection_visible_keys = ( 'id', 'collection_type' )
+ dict_element_visible_keys = ( 'id', 'collection_type' )
def __init__(
self,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Merged in iracooke/galaxy-central (pull request #434)
by commits-noreply＠bitbucket.org 24 Jul '14
by commits-noreply＠bitbucket.org 24 Jul '14
24 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/56a7b27577de/
Changeset: 56a7b27577de
User: dannon
Date: 2014-07-25 00:29:57
Summary: Merged in iracooke/galaxy-central (pull request #434)
Add sqlite datatype and corresponding dataprovider
Affected #: 3 files
diff -r f03f9c5a5efc7fecb4ca131f66c441d55cc5d353 -r 56a7b27577dec0dac17ef94d4c131e7f1f61cb15 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -177,6 +177,7 @@
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
+ <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
@@ -262,6 +263,7 @@
--><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/>
+ <sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/>
diff -r f03f9c5a5efc7fecb4ca131f66c441d55cc5d353 -r 56a7b27577dec0dac17ef94d4c131e7f1f61cb15 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -12,6 +12,7 @@
import subprocess
import tempfile
import zipfile
+import sqlite3
from urllib import urlencode, quote_plus
from galaxy import eggs
@@ -545,3 +546,45 @@
return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size()))
Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit)
+
+
+(a)dataproviders.decorators.has_dataproviders
+class SQlite ( Binary ):
+ file_ext = "sqlite"
+
+ # Connects and runs a query that should work on any real database
+ # If the file is not sqlite, an exception will be thrown and the sniffer will return false
+ def sniff( self, filename ):
+ try:
+ conn = sqlite3.connect(filename)
+ schema_version=conn.cursor().execute("pragma schema_version").fetchone()
+ conn.close()
+ if schema_version is not None:
+ return True
+ return False
+ except:
+ return False
+
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ dataset.peek = "SQLite Database"
+ dataset.blurb = data.nice_size( dataset.get_size() )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def display_peek( self, dataset ):
+ try:
+ return dataset.peek
+ except:
+ return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+
+ @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
+ def sqlite_dataprovider( self, dataset, **settings ):
+ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
+ return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings )
+
+
+Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite)
+
diff -r f03f9c5a5efc7fecb4ca131f66c441d55cc5d353 -r 56a7b27577dec0dac17ef94d4c131e7f1f61cb15 lib/galaxy/datatypes/dataproviders/dataset.py
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -11,6 +11,8 @@
import line
import column
import external
+import sqlite3
+import re
from galaxy import eggs
eggs.require( 'bx-python' )
@@ -700,3 +702,39 @@
#TODO: as samtools - need more info on output format
raise NotImplementedError()
super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs )
+
+
+
+class SQliteDataProvider ( base.DataProvider ):
+ """
+ Data provider that uses a sqlite database file as its source.
+
+ Allows any query to be run and returns the resulting rows as sqlite3 row objects
+ """
+ settings = {
+ 'query' : 'str'
+ }
+
+ def __init__( self, source, query=None, **kwargs ):
+ self.query=query
+ self.connection = sqlite3.connect(source.dataset.file_name);
+ self.connection.row_factory = sqlite3.Row
+ super( SQliteDataProvider, self ).__init__( source, **kwargs )
+
+ def query_matches_whitelist(self,query):
+ if re.match("select ",query,re.IGNORECASE):
+ if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query):
+ return False
+ else:
+ return True
+ return False
+
+
+
+ def __iter__( self ):
+ if (self.query is not None) and self.query_matches_whitelist(self.query):
+ for row in self.connection.cursor().execute(self.query):
+ yield row
+ else:
+ yield
+
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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4 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/47c6c6bb8eec/
Changeset: 47c6c6bb8eec
User: iracooke
Date: 2014-07-07 03:16:09
Summary: Add sqlite datatype and corresponding dataprovider
Affected #: 3 files
diff -r 6d50cd22380253129121e3e7359a6286ee9b1663 -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -177,6 +177,7 @@
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
+ <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
@@ -262,6 +263,7 @@
--><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/>
+ <sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/>
diff -r 6d50cd22380253129121e3e7359a6286ee9b1663 -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -12,6 +12,7 @@
import subprocess
import tempfile
import zipfile
+import sqlite3
from urllib import urlencode, quote_plus
from galaxy import eggs
@@ -545,3 +546,45 @@
return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size()))
Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit)
+
+
+(a)dataproviders.decorators.has_dataproviders
+class SQlite ( Binary ):
+ file_ext = "sqlite"
+
+ # Connects and runs a query that should work on any real database
+ # If the file is not sqlite, an exception will be thrown and the sniffer will return false
+ def sniff( self, filename ):
+ try:
+ conn = sqlite3.connect(filename)
+ schema_version=conn.cursor().execute("pragma schema_version").fetchone()
+ conn.close()
+ if schema_version is not None:
+ return True
+ return False
+ except:
+ return False
+
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ dataset.peek = "SQLite Database"
+ dataset.blurb = data.nice_size( dataset.get_size() )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def display_peek( self, dataset ):
+ try:
+ return dataset.peek
+ except:
+ return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+
+ @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
+ def sqlite_dataprovider( self, dataset, **settings ):
+ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
+ return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings )
+
+
+Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite)
+
diff -r 6d50cd22380253129121e3e7359a6286ee9b1663 -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 lib/galaxy/datatypes/dataproviders/dataset.py
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -11,6 +11,7 @@
import line
import column
import external
+import sqlite3
from galaxy import eggs
eggs.require( 'bx-python' )
@@ -700,3 +701,29 @@
#TODO: as samtools - need more info on output format
raise NotImplementedError()
super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs )
+
+
+
+class SQliteDataProvider ( base.DataProvider ):
+ """
+ Data provider that uses a sqlite database file as its source.
+
+ Allows any query to be run and returns the resulting rows as sqlite3 row objects
+ """
+ settings = {
+ 'query' : 'str'
+ }
+
+ def __init__( self, source, query=None, **kwargs ):
+ self.query=query
+ self.connection = sqlite3.connect(source.dataset.file_name);
+ self.connection.row_factory = sqlite3.Row
+ super( SQliteDataProvider, self ).__init__( source, **kwargs )
+
+ def __iter__( self ):
+ if self.query is not None:
+ for row in self.connection.cursor().execute(self.query):
+ yield row
+ else:
+ yield
+
https://bitbucket.org/galaxy/galaxy-central/commits/034c0159c0cf/
Changeset: 034c0159c0cf
User: iracooke
Date: 2014-07-24 06:30:17
Summary: Merged galaxy/galaxy-central into default
Affected #: 278 files
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -11,6 +11,9 @@
scripts/scramble/lib
scripts/scramble/archives
+# Python virtualenv
+.venv
+
# Database stuff
database/beaker_sessions
database/community_files
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -12,7 +12,6 @@
from galaxy.visualization.data_providers.registry import DataProviderRegistry
from galaxy.visualization.registry import VisualizationsRegistry
from galaxy.tools.imp_exp import load_history_imp_exp_tools
-from galaxy.tools.genome_index import load_genome_index_tools
from galaxy.sample_tracking import external_service_types
from galaxy.openid.providers import OpenIDProviders
from galaxy.tools.data_manager.manager import DataManagers
@@ -93,8 +92,6 @@
self.datatypes_registry.load_external_metadata_tool( self.toolbox )
# Load history import/export tools.
load_history_imp_exp_tools( self.toolbox )
- # Load genome indexer tool.
- load_genome_index_tools( self.toolbox )
# visualizations registry: associates resources with visualizations, controls how to render
self.visualizations_registry = None
if self.config.visualization_plugins_directory:
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -15,13 +15,12 @@
from galaxy.web.formatting import expand_pretty_datetime_format
from galaxy.util import string_as_bool
from galaxy.util import listify
-from galaxy.util import parse_xml
from galaxy.util.dbkeys import GenomeBuilds
from galaxy import eggs
-import pkg_resources
log = logging.getLogger( __name__ )
+
def resolve_path( path, root ):
"""If 'path' is relative make absolute by prepending 'root'"""
if not( os.path.isabs( path ) ):
@@ -40,9 +39,9 @@
self.config_dict = kwargs
self.root = kwargs.get( 'root_dir', '.' )
# Collect the umask and primary gid from the environment
- self.umask = os.umask( 077 ) # get the current umask
- os.umask( self.umask ) # can't get w/o set, so set it back
- self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
+ self.umask = os.umask( 077 ) # get the current umask
+ os.umask( self.umask ) # can't get w/o set, so set it back
+ self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
# Database related configuration
self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root )
@@ -75,7 +74,7 @@
self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) )
self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
- self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root )
+ self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'chrom') ), self.root )
self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
# The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution
# and moved to the tool shed.
@@ -169,7 +168,7 @@
self.admin_users = kwargs.get( "admin_users", "" )
self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u]
self.reset_password_length = int( kwargs.get('reset_password_length', '15') )
- self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu")
+ self.mailing_join_addr = kwargs.get('mailing_join_addr', 'galaxy-announce-join(a)bx.psu.edu')
self.error_email_to = kwargs.get( 'error_email_to', None )
self.activation_email = kwargs.get( 'activation_email', None )
self.user_activation_on = string_as_bool( kwargs.get( 'user_activation_on', False ) )
@@ -271,9 +270,9 @@
self.object_store_cache_path = resolve_path( kwargs.get( "object_store_cache_path", "database/object_store_cache" ), self.root )
# Handle AWS-specific config options for backward compatibility
if kwargs.get( 'aws_access_key', None) is not None:
- self.os_access_key= kwargs.get( 'aws_access_key', None )
- self.os_secret_key= kwargs.get( 'aws_secret_key', None )
- self.os_bucket_name= kwargs.get( 's3_bucket', None )
+ self.os_access_key = kwargs.get( 'aws_access_key', None )
+ self.os_secret_key = kwargs.get( 'aws_secret_key', None )
+ self.os_bucket_name = kwargs.get( 's3_bucket', None )
self.os_use_reduced_redundancy = kwargs.get( 'use_reduced_redundancy', False )
else:
self.os_access_key = kwargs.get( 'os_access_key', None )
@@ -376,6 +375,8 @@
self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) )
# visualization plugin framework
self.visualization_plugins_directory = kwargs.get( 'visualization_plugins_directory', None )
+ # Default chunk size for chunkable datatypes -- 64k
+ self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
@property
def sentry_dsn_public( self ):
@@ -452,19 +453,13 @@
except Exception, e:
raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) )
# Create the directories that it makes sense to create
- for path in self.file_path, \
- self.new_file_path, \
- self.job_working_directory, \
- self.cluster_files_directory, \
- self.template_cache, \
- self.ftp_upload_dir, \
- self.library_import_dir, \
- self.user_library_import_dir, \
- self.nginx_upload_store, \
- './static/genetrack/plots', \
- self.whoosh_index_dir, \
- self.object_store_cache_path, \
- os.path.join( self.tool_data_path, 'shared', 'jars' ):
+ for path in (self.file_path, self.new_file_path,
+ self.job_working_directory, self.cluster_files_directory,
+ self.template_cache, self.ftp_upload_dir,
+ self.library_import_dir, self.user_library_import_dir,
+ self.nginx_upload_store, './static/genetrack/plots',
+ self.whoosh_index_dir, self.object_store_cache_path,
+ os.path.join( self.tool_data_path, 'shared', 'jars' )):
self._ensure_directory( path )
# Check that required files exist
tool_configs = self.tool_configs
@@ -480,7 +475,7 @@
if key in self.deprecated_options:
log.warning( "Config option '%s' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file." % key )
- def is_admin_user( self,user ):
+ def is_admin_user( self, user ):
"""
Determine if the provided user is listed in `admin_users`.
@@ -495,12 +490,13 @@
"""
return resolve_path( path, self.root )
+
def get_database_engine_options( kwargs, model_prefix='' ):
"""
Allow options for the SQLAlchemy database engine to be passed by using
the prefix "database_engine_option".
"""
- conversions = {
+ conversions = {
'convert_unicode': string_as_bool,
'pool_timeout': int,
'echo': string_as_bool,
@@ -522,6 +518,7 @@
rval[ key ] = value
return rval
+
def configure_logging( config ):
"""
Allow some basic logging configuration to be read from ini file.
