commit/galaxy-central: greg: Display the "Skip automated testing" checkbox on repositories of type tool_dependency_definition in the tool shed.
by commits-noreply＠bitbucket.org 20 Nov '13
by commits-noreply＠bitbucket.org 20 Nov '13
20 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f8bebd9e12f5/
Changeset: f8bebd9e12f5
User: greg
Date: 2013-11-20 21:24:14
Summary: Display the "Skip automated testing" checkbox on repositories of type tool_dependency_definition in the tool shed.
Affected #: 1 file
diff -r 3d8ecec9515505f276fdaaa54c2f1af1c1d390b4 -r f8bebd9e12f53fca874739df55a34b73be224c0b templates/webapps/tool_shed/repository/manage_repository.mako
--- a/templates/webapps/tool_shed/repository/manage_repository.mako
+++ b/templates/webapps/tool_shed/repository/manage_repository.mako
@@ -7,6 +7,7 @@
<%
from galaxy.web.framework.helpers import time_ago
from tool_shed.util.shed_util_common import changeset_is_malicious
+ from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION
if repository.metadata_revisions:
has_metadata = True
@@ -199,17 +200,25 @@
</div></div>
${render_repository_items( metadata, containers_dict, can_set_metadata=True, render_repository_actions_for='tool_shed' )}
-%if includes_tools:
+%if includes_tools or repository.type == TOOL_DEPENDENCY_DEFINITION:
<p/><div class="toolForm"><div class="toolFormTitle">Automated tool tests</div><div class="toolFormBody"><form name="skip_tool_tests" id="skip_tool_tests" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository_metadata.changeset_revision )}" method="post" ><div class="form-row">
- <label>Skip automated testing of tools in this revision:</label>
+ %if repository.type == TOOL_DEPENDENCY_DEFINITION:
+ <label>Skip automated testing of this tool dependency recipe</label>
+ %else:
+ <label>Skip automated testing of tools in this revision:</label>
+ %endif
${skip_tool_tests_check_box.get_html()}
<div class="toolParamHelp" style="clear: both;">
- Check the box and click <b>Save</b> to skip automated testing of the tools in this revision.
+ %if repository.type == TOOL_DEPENDENCY_DEFINITION:
+ Check the box and click <b>Save</b> to skip automated testing of this tool dependency recipe.
+ %else:
+ Check the box and click <b>Save</b> to skip automated testing of the tools in this revision.
+ %endif
</div></div><div style="clear: both"></div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Enhance the tool shed repository's tool test inspection components to categorize empty <tests> or <test> tag sets defined in tool configs as "tool missing tests" instead of testing the tools with resulting test failures.
by commits-noreply＠bitbucket.org 20 Nov '13
by commits-noreply＠bitbucket.org 20 Nov '13
20 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3d8ecec95155/
Changeset: 3d8ecec95155
User: greg
Date: 2013-11-20 19:20:14
Summary: Enhance the tool shed repository's tool test inspection components to categorize empty <tests> or <test> tag sets defined in tool configs as "tool missing tests" instead of testing the tools with resulting test failures.
Affected #: 1 file
diff -r ec6c12a576850401bc502af2aa679a6c18568219 -r 3d8ecec9515505f276fdaaa54c2f1af1c1d390b4 lib/tool_shed/scripts/check_repositories_for_functional_tests.py
--- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py
+++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py
@@ -284,18 +284,38 @@
# If there are no tests, this tool should not be tested, since the tool functional tests only report failure if the test itself fails,
# not if it's missing or undefined. Filtering out those repositories at this step will reduce the number of "false negatives" the
# automated functional test framework produces.
- tool_has_tests = True
- if 'tests' not in tool_metadata or not tool_metadata[ 'tests' ]:
- tool_has_tests = False
- if verbosity >= 2:
- print '# No functional tests defined for %s.' % tool_id
- no_tests += 1
- else:
- tool_has_tests = True
+ tool_has_tests = False
+ defined_test_dicts = tool_metadata.get( 'tests', None )
+ if defined_test_dicts is not None:
+ # We need to inspect the <test> tags because the following tags...
+ # <tests>
+ # </tests>
+ # ...will produce the following metadata:
+ # "tests": []
+ # And the following tags...
+ # <tests>
+ # <test>
+ # </test>
+ # </tests>
+ # ...will produce the following metadata:
+ # "tests":
+ # [{"inputs": [], "name": "Test-1", "outputs": [], "required_files": []}]
+ for defined_test_dict in defined_test_dicts:
+ inputs = defined_test_dict.get( 'inputs', [] )
+ outputs = defined_test_dict.get( 'outputs', [] )
+ if inputs and outputs:
+ # At least one tool within the repository has a valid <test> tag.
+ tool_has_tests = True
+ break
+ if tool_has_tests:
if verbosity >= 2:
print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \
( tool_id, changeset_revision, name )
has_tests += 1
+ else:
+ if verbosity >= 2:
+ print '# No functional tests defined for %s.' % tool_id
+ no_tests += 1
failure_reason = ''
problem_found = False
missing_test_files = []
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: HDA UI: remove visualizations button for anon users, fix tooltip/popup when only one visualization is found
by commits-noreply＠bitbucket.org 20 Nov '13
by commits-noreply＠bitbucket.org 20 Nov '13
20 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ec6c12a57685/
Changeset: ec6c12a57685
User: carlfeberhard
Date: 2013-11-20 17:25:41
Summary: HDA UI: remove visualizations button for anon users, fix tooltip/popup when only one visualization is found
Affected #: 2 files
diff -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 -r ec6c12a576850401bc502af2aa679a6c18568219 static/scripts/mvc/dataset/hda-edit.js
--- a/static/scripts/mvc/dataset/hda-edit.js
+++ b/static/scripts/mvc/dataset/hda-edit.js
@@ -156,7 +156,8 @@
*/
_render_visualizationsButton : function(){
var visualizations = this.model.get( 'visualizations' );
- if( ( !this.model.hasData() )
+ if( ( !this.hasUser )
+ || ( !this.model.hasData() )
|| ( _.isEmpty( visualizations ) ) ){
return null;
}
@@ -209,8 +210,8 @@
}
// No need for popup menu because there's a single visualization.
- if ( visualizations.length === 1 ) {
- $icon.attr( 'title', visualizations[0] );
+ if( visualizations.length === 1 ){
+ $icon.attr( 'data-original-title', visualizations[0] );
$icon.click( create_viz_action( visualizations[0] ) );
// >1: Populate menu dict with visualization fns, make the popupmenu
diff -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 -r ec6c12a576850401bc502af2aa679a6c18568219 static/scripts/packed/mvc/dataset/hda-edit.js
--- a/static/scripts/packed/mvc/dataset/hda-edit.js
+++ b/static/scripts/packed/mvc/dataset/hda-edit.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="galaxy_main">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("data-original-title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="galaxy_main">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: HDA UI: implement multi select; pack scripts
by commits-noreply＠bitbucket.org 20 Nov '13
by commits-noreply＠bitbucket.org 20 Nov '13
20 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/df7d45db5d2b/
Changeset: df7d45db5d2b
User: carlfeberhard
Date: 2013-11-20 17:01:24
Summary: HDA UI: implement multi select; pack scripts
Affected #: 18 files
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -40,6 +40,11 @@
this._render_showParamsButton
];
+ /** is the view currently in selection mode? */
+ //this.selectable = attributes.selectable || false;
+ this.selectable = false;
+ /** is the view currently selected? */
+ this.selected = false;
/** is the body of this hda view expanded/not. */
this.expanded = attributes.expanded || false;
this._setUpListeners();
@@ -88,13 +93,14 @@
var $newRender = $( HDABaseView.templates.skeleton( this.model.toJSON() ) );
$newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() );
$newRender.children( '.dataset-body' ).replaceWith( this._render_body() );
+ //this._renderSelectable( $newRender );
this._setUpBehaviors( $newRender );
// fade the old render out (if desired)
if( fade ){
$( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); });
}
- // empty the old render, update to any new HDA state, swap in the new render contents
+ // empty the old render, update to any new HDA state, swap in the new render contents, handle multi-select
$( view ).queue( function( next ){
this.$el.empty()
.attr( 'class', view.className ).addClass( 'state-' + view.model.get( 'state' ) )
@@ -111,6 +117,7 @@
if( this.model.inReadyState() ){
this.trigger( 'rendered:ready', view );
}
+ if( this.selectable ){ this.showSelect(); }
next();
});
return this;
@@ -183,7 +190,7 @@
displayBtnData.faIcon = 'fa-eye';
return faIconButton( displayBtnData );
},
-
+
// ......................................................................... primary actions
/** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this hda.
* @returns {jQuery} rendered DOM
@@ -387,7 +394,9 @@
/** event map */
events : {
// expand the body when the title is clicked
- 'click .dataset-title-bar' : 'toggleBodyVisibility'
+ 'click .dataset-title-bar' : 'toggleBodyVisibility',
+ // toggle selected state
+ 'click .dataset-selector' : 'select'
},
/** Show or hide the body/details of an HDA.
@@ -405,6 +414,7 @@
} else {
this.collapseBody();
}
+ return false;
},
/** Render and show the full, detailed body of this view including extra data and controls.
@@ -414,10 +424,16 @@
var hdaView = this;
function _renderBodyAndExpand(){
- hdaView.render( false ).$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){
- hdaView.expanded = true;
- hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) );
- });
+ hdaView.$el.children( '.dataset-body' ).replaceWith( hdaView._render_body() );
+ hdaView.$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){
+ hdaView.expanded = true;
+ hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) );
+ });
+
+ //hdaView.render( false ).$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){
+ // hdaView.expanded = true;
+ // hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) );
+ //});
}
// fetch first if no details in the model
if( this.model.inReadyState() && !this.model.hasDetails() ){
@@ -440,6 +456,65 @@
});
},
+ // ......................................................................... selection
+ /** display a (fa-icon) checkbox on the left of the hda that fires events when checked
+ * Note: this also hides the primary actions
+ */
+ showSelect : function( speed ){
+ // if already shown, do nothing
+ if( this.$el.find( '.dataset-selector' ).css( 'display' ) !== 'none' ){ return; }
+ speed = ( speed !== undefined )?( speed ):( this.fxSpeed );
+
+ // create a jq fx queue to do this sequentially: fadeout the buttons, embiggen the selector
+ var hdaView = this,
+ SELECTOR_WIDTH = 32;
+
+ this.$el.queue( 'fx', function( next ){
+ $( this ).find( '.dataset-primary-actions' ).fadeOut( speed, next );
+ });
+ this.$el.queue( 'fx', function( next ){
+ $( this ).find( '.dataset-selector' ).show()
+ // height is height of titlebar, width will animate from 0 to WIDTH
+ .css({
+ height: $( this ).find( '.dataset-title-bar' ).innerHeight()
+ })
+ .animate({ width: SELECTOR_WIDTH }, speed, next );
+ hdaView.selectable = true;
+ hdaView.trigger( 'selectable', true, hdaView );
+ });
+ },
+
+ /** remove the selection checkbox */
+ hideSelect : function( speed ){
+ speed = ( speed !== undefined )?( speed ):( this.fxSpeed );
+
+ // reverse the process from showSelect
+ this.selectable = false;
+ this.trigger( 'selectable', false, this );
+ this.$el.queue( 'fx', function( next ){
+ $( this ).find( '.dataset-selector' ).animate({ width: '0px' }, speed, function(){
+ $( this ).hide();
+ next();
+ });
+ });
+ this.$el.queue( 'fx', function( next ){
+ $( this ).find( '.dataset-primary-actions' ).fadeIn( speed, next );
+ });
+ },
+
+ /** event handler for selection (also programmatic selection)
+ * @param {boolean} selected T/F select/de-select this hda
+ */
+ select : function( event, selected ){
+ // do nothing if selected is passed and selector already in desired state
+ if( selected !== undefined && selected === this.selected ){ return false; }
+ // switch icon, set selected, and trigger event
+ this.$el.find( '.dataset-selector span' ).toggleClass( 'fa-square-o fa-check-square-o' );
+ this.selected = !this.selected;
+ this.trigger( ( this.selected )?( 'selected' ):( 'de-selected' ), this );
+ return false;
+ },
+
// ......................................................................... removal
/** Remove this view's html from the DOM and remove all event listeners.