@@ -556,7 +553,7 @@
root.addHandler( handler )
# If sentry is configured, also log to it
if config.sentry_dsn:
- pkg_resources.require( "raven" )
+ eggs.require( "raven" )
from raven.handlers.logging import SentryHandler
sentry_handler = SentryHandler( config.sentry_dsn )
sentry_handler.setLevel( logging.WARN )
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -126,10 +126,21 @@
rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy )
return rval
- def from_JSON_dict( self, filename, path_rewriter=None ):
+ def from_JSON_dict( self, filename=None, path_rewriter=None, json_dict=None ):
dataset = self.parent
- log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
- JSONified_dict = json.load( open( filename ) )
+ if filename is not None:
+ log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ JSONified_dict = json.load( open( filename ) )
+ elif json_dict is not None:
+ log.debug( 'loading metadata from dict for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ if isinstance( json_dict, basestring ):
+ JSONified_dict = json.loads( json_dict )
+ elif isinstance( json_dict, dict ):
+ JSONified_dict = json_dict
+ else:
+ raise ValueError( "json_dict must be either a dictionary or a string, got %s." % ( type( json_dict ) ) )
+ else:
+ raise ValueError( "You must provide either a filename or a json_dict" )
for name, spec in self.spec.items():
if name in JSONified_dict:
from_ext_kwds = {}
@@ -143,13 +154,15 @@
#metadata associated with our dataset, we'll delete it from our dataset's metadata dict
del dataset._metadata[ name ]
- def to_JSON_dict( self, filename ):
+ def to_JSON_dict( self, filename=None ):
#galaxy.model.customtypes.json_encoder.encode()
meta_dict = {}
dataset_meta_dict = self.parent._metadata
for name, spec in self.spec.items():
if name in dataset_meta_dict:
meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] )
+ if filename is None:
+ return json.dumps( meta_dict )
json.dump( meta_dict, open( filename, 'wb+' ) )
def __getstate__( self ):
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -25,7 +25,6 @@
# All tabular data is chunkable.
CHUNKABLE = True
- CHUNK_SIZE = 10000
"""Add metadata elements"""
MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 )
@@ -262,13 +261,13 @@
def get_chunk(self, trans, dataset, chunk):
ck_index = int(chunk)
f = open(dataset.file_name)
- f.seek(ck_index * self.CHUNK_SIZE)
+ f.seek(ck_index * trans.app.config.display_chunk_size)
# If we aren't at the start of the file, seek to next newline. Do this better eventually.
if f.tell() != 0:
cursor = f.read(1)
while cursor and cursor != '\n':
cursor = f.read(1)
- ck_data = f.read(self.CHUNK_SIZE)
+ ck_data = f.read(trans.app.config.display_chunk_size)
cursor = f.read(1)
while cursor and ck_data[-1] != '\n':
ck_data += cursor
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/exceptions/__init__.py
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -86,6 +86,11 @@
err_code = error_codes.USER_REQUEST_INVALID_PARAMETER
+class AuthenticationFailed( MessageException ):
+ status_code = 401
+ err_code = error_codes.USER_AUTHENTICATION_FAILED
+
+
class AuthenticationRequired( MessageException ):
status_code = 403
#TODO: as 401 and send WWW-Authenticate: ???
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/exceptions/error_codes.json
--- a/lib/galaxy/exceptions/error_codes.json
+++ b/lib/galaxy/exceptions/error_codes.json
@@ -60,6 +60,11 @@
"message": "Supplied incorrect or incompatible tool meta parameters."
},
{
+ "name": "USER_AUTHENTICATION_FAILED",
+ "code": 401001,
+ "message": "Authentication failed, invalid credentials supplied."
+ },
+ {
"name": "USER_NO_API_KEY",
"code": 403001,
"message": "API authentication required for this request"
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1192,9 +1192,6 @@
param_dict = self.tool.params_from_strings( param_dict, self.app )
# Check for and move associated_files
self.tool.collect_associated_files(out_data, self.working_directory)
- gitd = self.sa_session.query( model.GenomeIndexToolData ).filter_by( job=job ).first()
- if gitd:
- self.tool.collect_associated_files({'': gitd}, self.working_directory)
# Create generated output children and primary datasets and add to param_dict
collected_datasets = {
'children': self.tool.collect_child_datasets(out_data, self.working_directory),
@@ -1248,7 +1245,6 @@
self.external_output_metadata.cleanup_external_metadata( self.sa_session )
galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session )
galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.app, self.job_id ).cleanup_after_job()
- galaxy.tools.genome_index.GenomeIndexToolWrapper( self.job_id ).postprocessing( self.sa_session, self.app )
if delete_files:
self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id))
except:
@@ -1351,10 +1347,8 @@
dataset_path_rewriter = self.dataset_path_rewriter
job = self.get_job()
- # Job output datasets are combination of history, library, jeha and gitd datasets.
+ # Job output datasets are combination of history, library, and jeha datasets.
special = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first()
- if not special:
- special = self.sa_session.query( model.GenomeIndexToolData ).filter_by( job=job ).first()
false_path = None
results = []
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/jobs/actions/post.py
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -215,8 +215,17 @@
p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\
<input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>";
}
+ inputlist = [];
+ $.each(node.input_terminals, function(i, v){
+ inputlist.push(v.name);
+ });
+ if (inputlist !== []){
+ p_str += "Available inputs are: <strong>" + inputlist.join(', ') + "</strong>";
+ }else{
+ p_str += "No inputs are available for templating into this action.";
+ }
"""
- return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.")
+ return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset. See <a href='https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables'>the wiki</a> for usage information.")
@classmethod
def get_short_str(cls, pja):
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/jobs/deferred/genome_index.py
--- a/lib/galaxy/jobs/deferred/genome_index.py
+++ /dev/null
@@ -1,43 +0,0 @@
-"""
-Module for managing genome transfer jobs.
-"""
-from __future__ import with_statement
-
-import logging, shutil, gzip, bz2, zipfile, tempfile, tarfile, sys, os
-
-from galaxy import eggs
-from sqlalchemy import and_
-from data_transfer import *
-
-log = logging.getLogger( __name__ )
-
-__all__ = [ 'GenomeIndexPlugin' ]
-
-class GenomeIndexPlugin( DataTransfer ):
-
- def __init__( self, app ):
- super( GenomeIndexPlugin, self ).__init__( app )
- self.app = app
- self.tool = app.toolbox.tools_by_id['__GENOME_INDEX__']
- self.sa_session = app.model.context.current
-
- def create_job( self, trans, path, indexes, dbkey, intname ):
- params = dict( user=trans.user.id, path=path, indexes=indexes, dbkey=dbkey, intname=intname )
- deferred = trans.app.model.DeferredJob( state = self.app.model.DeferredJob.states.NEW, plugin = 'GenomeIndexPlugin', params = params )
- self.sa_session.add( deferred )
- self.sa_session.flush()
- log.debug( 'Job created, id %d' % deferred.id )
- return deferred.id
-
- def check_job( self, job ):
- log.debug( 'Job check' )
- return 'ready'
-
- def run_job( self, job ):
- incoming = dict( path=os.path.abspath( job.params[ 'path' ] ), indexer=job.params[ 'indexes' ][0], user=job.params[ 'user' ] )
- indexjob = self.tool.execute( self, set_output_hid=False, history=None, incoming=incoming, transfer=None, deferred=job )
- job.params[ 'indexjob' ] = indexjob[0].id
- job.state = self.app.model.DeferredJob.states.RUNNING
- self.sa_session.add( job )
- self.sa_session.flush()
- return self.app.model.DeferredJob.states.RUNNING
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/jobs/deferred/genome_transfer.py
--- a/lib/galaxy/jobs/deferred/genome_transfer.py
+++ /dev/null
@@ -1,250 +0,0 @@
-"""
-Module for managing genome transfer jobs.
-"""
-from __future__ import with_statement
-
-import logging, shutil, gzip, bz2, zipfile, tempfile, tarfile, sys
-
-from galaxy import eggs
-from sqlalchemy import and_
-
-from galaxy.util.odict import odict
-from galaxy.workflow.modules import module_factory
-from galaxy.jobs.actions.post import ActionBox
-
-from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter
-from galaxy.tools.data import ToolDataTableManager
-
-from galaxy.datatypes.checkers import *
-from galaxy.datatypes.sequence import Fasta
-from data_transfer import *
-
-log = logging.getLogger( __name__ )
-
-__all__ = [ 'GenomeTransferPlugin' ]
-
-class GenomeTransferPlugin( DataTransfer ):
-
- locations = {}
-
- def __init__( self, app ):
- super( GenomeTransferPlugin, self ).__init__( app )
- self.app = app
- self.tool = app.toolbox.tools_by_id['__GENOME_INDEX__']
- self.sa_session = app.model.context.current
- tdtman = ToolDataTableManager( app.config.tool_data_path )
- xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path )
- for node in xmltree:
- table = node.get('name')
- location = node.findall('file')[0].get('path')
- self.locations[table] = location
-
- def create_job( self, trans, url, dbkey, intname, indexes ):
- job = trans.app.transfer_manager.new( protocol='http', url=url )
- params = dict( user=trans.user.id, transfer_job_id=job.id, protocol='http', type='init_transfer', url=url, dbkey=dbkey, indexes=indexes, intname=intname, liftover=None )
- deferred = trans.app.model.DeferredJob( state = self.app.model.DeferredJob.states.NEW, plugin = 'GenomeTransferPlugin', params = params )
- self.sa_session.add( deferred )
- self.sa_session.flush()
- return deferred.id
-
- def check_job( self, job ):
- if job.params['type'] == 'init_transfer':
- if not hasattr(job, 'transfer_job'):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- if job.transfer_job.state == 'done':
- transfer = job.transfer_job
- transfer.state = 'downloaded'
- job.params['type'] = 'extract_transfer'
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- self.sa_session.flush()
- return self.job_states.READY
- elif job.transfer_job.state == 'running':
- return self.job_states.WAIT
- elif job.transfer_job.state == 'new':
- assert job.params[ 'protocol' ] in [ 'http', 'ftp', 'https' ], 'Unknown protocol %s' % job.params[ 'protocol' ]
- self.app.transfer_manager.run( job.transfer_job )
- self.sa_session.add( job.transfer_job )
- self.sa_session.flush()
- return self.job_states.WAIT
- else:
- log.error( "An error occurred while downloading from %s" % job.params[ 'url' ] )
- return self.job_states.INVALID
- elif job.params[ 'type' ] == 'extract_transfer':
- return self.job_states.READY
-
- def get_job_status( self, jobid ):
- job = self.sa_session.query( self.app.model.DeferredJob ).get( int( jobid ) )
- if 'transfer_job_id' in job.params:
- if not hasattr( job, 'transfer_job' ):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- return job
-
- def run_job( self, job ):
- params = job.params
- dbkey = params[ 'dbkey' ]
- if not hasattr( job, 'transfer_job' ):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- transfer = job.transfer_job
- if params[ 'type' ] == 'extract_transfer':
- CHUNK_SIZE = 2**20
- destpath = os.path.join( self.app.config.get( 'genome_data_path', 'tool-data/genome' ), job.params[ 'dbkey' ], 'seq' )
- destfile = '%s.fa' % job.params[ 'dbkey' ]
- destfilepath = os.path.join( destpath, destfile )
- tmpprefix = '%s_%s_download_unzip_' % ( job.params['dbkey'], job.params[ 'transfer_job_id' ] )
- tmppath = os.path.dirname( os.path.abspath( transfer.path ) )
- if not os.path.exists( destpath ):
- os.makedirs( destpath )
- protocol = job.params[ 'protocol' ]
- data_type = self._check_compress( transfer.path )
- if data_type is None:
- sniffer = Fasta()
- if sniffer.sniff( transfer.path ):
- data_type = 'fasta'
- fd, uncompressed = tempfile.mkstemp( prefix=tmpprefix, dir=tmppath, text=False )
- if data_type in [ 'tar.gzip', 'tar.bzip' ]:
- fp = open( transfer.path, 'r' )
- tar = tarfile.open( mode = 'r:*', bufsize = CHUNK_SIZE, fileobj = fp )
- files = tar.getmembers()
- for filename in files:
- z = tar.extractfile(filename)
- while 1:
- try:
- chunk = z.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.write( fd, '\n' )
- os.close( fd )
- tar.close()
- fp.close()
- elif data_type == 'gzip':
- compressed = gzip.open( transfer.path, mode = 'rb' )
- while 1:
- try:
- chunk = compressed.read( CHUNK_SIZE )
- except IOError:
- compressed.close()
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- compressed.close()
- elif data_type == 'bzip':
- compressed = bz2.BZ2File( transfer.path, mode = 'r' )
- while 1:
- try:
- chunk = compressed.read( CHUNK_SIZE )
- except IOError:
- compressed.close()
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- compressed.close()
- elif data_type == 'zip':
- uncompressed_name = None
- unzipped = False
- z = zipfile.ZipFile( transfer.path )
- z.debug = 3
- for name in z.namelist():
- if name.endswith('/'):
- continue
- zipped_file = z.open( name )
- while 1:
- try:
- chunk = zipped_file.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- log.error( 'Problem decompressing zipped data' )
- return self.app.model.DeferredJob.states.INVALID
- if not chunk:
- break
- os.write( fd, chunk )
- zipped_file.close()
- os.close( fd )
- z.close()
- elif data_type == 'fasta':
- uncompressed = transfer.path
- else:
- job.state = self.app.model.DeferredJob.states.INVALID
- log.error( "Unrecognized compression format for file %s." % transfer.path )
- self.sa_session.add( job )
- self.sa_session.flush()
- return
- shutil.move( uncompressed, destfilepath )
- if os.path.exists( transfer.path ):
- os.remove( transfer.path )
- os.chmod( destfilepath, 0644 )
- fastaline = '\t'.join( [ dbkey, dbkey, params[ 'intname' ], os.path.abspath( destfilepath ) ] )
- self._add_line( 'all_fasta', fastaline )
- if params[ 'indexes' ] is not None:
- job.state = self.app.model.DeferredJob.states.WAITING
- job.params[ 'indexjobs' ] = []
- else:
- job.state = self.app.model.DeferredJob.states.OK
- job.params[ 'type' ] = 'finish_transfer'
- transfer.path = os.path.abspath(destfilepath)
- transfer.state = 'done'
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- if transfer.state == 'done':
- if params[ 'indexes' ] is not None:
- for indexer in params[ 'indexes' ]:
- incoming = dict(indexer=indexer, dbkey=params[ 'dbkey' ], intname=params[ 'intname' ], path=transfer.path, user=params['user'] )
- deferred = self.tool.execute( self, set_output_hid=False, history=None, incoming=incoming, transfer=transfer, deferred=job )
- job.params[ 'indexjobs' ].append( deferred[0].id )
- else:
- job.state = self.app.model.DeferredJob.states.OK
- self.sa_session.add( job )
- self.sa_session.flush()
- return self.app.model.DeferredJob.states.OK
-
- def _check_compress( self, filepath ):
- retval = ''
- if tarfile.is_tarfile( filepath ):
- retval = 'tar.'
- if check_zip( filepath ):
- return 'zip'
- is_bzipped, is_valid = check_bz2( filepath )
- if is_bzipped and is_valid:
- return retval + 'bzip'
- is_gzipped, is_valid = check_gzip( filepath )
- if is_gzipped and is_valid:
- return retval + 'gzip'
- return None
-
- def _add_line( self, locfile, newline ):
- filepath = self.locations[ locfile ]
- origlines = []
- output = []
- comments = []
- with open( filepath, 'r' ) as destfile:
- for line in destfile:
- if line.startswith( '#' ):
- comments.append( line.strip() )
- else:
- origlines.append( line.strip() )
- if newline not in origlines:
- origlines.append( newline )
- output.extend( comments )
- origlines.sort()
- output.extend( origlines )
- with open( filepath, 'w+' ) as destfile:
- destfile.write( '\n'.join( output ) )
-
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/jobs/deferred/liftover_transfer.py
--- a/lib/galaxy/jobs/deferred/liftover_transfer.py
+++ /dev/null
@@ -1,158 +0,0 @@
-"""
-Module for managing genome transfer jobs.
-"""
-from __future__ import with_statement
-
-import logging, shutil, gzip, tempfile, sys
-
-from galaxy import eggs
-from sqlalchemy import and_
-
-from galaxy.util.odict import odict
-from galaxy.workflow.modules import module_factory
-from galaxy.jobs.actions.post import ActionBox
-
-from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter
-
-from galaxy.datatypes.checkers import *
-
-from data_transfer import *
-
-log = logging.getLogger( __name__ )
-
-__all__ = [ 'LiftOverTransferPlugin' ]
-
-class LiftOverTransferPlugin( DataTransfer ):
-
- locations = {}
-
- def __init__( self, app ):
- super( LiftOverTransferPlugin, self ).__init__( app )
- self.app = app
- self.sa_session = app.model.context.current
-
- def create_job( self, trans, url, dbkey, from_genome, to_genome, destfile, parentjob ):
- job = trans.app.transfer_manager.new( protocol='http', url=url )
- params = dict( user=trans.user.id, transfer_job_id=job.id, protocol='http',
- type='init_transfer', dbkey=dbkey, from_genome=from_genome,
- to_genome=to_genome, destfile=destfile, parentjob=parentjob )
- deferred = trans.app.model.DeferredJob( state = self.app.model.DeferredJob.states.NEW, plugin = 'LiftOverTransferPlugin', params = params )
- self.sa_session.add( deferred )
- self.sa_session.flush()
- return deferred.id
-
- def check_job( self, job ):
- if job.params['type'] == 'init_transfer':
- if not hasattr(job, 'transfer_job'):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- if job.transfer_job.state == 'done':
- transfer = job.transfer_job
- transfer.state = 'downloaded'
- job.params['type'] = 'extract_transfer'
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- self.sa_session.flush()
- return self.job_states.READY
- elif job.transfer_job.state == 'running':
- return self.job_states.WAIT
- elif job.transfer_job.state == 'new':
- assert job.params[ 'protocol' ] in [ 'http', 'ftp', 'https' ], 'Unknown protocol %s' % job.params[ 'protocol' ]
- ready = True
- parent = self.sa_session.query( self.app.model.DeferredJob ).get( int( job.params[ 'parentjob' ] ) )
- if not hasattr( parent, 'transfer_job' ):
- parent.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( parent.params[ 'transfer_job_id' ] ) )
- if parent.transfer_job.state not in [ 'ok', 'error', 'done' ]:
- ready = False
- for lo_job in parent.params[ 'liftover' ]:
- liftoverjob = self.sa_session.query( self.app.model.TransferJob ).get( int( lo_job ) )
- if liftoverjob:
- if liftoverjob.state not in [ 'ok', 'error', 'new', 'done' ]:
- ready = False
- if ready:
- self.app.transfer_manager.run( job.transfer_job )
- self.sa_session.add( job.transfer_job )
- self.sa_session.flush()
- return self.job_states.WAIT
- else:
- log.error( "An error occurred while downloading from %s" % job.transfer_job.params[ 'url' ] )
- return self.job_states.INVALID
- elif job.params[ 'type' ] == 'extract_transfer':
- return self.job_states.READY
-
- def get_job_status( self, jobid ):
- job = self.sa_session.query( self.app.model.DeferredJob ).get( int( jobid ) )
- return job
-
- def run_job( self, job ):
- params = job.params
- dbkey = params[ 'dbkey' ]
- source = params[ 'from_genome' ]
- target = params[ 'to_genome' ]
- if not hasattr( job, 'transfer_job' ):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- transfer = job.transfer_job
- if params[ 'type' ] == 'extract_transfer':
- CHUNK_SIZE = 2**20
- destpath = os.path.join( self.app.config.get( 'genome_data_path', 'tool-data/genome' ), source, 'liftOver' )
- if not os.path.exists( destpath ):
- os.makedirs( destpath )
- destfile = job.params[ 'destfile' ]
- destfilepath = os.path.join( destpath, destfile )
- tmpprefix = '%s_%s_download_unzip_' % ( job.params['dbkey'], job.params[ 'transfer_job_id' ] )
- tmppath = os.path.dirname( os.path.abspath( transfer.path ) )
- if not os.path.exists( destpath ):
- os.makedirs( destpath )
- fd, uncompressed = tempfile.mkstemp( prefix=tmpprefix, dir=tmppath, text=False )
- chain = gzip.open( transfer.path, 'rb' )
- while 1:
- try:
- chunk = chain.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- chain.close()
- # Replace the gzipped file with the decompressed file if it's safe to do so
- shutil.move( uncompressed, destfilepath )
- os.remove( transfer.path )
- os.chmod( destfilepath, 0644 )
- locline = '\t'.join( [ source, target, os.path.abspath( destfilepath ) ] )
- self._add_line( locline )
- job.state = self.app.model.DeferredJob.states.OK
- job.params[ 'type' ] = 'finish_transfer'
- transfer.path = os.path.abspath(destfilepath)
- transfer.state = 'done'
- parentjob = self.sa_session.query( self.app.model.DeferredJob ).get( int( job.params[ 'parentjob' ] ) )
- finished = True
- for i in parentjob.params[ 'liftover' ]:
- sibling = self.sa_session.query( self.app.model.DeferredJob ).get( int( i ) )
- if sibling.state not in [ 'done', 'ok', 'error' ]:
- finished = False
- if finished:
- parentjob.state = self.app.model.DeferredJob.states.OK
- self.sa_session.add( parentjob )
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- self.sa_session.flush()
- return self.app.model.DeferredJob.states.OK
-
- def _add_line( self, newline ):
- filepath = 'tool-data/liftOver.loc'
- origlines = []
- with open( filepath, 'r' ) as destfile:
- for line in destfile:
- origlines.append( line.strip() )
- if newline not in origlines:
- origlines.append( newline )
- with open( filepath, 'w+' ) as destfile:
- destfile.write( '\n'.join( origlines ) )
-
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/jobs/mapper.py
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -83,7 +83,7 @@
if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names or "resource_params" in function_arg_names:
job = self.job_wrapper.get_job()
history = job.history
- user = history and history.user
+ user = job.user
user_email = user and str(user.email)
if "job" in function_arg_names:
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/jobs/metrics/formatting.py
--- a/lib/galaxy/jobs/metrics/formatting.py
+++ b/lib/galaxy/jobs/metrics/formatting.py
@@ -15,4 +15,4 @@
elif value < 3600:
return "%s minutes" % ( value / 60 )
else:
- return "%s days and %s minutes" % ( value / 3600, ( value % 3600 ) / 60 )
+ return "%s hours and %s minutes" % ( value / 3600, ( value % 3600 ) / 60 )
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/managers/__init__.py
--- a/lib/galaxy/managers/__init__.py
+++ b/lib/galaxy/managers/__init__.py
@@ -1,4 +1,33 @@
-""" 'Business logic' independent of web transactions/user context (trans)
-should be pushed into models - but logic that requires the context trans
-should be placed under this module.
"""
+Classes that manage resources (models, tools, etc.) by using the current
+Transaction.
+
+Encapsulates the intersection of trans (or trans.sa_session), models,
+and Controllers.
+
+Responsibilities:
+ model operations that involve the trans/sa_session (CRUD)
+ security:
+ ownership, accessibility
+ common aspect-oriented operations via new mixins:
+ sharable, annotatable, tagable, ratable
+
+Not responsible for:
+ encoding/decoding ids
+ any http gobblygook
+ formatting of returned data (always python structures)
+ formatting of raised errors
+
+The goal is to have Controllers only handle:
+ query-string/payload parsing and encoding/decoding ids
+ http
+ return formatting
+
+and:
+ control, improve namespacing in Controllers
+ DRY for Controller ops (define here - use in both UI/API Controllers)
+
+In other words, 'Business logic' independent of web transactions/user context
+(trans) should be pushed into models - but logic that requires the context
+trans should be placed under this module.
+"""
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/managers/base.py
--- /dev/null
+++ b/lib/galaxy/managers/base.py
@@ -0,0 +1,7 @@
+
+
+class ModelManager( object ):
+ pass
+
+class ModelSerializer( object ):
+ pass
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/managers/hdas.py
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -1,16 +1,35 @@
+"""
+Manager and Serializer for HDAs.
+
+HistoryDatasetAssociations (HDAs) are datasets contained or created in a
+history.
+"""
+
from galaxy import exceptions
-from ..managers import histories
+from galaxy.managers import base as manager_base
+from galaxy.managers import histories as history_manager
-class HDAManager( object ):
+import galaxy.web
+import galaxy.datatypes.metadata
+from galaxy import objectstore
+
+class HDAManager( manager_base.ModelManager ):
+ """
+ Interface/service object for interacting with HDAs.
+ """
def __init__( self ):
- self.histories_mgr = histories.HistoryManager()
+ """
+ Set up and initialize other managers needed by hdas.
+ """
+ self.histories_mgr = history_manager.HistoryManager()
def get( self, trans, unencoded_id, check_ownership=True, check_accessible=True ):
"""
+ Get an HDA by its unencoded db id, checking ownership (via its history)
+ or accessibility (via dataset shares/permissions).
"""
- # this is a replacement for UsesHistoryDatasetAssociationMixin because mixins are a bad soln/structure
hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( unencoded_id )
if hda is None:
raise exceptions.ObjectNotFound()
@@ -19,7 +38,8 @@
def secure( self, trans, hda, check_ownership=True, check_accessible=True ):
"""
- checks if (a) user owns item or (b) item is accessible to user.
+ check ownership (via its history) or accessibility (via dataset
+ shares/permissions).
"""
# all items are accessible to an admin
if trans.user and trans.user_is_admin():
@@ -31,12 +51,18 @@
return hda
def can_access_dataset( self, trans, hda ):
+ """
+ Use security agent to see if current user has access to dataset.
+ """
current_user_roles = trans.get_current_user_roles()
return trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset )
#TODO: is_owner, is_accessible
def check_ownership( self, trans, hda ):
+ """
+ Use history to see if current user owns HDA.
+ """
if not trans.user:
#if hda.history == trans.history:
# return hda
@@ -51,6 +77,9 @@
"HistoryDatasetAssociation is not owned by the current user", type='error' )
def check_accessible( self, trans, hda ):
+ """
+ Raise error if HDA is not accessible.
+ """
if trans.user and trans.user_is_admin():
return hda
# check for access of the containing history...
@@ -62,6 +91,151 @@
"HistoryDatasetAssociation is not accessible to the current user", type='error' )
def err_if_uploading( self, trans, hda ):
+ """
+ Raise error if HDA is still uploading.
+ """
if hda.state == trans.model.Dataset.states.UPLOAD:
raise exceptions.Conflict( "Please wait until this dataset finishes uploading" )
return hda
+
+ def get_hda_dict( self, trans, hda ):
+ """
+ Return full details of this HDA in dictionary form.
+ """
+ #precondition: the user's access to this hda has already been checked
+ #TODO:?? postcondition: all ids are encoded (is this really what we want at this level?)
+ expose_dataset_path = trans.user_is_admin() or trans.app.config.expose_dataset_path
+ hda_dict = hda.to_dict( view='element', expose_dataset_path=expose_dataset_path )
+ hda_dict[ 'api_type' ] = "file"
+
+ # Add additional attributes that depend on trans must be added here rather than at the model level.
+ can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+ can_access_hda = ( trans.user_is_admin() or can_access_hda )
+ if not can_access_hda:
+ return self.get_inaccessible_hda_dict( trans, hda )
+ hda_dict[ 'accessible' ] = True
+
+ #TODO: I'm unclear as to which access pattern is right
+ hda_dict[ 'annotation' ] = hda.get_item_annotation_str( trans.sa_session, hda.history.user, hda )
+ #annotation = getattr( hda, 'annotation', hda.get_item_annotation_str( trans.sa_session, trans.user, hda ) )
+
+ # ---- return here if deleted AND purged OR can't access
+ purged = ( hda.purged or hda.dataset.purged )
+ if ( hda.deleted and purged ):
+ #TODO: to_dict should really go AFTER this - only summary data
+ return trans.security.encode_dict_ids( hda_dict )
+
+ if expose_dataset_path:
+ try:
+ hda_dict[ 'file_name' ] = hda.file_name
+ except objectstore.ObjectNotFound:
+ log.exception( 'objectstore.ObjectNotFound, HDA %s.', hda.id )
+
+ hda_dict[ 'download_url' ] = galaxy.web.url_for( 'history_contents_display',
+ history_id = trans.security.encode_id( hda.history.id ),
+ history_content_id = trans.security.encode_id( hda.id ) )
+
+ # indeces, assoc. metadata files, etc.