* @param {Function} callback an optional function called when removal is done
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/mvc/dataset/hda-edit.js
--- a/static/scripts/mvc/dataset/hda-edit.js
+++ b/static/scripts/mvc/dataset/hda-edit.js
@@ -32,6 +32,7 @@
// HDAEdit gets the rerun button on almost all states
this._render_rerunButton
];
+
},
// ......................................................................... edit attr, delete
@@ -336,12 +337,11 @@
// ......................................................................... events
/** event map */
- events : {
- 'click .dataset-title-bar' : 'toggleBodyVisibility',
+ events : _.extend( _.clone( hdaBase.HDABaseView.prototype.events ), {
'click .dataset-undelete' : function( ev ){ this.model.undelete(); return false; },
'click .dataset-unhide' : function( ev ){ this.model.unhide(); return false; },
'click .dataset-purge' : 'confirmPurge'
- },
+ }),
/** listener for item purge */
confirmPurge : function _confirmPurge( ev ){
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/mvc/dataset/hda-model.js
--- a/static/scripts/mvc/dataset/hda-model.js
+++ b/static/scripts/mvc/dataset/hda-model.js
@@ -395,8 +395,11 @@
// ........................................................................ ajax
/** fetch detailed model data for all HDAs in this collection */
- fetchAllDetails : function(){
- return this.fetch({ data : { details : 'all' } });
+ fetchAllDetails : function( options ){
+ options = options || {};
+ var detailsFlag = { details: 'all' };
+ options.data = ( options.data )?( _.extend( options.data, detailsFlag ) ):( detailsFlag );
+ return this.fetch( options );
},
// ........................................................................ sorting/filtering
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -763,6 +763,25 @@
return this.storage.get( 'show_hidden' );
},
+ // ........................................................................ multi-select of hdas
+ showSelect : function( speed ){
+ _.each( this.hdaViews, function( view ){
+ view.showSelect( speed );
+ });
+ },
+
+ hideSelect : function( speed ){
+ _.each( this.hdaViews, function( view ){
+ view.hideSelect( speed );
+ });
+ },
+
+ getSelectedHdaViews : function(){
+ return _.filter( this.hdaViews, function( v ){
+ return v.selected;
+ });
+ },
+
// ........................................................................ loading indicator
/** hide the panel and display a loading indicator (in the panel's parent) when history model's are switched */
showLoadingIndicator : function( msg, speed, callback ){
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/galaxy.upload.js
--- a/static/scripts/packed/galaxy.upload.js
+++ b/static/scripts/packed/galaxy.upload.js
@@ -1,1 +1,1 @@
-define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c,d){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],state:{init:"fa fa-trash-o",queued:"fa fa-spinner fa-spin",running:"__running__",success:"fa fa-check",error:"fa fa-exclamation-triangle"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}var e=this;this.button_show=new c.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},on_unload:function(){if(e.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var e=this;d.jsonFromUrl(galaxy_config.root+"api/datatypes",function(f){for(key in f){e.select_extension.push([f[key],f[key]])}});d.jsonFromUrl(galaxy_config.root+"api/genomes",function(f){var g=e.select_genome[0];e.select_genome=[];for(key in f){if(f[key].length>1){if(f[key][1]!==g[1]){e.select_genome.push(f[key])}}}e.select_genome.sort(function(i,h){return i[0]>h[0]?1:i[0]<h[0]?-1:0});e.select_genome.unshift(g)})},event_dragover:function(f){},event_dragleave:function(f){},event_announce:function(i,g,n){var f="#upload-"+i;$(this.el).find("tbody:last").append(this.template_row(f));var h=this.get_upload_item(i);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var m=this;h.find("#symbol").on("click",function(){m.event_remove(i)});h.find("#text-content").on("keyup",function(){var o=h.find("#text-content").val().length;h.find("#size").html(m.size_to_string(o))});this.event_progress(i,g,0);this.counter.announce++;this.update_screen();if(g.size==-1){var l=h.find("#text");var j=8;var e=h.width()-2*j;var k=h.height()-j;l.css("width",e+"px");l.css("top",k+"px");h.height(k+l.height()+2*j);l.show()}},event_initialize:function(i,e,n){this.button_show.number(this.counter.announce);var g=this.get_upload_item(i);var k=g.find("#symbol");k.addClass(this.state.running);var j=Galaxy.currHistoryPanel.model.get("id");var f=g.find("#extension").val();var m=g.find("#genome").val();var l=g.find("#text-content").val();var h=g.find("#space_to_tabs").is(":checked");if(!l&&!(e.size>0)){return null}this.uploadbox.configure({url:galaxy_config.root+"api/tools",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=f;tool_input["files_0|NAME"]=e.name;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=h;data={};data.history_id=j;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refreshHdas()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_start:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#text-content").attr("disabled",true);$(this).find("#genome").attr("disabled",true);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.start()},event_stop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#text-content").attr("disabled",false);$(this).find("#genome").attr("disabled",false);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_create:function(){this.uploadbox.add([{name:"New File",size:-1}])},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Create:function(){f.event_create()},Upload:function(){f.event_start()},Pause:function(){f.event_stop()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()},},height:"400",width:"900"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{if(e>0){e=e*10;f="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(f){var e='<tr id="'+f.substr(1)+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You may specify a list of URLs (one per line) or paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';e+='<td><select id="extension" class="extension">';for(key in this.select_extension){e+='<option value="'+this.select_extension[key][1]+'">'+this.select_extension[key][0]+"</option>"}e+="</select></td>";e+='<td><select id="genome" class="genome">';for(key in this.select_genome){e+='<option value="'+this.select_genome[key][1]+'">'+this.select_genome[key][0]+"</option>"}e+="</select></td>";e+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}});
\ No newline at end of file
+define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c,d){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],state:{init:"fa fa-trash-o",queued:"fa fa-spinner fa-spin",running:"__running__",success:"fa fa-check",error:"fa fa-exclamation-triangle"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(f){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}var e=this;this.button_show=new c.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(g){e.event_show(g)},on_unload:function(){if(e.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var e=this;d.jsonFromUrl(galaxy_config.root+"api/datatypes",function(g){for(key in g){e.select_extension.push([g[key],g[key]])}});d.jsonFromUrl(galaxy_config.root+"api/genomes",function(g){var h=e.select_genome[0];e.select_genome=[];for(key in g){if(g[key].length>1){if(g[key][1]!==h[1]){e.select_genome.push(g[key])}}}e.select_genome.sort(function(j,i){return j[0]>i[0]?1:j[0]<i[0]?-1:0});e.select_genome.unshift(h)});if(f){this.options=_.defaults(f,this.options)}},event_dragover:function(f){},event_dragleave:function(f){},event_announce:function(i,g,n){var f="#upload-"+i;$(this.el).find("tbody:last").append(this.template_row(f));var h=this.get_upload_item(i);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var m=this;h.find("#symbol").on("click",function(){m.event_remove(i)});h.find("#text-content").on("keyup",function(){var o=h.find("#text-content").val().length;h.find("#size").html(m.size_to_string(o))});var m=this;h.find("#genome").on("change",function(q){var p=$(q.target).val();var o=$(m.el).find(".upload-item");o.each(function(){var s=$(this).find("#symbol");var r=$(this).find("#genome");if(s.hasClass(m.state.init)&&r.val()=="?"){r.val(p)}})});this.event_progress(i,g,0);this.counter.announce++;this.update_screen();if(g.size==-1){var l=h.find("#text");var j=8;var e=h.width()-2*j;var k=h.height()-j;l.css("width",e+"px");l.css("top",k+"px");h.height(k+l.height()+2*j);l.show()}},event_initialize:function(i,e,n){this.button_show.number(this.counter.announce);var g=this.get_upload_item(i);var k=g.find("#symbol");k.addClass(this.state.running);var j=Galaxy.currHistoryPanel.model.get("id");var f=g.find("#extension").val();var m=g.find("#genome").val();var l=g.find("#text-content").val();var h=g.find("#space_to_tabs").is(":checked");if(!l&&!(e.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=f;tool_input["files_0|NAME"]=e.name;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=h;data={};data.history_id=j;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refreshHdas()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_start:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#text-content").attr("disabled",true);$(this).find("#genome").attr("disabled",true);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.start()},event_stop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#text-content").attr("disabled",false);$(this).find("#genome").attr("disabled",false);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_create:function(){this.uploadbox.add([{name:"New File",size:-1}])},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Create:function(){f.event_create()},Upload:function(){f.event_start()},Pause:function(){f.event_stop()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()},},height:"400",width:"900"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{if(e>0){e=e*10;f="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(f){var e='<tr id="'+f.substr(1)+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You may specify a list of URLs (one per line) or paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';e+='<td><select id="extension" class="extension">';for(key in this.select_extension){e+='<option value="'+this.select_extension[key][1]+'">'+this.select_extension[key][0]+"</option>"}e+="</select></td>";e+='<td><select id="genome" class="genome">';for(key in this.select_genome){e+='<option value="'+this.select_genome[key][1]+'">'+this.select_genome[key][0]+"</option>"}e+="</select></td>";e+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}});
\ No newline at end of file
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/mvc/dataset/hda-base.js
--- a/static/scripts/packed/mvc/dataset/hda-base.js
+++ b/static/scripts/packed/mvc/dataset/hda-base.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:"galaxy_main",classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}});
\ No newline at end of file
+define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.selectable=false;this.selected=false;this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.selectable){this.showSelect()}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:"galaxy_main",classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"select"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelect:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);var d=this,c=32;this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().css({height:$(this).find(".dataset-title-bar").innerHeight()}).animate({width:c},e,f);d.selectable=true;d.trigger("selectable",true,d)})},hideSelect:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);this.$el.queue("fx",function(d){$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})},select:function(d,c){if(c!==undefined&&c===this.selected){return false}this.$el.find(".dataset-selector span").toggleClass("fa-square-o fa-check-square-o");this.selected=!this.selected;this.trigger((this.selected)?("selected"):("de-selected"),this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}});
\ No newline at end of file
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/mvc/dataset/hda-edit.js
--- a/static/scripts/packed/mvc/dataset/hda-edit.js
+++ b/static/scripts/packed/mvc/dataset/hda-edit.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="galaxy_main">?</a>').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"},confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="galaxy_main">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}});
\ No newline at end of file
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/mvc/dataset/hda-model.js
--- a/static/scripts/packed/mvc/dataset/hda-model.js
+++ b/static/scripts/packed/mvc/dataset/hda-model.js
@@ -1,1 +1,1 @@