+ meta_files = []
+ for meta_type in hda.metadata.spec.keys():
+ if isinstance( hda.metadata.spec[ meta_type ].param, galaxy.datatypes.metadata.FileParameter ):
+ meta_files.append( dict( file_type=meta_type ) )
+ if meta_files:
+ hda_dict[ 'meta_files' ] = meta_files
+
+ # currently, the viz reg is optional - handle on/off
+ if trans.app.visualizations_registry:
+ hda_dict[ 'visualizations' ] = trans.app.visualizations_registry.get_visualizations( trans, hda )
+ else:
+ hda_dict[ 'visualizations' ] = hda.get_visualizations()
+ #TODO: it may also be wiser to remove from here and add as API call that loads the visualizations
+ # when the visualizations button is clicked (instead of preloading/pre-checking)
+
+ # ---- return here if deleted
+ if hda.deleted and not purged:
+ return trans.security.encode_dict_ids( hda_dict )
+
+ return trans.security.encode_dict_ids( hda_dict )
+
+ def get_inaccessible_hda_dict( self, trans, hda ):
+ """
+ Return truncated serialization of HDA when inaccessible to user.
+ """
+ return trans.security.encode_dict_ids({
+ 'id' : hda.id,
+ 'history_id': hda.history.id,
+ 'hid' : hda.hid,
+ 'name' : hda.name,
+ 'state' : hda.state,
+ 'deleted' : hda.deleted,
+ 'visible' : hda.visible,
+ 'accessible': False
+ })
+
+ def get_hda_dict_with_error( self, trans, hda=None, history_id=None, id=None, error_msg='Error' ):
+ """
+ Return truncated serialization of HDA when error raised getting
+ details.
+ """
+ return trans.security.encode_dict_ids({
+ 'id' : hda.id if hda else id,
+ 'history_id': hda.history.id if hda else history_id,
+ 'hid' : hda.hid if hda else '(unknown)',
+ 'name' : hda.name if hda else '(unknown)',
+ 'error' : error_msg,
+ 'state' : trans.model.Dataset.states.NEW
+ })
+
+ def get_display_apps( self, trans, hda ):
+ """
+ Return dictionary containing new-style display app urls.
+ """
+ display_apps = []
+ for display_app in hda.get_display_applications( trans ).itervalues():
+
+ app_links = []
+ for link_app in display_app.links.itervalues():
+ app_links.append({
+ 'target': link_app.url.get( 'target_frame', '_blank' ),
+ 'href' : link_app.get_display_url( hda, trans ),
+ 'text' : gettext( link_app.name )
+ })
+ if app_links:
+ display_apps.append( dict( label=display_app.name, links=app_links ) )
+
+ return display_apps
+
+ def get_old_display_applications( self, trans, hda ):
+ """
+ Return dictionary containing old-style display app urls.
+ """
+ display_apps = []
+ if not trans.app.config.enable_old_display_applications:
+ return display_apps
+
+ for display_app in hda.datatype.get_display_types():
+ target_frame, display_links = hda.datatype.get_display_links( hda,
+ display_app, trans.app, trans.request.base )
+
+ if len( display_links ) > 0:
+ display_label = hda.datatype.get_display_label( display_app )
+
+ app_links = []
+ for display_name, display_link in display_links:
+ app_links.append({
+ 'target': target_frame,
+ 'href' : display_link,
+ 'text' : gettext( display_name )
+ })
+ if app_links:
+ display_apps.append( dict( label=display_label, links=app_links ) )
+
+ return display_apps
+
+
+# =============================================================================
+class HistorySerializer( manager_base.ModelSerializer ):
+ """
+ Interface/service object for serializing HDAs into dictionaries.
+ """
+ pass
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/managers/histories.py
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -1,9 +1,32 @@
+"""
+Manager and Serializer for histories.
+
+Histories are containers for datasets or dataset collections
+created (or copied) by users over the course of an analysis.
+"""
+
from galaxy import exceptions
from galaxy.model import orm
+from galaxy.managers import base as manager_base
+import galaxy.managers.hdas
-class HistoryManager( object ):
+import galaxy.web
+import galaxy.dataset_collections.util
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+# =============================================================================
+class HistoryManager( manager_base.ModelManager ):
+ """
+ Interface/service object for interacting with HDAs.
+ """
+
#TODO: all the following would be more useful if passed the user instead of defaulting to trans.user
+ def __init__( self, *args, **kwargs ):
+ super( HistoryManager, self ).__init__( *args, **kwargs )
def get( self, trans, unencoded_id, check_ownership=True, check_accessible=True, deleted=None ):
"""
@@ -44,7 +67,7 @@
def secure( self, trans, history, check_ownership=True, check_accessible=True ):
"""
- checks if (a) user owns item or (b) item is accessible to user.
+ Checks if (a) user owns item or (b) item is accessible to user.
"""
# all items are accessible to an admin
if trans.user and trans.user_is_admin():
@@ -56,15 +79,28 @@
return history
def is_current( self, trans, history ):
+ """
+ True if the given history is the user's current history.
+
+ Returns False if the session has no current history.
+ """
+ if trans.history is None:
+ return False
return trans.history == history
def is_owner( self, trans, history ):
+ """
+ True if the current user is the owner of the given history.
+ """
# anon users are only allowed to view their current history
if not trans.user:
return self.is_current( trans, history )
return trans.user == history.user
def check_ownership( self, trans, history ):
+ """
+ Raises error if the current user is not the owner of the history.
+ """
if trans.user and trans.user_is_admin():
return history
if not trans.user and not self.is_current( trans, history ):
@@ -74,6 +110,9 @@
raise exceptions.ItemOwnershipException( "History is not owned by the current user", type='error' )
def is_accessible( self, trans, history ):
+ """
+ True if the user can access (read) the current history.
+ """
# admin always have access
if trans.user and trans.user_is_admin():
return True
@@ -88,6 +127,103 @@
return False
def check_accessible( self, trans, history ):
+ """
+ Raises error if the current user can't access the history.
+ """
if self.is_accessible( trans, history ):
return history
raise exceptions.ItemAccessibilityException( "History is not accessible to the current user", type='error' )
+
+ #TODO: bleh...
+ def _get_history_data( self, trans, history ):
+ """
+ Returns a dictionary containing ``history`` and ``contents``, serialized
+ history and an array of serialized history contents respectively.
+ """
+ hda_mgr = galaxy.managers.hdas.HDAManager()
+ collection_dictifier = galaxy.dataset_collections.util.dictify_dataset_collection_instance
+
+ history_dictionary = {}
+ contents_dictionaries = []
+ try:
+ #for content in history.contents_iter( **contents_kwds ):
+ for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
+ hda_dict = {}
+
+ if isinstance( content, trans.app.model.HistoryDatasetAssociation ):
+ try:
+ hda_dict = hda_mgr.get_hda_dict( trans, content )
+ except Exception, exc:
+ # don't fail entire list if hda err's, record and move on
+ log.exception( 'Error bootstrapping hda: %s', exc )
+ hda_dict = hda_mgr.get_hda_dict_with_error( trans, content, str( exc ) )
+
+ elif isinstance( content, trans.app.model.HistoryDatasetCollectionAssociation ):
+ try:
+ service = trans.app.dataset_collections_service
+ dataset_collection_instance = service.get_dataset_collection_instance(
+ trans=trans,
+ instance_type='history',
+ id=trans.security.encode_id( content.id ),
+ )
+ hda_dict = collection_dictifier( dataset_collection_instance,
+ security=trans.security, parent=dataset_collection_instance.history, view="element" )
+
+ except Exception, exc:
+ log.exception( "Error in history API at listing dataset collection: %s", exc )
+ #TODO: return some dict with the error
+
+ contents_dictionaries.append( hda_dict )
+
+ # re-use the hdas above to get the history data...
+ history_dictionary = self.get_history_dict( trans, history, contents_dictionaries=contents_dictionaries )
+
+ except Exception, exc:
+ user_id = str( trans.user.id ) if trans.user else '(anonymous)'
+ log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) )
+ message = ( 'An error occurred getting the history data from the server. '
+ + 'Please contact a Galaxy administrator if the problem persists.' )
+ history_dictionary[ 'error' ] = message
+
+ return {
+ 'history' : history_dictionary,
+ 'contents' : contents_dictionaries
+ }
+
+ def get_history_dict( self, trans, history, contents_dictionaries=None ):
+ """
+ Returns history data in the form of a dictionary.
+ """
+ #TODO: to serializer
+ history_dict = history.to_dict( view='element', value_mapper={ 'id':trans.security.encode_id })
+ history_dict[ 'user_id' ] = None
+ if history.user_id:
+ history_dict[ 'user_id' ] = trans.security.encode_id( history.user_id )
+
+ history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True )
+ history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, history.user, history )
+ if not history_dict[ 'annotation' ]:
+ history_dict[ 'annotation' ] = ''
+
+ #TODO: item_slug url
+ if history_dict[ 'importable' ] and history_dict[ 'slug' ]:
+ username_and_slug = ( '/' ).join(( 'u', history.user.username, 'h', history_dict[ 'slug' ] ))
+ history_dict[ 'username_and_slug' ] = username_and_slug
+
+#TODO: re-add
+ #hda_summaries = hda_dictionaries if hda_dictionaries else self.get_hda_summary_dicts( trans, history )
+ ##TODO remove the following in v2
+ #( state_counts, state_ids ) = self._get_hda_state_summaries( trans, hda_summaries )
+ #history_dict[ 'state_details' ] = state_counts
+ #history_dict[ 'state_ids' ] = state_ids
+ #history_dict[ 'state' ] = self._get_history_state_from_hdas( trans, history, state_counts )
+
+ return history_dict
+
+
+# =============================================================================
+class HistorySerializer( manager_base.ModelSerializer ):
+ """
+ Interface/service object for serializing histories into dictionaries.
+ """
+ pass
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
--- a/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
+++ b/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
@@ -23,6 +23,8 @@
handler.setFormatter( formatter )
log.addHandler( handler )
+metadata = MetaData()
+context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) )
class DeferredJob( object ):
states = Bunch( NEW = 'new',
@@ -37,12 +39,8 @@
self.params = params
def upgrade(migrate_engine):
- metadata = MetaData()
metadata.bind = migrate_engine
- Session = sessionmaker( bind=migrate_engine)
- context = Session()
-
DeferredJob.table = Table( "deferred_job", metadata,
Column( "id", Integer, primary_key=True ),
Column( "create_time", DateTime, default=now ),
@@ -70,12 +68,8 @@
context.flush()
def downgrade(migrate_engine):
- metadata = MetaData()
metadata.bind = migrate_engine
- Session = sessionmaker( bind=migrate_engine)
- context = Session()
-
jobs = context.query( DeferredJob ).filter_by( plugin='GenomeTransferPlugin' ).all()
for job in jobs:
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -3213,7 +3213,9 @@
# Populate tool_type to ToolClass mappings
tool_types = {}
-for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool, DataManagerTool ]:
+for tool_class in [ Tool, SetMetadataTool, OutputParameterJSONTool,
+ DataManagerTool, DataSourceTool, AsyncDataSourceTool,
+ DataDestinationTool ]:
tool_types[ tool_class.tool_type ] = tool_class
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/tools/actions/index_genome.py
--- a/lib/galaxy/tools/actions/index_genome.py
+++ /dev/null
@@ -1,67 +0,0 @@
-import tempfile
-from __init__ import ToolAction
-from galaxy.util.odict import odict
-from galaxy.tools.genome_index import *
-
-import logging
-log = logging.getLogger( __name__ )
-
-class GenomeIndexToolAction( ToolAction ):
- """Tool action used for exporting a history to an archive. """
-
- def execute( self, tool, trans, *args, **kwargs ):
- #
- # Get genome to index.
- #
- incoming = kwargs['incoming']
- #
- # Create the job and output dataset objects
- #
- job = trans.app.model.Job()
- job.tool_id = tool.id
- job.user_id = incoming['user']
- start_job_state = job.state # should be job.states.NEW
- job.state = job.states.WAITING # we need to set job state to something other than NEW,
- # or else when tracking jobs in db it will be picked up
- # before we have added input / output parameters
- trans.sa_session.add( job )
-
- # Create dataset that will serve as archive.
- temp_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.NEW )
- trans.sa_session.add( temp_dataset )
-
- trans.sa_session.flush() # ensure job.id and archive_dataset.id are available
- trans.app.object_store.create( temp_dataset ) # set the object store id, create dataset (because galaxy likes having datasets)
-
- #
- # Setup job and job wrapper.
- #
-
- # Add association for keeping track of index jobs, transfer jobs, and so on.
- user = trans.sa_session.query( trans.app.model.User ).get( int( incoming['user'] ) )
- assoc = trans.app.model.GenomeIndexToolData( job=job, dataset=temp_dataset, fasta_path=incoming['path'], \
- indexer=incoming['indexer'], user=user, \
- deferred_job=kwargs['deferred'], transfer_job=kwargs['transfer'] )
- trans.sa_session.add( assoc )
-
- job_wrapper = GenomeIndexToolWrapper( job )
- cmd_line = job_wrapper.setup_job( assoc )
-
- #
- # Add parameters to job_parameter table.