-define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:null},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);h.misc_info=jQuery.trim(h.misc_info);return h},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){return this.save({deleted:true},h)},undelete:function a(h){return this.save({deleted:false},h)},hide:function b(h){return this.save({visible:false},h)},unhide:function g(h){return this.save({visible:true},h)},purge:function f(h){h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set("purged",true)});j.fail(function(o,k,n){var l=_l("Unable to purge this dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})})},searchKeys:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],search:function(h){var i=this;h=h.toLowerCase();return _.filter(this.searchKeys,function(k){var j=i.get(k);return(_.isString(j)&&j.toLowerCase().indexOf(h)!==-1)})},matches:function(h){return !!this.search(h).length},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,i){return this.filter(function(j){return j.isVisible(h,i)})},fetchAllDetails:function(){return this.fetch({data:{details:"all"}})},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return("HDACollection()")}});return{HistoryDatasetAssociation:d,HDACollection:e}});
\ No newline at end of file
+define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:null},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);h.misc_info=jQuery.trim(h.misc_info);return h},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){return this.save({deleted:true},h)},undelete:function a(h){return this.save({deleted:false},h)},hide:function b(h){return this.save({visible:false},h)},unhide:function g(h){return this.save({visible:true},h)},purge:function f(h){h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set("purged",true)});j.fail(function(o,k,n){var l=_l("Unable to purge this dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})})},searchKeys:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],search:function(h){var i=this;h=h.toLowerCase();return _.filter(this.searchKeys,function(k){var j=i.get(k);return(_.isString(j)&&j.toLowerCase().indexOf(h)!==-1)})},matches:function(h){return !!this.search(h).length},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,i){return this.filter(function(j){return j.isVisible(h,i)})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return("HDACollection()")}});return{HistoryDatasetAssociation:d,HDACollection:e}});
\ No newline at end of file
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/mvc/history/history-panel.js
--- a/static/scripts/packed/mvc/history/history-panel.js
+++ b/static/scripts/packed/mvc/history/history-panel.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(d,b,a){var c=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(e){e=e||{};if(e.logger){this.logger=e.logger}this.log(this+".initialize:",e);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);if(this.model){this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden);this._setUpModelEventHandlers()}if(e.onready){e.onready.call(this)}},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(e){this.log(this+"",arguments)},this)}},errorHandler:function(g,j,f,i,h){var e=this._parseErrorMessage(g,j,f,i,h);if(j&&j.status===0&&j.readyState===0){}else{if(j&&j.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",e.message,e.details)})}else{this.displayMessage("error",e.message,e.details)}}}},_parseErrorMessage:function(h,l,g,k,j){var f=Galaxy.currUser,e={message:this._bePolite(k),details:{user:(f instanceof User)?(f.toJSON()):(f+""),source:(h instanceof Backbone.Model)?(h.toJSON()):(h+""),xhr:l,options:(l)?(_.omit(g,"xhr")):(g)}};_.extend(e.details,j||{});if(l&&_.isFunction(l.getAllResponseHeaders)){var i=l.getAllResponseHeaders();i=_.compact(i.split("\n"));i=_.map(i,function(m){return m.split(": ")});e.details.xhr.responseHeaders=_.object(i)}return e},_bePolite:function(e){e=e||_l("An error occurred while getting updates from the server");return e+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(f){var e=this;return this.loadHistoryWithHDADetails("current",f).then(function(h,g){e.trigger("current-history",e)})},switchToHistory:function(h,g){var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories/"+h+"/set_as_current")};return this.loadHistoryWithHDADetails(h,g,f).then(function(j,i){e.trigger("switched-history",e)})},createNewHistory:function(g){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,g,f).then(function(i,h){e.trigger("new-history",e)})},loadHistoryWithHDADetails:function(h,g,f,j){var e=this,i=function(k){return e.getExpandedHdaIds(k.id)};return this.loadHistory(h,g,f,j,i)},loadHistory:function(h,g,f,k,i){this.trigger("loading-history",this);g=g||{};var e=this;var j=d.History.getHistoryData(h,{historyFn:f,hdaFn:k,hdaDetailIds:g.initiallyExpanded||i});return this._loadHistoryFromXHR(j,g).fail(function(n,l,m){e.trigger("error",e,n,g,_l("An error was encountered while "+l),{historyId:h,history:m||{}})}).always(function(){e.trigger("loading-done",e)})},_loadHistoryFromXHR:function(g,f){var e=this;g.then(function(h,i){e.setModel(h,i,f)});g.fail(function(i,h){e.render()});return g},setModel:function(g,e,f){f=f||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){g.user=Galaxy.currUser.toJSON()}this.model=new d.History(g,e,f);this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(f,e){if(this.model){return this.model.refresh(f,e)}return $.when()},_setUpWebStorage:function(f,e,g){this.storage=new PersistentStorage(this._getStorageKey(this.model.get("id")),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(f){this.storage.set("exandedHdas",f)}if((e===true)||(e===false)){this.storage.set("show_deleted",e)}if((g===true)||(g===false)){this.storage.set("show_hidden",g)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},_getStorageKey:function(e){if(!e){throw new Error("_getStorageKey needs valid id: "+e)}return("history:"+e)},clearWebStorage:function(){for(var e in sessionStorage){if(e.indexOf("history:")===0){sessionStorage.removeItem(e)}}},getStoredOptions:function(f){if(!f||f==="current"){return(this.storage)?(this.storage.get()):({})}var e=sessionStorage.getItem(this._getStorageKey(f));return(e===null)?({}):(JSON.parse(e))},getExpandedHdaIds:function(e){var f=this.getStoredOptions(e).expandedHdas;return((_.isEmpty(f))?([]):(_.keys(f)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(f,h,e,g){this.errorHandler(f,h,e,g)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this);this.model.hdas.on("state:ready",function(f,g,e){if((!f.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[f.id])}},this)},addHdaView:function(h){this.log("add."+this,h);var f=this;if(!h.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function g(j){var i=f.$el.find(f.emptyMsgSelector);if(i.is(":visible")){i.fadeOut(f.fxSpeed,j)}else{j()}},function e(j){f.scrollToTop();var i=f.$el.find(f.datasetsSelector);f.createHdaView(h).$el.hide().prependTo(i).slideDown(f.fxSpeed)}])},createHdaView:function(g){var f=g.get("id"),e=this.storage.get("expandedHdas").get(f),h=new this.HDAView({model:g,expanded:e,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(h);this.hdaViews[f]=h;return h.render()},_setUpHdaListeners:function(f){var e=this;f.on("body-expanded",function(g){e.storage.get("expandedHdas").set(g,true)});f.on("body-collapsed",function(g){e.storage.get("expandedHdas").deleteKey(g)});f.on("error",function(h,j,g,i){e.errorHandler(h,j,g,i)})},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},render:function(g){var e=this,f;if(this.model){f=this.renderModel()}else{f=this.renderWithoutModel()}$(e).queue("fx",[function(h){if(e.$el.is(":visible")){e.$el.fadeOut(e.fxSpeed,h)}else{h()}},function(h){e.$el.empty();if(f){e.$el.append(f.children())}e.$el.fadeIn(e.fxSpeed,h)},function(h){if(g){g.call(this)}e.trigger("rendered",this)}]);return this},renderWithoutModel:function(){var e=$("<div/>"),f=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return e.append(f)},renderModel:function(){var e=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){e.append(c.templates.anonHistoryPanel(this.model.toJSON()))}else{e.append(c.templates.historyPanel(this.model.toJSON()));this._renderTags(e);this._renderAnnotation(e)}this._setUpBehaviours(e);if(!this.model.hdas.length||!this.renderHdas(e.find(this.datasetsSelector))){e.find(this.emptyMsgSelector).show()}return e},_renderTags:function(e){this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var f=this;e.find(".history-name").make_text_editable({on_finish:function(g){e.find(".history-name").text(g);f.model.save({name:g}).fail(function(){e.find(".history-name").text(f.model.previous("name"))})}})},renderHdas:function(f){this.hdaViews={};var e=this,g=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(g,function(h){f.prepend(e.createHdaView(h).$el)});return g.length},events:{"click .message-container":"clearMessages"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(e){e.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},showLoadingIndicator:function(f,e,g){e=(e!==undefined)?(e):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,g)}else{this.$el.fadeOut(e);this.indicator.show(f,e,g)}},hideLoadingIndicator:function(e,f){e=(e!==undefined)?(e):(this.fxSpeed);if(this.indicator){this.indicator.hide(e,f)}},displayMessage:function(j,k,i){var g=this;this.scrollToTop();var h=this.$el.find(this.msgsSelector),e=$("<div/>").addClass(j+"message").html(k);if(!_.isEmpty(i)){var f=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(g.messageToModalOptions(j,k,i));return false});e.append(" ",f)}return h.html(e)},messageToModalOptions:function(i,k,h){var e=this,j=$("<div/>"),g={title:"Details"};function f(l){l=_.omit(l,_.functions(l));return["<table>",_.map(l,function(n,m){n=(_.isObject(n))?(f(n)):(n);return'<tr><td style="vertical-align: top; color: grey">'+m+'</td><td style="padding-left: 8px">'+n+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(h)){g.body=j.append(f(h))}else{g.body=j.html(h)}g.buttons={Ok:function(){Galaxy.modal.hide();e.clearMessages()}};return g},clearMessages:function(){var e=this.$el.find(this.msgsSelector);e.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(e){this.$el.parent().scrollTop(e)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(f,g){if(!g){this.$el.parent().parent().scrollTop(f);return this}var e=window,h=this.$el.parent().parent(),j=$(e).innerHeight(),i=(j/2)-(g/2);$(h).scrollTop(f-i);return this},scrollToId:function(f){if((!f)||(!this.hdaViews[f])){return this}var e=this.hdaViews[f].$el;this.scrollIntoView(e.offset().top,e.outerHeight());return this},scrollToHid:function(e){var f=this.model.hdas.getByHid(e);if(!f){return this}return this.scrollToId(f.id)},connectToQuotaMeter:function(e){if(!e){return this}this.listenTo(e,"quota:over",this.showQuotaMessage);this.listenTo(e,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(e&&e.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var e=this.$el.find(".quota-message");if(e.is(":hidden")){e.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var e=this.$el.find(".quota-message");if(!e.is(":hidden")){e.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(e){if(!e){return this}this.on("new-storage",function(g,f){if(e&&g){e.findItemByHtml(_l("Include Deleted Datasets")).checked=g.get("show_deleted");e.findItemByHtml(_l("Include Hidden Datasets")).checked=g.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});c.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:c}});
\ No newline at end of file
+define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(d,b,a){var c=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(e){e=e||{};if(e.logger){this.logger=e.logger}this.log(this+".initialize:",e);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);if(this.model){this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden);this._setUpModelEventHandlers()}if(e.onready){e.onready.call(this)}},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(e){this.log(this+"",arguments)},this)}},errorHandler:function(g,j,f,i,h){var e=this._parseErrorMessage(g,j,f,i,h);if(j&&j.status===0&&j.readyState===0){}else{if(j&&j.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",e.message,e.details)})}else{this.displayMessage("error",e.message,e.details)}}}},_parseErrorMessage:function(h,l,g,k,j){var f=Galaxy.currUser,e={message:this._bePolite(k),details:{user:(f instanceof User)?(f.toJSON()):(f+""),source:(h instanceof Backbone.Model)?(h.toJSON()):(h+""),xhr:l,options:(l)?(_.omit(g,"xhr")):(g)}};_.extend(e.details,j||{});if(l&&_.isFunction(l.getAllResponseHeaders)){var i=l.getAllResponseHeaders();i=_.compact(i.split("\n"));i=_.map(i,function(m){return m.split(": ")});e.details.xhr.responseHeaders=_.object(i)}return e},_bePolite:function(e){e=e||_l("An error occurred while getting updates from the server");return e+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(f){var e=this;return this.loadHistoryWithHDADetails("current",f).then(function(h,g){e.trigger("current-history",e)})},switchToHistory:function(h,g){var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories/"+h+"/set_as_current")};return this.loadHistoryWithHDADetails(h,g,f).then(function(j,i){e.trigger("switched-history",e)})},createNewHistory:function(g){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,g,f).then(function(i,h){e.trigger("new-history",e)})},loadHistoryWithHDADetails:function(h,g,f,j){var e=this,i=function(k){return e.getExpandedHdaIds(k.id)};return this.loadHistory(h,g,f,j,i)},loadHistory:function(h,g,f,k,i){this.trigger("loading-history",this);g=g||{};var e=this;var j=d.History.getHistoryData(h,{historyFn:f,hdaFn:k,hdaDetailIds:g.initiallyExpanded||i});return this._loadHistoryFromXHR(j,g).fail(function(n,l,m){e.trigger("error",e,n,g,_l("An error was encountered while "+l),{historyId:h,history:m||{}})}).always(function(){e.trigger("loading-done",e)})},_loadHistoryFromXHR:function(g,f){var e=this;g.then(function(h,i){e.setModel(h,i,f)});g.fail(function(i,h){e.render()});return g},setModel:function(g,e,f){f=f||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){g.user=Galaxy.currUser.toJSON()}this.model=new d.History(g,e,f);this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(f,e){if(this.model){return this.model.refresh(f,e)}return $.when()},_setUpWebStorage:function(f,e,g){this.storage=new PersistentStorage(this._getStorageKey(this.model.get("id")),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(f){this.storage.set("exandedHdas",f)}if((e===true)||(e===false)){this.storage.set("show_deleted",e)}if((g===true)||(g===false)){this.storage.set("show_hidden",g)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},_getStorageKey:function(e){if(!e){throw new Error("_getStorageKey needs valid id: "+e)}return("history:"+e)},clearWebStorage:function(){for(var e in sessionStorage){if(e.indexOf("history:")===0){sessionStorage.removeItem(e)}}},getStoredOptions:function(f){if(!f||f==="current"){return(this.storage)?