- #
- incoming[ '__GENOME_INDEX_COMMAND__' ] = cmd_line
- for name, value in tool.params_to_strings( incoming, trans.app ).iteritems():
- job.add_parameter( name, value )
-
- job.state = start_job_state # job inputs have been configured, restore initial job state
- job.set_handler(tool.get_job_handler(None))
- trans.sa_session.flush()
-
-
- # Queue the job for execution
- trans.app.job_queue.put( job.id, tool.id )
- log.info( "Added genome index job to the job queue, id: %s" % str( job.id ) )
-
- return job, odict()
-
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/tools/deps/containers.py
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -191,19 +191,26 @@
# TODO: Remove redundant volumes...
volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw)
volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
- return docker_util.build_docker_run_command(
+
+ docker_host_props = dict(
+ docker_cmd=prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND),
+ sudo=asbool(prop("sudo", docker_util.DEFAULT_SUDO)),
+ sudo_cmd=prop("sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND),
+ host=prop("host", docker_util.DEFAULT_HOST),
+ )
+
+ cache_command = docker_util.build_docker_cache_command(self.container_id, **docker_host_props)
+ run_command = docker_util.build_docker_run_command(
command,
self.container_id,
volumes=volumes,
volumes_from=volumes_from,
env_directives=env_directives,
working_directory=working_directory,
- docker_cmd=prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND),
- sudo=asbool(prop("sudo", docker_util.DEFAULT_SUDO)),
- sudo_cmd=prop("sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND),
- host=prop("host", docker_util.DEFAULT_HOST),
- net=prop("net", "none") # By default, docker instance has networking disabled
+ net=prop("net", "none"), # By default, docker instance has networking disabled
+ **docker_host_props
)
+ return "%s\n%s" % (cache_command, run_command)
def __expand_str(self, value):
if not value:
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/tools/deps/docker_util.py
--- a/lib/galaxy/tools/deps/docker_util.py
+++ b/lib/galaxy/tools/deps/docker_util.py
@@ -50,28 +50,41 @@
return ":".join([self.from_path, self.to_path, self.how])
+def build_docker_cache_command(
+ image,
+ docker_cmd=DEFAULT_DOCKER_COMMAND,
+ sudo=DEFAULT_SUDO,
+ sudo_cmd=DEFAULT_SUDO_COMMAND,
+ host=DEFAULT_HOST,
+):
+ inspect_command_parts = __docker_prefix(docker_cmd, sudo, sudo_cmd, host)
+ inspect_command_parts.extend(["inspect", image])
+ inspect_image_command = " ".join(inspect_command_parts)
+
+ pull_command_parts = __docker_prefix(docker_cmd, sudo, sudo_cmd, host)
+ pull_command_parts.extend(["pull", image])
+ pull_image_command = " ".join(pull_command_parts)
+ cache_command = "%s > /dev/null 2>&1\n[ $? -ne 0 ] && %s > /dev/null 2>&1\n" % (inspect_image_command, pull_image_command)
+ return cache_command
+
+
def build_docker_run_command(
container_command,
image,
tag=None,
- docker_cmd=DEFAULT_DOCKER_COMMAND,
volumes=[],
volumes_from=DEFAULT_VOLUMES_FROM,
memory=DEFAULT_MEMORY,
env_directives=[],
working_directory=DEFAULT_WORKING_DIRECTORY,
+ name=None,
+ net=DEFAULT_NET,
+ docker_cmd=DEFAULT_DOCKER_COMMAND,
sudo=DEFAULT_SUDO,
sudo_cmd=DEFAULT_SUDO_COMMAND,
- name=None,
host=DEFAULT_HOST,
- net=DEFAULT_NET,
):
- command_parts = []
- if sudo:
- command_parts.append(sudo_cmd)
- command_parts.append(docker_cmd)
- if host:
- command_parts.append(["-H", host])
+ command_parts = __docker_prefix(docker_cmd, sudo, sudo_cmd, host)
command_parts.append("run")
for env_directive in env_directives:
command_parts.extend(["-e", env_directive])
@@ -93,3 +106,15 @@
command_parts.append(full_image)
command_parts.append(container_command)
return " ".join(command_parts)
+
+
+def __docker_prefix(docker_cmd, sudo, sudo_cmd, host):
+ """ Prefix to issue a docker command.
+ """
+ command_parts = []
+ if sudo:
+ command_parts.append(sudo_cmd)
+ command_parts.append(docker_cmd)
+ if host:
+ command_parts.append(["-H", host])
+ return command_parts
diff -r 47c6c6bb8eec81060cbf2ddb2396c19e78444747 -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b lib/galaxy/tools/genome_index/__init__.py
--- a/lib/galaxy/tools/genome_index/__init__.py
+++ /dev/null
@@ -1,243 +0,0 @@
-from __future__ import with_statement
-
-import json
-import logging
-import os
-import shutil
-import tarfile
-import tempfile
-
-from galaxy import model, util
-from galaxy.web.framework.helpers import to_unicode
-from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.util.json import *
-from galaxy.web.base.controller import UsesHistoryMixin
-from galaxy.tools.data import ToolDataTableManager
-
-
-log = logging.getLogger(__name__)
-
-def load_genome_index_tools( toolbox ):
- """ Adds tools for indexing genomes via the main job runner. """
- # Create XML for loading the tool.
- tool_xml_text = """
- <tool id="__GENOME_INDEX__" name="Index Genome" version="0.1" tool_type="genome_index">
- <type class="GenomeIndexTool" module="galaxy.tools"/>
- <action module="galaxy.tools.actions.index_genome" class="GenomeIndexToolAction"/>
- <command>$__GENOME_INDEX_COMMAND__ $output_file $output_file.files_path "$__app__.config.rsync_url" "$__app__.config.tool_data_path"</command>
- <inputs>
- <param name="__GENOME_INDEX_COMMAND__" type="hidden"/>
- </inputs>
- <outputs>
- <data format="txt" name="output_file"/>
- </outputs>
- <stdio>
- <exit_code range="1:" err_level="fatal" />
- </stdio>
- </tool>
- """
-
- # Load index tool.
- tmp_name = tempfile.NamedTemporaryFile()
- tmp_name.write( tool_xml_text )
- tmp_name.flush()
- genome_index_tool = toolbox.load_tool( tmp_name.name )
- toolbox.tools_by_id[ genome_index_tool.id ] = genome_index_tool
- log.debug( "Loaded genome index tool: %s", genome_index_tool.id )
-
-class GenomeIndexToolWrapper( object ):
- """ Provides support for performing jobs that index a genome. """
- def __init__( self, job_id ):
- self.locations = dict()
- self.job_id = job_id
-
- def setup_job( self, genobj ):
- """ Perform setup for job to index a genome and return an archive. Method generates
- attribute files, sets the corresponding attributes in the associated database
- object, and returns a command line for running the job. The command line
- includes the command, inputs, and options; it does not include the output
- file because it must be set at runtime. """
-
- #
- # Create and return command line for running tool.
- #
- scriptpath = os.path.join( os.path.abspath( os.getcwd() ), "lib/galaxy/tools/genome_index/index_genome.py" )
- return "python %s %s %s" % ( scriptpath, genobj.indexer, genobj.fasta_path )
-
- def postprocessing( self, sa_session, app ):
- """ Finish the job, move the finished indexes to their final resting place,
- and update the .loc files where applicable. """
- gitd = sa_session.query( model.GenomeIndexToolData ).filter_by( job_id=self.job_id ).first()
- indexdirs = dict( bfast='bfast_index', bowtie='bowtie_index', bowtie2='bowtie2_index',
- bwa='bwa_index', perm='perm_%s_index', picard='srma_index', sam='sam_index' )
-
-
- if gitd:
- fp = open( gitd.dataset.get_file_name(), 'r' )
- deferred = sa_session.query( model.DeferredJob ).filter_by( id=gitd.deferred_job_id ).first()
- try:
- logloc = json.load( fp )
- except ValueError:
- deferred.state = app.model.DeferredJob.states.ERROR
- sa_session.add( deferred )
- sa_session.flush()
- log.debug( 'Indexing job failed, setting deferred job state to error.' )
- return False
- finally:
- fp.close()
- destination = None
- tdtman = ToolDataTableManager( app.config.tool_data_path )
- xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path )
- for node in xmltree:
- table = node.get('name')
- location = node.findall('file')[0].get('path')
- self.locations[table] = os.path.abspath( location )
- locbase = os.path.abspath( os.path.split( self.locations['all_fasta'] )[0] )
- params = deferred.params
- dbkey = params[ 'dbkey' ]
- basepath = os.path.join( os.path.abspath( app.config.genome_data_path ), dbkey )
- intname = params[ 'intname' ]
- indexer = gitd.indexer
- workingdir = os.path.abspath( gitd.dataset.extra_files_path )
- location = []
- indexdata = gitd.dataset.extra_files_path
- if indexer == '2bit':
- indexdata = os.path.join( workingdir, '%s.2bit' % dbkey )
- destination = os.path.join( basepath, 'seq', '%s.2bit' % dbkey )
- location.append( dict( line='\t'.join( [ 'seq', dbkey, destination ] ), file= os.path.join( locbase, 'alignseq.loc' ) ) )
- elif indexer == 'bowtie':
- self._ex_tar( workingdir, 'cs.tar' )
- destination = os.path.join( basepath, 'bowtie_index' )
- for var in [ 'nt', 'cs' ]:
- for line in logloc[ var ]:
- idx = line
- if var == 'nt':
- locfile = self.locations[ 'bowtie_indexes' ]
- locdir = os.path.join( destination, idx )
- else:
- locfile = self.locations[ 'bowtie_indexes_color' ]
- locdir = os.path.join( destination, var, idx )
- location.append( dict( line='\t'.join( [ dbkey, dbkey, intname, locdir ] ), file=locfile ) )
- elif indexer == 'bowtie2':
- destination = os.path.join( basepath, 'bowtie2_index' )
- for line in logloc[ 'nt' ]:
- idx = line
- locfile = self.locations[ 'bowtie2_indexes' ]
- locdir = os.path.join( destination, idx )
- location.append( dict( line='\t'.join( [ dbkey, dbkey, intname, locdir ] ), file=locfile ) )
- elif indexer == 'bwa':
- self._ex_tar( workingdir, 'cs.tar' )
- destination = os.path.join( basepath, 'bwa_index' )
- for var in [ 'nt', 'cs' ]:
- for line in logloc[ var ]:
- idx = line
- if var == 'nt':
- locfile = self.locations[ 'bwa_indexes' ]
- locdir = os.path.join( destination, idx )
- else:
- locfile = self.locations[ 'bwa_indexes_color' ]
- locdir = os.path.join( destination, var, idx )
- location.append( dict( line='\t'.join( [ dbkey, dbkey, intname, locdir ] ), file=locfile ) )
- elif indexer == 'perm':
- self._ex_tar( workingdir, 'cs.tar' )
- destination = os.path.join( basepath, 'perm_index' )
- for var in [ 'nt', 'cs' ]:
- for line in logloc[ var ]:
- idx = line.pop()
- if var == 'nt':
- locfile = self.locations[ 'perm_base_indexes' ]
- locdir = os.path.join( destination, idx )
- else:
- locfile = self.locations[ 'perm_color_indexes' ]
- locdir = os.path.join( destination, var, idx )
- line.append( locdir )
- location.append( dict( line='\t'.join( line ), file=locfile ) )
- elif indexer == 'picard':
- destination = os.path.join( basepath, 'srma_index' )
- for var in [ 'nt' ]:
- for line in logloc[ var ]:
- idx = line
- locfile = self.locations[ 'picard_indexes' ]
- locdir = os.path.join( destination, idx )
- location.append( dict( line='\t'.join( [ dbkey, dbkey, intname, locdir ] ), file=locfile ) )
- elif indexer == 'sam':
- destination = os.path.join( basepath, 'sam_index' )
- for var in [ 'nt' ]:
- for line in logloc[ var ]:
- locfile = self.locations[ 'sam_fa_indexes' ]
- locdir = os.path.join( destination, line )
- location.append( dict( line='\t'.join( [ 'index', dbkey, locdir ] ), file=locfile ) )
-
- if destination is not None and os.path.exists( os.path.split( destination )[0] ) and not os.path.exists( destination ):
- log.debug( 'Moving %s to %s' % ( indexdata, destination ) )
- shutil.move( indexdata, destination )
- if indexer not in [ '2bit' ]:
- genome = '%s.fa' % dbkey
- target = os.path.join( destination, genome )
- fasta = os.path.abspath( os.path.join( basepath, 'seq', genome ) )
- self._check_link( fasta, target )
- if os.path.exists( os.path.join( destination, 'cs' ) ):
- target = os.path.join( destination, 'cs', genome )
- fasta = os.path.abspath( os.path.join( basepath, 'seq', genome ) )
- self._check_link( fasta, target )
- for line in location:
- self._add_line( line[ 'file' ], line[ 'line' ] )
- deferred.state = app.model.DeferredJob.states.OK
- sa_session.add( deferred )
- sa_session.flush()
-
-
- def _check_link( self, targetfile, symlink ):
- target = os.path.relpath( targetfile, os.path.dirname( symlink ) )
- filename = os.path.basename( targetfile )
- if not os.path.exists( targetfile ): # this should never happen.
- raise Exception, "%s not found. Unable to proceed without a FASTA file. Aborting." % targetfile
- if os.path.exists( symlink ) and os.path.islink( symlink ):
- if os.path.realpath( symlink ) == os.path.abspath( targetfile ): # symlink exists, points to the correct FASTA file.
- return
- else: # no it doesn't. Make a new one, and this time do it right.
- os.remove( symlink )
- os.symlink( target, symlink )
- return
- elif not os.path.exists( symlink ): # no symlink to the FASTA file. Create one.
- os.symlink( target, symlink )
- return
- elif os.path.exists( symlink ) and not os.path.islink( symlink ):
- if self._hash_file( targetfile ) == self._hash_file( symlink ): # files are identical. No need to panic.
- return
- else:
- if os.path.getsize( symlink ) == 0: # somehow an empty file got copied instead of the symlink. Delete with extreme prejudice.
- os.remove( symlink )
- os.symlink( target, symlink )
- return
- else:
- raise Exception, "Regular file %s exists, is not empty, contents do not match %s." % ( symlink, targetfile )
-
- def _hash_file( self, filename ):
- import hashlib
- md5 = hashlib.md5()
- with open( filename, 'rb' ) as f:
- for chunk in iter( lambda: f.read( 8192 ), '' ):
- md5.update( chunk )
- return md5.digest()
-
-
- def _ex_tar( self, directory, filename ):
- fh = tarfile.open( os.path.join( directory, filename ) )
- fh.extractall( path=directory )
- fh.close()
- os.remove( os.path.join( directory, filename ) )
-
- def _add_line( self, locfile, newline ):
- filepath = locfile
- origlines = []
- output = []
- comments = []
- with open( filepath, 'r' ) as destfile:
- for line in destfile:
- origlines.append( line.strip() )
- if newline not in origlines:
- origlines.append( newline )
- with open( filepath, 'w+' ) as destfile:
- origlines.append( '' )
- destfile.write( '\n'.join( origlines ) )
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/4ca1677c8d5b/
Changeset: 4ca1677c8d5b
User: iracooke
Date: 2014-07-24 09:16:24
Summary: Added whitelisting to sqlite data provider
Affected #: 1 file
diff -r 034c0159c0cfbc7736eeee4132fbedda8a465c6b -r 4ca1677c8d5bc6486b0b1dff50372a23dfaf307d lib/galaxy/datatypes/dataproviders/dataset.py
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -12,6 +12,7 @@
import column
import external
import sqlite3
+import re
from galaxy import eggs
eggs.require( 'bx-python' )
@@ -720,8 +721,18 @@
self.connection.row_factory = sqlite3.Row
super( SQliteDataProvider, self ).__init__( source, **kwargs )
+ def query_matches_whitelist(self,query):
+ if re.match("select ",query,re.IGNORECASE):
+ if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query):
+ return False
+ else:
+ return True
+ return False
+
+
+
def __iter__( self ):
- if self.query is not None:
+ if (self.query is not None) and self.query_matches_whitelist(self.query):
for row in self.connection.cursor().execute(self.query):
yield row
else:
https://bitbucket.org/galaxy/galaxy-central/commits/56a7b27577de/
Changeset: 56a7b27577de
User: dannon
Date: 2014-07-25 00:29:57
Summary: Merged in iracooke/galaxy-central (pull request #434)
Add sqlite datatype and corresponding dataprovider
Affected #: 3 files
diff -r f03f9c5a5efc7fecb4ca131f66c441d55cc5d353 -r 56a7b27577dec0dac17ef94d4c131e7f1f61cb15 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -177,6 +177,7 @@
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
+ <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
@@ -262,6 +263,7 @@
--><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/>
+ <sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/>
diff -r f03f9c5a5efc7fecb4ca131f66c441d55cc5d353 -r 56a7b27577dec0dac17ef94d4c131e7f1f61cb15 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -12,6 +12,7 @@
import subprocess
import tempfile
import zipfile
+import sqlite3
from urllib import urlencode, quote_plus
from galaxy import eggs
@@ -545,3 +546,45 @@
return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size()))
Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit)
+
+
+(a)dataproviders.decorators.has_dataproviders
+class SQlite ( Binary ):
+ file_ext = "sqlite"
+
+ # Connects and runs a query that should work on any real database
+ # If the file is not sqlite, an exception will be thrown and the sniffer will return false
+ def sniff( self, filename ):
+ try:
+ conn = sqlite3.connect(filename)
+ schema_version=conn.cursor().execute("pragma schema_version").fetchone()
+ conn.close()
+ if schema_version is not None:
+ return True
+ return False
+ except:
+ return False
+
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ dataset.peek = "SQLite Database"
+ dataset.blurb = data.nice_size( dataset.get_size() )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def display_peek( self, dataset ):
+ try:
+ return dataset.peek
+ except:
+ return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+
+ @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
+ def sqlite_dataprovider( self, dataset, **settings ):
+ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
+ return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings )
+
+
+Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite)
+
diff -r f03f9c5a5efc7fecb4ca131f66c441d55cc5d353 -r 56a7b27577dec0dac17ef94d4c131e7f1f61cb15 lib/galaxy/datatypes/dataproviders/dataset.py
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -11,6 +11,8 @@
import line
import column
import external
+import sqlite3
+import re
from galaxy import eggs
eggs.require( 'bx-python' )
@@ -700,3 +702,39 @@
#TODO: as samtools - need more info on output format
raise NotImplementedError()
super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs )
+
+
+
+class SQliteDataProvider ( base.DataProvider ):
+ """
+ Data provider that uses a sqlite database file as its source.
+
+ Allows any query to be run and returns the resulting rows as sqlite3 row objects
+ """
+ settings = {
+ 'query' : 'str'
+ }
+
+ def __init__( self, source, query=None, **kwargs ):
+ self.query=query
+ self.connection = sqlite3.connect(source.dataset.file_name);
+ self.connection.row_factory = sqlite3.Row
+ super( SQliteDataProvider, self ).__init__( source, **kwargs )
+
+ def query_matches_whitelist(self,query):
+ if re.match("select ",query,re.IGNORECASE):
+ if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query):
+ return False
+ else:
+ return True
+ return False
+
+
+
+ def __iter__( self ):
+ if (self.query is not None) and self.query_matches_whitelist(self.query):
+ for row in self.connection.cursor().execute(self.query):
+ yield row
+ else:
+ yield
+
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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7 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e80c212ba514/
Changeset: e80c212ba514
User: dannon
Date: 2014-07-23 23:24:33
Summary: Strip whitespace in manage_info template.
Affected #: 1 file
diff -r 6fbe4d95a8dc64bd222dbf1170bdadcc5321e855 -r e80c212ba514b4960c01f681cf15a2bc8b2b4882 templates/webapps/galaxy/user/manage_info.mako
--- a/templates/webapps/galaxy/user/manage_info.mako
+++ b/templates/webapps/galaxy/user/manage_info.mako
@@ -49,7 +49,7 @@
<div class="form-row"><div class="grid-header">
%for i, filter in enumerate( ['Active', 'Deleted', 'All'] ):
- %if i > 0:
+ %if i > 0:
<span>|</span>
%endif
%if show_filter == filter:
@@ -62,10 +62,10 @@
</div><table class="grid"><tbody>
- %for index, address in enumerate(addresses):
+ %for index, address in enumerate(addresses):
<tr class="libraryRow libraryOrFolderRow" id="libraryRow"><td>
- <div class="form-row">
+ <div class="form-row"><label>${address.desc}:</label>
${address.get_html()}
</div>
@@ -82,7 +82,7 @@
</ul></div></td>
- </tr>
+ </tr>
%endfor
</tbody></table>
https://bitbucket.org/galaxy/galaxy-central/commits/65f2c8c30d47/
Changeset: 65f2c8c30d47
User: dannon
Date: 2014-07-24 22:04:39
Summary: Sanitize user addresses. This should be revisited at some point -- not sure why these html stubs (and only these) generated in the model.
Affected #: 1 file
diff -r e80c212ba514b4960c01f681cf15a2bc8b2b4882 -r 65f2c8c30d477eb1008bf4e3b40c8695f5ac2df6 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -34,6 +34,7 @@
from galaxy.util.bunch import Bunch
from galaxy.util.hash_util import new_secure_hash
from galaxy.util.directory_hash import directory_hash_id
+from galaxy.util.sanitize_html import sanitize_html
from galaxy.web.framework.helpers import to_unicode
from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField,
PasswordField, SelectField, TextArea, TextField, WorkflowField,
@@ -3703,23 +3704,27 @@
self.country = country
self.phone = phone
def get_html(self):
+ # This should probably be deprecated eventually. It should currently
+ # sanitize.
+ # TODO Find out where else uses this and replace with
+ # templates
html = ''
if self.name:
- html = html + self.name
+ html = html + sanitize_html(self.name)
if self.institution:
- html = html + '<br/>' + self.institution
+ html = html + '<br/>' + sanitize_html(self.institution)
if self.address:
- html = html + '<br/>' + self.address
+ html = html + '<br/>' + sanitize_html(self.address)
if self.city:
- html = html + '<br/>' + self.city
+ html = html + '<br/>' + sanitize_html(self.city)
if self.state:
- html = html + ' ' + self.state
+ html = html + ' ' + sanitize_html(self.state)
if self.postal_code:
- html = html + ' ' + self.postal_code
+ html = html + ' ' + sanitize_html(self.postal_code)
if self.country:
- html = html + '<br/>' + self.country
+ html = html + '<br/>' + sanitize_html(self.country)
if self.phone:
- html = html + '<br/>' + 'Phone: ' + self.phone
+ html = html + '<br/>' + 'phone: ' + sanitize_html(self.phone)
return html
class UserOpenID( object ):
https://bitbucket.org/galaxy/galaxy-central/commits/e39c3a510cc1/
Changeset: e39c3a510cc1
User: dannon
Date: 2014-07-24 22:06:21
Summary: Sanitize address description display in the manage_info field.
Affected #: 1 file
diff -r 65f2c8c30d477eb1008bf4e3b40c8695f5ac2df6 -r e39c3a510cc17b47f3e54b0dcdc1965be8287be8 templates/webapps/galaxy/user/manage_info.mako
--- a/templates/webapps/galaxy/user/manage_info.mako
+++ b/templates/webapps/galaxy/user/manage_info.mako
@@ -66,7 +66,7 @@
<tr class="libraryRow libraryOrFolderRow" id="libraryRow"><td><div class="form-row">
- <label>${address.desc}:</label>
+ <label>${address.desc | h}:</label>
${address.get_html()}
</div><div class="form-row">
https://bitbucket.org/galaxy/galaxy-central/commits/6e6e184ec4e1/
Changeset: 6e6e184ec4e1
User: dannon
Date: 2014-07-24 22:06:37
Summary: Merge.
Affected #: 6 files
diff -r e39c3a510cc17b47f3e54b0dcdc1965be8287be8 -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1712,10 +1712,15 @@
if self.__display_multirun_option():
# Select multiple datasets, run multiple jobs.
multirun_key = "%s|__multirun__" % self.name
+ collection_multirun_key = "%s|__collection_multirun__" % self.name
if multirun_key in (other_values or {}):
multirun_value = listify( other_values[ multirun_key ] )
if multirun_value and len( multirun_value ) > 1:
default_field = "select_multiple"
+ elif collection_multirun_key in (other_values or {}):
+ multirun_value = listify( other_values[ collection_multirun_key ] )
+ if multirun_value:
+ default_field = "select_collection"
else:
multirun_value = value
multi_dataset_matcher = DatasetMatcher( trans, self, multirun_value, other_values )
@@ -2014,9 +2019,17 @@
default_field = "select_single_collection"
fields = odict()
+ collection_multirun_key = "%s|__collection_multirun__" % self.name
+ if collection_multirun_key in (other_values or {}):
+ multirun_value = other_values[ collection_multirun_key ]
+ if multirun_value:
+ default_field = "select_map_over_collections"
+ else:
+ multirun_value = value
+
history = self._get_history( trans )
fields[ "select_single_collection" ] = self._get_single_collection_field( trans=trans, history=history, value=value, other_values=other_values )
- fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=value, other_values=other_values )
+ fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=multirun_value, other_values=other_values )
return self._switch_fields( fields, default_field=default_field )
diff -r e39c3a510cc17b47f3e54b0dcdc1965be8287be8 -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae static/scripts/galaxy.tools.js
--- a/static/scripts/galaxy.tools.js
+++ b/static/scripts/galaxy.tools.js
@@ -86,7 +86,7 @@
}).attr(
'title',
selectionType['select_by']
- );
+ ).data( "index", iIndex );
view.formRow().find( "label" ).append( button );
}
});
@@ -114,11 +114,13 @@
} else {
$("div#remap-row").css("display", "none");
}
- this.formRow().find( "i" ).each(function(index, iElement) {
+ this.formRow().find( "i" ).each(function(_, iElement) {
+ var $iElement = $(iElement);
+ var index = $iElement.data("index");
if(index == enableIndex) {
- $(iElement).css('color', 'black');
+ $iElement.css('color', 'black');
} else {
- $(iElement).css('color', 'Gray');
+ $iElement.css('color', 'Gray');
}
});
var $select = this.$( "select" );
diff -r e39c3a510cc17b47f3e54b0dcdc1965be8287be8 -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -103,8 +103,9 @@
var self = this,
menu = create_icon_buttons_menu([
{ icon_class: 'plus-button', title: 'Add tracks', on_click: function() {
- visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
- _.each(tracks, function(track) {
+ visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey },
+ function(new_tracks) {
+ _.each(new_tracks, function(track) {
view.add_drawable( tracks.object_from_template(track, view, view) );
});
});
diff -r e39c3a510cc17b47f3e54b0dcdc1965be8287be8 -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae test/functional/tools/collection_two_paired.xml
--- /dev/null
+++ b/test/functional/tools/collection_two_paired.xml
@@ -0,0 +1,69 @@
+<tool id="collection_two_paired" name="collection_two_paired" version="0.1.0">
+ <command>
+ #if $kind.collection_type == "paired"
+ cat $kind.f1.forward $kind.f1['reverse'] >> $out1;
+ cat $kind.f2.forward $kind.f2['reverse'] >> $out1;
+ #else
+ #for $i, $_ in enumerate($kind.f1):
+ cat $kind.f1[$i] $kind.f2[$i] >> $out1;
+ #end for
+ #end if
+ </command>
+ <inputs>
+ <conditional name="kind">
+ <param type="select" name="collection_type">
+ <option value="paired">Paired Datasets</option>
+ <option value="list">List of Datasets</option>
+ </param>
+ <when value="paired">
+ <param name="f1" type="data_collection" collection_type="paired" />
+ <param name="f2" type="data_collection" collection_type="paired" />
+ </when>
+ <when value="list">
+ <param name="f1" type="data_collection" collection_type="paired" />
+ <param name="f2" type="data_collection" collection_type="paired" />
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <data format="txt" name="out1" />
+ </outputs>
+ <tests>
+ <test>
+ <conditional name="kind">
+ <param name="collection_type" value="paired" />
+ <param name="f1">
+ <collection type="paired">
+ <element name="forward" value="simple_line.txt" />
+ <element name="reverse" value="simple_line_alternative.txt" />
+ </collection>
+ </param>
+ <param name="f2">
+ <collection type="paired">
+ <element name="forward" value="simple_line.txt" />
+ <element name="reverse" value="simple_line_alternative.txt" />
+ </collection>
+ </param>
+ </conditional>
+ <output name="out1" file="simple_lines_interleaved.txt"/>
+ </test>
+ <test>
+ <conditional name="kind">
+ <param name="collection_type" value="list" />
+ <param name="f1">
+ <collection type="list">
+ <element name="l11" value="simple_line.txt" />
+ <element name="l12" value="simple_line.txt" />
+ </collection>
+ </param>
+ <param name="f2">
+ <collection type="list">
+ <element name="l21" value="simple_line_alternative.txt" />
+ <element name="l22" value="simple_line_alternative.txt" />
+ </collection>
+ </param>
+ </conditional>
+ <output name="out1" file="simple_lines_interleaved.txt"/>
+ </test>
+ </tests>
+</tool>
diff -r e39c3a510cc17b47f3e54b0dcdc1965be8287be8 -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae test/functional/tools/samples_tool_conf.xml
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -21,4 +21,5 @@
<tool file="collection_paired_test.xml" /><tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" />
+ <tool file="collection_two_paired.xml" /></toolbox>
\ No newline at end of file
diff -r e39c3a510cc17b47f3e54b0dcdc1965be8287be8 -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae test/unit/tools/test_execution.py
--- a/test/unit/tools/test_execution.py
+++ b/test/unit/tools/test_execution.py
@@ -16,13 +16,12 @@
eggs.require( "Paste" )
from paste import httpexceptions
-# Tool with a repeat parameter, to test state update.
-REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
+BASE_REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"><command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command><inputs><param type="text" name="param1" value="" /><repeat name="repeat1" label="Repeat 1">
- <param type="text" name="param2" value="" />
+ %s
</repeat></inputs><outputs>
@@ -31,6 +30,10 @@
</tool>
'''
+# Tool with a repeat parameter, to test state update.
+REPEAT_TOOL_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="text" name="param2" value="" />'''
+REPEAT_COLLECTION_PARAM_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="data_collection" name="param2" collection_type="paired" />'''
+
class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.UsesTools ):
@@ -287,13 +290,48 @@
} )
self.__assert_exeuted( template, template_vars )
- def __history_dataset_collection_for( self, hdas, id=1234 ):
- collection = galaxy.model.DatasetCollection()
+ def test_subcollection_multirun_with_state_updates( self ):
+ self._init_tool( REPEAT_COLLECTION_PARAM_CONTENTS )
+ hda1, hda2 = self.__add_dataset( 1 ), self.__add_dataset( 2 )
+ collection = self.__history_dataset_collection_for( [ hda1, hda2 ], collection_type="list:paired" )
+ collection_id = self.app.security.encode_id( collection.id )
+ self.app.dataset_collections_service = Bunch(
+ match_collections=lambda collections: None
+ )
+ template, template_vars = self.__handle_with_incoming(
+ repeat1_add="dummy",
+ )
+ state = self.__assert_rerenders_tool_without_errors( template, template_vars )
+ assert len( state.inputs[ "repeat1" ] ) == 1
+ template, template_vars = self.__handle_with_incoming( state, **{
+ "repeat1_0|param2|__collection_multirun__": "%s|paired" % collection_id,
+ "repeat1_add": "dummy",
+ } )
+ state = self.__assert_rerenders_tool_without_errors( template, template_vars )
+ assert state.inputs[ "repeat1" ][ 0 ][ "param2|__collection_multirun__" ] == "%s|paired" % collection_id
+
+ def __history_dataset_collection_for( self, hdas, collection_type="list", id=1234 ):
+ collection = galaxy.model.DatasetCollection(
+ collection_type=collection_type,
+ )
to_element = lambda hda: galaxy.model.DatasetCollectionElement(
collection=collection,
element=hda,
)
- collection.datasets = map(to_element, hdas)
+ elements = map(to_element, hdas)
+ if collection_type == "list:paired":
+ paired_collection = galaxy.model.DatasetCollection(
+ collection_type="paired",
+ )
+ paired_collection.elements = elements
+ list_dce = galaxy.model.DatasetCollectionElement(
+ collection=collection,
+ element=paired_collection,
+ )
+ elements = [ list_dce ]
+
+ collection.elements = elements
+
history_dataset_collection_association = galaxy.model.HistoryDatasetCollectionAssociation(
id=id,
collection=collection,
@@ -349,13 +387,13 @@
self.history.datasets.append( hda )
return hda
- def __add_collection_dataset( self, id, *hdas ):
+ def __add_collection_dataset( self, id, collection_type="paired", *hdas ):
hdca = galaxy.model.HistoryDatasetCollectionAssociation()
hdca.id = id
collection = galaxy.model.DatasetCollection()
hdca.collection = collection
collection.elements = [ galaxy.model.DatasetCollectionElement(element=self.__add_dataset( 1 )) ]
-
+ collection.type = collection_type
self.trans.sa_session.model_objects[ galaxy.model.HistoryDatasetCollectionAssociation ][ id ] = hdca
self.history.dataset_collections.append( hdca )
return hdca
https://bitbucket.org/galaxy/galaxy-central/commits/3686de5c8280/
Changeset: 3686de5c8280
User: dannon
Date: 2014-07-24 23:29:51
Summary: merge
Affected #: 2 files
diff -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae -r 3686de5c8280c18c197323948c5e2ea79e642a0b lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1391,7 +1391,7 @@
# Load parameters (optional)
input_elem = root.find("inputs")
enctypes = set()
- if input_elem:
+ if input_elem is not None:
# Handle properties of the input form
self.check_values = string_as_bool( input_elem.get("check_values", self.check_values ) )
self.nginx_upload = string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) )
diff -r 6e6e184ec4e1e00ff12b23ec36c9b7d3671e19ae -r 3686de5c8280c18c197323948c5e2ea79e642a0b test/functional/tools/collection_two_paired.xml
--- a/test/functional/tools/collection_two_paired.xml
+++ b/test/functional/tools/collection_two_paired.xml
@@ -20,8 +20,8 @@
<param name="f2" type="data_collection" collection_type="paired" /></when><when value="list">
- <param name="f1" type="data_collection" collection_type="paired" />
- <param name="f2" type="data_collection" collection_type="paired" />
+ <param name="f1" type="data_collection" collection_type="list" />
+ <param name="f2" type="data_collection" collection_type="list" /></when></conditional></inputs>
https://bitbucket.org/galaxy/galaxy-central/commits/dd39f52ba6fc/
Changeset: dd39f52ba6fc
User: dannon
Date: 2014-07-24 23:52:30
Summary: Cleanup in galaxy.util
Affected #: 1 file
diff -r 3686de5c8280c18c197323948c5e2ea79e642a0b -r dd39f52ba6fc0cea9328d1437842904ac1d020c9 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -48,10 +48,10 @@
from .inflection import Inflector, English
inflector = Inflector(English)
-log = logging.getLogger(__name__)
+log = logging.getLogger(__name__)
_lock = threading.RLock()
-CHUNK_SIZE = 65536 #64k
+CHUNK_SIZE = 65536 # 64k
DATABASE_MAX_STRING_SIZE = 32768
DATABASE_MAX_STRING_SIZE_PRETTY = '32K'
@@ -62,6 +62,7 @@
NULL_CHAR = '\000'
BINARY_CHARS = [ NULL_CHAR ]
+
def is_multi_byte( chars ):
for char in chars:
try:
@@ -69,18 +70,15 @@
except UnicodeDecodeError:
# Probably binary
return False
- if wchartype.is_asian( char ) or \
- wchartype.is_full_width( char ) or \
- wchartype.is_kanji( char ) or \
- wchartype.is_hiragana( char ) or \
- wchartype.is_katakana( char ) or \
- wchartype.is_half_katakana( char ) or \
- wchartype.is_hangul( char ) or \
- wchartype.is_full_digit( char ) or \
- wchartype.is_full_letter( char ):
+ if ( wchartype.is_asian( char ) or wchartype.is_full_width( char ) or
+ wchartype.is_kanji( char ) or wchartype.is_hiragana( char ) or
+ wchartype.is_katakana( char ) or wchartype.is_half_katakana( char )
+ or wchartype.is_hangul( char ) or wchartype.is_full_digit( char )
+ or wchartype.is_full_letter( char )):
return True
return False
+
def is_binary( value, binary_chars=None ):
"""
File is binary if it contains a null-byte by default (e.g. behavior of grep, etc.).
@@ -99,6 +97,7 @@
return True
return False
+
def get_charset_from_http_headers( headers, default=None ):
rval = headers.get('content-type', None )
if rval and 'charset=' in rval:
@@ -107,16 +106,18 @@
return rval
return default
+
def synchronized(func):
"""This wrapper will serialize access to 'func' to a single thread. Use it as a decorator."""
def caller(*params, **kparams):
- _lock.acquire(True) # Wait
+ _lock.acquire(True) # Wait
try:
return func(*params, **kparams)
finally:
_lock.release()
return caller
+
def file_iter(fname, sep=None):
"""
This generator iterates over a file and yields its lines
@@ -131,6 +132,7 @@
if line and line[0] != '#':
yield line.split(sep)
+
def file_reader( fp, chunk_size=CHUNK_SIZE ):
"""This generator yields the open fileobject in chunks (default 64k). Closes the file at the end"""
while 1:
@@ -140,6 +142,7 @@
yield data
fp.close()
+
def unique_id(KEY_SIZE=128):
"""
Generates an unique id
@@ -148,8 +151,8 @@
>>> len(set(ids))
1000
"""
- id = str( random.getrandbits( KEY_SIZE ) )
- return md5(id).hexdigest()
+ return md5(str( random.getrandbits( KEY_SIZE ) )).hexdigest()
+
def parse_xml(fname):
"""Returns a parsed xml tree"""
@@ -163,6 +166,7 @@
tree = ElementTree.fromstring(xml_string)
return tree
+
def xml_to_string( elem, pretty=False ):
"""Returns a string from an xml tree"""
if pretty:
@@ -170,12 +174,13 @@
try:
return ElementTree.tostring( elem )
except TypeError, e:
- #assume this is a comment
+ # we assume this is a comment
if hasattr( elem, 'text' ):
return "<!-- %s -->\n" % ( elem.text )
else:
raise e
+
def xml_element_compare( elem1, elem2 ):
if not isinstance( elem1, dict ):
elem1 = xml_element_to_dict( elem1 )
@@ -183,9 +188,11 @@
elem2 = xml_element_to_dict( elem2 )
return elem1 == elem2
+
def xml_element_list_compare( elem_list1, elem_list2 ):
return [ xml_element_to_dict( elem ) for elem in elem_list1 ] == [ xml_element_to_dict( elem ) for elem in elem_list2 ]
+
def xml_element_to_dict( elem ):
rval = {}
if elem.attrib:
@@ -220,7 +227,6 @@
return rval
-
def pretty_print_xml( elem, level=0 ):
pad = ' '
i = "\n" + level * pad
@@ -238,26 +244,28 @@
elem.tail = i + pad
return elem
+
def get_file_size( value, default=None ):
try:
- #try built-in
+ # try built-in
return os.path.getsize( value )
except:
try:
- #try built-in one name attribute
+ # try built-in one name attribute
return os.path.getsize( value.name )
except:
try:
- #try tell() of end of object
+ # try tell() of end of object
offset = value.tell()
value.seek( 0, 2 )
rval = value.tell()
value.seek( offset )
return rval
except:
- #return default value
+ # return default value
return default
+
def shrink_stream_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ):
rval = ''
if get_file_size( value ) > size:
@@ -292,6 +300,7 @@
rval += data
return rval
+
def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ):
if len( value ) > size:
len_join_by = len( join_by )
@@ -311,29 +320,30 @@
value = "%s%s%s" % ( value[:left_index], join_by, value[-right_index:] )
return value
+
def pretty_print_json(json_data, is_json_string=False):
if is_json_string:
json_data = json.from_json_string(json_data)
return json.to_json_string(json_data, sort_keys=True, indent=4)
# characters that are valid
-valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")
+valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")
# characters that are allowed but need to be escaped
-mapped_chars = { '>' :'__gt__',
- '<' :'__lt__',
- "'" :'__sq__',
- '"' :'__dq__',
- '[' :'__ob__',
- ']' :'__cb__',
- '{' :'__oc__',
- '}' :'__cc__',
- '@' : '__at__',
- '\n' : '__cn__',
- '\r' : '__cr__',
- '\t' : '__tc__',
- '#' : '__pd__'
- }
+mapped_chars = { '>': '__gt__',
+ '<': '__lt__',
+ "'": '__sq__',
+ '"': '__dq__',
+ '[': '__ob__',
+ ']': '__cb__',
+ '{': '__oc__',
+ '}': '__cc__',
+ '@': '__at__',
+ '\n': '__cn__',
+ '\r': '__cr__',
+ '\t': '__tc__',
+ '#': '__pd__'}
+
def restore_text(text):
"""Restores sanitized text"""
@@ -343,6 +353,7 @@
text = text.replace(value, key)
return text
+
def sanitize_text(text):
"""
Restricts the characters that are allowed in text; accepts both strings
@@ -353,6 +364,7 @@
elif isinstance( text, list ):
return [ _sanitize_text_helper(t) for t in text ]
+
def _sanitize_text_helper(text):
"""Restricts the characters that are allowed in a string"""
@@ -363,9 +375,10 @@
elif c in mapped_chars:
out.append(mapped_chars[c])
else:
- out.append('X') # makes debugging easier
+ out.append('X') # makes debugging easier
return ''.join(out)
+
def sanitize_param(value):
"""Clean incoming parameters (strings or lists)"""
if isinstance( value, basestring ):
@@ -373,10 +386,12 @@
elif isinstance( value, list ):
return map(sanitize_text, value)
else:
- raise Exception, 'Unknown parameter type (%s)' % ( type( value ) )
+ raise Exception('Unknown parameter type (%s)' % ( type( value ) ))
valid_filename_chars = set( string.ascii_letters + string.digits + '_.' )
invalid_filenames = [ '', '.', '..' ]
+
+
def sanitize_for_filename( text, default=None ):
"""
Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name.