(this.storage.get()):({})}var e=sessionStorage.getItem(this._getStorageKey(f));return(e===null)?({}):(JSON.parse(e))},getExpandedHdaIds:function(e){var f=this.getStoredOptions(e).expandedHdas;return((_.isEmpty(f))?([]):(_.keys(f)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(f,h,e,g){this.errorHandler(f,h,e,g)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this);this.model.hdas.on("state:ready",function(f,g,e){if((!f.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[f.id])}},this)},addHdaView:function(h){this.log("add."+this,h);var f=this;if(!h.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function g(j){var i=f.$el.find(f.emptyMsgSelector);if(i.is(":visible")){i.fadeOut(f.fxSpeed,j)}else{j()}},function e(j){f.scrollToTop();var i=f.$el.find(f.datasetsSelector);f.createHdaView(h).$el.hide().prependTo(i).slideDown(f.fxSpeed)}])},createHdaView:function(g){var f=g.get("id"),e=this.storage.get("expandedHdas").get(f),h=new this.HDAView({model:g,expanded:e,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(h);this.hdaViews[f]=h;return h.render()},_setUpHdaListeners:function(f){var e=this;f.on("body-expanded",function(g){e.storage.get("expandedHdas").set(g,true)});f.on("body-collapsed",function(g){e.storage.get("expandedHdas").deleteKey(g)});f.on("error",function(h,j,g,i){e.errorHandler(h,j,g,i)})},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},render:function(g){var e=this,f;if(this.model){f=this.renderModel()}else{f=this.renderWithoutModel()}$(e).queue("fx",[function(h){if(e.$el.is(":visible")){e.$el.fadeOut(e.fxSpeed,h)}else{h()}},function(h){e.$el.empty();if(f){e.$el.append(f.children())}e.$el.fadeIn(e.fxSpeed,h)},function(h){if(g){g.call(this)}e.trigger("rendered",this)}]);return this},renderWithoutModel:function(){var e=$("<div/>"),f=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return e.append(f)},renderModel:function(){var e=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){e.append(c.templates.anonHistoryPanel(this.model.toJSON()))}else{e.append(c.templates.historyPanel(this.model.toJSON()));this._renderTags(e);this._renderAnnotation(e)}this._setUpBehaviours(e);if(!this.model.hdas.length||!this.renderHdas(e.find(this.datasetsSelector))){e.find(this.emptyMsgSelector).show()}return e},_renderTags:function(e){this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var f=this;e.find(".history-name").make_text_editable({on_finish:function(g){e.find(".history-name").text(g);f.model.save({name:g}).fail(function(){e.find(".history-name").text(f.model.previous("name"))})}})},renderHdas:function(f){this.hdaViews={};var e=this,g=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(g,function(h){f.prepend(e.createHdaView(h).$el)});return g.length},events:{"click .message-container":"clearMessages"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(e){e.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},showSelect:function(e){_.each(this.hdaViews,function(f){f.showSelect(e)})},hideSelect:function(e){_.each(this.hdaViews,function(f){f.hideSelect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},showLoadingIndicator:function(f,e,g){e=(e!==undefined)?(e):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,g)}else{this.$el.fadeOut(e);this.indicator.show(f,e,g)}},hideLoadingIndicator:function(e,f){e=(e!==undefined)?(e):(this.fxSpeed);if(this.indicator){this.indicator.hide(e,f)}},displayMessage:function(j,k,i){var g=this;this.scrollToTop();var h=this.$el.find(this.msgsSelector),e=$("<div/>").addClass(j+"message").html(k);if(!_.isEmpty(i)){var f=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(g.messageToModalOptions(j,k,i));return false});e.append(" ",f)}return h.html(e)},messageToModalOptions:function(i,k,h){var e=this,j=$("<div/>"),g={title:"Details"};function f(l){l=_.omit(l,_.functions(l));return["<table>",_.map(l,function(n,m){n=(_.isObject(n))?(f(n)):(n);return'<tr><td style="vertical-align: top; color: grey">'+m+'</td><td style="padding-left: 8px">'+n+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(h)){g.body=j.append(f(h))}else{g.body=j.html(h)}g.buttons={Ok:function(){Galaxy.modal.hide();e.clearMessages()}};return g},clearMessages:function(){var e=this.$el.find(this.msgsSelector);e.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(e){this.$el.parent().scrollTop(e)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(f,g){if(!g){this.$el.parent().parent().scrollTop(f);return this}var e=window,h=this.$el.parent().parent(),j=$(e).innerHeight(),i=(j/2)-(g/2);$(h).scrollTop(f-i);return this},scrollToId:function(f){if((!f)||(!this.hdaViews[f])){return this}var e=this.hdaViews[f].$el;this.scrollIntoView(e.offset().top,e.outerHeight());return this},scrollToHid:function(e){var f=this.model.hdas.getByHid(e);if(!f){return this}return this.scrollToId(f.id)},connectToQuotaMeter:function(e){if(!e){return this}this.listenTo(e,"quota:over",this.showQuotaMessage);this.listenTo(e,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(e&&e.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var e=this.$el.find(".quota-message");if(e.is(":hidden")){e.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var e=this.$el.find(".quota-message");if(!e.is(":hidden")){e.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(e){if(!e){return this}this.on("new-storage",function(g,f){if(e&&g){e.findItemByHtml(_l("Include Deleted Datasets")).checked=g.get("show_deleted");e.findItemByHtml(_l("Include Hidden Datasets")).checked=g.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});c.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:c}});
\ No newline at end of file
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/templates/compiled/history-templates.js
--- a/static/scripts/packed/templates/compiled/history-templates.js
+++ b/static/scripts/packed/templates/compiled/history-templates.js
@@ -1,1 +1,1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+='\n </div>\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';return A}function m(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';B=p["if"].call(D,D.misc_blurb,{hash:{},inverse:o.noop,fn:o.program(4,l,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.data_type,{hash:{},inverse:o.noop,fn:o.program(6,j,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.metadata_dbkey,{hash:{},inverse:o.noop,fn:o.program(9,f,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.misc_info,{hash:{},inverse:o.noop,fn:o.program(12,x,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';B=p.unless.call(D,D.deleted,{hash:{},inverse:o.noop,fn:o.program(14,w,C),data:C});if(B||B===0){A+=B}A+="\n\n ";return A}function l(D,C){var A="",B;A+='\n <div class="dataset-blurb">\n <span class="value">';if(B=p.misc_blurb){B=B.call(D,{hash:{},data:C})}else{B=D.misc_blurb;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function j(E,D){var A="",C,B;A+='\n <div class="dataset-datatype">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(7,i,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">';if(C=p.data_type){C=C.call(E,{hash:{},data:D})}else{C=E.data_type;C=typeof C===e?C.apply(E):C}A+=d(C)+"</span>\n </div>\n ";return A}function i(B,A){return"format"}function f(E,D){var A="",C,B;A+='\n <div class="dataset-dbkey">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(10,y,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">\n ';if(C=p.metadata_dbkey){C=C.call(E,{hash:{},data:D})}else{C=E.metadata_dbkey;C=typeof C===e?C.apply(E):C}A+=d(C)+"\n </span>\n </div>\n ";return A}function y(B,A){return"database"}function x(D,C){var A="",B;A+='\n <div class="dataset-info">\n <span class="value">';if(B=p.misc_info){B=B.call(D,{hash:{},data:C})}else{B=D.misc_info;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function w(D,C){var A="",B;A+='\n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="dataset-display-applications">\n ';B=p.each.call(D,D.display_apps,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p.each.call(D,D.display_types,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-peek">\n ';B=p["if"].call(D,D.peek,{hash:{},inverse:o.noop,fn:o.program(19,s,C),data:C});if(B||B===0){A+=B}A+="\n </div>\n\n ";return A}function v(D,C){var A="",B;A+='\n <div class="display-application">\n <span class="display-application-location">';if(B=p.label){B=B.call(D,{hash:{},data:C})}else{B=D.label;B=typeof B===e?B.apply(D):B}A+=d(B)+'</span>\n <span class="display-application-links">\n ';B=p.each.call(D,D.links,{hash:{},inverse:o.noop,fn:o.program(16,u,C),data:C});if(B||B===0){A+=B}A+="\n </span>\n </div>\n ";return A}function u(E,D){var A="",C,B;A+='\n <a target="';if(C=p.target){C=C.call(E,{hash:{},data:D})}else{C=E.target;C=typeof C===e?C.apply(E):C}A+=d(C)+'" href="';if(C=p.href){C=C.call(E,{hash:{},data:D})}else{C=E.href;C=typeof C===e?C.apply(E):C}A+=d(C)+'">';B={hash:{},inverse:o.noop,fn:o.program(17,t,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+="</a>\n ";return A}function t(C,B){var A;if(A=p.text){A=A.call(C,{hash:{},data:B})}else{A=C.text;A=typeof A===e?A.apply(C):A}return d(A)}function s(D,C){var A="",B;A+='\n <pre class="peek">';if(B=p.peek){B=B.call(D,{hash:{},data:C})}else{B=D.peek;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+="</pre>\n ";return A}q+='<div class="dataset-body">\n ';h=p["if"].call(r,r.body,{hash:{},inverse:o.program(3,m,z),fn:o.program(1,n,z),data:z});if(h||h===0){q+=h}q+="\n</div>";return q})})();(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-skeleton"]=b(function(f,r,p,k,w){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,f.helpers);w=w||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(B,A){var x="",z,y;x+='\n <div class="errormessagesmall">\n ';y={hash:{},inverse:o.noop,fn:o.program(2,m,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+=":\n ";y={hash:{},inverse:o.noop,fn:o.program(4,l,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </div>\n ";return x}function m(y,x){return"There was an error getting the data for this dataset"}function l(z,y){var x;if(x=p.error){x=x.call(z,{hash:{},data:y})}else{x=z.error;x=typeof x===e?x.apply(z):x}return d(x)}function j(A,z){var x="",y;x+="\n ";y=p["if"].call(A,A.purged,{hash:{},inverse:o.program(10,v,z),fn:o.program(7,i,z),data:z});if(y||y===0){x+=y}x+="\n ";return x}function i(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(8,g,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n\n ";return x}function g(y,x){return"This dataset has been deleted and removed from disk."}function v(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(11,u,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='\n \n \n Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it\n or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk\n </strong></div>\n ';return x}function u(y,x){return"This dataset has been deleted."}function t(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(14,s,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='\n \n Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it\n </strong></div>\n ';return x}function s(y,x){return"This dataset has been hidden."}q+='<div class="dataset hda">\n <div class="dataset-warnings">\n ';h=p["if"].call(r,r.error,{hash:{},inverse:o.noop,fn:o.program(1,n,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p["if"].call(r,r.deleted,{hash:{},inverse:o.noop,fn:o.program(6,j,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p.unless.call(r,r.visible,{hash:{},inverse:o.noop,fn:o.program(13,t,w),data:w});if(h||h===0){q+=h}q+='\n </div>\n\n <div class="dataset-primary-actions"></div>\n <div class="dataset-title-bar clear">\n <span class="dataset-state-icon state-icon"></span>\n <div class="dataset-title">\n <span class="hda-hid">';if(h=p.hid){h=h.call(r,{hash:{},data:w})}else{h=r.hid;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n <span class="dataset-name">';if(h=p.name){h=h.call(r,{hash:{},data:w})}else{h=r.name;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n </div>\n </div>\n\n <div class="dataset-body"></div>\n</div>';return q})})();(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel-anon"]=b(function(g,r,p,k,u){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);u=u||{};var q="",i,f,o=this,e="function",c=p.blockHelperMissing,d=this.escapeExpression;function n(z,y){var v="",x,w;v+='\n <div class="history-name" title="';w={hash:{},inverse:o.noop,fn:o.program(2,m,y),data:y};if(x=p.local){x=x.call(z,w)}else{x=z.local;x=typeof x===e?x.apply(z):x}if(!p.local){x=c.call(z,x,w)}if(x||x===0){v+=x}v+='">\n ';if(x=p.name){x=x.call(z,{hash:{},data:y})}else{x=z.name;x=typeof x===e?x.apply(z):x}v+=d(x)+"\n </div>\n ";return v}function m(w,v){return"You must be logged in to edit your history name"}function l(y,x){var v="",w;v+='\n <div class="history-size">';if(w=p.nice_size){w=w.call(y,{hash:{},data:x})}else{w=y.nice_size;w=typeof w===e?w.apply(y):w}v+=d(w)+"</div>\n ";return v}function j(y,x){var v="",w;v+='\n \n <div class="';if(w=p.status){w=w.call(y,{hash:{},data:x})}else{w=y.status;w=typeof w===e?w.apply(y):w}v+=d(w)+'message">';if(w=p.message){w=w.call(y,{hash:{},data:x})}else{w=y.message;w=typeof w===e?w.apply(y):w}v+=d(w)+"</div>\n ";return v}function h(w,v){return"You are over your disk quota"}function t(w,v){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function s(w,v){return"Your history is empty. 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diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/templates/compiled/template-hda-skeleton.js
--- a/static/scripts/packed/templates/compiled/template-hda-skeleton.js
+++ b/static/scripts/packed/templates/compiled/template-hda-skeleton.js
@@ -1,1 +1,1 @@
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\ No newline at end of file
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-skeleton"]=b(function(f,r,p,k,w){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,f.helpers);w=w||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(B,A){var x="",z,y;x+='\n <div class="errormessagesmall">\n ';y={hash:{},inverse:o.noop,fn:o.program(2,m,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+=":\n ";y={hash:{},inverse:o.noop,fn:o.program(4,l,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </div>\n ";return x}function m(y,x){return"There was an error getting the data for this dataset"}function l(z,y){var x;if(x=p.error){x=x.call(z,{hash:{},data:y})}else{x=z.error;x=typeof x===e?x.apply(z):x}return d(x)}function j(A,z){var x="",y;x+="\n ";y=p["if"].call(A,A.purged,{hash:{},inverse:o.program(10,v,z),fn:o.program(7,i,z),data:z});if(y||y===0){x+=y}x+="\n ";return x}function i(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(8,g,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n\n ";return x}function g(y,x){return"This dataset has been deleted and removed from disk."}function v(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(11,u,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='\n \n \n Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it\n or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk\n </strong></div>\n ';return x}function u(y,x){return"This dataset has been deleted."}function t(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(14,s,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='\n \n Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it\n </strong></div>\n ';return x}function s(y,x){return"This dataset has been hidden."}q+='<div class="dataset hda">\n <div class="dataset-warnings">\n ';h=p["if"].call(r,r.error,{hash:{},inverse:o.noop,fn:o.program(1,n,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p["if"].call(r,r.deleted,{hash:{},inverse:o.noop,fn:o.program(6,j,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p.unless.call(r,r.visible,{hash:{},inverse:o.noop,fn:o.program(13,t,w),data:w});if(h||h===0){q+=h}q+='\n </div>\n\n <div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>\n <div class="dataset-primary-actions"></div>\n <div class="dataset-title-bar clear">\n <span class="dataset-state-icon state-icon"></span>\n <div class="dataset-title">\n <span class="hda-hid">';if(h=p.hid){h=h.call(r,{hash:{},data:w})}else{h=r.hid;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n <span class="dataset-name">';if(h=p.name){h=h.call(r,{hash:{},data:w})}else{h=r.name;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n </div>\n </div>\n\n <div class="dataset-body"></div>\n</div>';return q})})();
\ No newline at end of file
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/utils/galaxy.uploadbox.js
--- a/static/scripts/packed/utils/galaxy.uploadbox.js
+++ b/static/scripts/packed/utils/galaxy.uploadbox.js
@@ -1,1 +1,1 @@
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\ No newline at end of file
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diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/packed/viz/trackster/painters.js
--- a/static/scripts/packed/viz/trackster/painters.js
+++ b/static/scripts/packed/viz/trackster/painters.js
@@ -1,1 +1,1 @@
-define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=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_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){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_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
+define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=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);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.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);var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":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));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_start+9)}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))}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start,1);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){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)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.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),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}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))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}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))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/templates/compiled/history-templates.js
--- a/static/scripts/templates/compiled/history-templates.js
+++ b/static/scripts/templates/compiled/history-templates.js
@@ -291,7 +291,7 @@
buffer += "\n\n ";
stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data});
if(stack1 || stack1 === 0) { buffer += stack1; }
- buffer += "\n </div>\n\n <div class=\"dataset-primary-actions\"></div>\n <div class=\"dataset-title-bar clear\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">";
+ buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n <div class=\"dataset-title-bar clear\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">";
if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
buffer += escapeExpression(stack1)
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/templates/compiled/template-hda-skeleton.js
--- a/static/scripts/templates/compiled/template-hda-skeleton.js
+++ b/static/scripts/templates/compiled/template-hda-skeleton.js
@@ -112,7 +112,7 @@
buffer += "\n\n ";
stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data});
if(stack1 || stack1 === 0) { buffer += stack1; }
- buffer += "\n </div>\n\n <div class=\"dataset-primary-actions\"></div>\n <div class=\"dataset-title-bar clear\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">";
+ buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n <div class=\"dataset-title-bar clear\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">";
if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
buffer += escapeExpression(stack1)
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/scripts/templates/hda-templates.html
--- a/static/scripts/templates/hda-templates.html
+++ b/static/scripts/templates/hda-templates.html
@@ -35,6 +35,7 @@
{{/unless}}
</div>
+ <div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div><div class="dataset-primary-actions"></div><div class="dataset-title-bar clear"><span class="dataset-state-icon state-icon"></span>
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1539,6 +1539,7 @@
.dataset .dataset-padding{padding:6px 10px 6px 8px}
.dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%}
.dataset .help-text{font-weight:normal;font-style:italic;font-size:90%;color:#555}
+.dataset .dataset-selector{float:left;display:none;width:0px;margin:0 8px -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle}
.dataset .dataset-title-bar{cursor:pointer;padding:6px 10px 6px 8px}
.dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px}
.dataset .dataset-primary-actions{float:right;margin:6px 10px 0}.dataset .dataset-primary-actions .icon-btn{margin-left:2px}
diff -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 -r df7d45db5d2b284528ba9ca4a02ba10c953453a0 static/style/src/less/history.less
--- a/static/style/src/less/history.less
+++ b/static/style/src/less/history.less
@@ -241,9 +241,24 @@
color: #555;
}
+ .dataset-selector {
+ //background-color: red;
+ float: left;
+ // always initially hidden and zero width
+ display: none;
+ width: 0px;
+ //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish
+ margin: 0px 8px -@spacing-bottom 0px;
+ padding: ( @spacing-top - 1 ) 0px 2px @spacing-left;
+ cursor: pointer;
+ //text-align: center;
+ vertical-align: middle;
+ }
+
.dataset-title-bar {
cursor: pointer;
.dataset-padding;
+
.dataset-state-icon {
//display: inline-block;
//vertical-align: middle;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Upload: Modify selection rule
by commits-noreply＠bitbucket.org 20 Nov '13
by commits-noreply＠bitbucket.org 20 Nov '13
20 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/30a9490f9bf6/
Changeset: 30a9490f9bf6
User: guerler
Date: 2013-11-20 04:55:20
Summary: Upload: Modify selection rule
Affected #: 1 file
diff -r b042f0fac1abe5bace4ae32e93595a453b99d9de -r 30a9490f9bf6ce4a18f8a7e7974f5e70651c7ba6 static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -174,8 +174,9 @@
items.each(function()
{
var symbol = $(this).find('#symbol');
- if(symbol.hasClass(self.state.init)) {
- $(this).find('#genome').val(selected_genome);
+ var genome = $(this).find('#genome');
+ if(symbol.hasClass(self.state.init) && genome.val() == '?') {
+ genome.val(selected_genome);
}
});
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Upload: Fix genome selection feature
by commits-noreply＠bitbucket.org 20 Nov '13
by commits-noreply＠bitbucket.org 20 Nov '13
20 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b042f0fac1ab/
Changeset: b042f0fac1ab
User: guerler
Date: 2013-11-20 04:49:48
Summary: Upload: Fix genome selection feature
Affected #: 1 file
diff -r f78dcb9eb2897c452c3475d21bd601c0a91b63da -r b042f0fac1abe5bace4ae32e93595a453b99d9de static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -153,22 +153,30 @@
// add functionality to new row elements
var self = this;
+
+ // handle click event
it.find('#symbol').on('click', function() { self.event_remove (index) });
+
+ // handle text editing event
it.find('#text-content').on('keyup', function() {
var count = it.find('#text-content').val().length;
it.find('#size').html(self.size_to_string (count));
});
+
+ // handle genome selection event
+ var self = this;
it.find('#genome').on('change', function(e) {
- // identify target
- var $target = $(e.target);
- var selected_genome = $target.val();
+ // identify selected genome
+ var selected_genome = $(e.target).val();
- // identify other genome selectors
- var genomes = (self.$el).find('.genome');
- genomes.each(function() {
- var $select = $(this);
- if ($select.val() == '?')
- $select.val(selected_genome);
+ // update genome
+ var items = $(self.el).find('.upload-item');
+ items.each(function()
+ {
+ var symbol = $(this).find('#symbol');
+ if(symbol.hasClass(self.state.init)) {
+ $(this).find('#genome').val(selected_genome);
+ }
});
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Enhance and fix tool dependency installation from the tool shed to automatically source all tool dependency env.sh files defined within <setup_xxx+environment> tags. This change set also includes related code cleanup, enhanced logging and other related fixes.
by commits-noreply＠bitbucket.org 19 Nov '13
by commits-noreply＠bitbucket.org 19 Nov '13
19 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f78dcb9eb289/
Changeset: f78dcb9eb289
User: greg
Date: 2013-11-19 23:05:07
Summary: Enhance and fix tool dependency installation from the tool shed to automatically source all tool dependency env.sh files defined within <setup_xxx+environment> tags. This change set also includes related code cleanup, enhanced logging and other related fixes.
Affected #: 8 files
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -436,7 +436,9 @@
tool_dependencies=tool_dependencies )
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status == trans.app.model.ToolDependency.installation_status.ERROR:
- message += ' %s' % str( installed_tool_dependency.error_message )
+ text = util.unicodify( installed_tool_dependency.error_message )
+ if text is not None:
+ message += ' %s' % text
tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies ]
if message:
status = 'error'
@@ -681,8 +683,8 @@
action='uninstall_tool_dependencies',
**kwd ) )
else:
- kwd[ 'message' ] = 'All selected tool dependencies are already uninstalled.'
- kwd[ 'status' ] = 'error'
+ message = 'No selected tool dependencies can be uninstalled, you may need to use the <b>Repair repository</b> feature.'
+ status = 'error'
elif operation == "install":
if trans.app.config.tool_dependency_dir:
tool_dependencies_for_installation = []
@@ -694,13 +696,12 @@
if tool_dependencies_for_installation:
self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )
else:
- kwd[ 'message' ] = 'All selected tool dependencies are already installed.'