@@ -512,7 +527,7 @@
def __init__( self, params, sanitize=True ):
if sanitize:
for key, value in params.items():
- if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: #sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed.
+ if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: # sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed.
self.__dict__[ key ] = sanitize_param( value )
else:
self.__dict__[ key ] = value
@@ -525,7 +540,7 @@
"""
flat = []
for key, value in self.__dict__.items():
- if type(value) == type([]):
+ if isinstance(value, list):
for v in value:
flat.append( (key, v) )
else:
@@ -551,16 +566,19 @@
def update(self, values):
self.__dict__.update(values)
+
def rst_to_html( s ):
"""Convert a blob of reStructuredText to HTML"""
log = logging.getLogger( "docutils" )
+
class FakeStream( object ):
def write( self, str ):
if len( str ) > 0 and not str.isspace():
log.warn( str )
return unicodify( docutils.core.publish_string( s,
- writer=docutils.writers.html4css1.Writer(),
- settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) )
+ writer=docutils.writers.html4css1.Writer(),
+ settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) )
+
def xml_text(root, name=None):
"""Returns the text inside an element"""
@@ -582,6 +600,8 @@
# asbool implementation pulled from PasteDeploy
truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
+
+
def asbool(obj):
if isinstance(obj, basestring):
obj = obj.strip().lower()
@@ -600,6 +620,7 @@
else:
return False
+
def string_as_bool_or_none( string ):
"""
Returns True, None or False based on the argument:
@@ -618,6 +639,7 @@
else:
return False
+
def listify( item, do_strip=False ):
"""
Make a single item a single item list, or return a list if passed a
@@ -635,6 +657,7 @@
else:
return [ item ]
+
def commaify(amount):
orig = amount
new = re.sub("^(-?\d+)(\d{3})", '\g<1>,\g<2>', amount)
@@ -643,7 +666,8 @@
else:
return commaify(new)
-def roundify(amount, sfs = 2):
+
+def roundify(amount, sfs=2):
"""
Take a number in string form and truncate to 'sfs' significant figures.
"""
@@ -652,6 +676,7 @@
else:
return amount[0:sfs] + '0'*(len(amount) - sfs)
+
def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None ):
"""
Returns a unicode string or None
@@ -691,6 +716,7 @@
def object_to_string( obj ):
return binascii.hexlify( pickle.dumps( obj, 2 ) )
+
def string_to_object( s ):
return pickle.loads( binascii.unhexlify( s ) )
@@ -743,19 +769,23 @@
return False
return True
+
def get_ucsc_by_build(build):
sites = []
for site in ucsc_build_sites:
if build in site['builds']:
- sites.append((site['name'],site['url']))
+ sites.append((site['name'], site['url']))
return sites
+
+
def get_gbrowse_sites_by_build(build):
sites = []
for site in gbrowse_build_sites:
if build in site['builds']:
- sites.append((site['name'],site['url']))
+ sites.append((site['name'], site['url']))
return sites
+
def read_dbnames(filename):
""" Read build names from file """
class DBNames( list ):
@@ -764,30 +794,34 @@
db_names = DBNames()
try:
ucsc_builds = {}
- man_builds = [] #assume these are integers
+ man_builds = [] # assume these are integers
name_to_db_base = {}
for line in open(filename):
try:
- if line[0:1] == "#": continue
- fields = line.replace("\r","").replace("\n","").split("\t")
- #Special case of unspecified build is at top of list
+ if line[0:1] == "#":
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
+ # Special case of unspecified build is at top of list
if fields[0] == "?":
- db_names.insert(0,(fields[0],fields[1]))
+ db_names.insert(0, (fields[0], fields[1]))
continue
- try: #manual build (i.e. microbes)
+ try: # manual build (i.e. microbes)
int(fields[0])
man_builds.append((fields[1], fields[0]))
- except: #UCSC build
+ except: # UCSC build
db_base = fields[0].rstrip('0123456789')
if db_base not in ucsc_builds:
ucsc_builds[db_base] = []
name_to_db_base[fields[1]] = db_base
- #we want to sort within a species numerically by revision number
+ # we want to sort within a species numerically by revision number
build_rev = re.compile(r'\d+$')
- try: build_rev = int(build_rev.findall(fields[0])[0])
- except: build_rev = 0
- ucsc_builds[db_base].append((build_rev, fields[0],fields[1]))
- except: continue
+ try:
+ build_rev = int(build_rev.findall(fields[0])[0])
+ except:
+ build_rev = 0
+ ucsc_builds[db_base].append((build_rev, fields[0], fields[1]))
+ except:
+ continue
sort_names = name_to_db_base.keys()
sort_names.sort()
for name in sort_names:
@@ -796,16 +830,18 @@
ucsc_builds[db_base].reverse()
ucsc_builds[db_base] = [(build, name) for build_rev, build, name in ucsc_builds[db_base]]
db_names = DBNames( db_names + ucsc_builds[db_base] )
- if len( db_names ) > 1 and len( man_builds ) > 0: db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) )
+ if len( db_names ) > 1 and len( man_builds ) > 0:
+ db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) )
man_builds.sort()
- man_builds = [(build, name) for name, build in man_builds]
+ man_builds = [(build, name) for name, build in man_builds]
db_names = DBNames( db_names + man_builds )
except Exception, e:
print "ERROR: Unable to read builds file:", e
- if len(db_names)<1:
+ if len(db_names) < 1:
db_names = DBNames( [( db_names.default_value, db_names.default_name )] )
return db_names
+
def read_ensembl( filename, ucsc ):
""" Read Ensembl build names from file """
ucsc_builds = []
@@ -814,47 +850,55 @@
ensembl_builds = list()
try:
for line in open( filename ):
- if line[0:1] in [ '#', '\t' ]: continue
- fields = line.replace("\r","").replace("\n","").split("\t")
- if fields[0] in ucsc_builds: continue
+ if line[0:1] in [ '#', '\t' ]:
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
+ if fields[0] in ucsc_builds:
+ continue
ensembl_builds.append( dict( dbkey=fields[0], release=fields[1], name=fields[2].replace( '_', ' ' ) ) )
except Exception, e:
print "ERROR: Unable to read builds file:", e
return ensembl_builds
+
def read_ncbi( filename ):
""" Read NCBI build names from file """
ncbi_builds = list()
try:
for line in open( filename ):
- if line[0:1] in [ '#', '\t' ]: continue
- fields = line.replace("\r","").replace("\n","").split("\t")
+ if line[0:1] in [ '#', '\t' ]:
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
ncbi_builds.append( dict( dbkey=fields[0], name=fields[1] ) )
except Exception, e:
print "ERROR: Unable to read builds file:", e
return ncbi_builds
+
def read_build_sites( filename, check_builds=True ):
""" read db names to ucsc mappings from file, this file should probably be merged with the one above """
build_sites = []
try:
for line in open(filename):
try:
- if line[0:1] == "#": continue
- fields = line.replace("\r","").replace("\n","").split("\t")
+ if line[0:1] == "#":
+ continue
+ fields = line.replace("\r", "").replace("\n", "").split("\t")
site_name = fields[0]
site = fields[1]
if check_builds:
site_builds = fields[2].split(",")
- site_dict = {'name':site_name, 'url':site, 'builds':site_builds}
+ site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
else:
- site_dict = {'name':site_name, 'url':site}
+ site_dict = {'name': site_name, 'url': site}
build_sites.append( site_dict )
- except: continue
+ except:
+ continue
except:
- print "ERROR: Unable to read builds for site file %s" %filename
+ print "ERROR: Unable to read builds for site file %s" % filename
return build_sites
+
def relativize_symlinks( path, start=None, followlinks=False):
for root, dirs, files in os.walk( path, followlinks=followlinks ):
rel_start = None
@@ -871,23 +915,26 @@
os.remove( symlink_file_name )
os.symlink( rel_path, symlink_file_name )
+
def stringify_dictionary_keys( in_dict ):
- #returns a new dictionary
- #changes unicode keys into strings, only works on top level (does not recurse)
- #unicode keys are not valid for expansion into keyword arguments on method calls
+ # returns a new dictionary
+ # changes unicode keys into strings, only works on top level (does not recurse)
+ # unicode keys are not valid for expansion into keyword arguments on method calls
out_dict = {}
for key, value in in_dict.iteritems():
out_dict[ str( key ) ] = value
return out_dict
+
def recursively_stringify_dictionary_keys( d ):
if isinstance(d, dict):
- return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k,v in d.iteritems()])
+ return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k, v in d.iteritems()])
elif isinstance(d, list):
return [recursively_stringify_dictionary_keys(x) for x in d]
else:
return d
+
def mkstemp_ln( src, prefix='mkstemp_ln_' ):
"""
From tempfile._mkstemp_inner, generate a hard link in the same dir with a
@@ -904,9 +951,10 @@
return (os.path.abspath(file))
except OSError, e:
if e.errno == errno.EEXIST:
- continue # try again
+ continue # try again
raise
- raise IOError, (errno.EEXIST, "No usable temporary file name found")
+ raise IOError(errno.EEXIST, "No usable temporary file name found")
+
def umask_fix_perms( path, umask, unmasked_perms, gid=None ):
"""
@@ -923,7 +971,7 @@
try:
os.chmod( path, perms )
except Exception, e:
- log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ), \
+ log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ),
path,
oct( perms ),
oct( stat.S_IMODE( st.st_mode ) ),
@@ -939,11 +987,12 @@
except:
desired_group = gid
current_group = st.st_gid
- log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group, \
+ log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group,
path,
current_group,
e ) )
+
def docstring_trim(docstring):
"""Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/"""
if not docstring:
@@ -970,6 +1019,7 @@
# Return a single string:
return '\n'.join(trimmed)
+
def nice_size(size):
"""
Returns a readably formatted string with the size
@@ -989,14 +1039,15 @@
except:
return '??? bytes'
for ind, word in enumerate(words):
- step = 1024 ** (ind + 1)
+ step = 1024 ** (ind + 1)
if step > size:
size = size / float(1024 ** ind)
- if word == 'bytes': # No decimals for bytes
+ if word == 'bytes': # No decimals for bytes
return "%d bytes" % size
return "%.1f %s" % (size, word)
return '??? bytes'
+
def size_to_bytes( size ):
"""
Returns a number of bytes if given a reasonably formatted string with the size
@@ -1023,6 +1074,7 @@
elif multiple.startswith( 'b' ):
return int( size )
+
def send_mail( frm, to, subject, body, config ):
"""
Sends an email.
@@ -1072,6 +1124,7 @@
s.sendmail( frm, to, msg.as_string() )
s.quit()
+
def force_symlink( source, link_name ):
try:
os.symlink( source, link_name )
@@ -1082,12 +1135,13 @@
else:
raise e
+
def move_merge( source, target ):
- #when using shutil and moving a directory, if the target exists,
- #then the directory is placed inside of it
- #if the target doesn't exist, then the target is made into the directory
- #this makes it so that the target is always the target, and if it exists,
- #the source contents are moved into the target
+ # when using shutil and moving a directory, if the target exists,
+ # then the directory is placed inside of it
+ # if the target doesn't exist, then the target is made into the directory
+ # this makes it so that the target is always the target, and if it exists,
+ # the source contents are moved into the target
if os.path.isdir( source ) and os.path.exists( target ) and os.path.isdir( target ):
for name in os.listdir( source ):
move_merge( os.path.join( source, name ), os.path.join( target, name ) )
@@ -1103,7 +1157,7 @@
rv |= ord(x) ^ ord(y)
return rv == 0
-galaxy_root_path = os.path.join(__path__[0], "..","..","..")
+galaxy_root_path = os.path.join(__path__[0], "..", "..", "..")
# The dbnames list is used in edit attributes and the upload tool
dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) )
@@ -1114,6 +1168,7 @@
gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) )
dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names)
+
def galaxy_directory():
return os.path.abspath(galaxy_root_path)
https://bitbucket.org/galaxy/galaxy-central/commits/f03f9c5a5efc/
Changeset: f03f9c5a5efc
User: dannon
Date: 2014-07-24 23:53:37
Summary: Prevent redefinition of build_rev in list comprehension -- doesn't get used anyway
Affected #: 1 file
diff -r dd39f52ba6fc0cea9328d1437842904ac1d020c9 -r f03f9c5a5efc7fecb4ca131f66c441d55cc5d353 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -828,7 +828,7 @@
db_base = name_to_db_base[name]
ucsc_builds[db_base].sort()
ucsc_builds[db_base].reverse()
- ucsc_builds[db_base] = [(build, name) for build_rev, build, name in ucsc_builds[db_base]]
+ ucsc_builds[db_base] = [(build, name) for _, build, name in ucsc_builds[db_base]]
db_names = DBNames( db_names + ucsc_builds[db_base] )
if len( db_names ) > 1 and len( man_builds ) > 0:
db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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