- kwd[ 'status' ] = 'error'
+ message = 'All selected tool dependencies are already installed.'
+ status = 'error'
else:
message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) '
message += ' and restart your Galaxy server to install tool dependencies.'
- kwd[ 'message' ] = message
- kwd[ 'status' ] = 'error'
+ status = 'error'
installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
tool_shed_repository=tool_shed_repository,
name='inst_td_ids',
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ b/lib/tool_shed/galaxy_install/repository_util.py
@@ -795,12 +795,11 @@
for tool_dependency in repository.missing_tool_dependencies:
if tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR,
trans.model.ToolDependency.installation_status.INSTALLING ]:
- tool_dependency_util.set_tool_dependency_attributes( trans,
- tool_dependency,
- trans.model.ToolDependency.installation_status.UNINSTALLED,
- None,
- remove_from_disk=True )
- trans.sa_session.refresh( tool_dependency )
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( trans.app,
+ tool_dependency=tool_dependency,
+ status=trans.model.ToolDependency.installation_status.UNINSTALLED,
+ error_message=None,
+ remove_from_disk=True )
# Install tool dependencies.
suc.update_tool_shed_repository_status( trans.app,
repository,
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
@@ -28,6 +28,73 @@
INSTALLATION_LOG = 'INSTALLATION.log'
VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz'
+
+class EnvFileBuilder( object ):
+
+ def __init__( self, install_dir ):
+ self.install_dir = install_dir
+ self.return_code = 0
+
+ def append_line( self, skip_if_contained=True, make_executable=True, **kwd ):
+ env_var_dict = dict( **kwd )
+ env_entry, env_file = td_common_util.create_or_update_env_shell_file( self.install_dir, env_var_dict )
+ return_code = file_append( env_entry, env_file, skip_if_contained=skip_if_contained, make_executable=make_executable )
+ self.return_code = self.return_code or return_code
+ return self.return_code
+
+
+class InstallEnvironment( object ):
+ """Object describing the environment built up as part of the process of building and installing a package."""
+
+ def add_env_shell_file_paths( self, paths ):
+ for path in paths:
+ self.env_shell_file_paths.append( str( path ) )
+
+ def build_command( self, command, action_type='shell_command' ):
+ """
+ Build command line for execution from simple command, but
+ configuring environment described by this object.
+ """
+ env_cmds = self.environment_commands( action_type )
+ return '\n'.join( env_cmds + [ command ] )
+
+ def __call__( self, install_dir ):
+ with settings( warn_only=True, **td_common_util.get_env_var_values( install_dir ) ):
+ with prefix( self.__setup_environment() ):
+ yield
+
+ def environment_commands( self, action_type ):
+ """Build a list of commands used to construct the environment described by this object."""
+ cmds = []
+ for env_shell_file_path in self.env_shell_file_paths:
+ if os.path.exists( env_shell_file_path ):
+ for env_setting in open( env_shell_file_path ):
+ cmds.append( env_setting.strip( '\n' ) )
+ else:
+ log.debug( 'Invalid file %s specified, ignoring %s action.' % ( str( env_shell_file_path ), str( action_type ) ) )
+ return cmds
+
+ def environment_dict( self, action_type='template_command' ):
+ env_vars = dict()
+ for env_shell_file_path in self.env_shell_file_paths:
+ if os.path.exists( env_shell_file_path ):
+ for env_setting in open( env_shell_file_path ):
+ env_string = env_setting.split( ';' )[ 0 ]
+ env_name, env_path = env_string.split( '=' )
+ env_vars[ env_name ] = env_path
+ else:
+ log.debug( 'Invalid file %s specified, ignoring template_command action.' % str( env_shell_file_path ) )
+ return env_vars
+
+ def __init__( self ):
+ self.env_shell_file_paths = []
+
+ def __setup_environment( self ):
+ return "&&".join( [ ". %s" % file for file in self.__valid_env_shell_file_paths() ] )
+
+ def __valid_env_shell_file_paths( self ):
+ return [ file for file in self.env_shell_file_paths if os.path.exists( file ) ]
+
def check_fabric_version():
version = env.version
if int( version.split( "." )[ 0 ] ) < 1:
@@ -76,6 +143,11 @@
filtered_actions.append( action )
return filtered_actions
+def handle_action_shell_file_paths( env_file_builder, action_dict ):
+ shell_file_paths = action_dict.get( 'action_shell_file_paths', [] )
+ for shell_file_path in shell_file_paths:
+ env_file_builder.append_line( action="source", value=shell_file_path )
+
def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ):
sa_session = app.model.context.current
with settings( warn_only=True ):
@@ -200,79 +272,6 @@
shutil.move( full_path_to_dir, venv_dir )
return True
-
-class EnvFileBuilder( object ):
-
- def __init__( self, install_dir ):
- self.install_dir = install_dir
- self.return_code = 0
-
- def append_line( self, skip_if_contained=True, make_executable=True, **kwds ):
- env_var_dict = dict(**kwds)
- env_entry, env_file = td_common_util.create_or_update_env_shell_file( self.install_dir, env_var_dict )
- return_code = file_append( env_entry, env_file, skip_if_contained=skip_if_contained, make_executable=make_executable )
- self.return_code = self.return_code or return_code
- return self.return_code
-
-
-class InstallEnvironment( object ):
- """
- Object describing the environment built up as part of the process of building
- and installing a package.
- """
-
- def __init__( self ):
- self.env_shell_file_paths = []
-
- def build_command( self, command, action_type='shell_command' ):
- """
- Build command line for execution from simple command, but
- configuring environment described by this object.
- """
- env_cmds = self.environment_commands(action_type)
- return '\n'.join(env_cmds + [command])
-
- def environment_commands(self, action_type):
- """
- Build a list of commands used to construct the environment described by
- this object.
- """
- cmds = []
- for env_shell_file_path in self.env_shell_file_paths:
- if os.path.exists( env_shell_file_path ):
- for env_setting in open( env_shell_file_path ):
- cmds.append( env_setting.strip( '\n' ) )
- else:
- log.debug( 'Invalid file %s specified, ignoring %s action.', env_shell_file_path, action_type )
- return cmds
-
- def __call__( self, install_dir ):
- with settings( warn_only=True, **td_common_util.get_env_var_values( install_dir ) ):
- with prefix( self.__setup_environment() ):
- yield
-
- def __setup_environment(self):
- return "&&".join( [". %s" % file for file in self.__valid_env_shell_file_paths() ] )
-
- def __valid_env_shell_file_paths(self):
- return [ file for file in self.env_shell_file_paths if os.path.exists( file ) ]
-
- def environment_dict(self, action_type='template_command'):
- env_vars = dict()
- for env_shell_file_path in self.env_shell_file_paths:
- if os.path.exists( env_shell_file_path ):
- for env_setting in open( env_shell_file_path ):
- env_string = env_setting.split( ';' )[ 0 ]
- env_name, env_path = env_string.split( '=' )
- env_vars[ env_name ] = env_path
- else:
- log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path )
- return env_vars
-
- def add_env_shell_file_paths(self, paths):
- self.env_shell_file_paths.extend(paths)
-
-
def install_and_build_package( app, tool_dependency, actions_dict ):
"""Install a Galaxy tool dependency package either via a url or a mercurial or git clone command."""
sa_session = app.model.context.current
@@ -335,7 +334,6 @@
dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True )
if is_binary:
log_file = os.path.join( install_dir, INSTALLATION_LOG )
- log.debug( 'log_file: %s' % log_file )
if os.path.exists( log_file ):
logfile = open( log_file, 'ab' )
else:
@@ -349,7 +347,7 @@
filtered_actions = actions[ 1: ]
return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] )
if return_code:
- return
+ return tool_dependency
dir = package_name
elif action_type == 'download_file':
# <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action>
@@ -374,13 +372,15 @@
# <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package>
# </action>
filtered_actions = actions[ 1: ]
-
- if action_dict.get( 'env_shell_file_paths', False ):
- install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] )
+ env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None )
+ if env_shell_file_paths is None:
+ log.debug( 'Missing R environment. Please check your specified R installation exists.' )
+ return tool_dependency
else:
- log.warning( 'Missing R environment. Please check your specified R installation exists.' )
- return
- tarball_names = list()
+ install_environment.add_env_shell_file_paths( env_shell_file_paths )
+ log.debug( 'Handling setup_r_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s"' % \
+ ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) )
+ tarball_names = []
for url in action_dict[ 'r_packages' ]:
filename = url.split( '/' )[ -1 ]
tarball_names.append( filename )
@@ -391,20 +391,18 @@
with settings( warn_only=True ):
for tarball_name in tarball_names:
cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR &&
- Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % (tarball_name)
-
+ Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) )
cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
-
+ return tool_dependency
# R libraries are installed to $INSTALL_DIR (install_dir), we now set the R_LIBS path to that directory
env_file_builder = EnvFileBuilder( install_dir )
handle_action_shell_file_paths( env_file_builder, action_dict ) # Pull in R environment (runtime).
env_file_builder.append_line( name="R_LIBS", action="prepend_to", value=install_dir )
return_code = env_file_builder.return_code
if return_code:
- return
+ return tool_dependency
elif action_type == 'setup_ruby_environment':
# setup an Ruby environment
# <action type="setup_ruby_environment">
@@ -417,24 +415,27 @@
# <package>http://url-to-some-gem-file.de/protk.gem</package>
# </action>
filtered_actions = actions[ 1: ]
-
- if action_dict.get( 'env_shell_file_paths', False ):
- install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] )
+ env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None )
+ if env_shell_file_paths is None:
+ log.debug( 'Missing Ruby environment, make sure your specified Ruby installation exists.' )
+ return tool_dependency
else:
- log.warning( 'Missing Ruby environment. Please check if your specified Ruby installation exists.' )
- return
-
+ install_environment.add_env_shell_file_paths( env_shell_file_paths )
+ log.debug( 'Handling setup_ruby_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s"' % \
+ ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) )
dir = os.path.curdir
current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
with lcd( current_dir ):
with settings( warn_only=True ):
- for (gem, gem_version) in action_dict[ 'ruby_packages' ]:
+ ruby_package_tups = action_dict.get( 'ruby_package_tups', [] )
+ for ruby_package_tup in ruby_package_tups:
+ gem, gem_version = ruby_package_tup
if os.path.isfile( gem ):
# we assume a local shipped gem file
cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR &&
gem install --local %s''' % ( gem )
- elif gem.find('://') != -1:
- # we assume a URL to a gem file
+ elif gem.find( '://' ) != -1:
+ # We assume a URL to a gem file.
url = gem
gem_name = url.split( '/' )[ -1 ]
td_common_util.url_download( work_dir, gem_name, url, extract=False )
@@ -453,15 +454,15 @@
cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
-
+ return tool_dependency
env_file_builder = EnvFileBuilder( install_dir )
- handle_action_shell_file_paths( env_file_builder, action_dict ) # Pull in ruby dependencies (runtime).
+ # Pull in ruby dependencies (runtime).
+ handle_action_shell_file_paths( env_file_builder, action_dict )
env_file_builder.append_line( name="GEM_PATH", action="prepend_to", value=install_dir )
env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join(install_dir, 'bin') )
return_code = env_file_builder.return_code
if return_code:
- return
+ return tool_dependency
elif action_type == 'setup_perl_environment':
# setup an Perl environment
# <action type="setup_perl_environment">
@@ -473,65 +474,59 @@
# <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
# </action>
filtered_actions = actions[ 1: ]
-
- if action_dict.get( 'env_shell_file_paths', False ):
- install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] )
+ env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None )
+ if env_shell_file_paths is None:
+ log.debug( 'Missing Rerl environment, make sure your specified Rerl installation exists.' )
+ return tool_dependency
else:
- log.warning( 'Missing Rerl environment. Please check if your specified Rerl installation exists.' )
- return
-
+ install_environment.add_env_shell_file_paths( env_shell_file_paths )
+ log.debug( 'Handling setup_perl_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s"' % \
+ ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) )
dir = os.path.curdir
current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
with lcd( current_dir ):
with settings( warn_only=True ):
-
- for package in action_dict[ 'perl_packages' ]:
- """
- If set to a true value then MakeMaker's prompt function will always return the default without waiting for user input.
- """
+ perl_packages = action_dict.get( 'perl_packages', [] )
+ for perl_package in perl_packages:
+ # If set to a true value then MakeMaker's prompt function will always
+ # return the default without waiting for user input.
cmd = '''export PERL_MM_USE_DEFAULT=1 && '''
-
- if package.find('://') != -1:
- # we assume a URL to a gem file
- url = package
- package_name = url.split( '/' )[ -1 ]
- dir = td_common_util.url_download( work_dir, package_name, url, extract=True )
- # search for Build.PL or Makefile.PL (ExtUtils::MakeMaker vs. Module::Build)
-
- tmp_work_dir = os.path.join( work_dir, dir)
+ if perl_package.find( '://' ) != -1:
+ # We assume a URL to a gem file.
+ url = perl_package
+ perl_package_name = url.split( '/' )[ -1 ]
+ dir = td_common_util.url_download( work_dir, perl_package_name, url, extract=True )
+ # Search for Build.PL or Makefile.PL (ExtUtils::MakeMaker vs. Module::Build).
+ tmp_work_dir = os.path.join( work_dir, dir )
if os.path.exists( os.path.join( tmp_work_dir, 'Makefile.PL' ) ):
-
cmd += '''perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install'''
elif os.path.exists( os.path.join( tmp_work_dir, 'Build.PL' ) ):
cmd += '''perl Build.PL --install_base $INSTALL_DIR && perl Build && perl Build install'''
else:
- log.warning( 'No Makefile.PL or Build.PL file found in %s. Skip installation of %s.' % ( url, package_name ) )
- return
+ log.debug( 'No Makefile.PL or Build.PL file found in %s. Skipping installation of %s.' % ( url, perl_package_name ) )
+ return tool_dependency
with lcd( tmp_work_dir ):
cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
+ return tool_dependency
else:
- # perl package from CPAN without version number
- # cpanm should be installed with the parent perl distribution, otherwise this will not work
- cmd += '''cpanm --local-lib=$INSTALL_DIR %s''' % ( package )
-
+ # perl package from CPAN without version number.
+ # cpanm should be installed with the parent perl distribution, otherwise this will not work.
+ cmd += '''cpanm --local-lib=$INSTALL_DIR %s''' % ( perl_package )
cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
-
+ return tool_dependency
env_file_builder = EnvFileBuilder( install_dir )
+ # Pull in perl dependencies (runtime).
+ handle_action_shell_file_paths( env_file_builder, action_dict )
# Recursively add dependent PERL5LIB and PATH to env.sh & anything else needed.
- handle_action_shell_file_paths( env_file_builder, action_dict ) # Pull in ruby dependencies (runtime).
-
- env_file_builder.append_line( name="PERL5LIB", action="prepend_to", value=os.path.join(install_dir, 'lib', 'perl5') )
- env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join(install_dir, 'bin') )
+ env_file_builder.append_line( name="PERL5LIB", action="prepend_to", value=os.path.join( install_dir, 'lib', 'perl5' ) )
+ env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'bin' ) )
return_code = env_file_builder.return_code
if return_code:
- return
-
+ return tool_dependency
else:
# We're handling a complex repository dependency where we only have a set_environment tag set.
# <action type="set_environment">
@@ -577,7 +572,7 @@
env_file_builder.append_line( **env_var_dict )
return_code = env_file_builder.return_code
if return_code:
- return
+ return tool_dependency
elif action_type == 'set_environment_for_install':
# Currently the only action supported in this category is a list of paths to one or more tool dependency env.sh files,
# the environment setting in each of which will be injected into the environment for all <action type="shell_command">
@@ -588,7 +583,7 @@
venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) )
if not install_virtualenv( app, venv_src_directory ):
log.error( 'Unable to install virtualenv' )
- return
+ return tool_dependency
requirements = action_dict[ 'requirements' ]
if os.path.exists( os.path.join( dir, requirements ) ):
# requirements specified as path to a file
@@ -608,26 +603,26 @@
full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command )
return_code = handle_command( app, tool_dependency, install_dir, full_setup_command )
if return_code:
- return
+ return tool_dependency
site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( venv_directory, "bin", "python" )
output = handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True )
if output.return_code:
- return
+ return tool_dependency
if not os.path.exists( output.stdout ):
- log.error( "virtualenv's site-packages directory '%s' does not exist", output.stdout )
- return
+ log.debug( "virtualenv's site-packages directory '%s' does not exist", output.stdout )
+ return tool_dependency
env_file_builder = EnvFileBuilder( install_dir )
env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=output.stdout )
env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) )
return_code = env_file_builder.return_code
if return_code:
- return
+ return tool_dependency
elif action_type == 'shell_command':
with settings( warn_only=True ):
cmd = install_environment.build_command( action_dict[ 'command' ] )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
+ return tool_dependency
elif action_type == 'template_command':
env_vars = dict()
env_vars = install_environment.environment_dict()
@@ -639,7 +634,7 @@
cmd = fill_template( '#from fabric.api import env\n%s' % action_dict[ 'command' ], context=env_vars )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
+ return tool_dependency
elif action_type == 'make_install':
# make; make install; allow providing make options
with settings( warn_only=True ):
@@ -647,7 +642,7 @@
cmd = install_environment.build_command( 'make %s && make install' % make_opts )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
+ return tool_dependency
elif action_type == 'autoconf':
# Handle configure, make and make install allow providing configuration options
with settings( warn_only=True ):
@@ -659,7 +654,7 @@
cmd = install_environment.build_command( td_common_util.evaluate_template( pre_cmd, install_dir ) )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
- return
+ return tool_dependency
elif action_type == 'download_file':
# Download a single file to the current working directory.
url = action_dict[ 'url' ]
@@ -705,13 +700,7 @@
td_common_util.move_file( current_dir=work_dir,
source=downloaded_filename,
destination=full_path_to_dir )
-
-
-def handle_action_shell_file_paths( env_file_builder, action_dict ):
- shell_file_paths = action_dict.get( 'action_shell_file_paths', [])
- for shell_file_path in shell_file_paths:
- env_file_builder.append_line( action="source", value=shell_file_path )
-
+ return tool_dependency
def log_results( command, fabric_AttributeString, file_path ):
"""
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -92,7 +92,7 @@
return text
def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ):
- tool_dependency = None
+ handled_tool_dependencies = []
tool_shed = elem.attrib[ 'toolshed' ]
required_repository_name = elem.attrib[ 'name' ]
required_repository_owner = elem.attrib[ 'owner' ]
@@ -156,26 +156,28 @@
required_repository_owner,
required_repository_changeset_revision )
config_to_use = tmp_filename
- tool_dependency, actions_dict = populate_actions_dict( app=app,
- dependent_install_dir=dependent_install_dir,
- required_install_dir=required_repository_package_install_dir,
- tool_shed_repository=tool_shed_repository,
- required_repository=required_repository,
- package_name=package_name,
- package_version=package_version,
- tool_dependencies_config=config_to_use )
+ tool_dependencies, actions_dict = populate_actions_dict( app=app,
+ dependent_install_dir=dependent_install_dir,
+ required_install_dir=required_repository_package_install_dir,
+ tool_shed_repository=tool_shed_repository,
+ required_repository=required_repository,
+ package_name=package_name,
+ package_version=package_version,
+ tool_dependencies_config=config_to_use )
if tmp_filename:
try:
os.remove( tmp_filename )
except:
pass
- # Install and build the package via fabric.
- install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
+ for tool_dependency in tool_dependencies:
+ # Install and build the package via fabric and update the tool_dependency record accordingly..
+ tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
+ handled_tool_dependencies.append( tool_dependency )
else:
message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) )
raise Exception( message )
- return tool_dependency
+ return handled_tool_dependencies
def handle_set_environment_entry_for_package( app, install_dir, tool_shed_repository, package_name, package_version, elem, required_repository ):
"""
@@ -184,19 +186,24 @@
"""
action_dict = {}
actions = []
+ tool_dependencies = []
for package_elem in elem:
if package_elem.tag == 'install':
- # Create the tool_dependency record in the database.
+ # Create the new tool_dependency record in the database.
tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app,
tool_shed_repository=tool_shed_repository,
name=package_name,
version=package_version,
type='package',
- status=app.model.ToolDependency.installation_status.INSTALLING,
+ status=app.model.ToolDependency.installation_status.NEVER_INSTALLED,
set_status=True )
# Get the installation method version from a tag like: <install version="1.0">
package_install_version = package_elem.get( 'version', '1.0' )
if package_install_version == '1.0':
+ # Update the tool dependency's status.
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=app.model.ToolDependency.installation_status.INSTALLING )
# Since the required tool dependency is installed for a repository dependency, we first need to inspect the <actions> tag set to find
# the <action type="set_environment"> tag.
env_var_dicts = []
@@ -219,9 +226,10 @@
site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( install_dir, "venv", "bin", "python" )
output = fabric_util.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True )
if output.return_code:
- log.error( 'Dependency includes a setup_virtualenv action but venv python is broken:', output.stderr )
+ log.error( 'Tool dependency %s includes a setup_virtualenv action but venv python is broken: ' % \
+ ( str( tool_dependency.name ), str( output.stderr ) ) )
elif not os.path.exists( output.stdout ):
- log.error( "virtualenv's site-packages directory '%s' does not exist", output.stdout )
+ log.error( "virtualenv's site-packages directory '%s' does not exist", str( output.stdout ) )
else:
env_var_dicts.append( dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) )
env_var_dicts.append( dict( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'venv', 'bin' ) ) )
@@ -234,8 +242,8 @@
# we will replace the current "value" entries in each env_var_dict with the actual path taken from the env.sh
# file generated for the installed required repository. Each env_var_dict currently looks something like this:
# {'action': 'append_to', 'name': 'LD_LIBRARY_PATH', 'value': '$BOOST_ROOT_DIR/lib/'}
- # We'll read the contents of the received required_repository's env.sh file and replace the 'value' entry of each env_var_dict
- # with the associated value in the env.sh file.
+ # We'll read the contents of the received required_repository's env.sh file and replace the 'value' entry of
+ # each env_var_dict with the associated value in the env.sh file.
new_env_var_dicts = []
env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app,
repository_name=required_repository.name,
@@ -265,16 +273,25 @@
else:
action_dict[ 'environment_variable' ] = env_var_dicts
actions.append( ( 'set_environment', action_dict ) )
+ if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR,
+ app.model.ToolDependency.installation_status.INSTALLED ]:
+ # Update the tool dependency's status.
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=app.model.ToolDependency.installation_status.INSTALLED )
+ # Accumulate processed tool dependencies to return to the caller.
+ tool_dependencies.append( tool_dependency )
else:
raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' )
- return tool_dependency, actions
- return None, actions
+ return tool_dependencies, actions
+ return tool_dependencies, actions
def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ):
sa_session = app.model.context.current
try:
# There is currently only one fabric method.
- fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
+ tool_dependency = fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
except Exception, e:
log.exception( 'Error installing tool dependency %s version %s.', str( tool_dependency.name ), str( tool_dependency.version ) )
# Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must
@@ -284,10 +301,16 @@
tool_dependency,
error_message,
remove_installation_path=False )
- if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
- tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED
- sa_session.add( tool_dependency )
- sa_session.flush()
+ if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR,
+ app.model.ToolDependency.installation_status.INSTALLED ]:
+ log.debug( 'Changing status for tool dependency %s from %s to %s.' % \
+ ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) )
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=app.model.ToolDependency.installation_status.INSTALLED,
+ error_message=None,
+ remove_from_disk=False )
+ return tool_dependency
def install_package( app, elem, tool_shed_repository, tool_dependencies=None ):
# The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository.
@@ -300,9 +323,15 @@
for package_elem in elem:
if package_elem.tag == 'repository':
# We have a complex repository dependency definition.
- rd_tool_dependency = handle_complex_repository_dependency_for_package( app, package_elem, package_name, package_version, tool_shed_repository )
- if rd_tool_dependency and rd_tool_dependency.status == app.model.ToolDependency.installation_status.ERROR:
- print "Error installing tool dependency for required repository: %s" % str( rd_tool_dependency.error_message )
+ rd_tool_dependencies = handle_complex_repository_dependency_for_package( app,
+ package_elem,
+ package_name,
+ package_version,
+ tool_shed_repository )
+ for rd_tool_dependency in rd_tool_dependencies:
+ if rd_tool_dependency.status == app.model.ToolDependency.installation_status.ERROR:
+ # We'll log the error here, but continue installing packages since some may not require this dependency.
+ print "Error installing tool dependency for required repository: %s" % str( rd_tool_dependency.error_message )
elif package_elem.tag == 'install':
# <install version="1.0">
# Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository.
@@ -324,24 +353,27 @@
package_version,
'package' )
if tool_dependency.status == app.model.ToolDependency.installation_status.INSTALLING:
- # The tool dependency is in an Installing state, so we don't want to do anything to it.
+ # The tool dependency is in an Installing state, so we don't want to do anything to it. If the tool
+ # dependency is being installed by someone else, we don't want to interfere with that. This assumes
+ # the installation by "someone else" is not hung in an Installing state, which is a weakness if that
+ # "someone else" never repaired it.
log.debug( 'Skipping installation of tool dependency %s version %s because it has a status of %s' % \
- ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) )
+ ( str( tool_dependency.name ), str( tool_dependency.version ), str( tool_dependency.status ) ) )
can_install_tool_dependency = False
else:
- # If the tool dependency is being installed by someone else, we don't want to interfere with that.
- # This assumes the installation by "someone else" is not hung in an Installing state, which is a
- # weakness if "someone else" never repaired it.
tool_dependency_installation_directory_contents = os.listdir( install_dir )
if fabric_util.INSTALLATION_LOG in tool_dependency_installation_directory_contents:
- print '\nSkipping installation of tool dependency', package_name, 'version', package_version, \
- 'since it is installed in', install_dir, '\n'
+ # Since this tool dependency's installation directory contains an installation log, we consider it to be
+ # installed. In some cases the record may be missing from the database due to some activity outside of
+ # the control of the Tool Shed. Since a new record was created for it and we don't know the state of the
+ # files on disk, we will set it to an error state (unless we are running Tool Shed functional tests - see
+ # below).
+ log.debug( 'Skipping installation of tool dependency %s version %s because it is installed in %s' % \
+ ( str( tool_dependency.name ), str( tool_dependency.version ), str( install_dir ) ) )
can_install_tool_dependency = False
- # This tool dependency was previously installed, but the record was missing from the database due to some
- # activity outside of the control of the tool shed. Since a new record was created for it and we don't know
- # the state of the files on disk, we will set it to an error state. If we are running functional tests, the
- # state will be set to Installed, because previously compiled tool dependencies are not deleted by default.
if app.config.running_functional_tests:
+ # If we are running functional tests, the state will be set to Installed because previously compiled
+ # tool dependencies are not deleted by default, from the "install and test" framework..
tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED
else:
error_message = 'The installation directory for this tool dependency had contents, but the database had no record. '
@@ -351,9 +383,9 @@
tool_dependency.error_message = error_message
else:
error_message = '\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s' % \
- ( install_dir, package_name, package_version, fabric_util.INSTALLATION_LOG )
- error_message += ' is missing. This indicates an installation error, so the tool dependency is being'
- error_message += ' prepared for reinstallation.'
+ ( str( install_dir ), str( package_name ), str( package_version ), str( fabric_util.INSTALLATION_LOG ) )
+ error_message += ' is missing. This indicates an installation error so the tool dependency is being'
+ error_message += ' prepared for re-installation.'
print error_message
tool_dependency.status = app.model.ToolDependency.installation_status.NEVER_INSTALLED
try:
@@ -373,7 +405,7 @@
version=package_version,
type='package',
status=app.model.ToolDependency.installation_status.INSTALLING,
- set_status=False )
+ set_status=True )
# Get the information about the current platform in case the tool dependency definition includes tag sets for installing
# compiled binaries.
platform_info_dict = tool_dependency_util.get_platform_info_dict()
@@ -404,13 +436,12 @@
if binary_installed:
continue
# No platform-specific <actions> recipe has yet resulted in a successful installation.
- install_via_fabric( app,
- tool_dependency,
- install_dir,
- package_name=package_name,
- actions_elem=actions_elem,
- action_elem=None )
- sa_session.refresh( tool_dependency )
+ tool_dependency = install_via_fabric( app,
+ tool_dependency,
+ install_dir,
+ package_name=package_name,
+ actions_elem=actions_elem,
+ action_elem=None )
if tool_dependency.status == app.model.ToolDependency.installation_status.INSTALLED:
# If an <actions> tag was found that matches the current platform, and the install_via_fabric method
# did not result in an error state, set binary_installed to True in order to skip any remaining
@@ -419,47 +450,53 @@
else:
# Process the next matching <actions> tag, or any defined <actions> tags that do not contain platform
# dependent recipes.
- print 'Error downloading binary for %s version %s: %s' % \
- ( package_name, package_version, tool_dependency.error_message )
+ log.debug( 'Error downloading binary for tool dependency %s version %s: %s' % \
+ ( str( package_name ), str( package_version ), str( tool_dependency.error_message ) ) )
else:
# If no <actions> tags have been defined that match our current platform, or none of the matching
# <actions> tags resulted in a successful tool dependency status, proceed with one and only one
# <actions> tag that is not defined to be platform-specific.
if not binary_installed:
- print 'Binary installation did not occur, so proceeding with install and compile recipe.'
+ log.debug( 'Proceeding with install and compile recipe for tool dependency %s.' % str( tool_dependency.name ) )
# Make sure to reset for installation if attempt at binary installation resulted in an error.
+ can_install = True
if tool_dependency.status != app.model.ToolDependency.installation_status.NEVER_INSTALLED:
removed, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency )
- install_via_fabric( app,
- tool_dependency,
- install_dir,
- package_name=package_name,
- actions_elem=actions_elem,
- action_elem=None )
+ if not removed:
+ log.debug( 'Error removing old files from installation directory %s: %s' % \
+ ( str( tool_dependency.installation_directory( app ), str( error_message ) ) ) )
+ can_install = False
+ if can_install:
+ tool_dependency = install_via_fabric( app,
+ tool_dependency,
+ install_dir,
+ package_name=package_name,
+ actions_elem=actions_elem,
+ action_elem=None )
# Perform any final actions that have been defined within the actions_group tag set, but outside of
# an <actions> tag, such as a set_environment entry, or a download_file or download_by_url command to
# retrieve extra data for this tool dependency. Only do this if the tool dependency is not in an error
# state, otherwise skip this action.
if actions_elem.tag == 'action' and tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
- install_via_fabric( app,
- tool_dependency,
- install_dir,
- package_name=package_name,
- actions_elem=None,
- action_elem=actions_elem )
+ tool_dependency = install_via_fabric( app,
+ tool_dependency,
+ install_dir,
+ package_name=package_name,
+ actions_elem=None,
+ action_elem=actions_elem )
else:
# <actions> tags outside of an <actions_group> tag shall not check os or architecture, and if the attributes are
# defined, they will be ignored. All <actions> tags outside of an <actions_group> tag set shall always be processed.
# This is the default and original behavior of the install_package method.
- install_via_fabric( app,
- tool_dependency,
- install_dir,
- package_name=package_name,
- actions_elem=actions_elems,
- action_elem=None )
- sa_session.refresh( tool_dependency )
+ tool_dependency = install_via_fabric( app,
+ tool_dependency,
+ install_dir,
+ package_name=package_name,
+ actions_elem=actions_elems,
+ action_elem=None )
if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
- print package_name, 'version', package_version, 'installed in', install_dir
+ log.debug( 'Tool dependency %s version %s has been installed in %s.' % \
+ ( str( package_name ), str( package_version ), str( install_dir ) ) )
else:
error_message = 'Version %s of the %s package cannot be installed because ' % ( str( package_version ), str( package_name ) )
error_message += 'the recipe for installing the package is missing either an <actions> tag set or an <actions_group> '
@@ -489,7 +526,6 @@
def install_via_fabric( app, tool_dependency, install_dir, package_name=None, proprietary_fabfile_path=None, actions_elem=None, action_elem=None, **kwd ):
"""Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric."""
-
sa_session = app.model.context.current
if not os.path.exists( install_dir ):
os.makedirs( install_dir )
@@ -657,7 +693,7 @@
configure_opts = td_common_util.evaluate_template( action_elem.text, install_dir )
action_dict[ 'configure_opts' ] = configure_opts
elif action_type == 'setup_r_environment':
- # setup an R environment
+ # setup an R environment.
# <action type="setup_r_environment">
# <repository name="package_r_3_0_1" owner="bgruening">
# <package name="R" version="3.0.1" />
@@ -665,18 +701,19 @@
# <!-- allow installing an R packages -->
# <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package>
# </action>
- td_common_util.parse_setup_environment_repositories( app, all_env_shell_file_paths, action_elem, action_dict )
+ # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository.
+ # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict.
+ action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict )
r_packages = list()
for env_elem in action_elem:
if env_elem.tag == 'package':
r_packages.append( env_elem.text.strip() )
-
if r_packages:
action_dict[ 'r_packages' ] = r_packages
else:
continue
elif action_type == 'setup_ruby_environment':
- # setup an Ruby environment
+ # setup a Ruby environment.
# <action type="setup_ruby_environment">
# <repository name="package_ruby_2_0" owner="bgruening">
# <package name="ruby" version="2.0" />
@@ -686,33 +723,32 @@
# <package>protk=1.2.4</package>
# <package>http://url-to-some-gem-file.de/protk.gem</package>
# </action>
- td_common_util.parse_setup_environment_repositories( app, all_env_shell_file_paths, action_elem, action_dict )
- ruby_packages = list()
+ # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository.
+ # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict.
+ action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict )
+ ruby_package_tups = []
for env_elem in action_elem:
if env_elem.tag == 'package':
- """
- A valid gem definition can be:
- protk=1.2.4
- protk
- ftp://ftp.gruening.de/protk.gem
- """
- gem_token = env_elem.text.strip().split('=')
- if len(gem_token) == 2:
+ #A valid gem definition can be:
+ # protk=1.2.4
+ # protk
+ # ftp://ftp.gruening.de/protk.gem
+ gem_token = env_elem.text.strip().split( '=' )
+ if len( gem_token ) == 2:
# version string
- gem_name = gem_token[0]
- gem_version = gem_token[1]
- ruby_packages.append( [gem_name, gem_version] )
+ gem_name = gem_token[ 0 ]
+ gem_version = gem_token[ 1 ]
+ ruby_package_tups.append( ( gem_name, gem_version ) )
else:
# gem name for rubygems.org without version number
gem = env_elem.text.strip()
- ruby_packages.append( [gem, None] )
-
- if ruby_packages:
- action_dict[ 'ruby_packages' ] = ruby_packages
+ ruby_package_tups.append( ( gem, None ) )
+ if ruby_package_tups:
+ action_dict[ 'ruby_package_tups' ] = ruby_package_tups
else:
continue
elif action_type == 'setup_perl_environment':
- # setup an Perl environment
+ # setup a Perl environment.
# <action type="setup_perl_environment">
# <repository name="package_perl_5_18" owner="bgruening">
# <package name="perl" version="5.18.1" />
@@ -721,17 +757,17 @@
# <package>XML::Parser</package>
# <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
# </action>
- td_common_util.parse_setup_environment_repositories( app, all_env_shell_file_paths, action_elem, action_dict )
- perl_packages = list()
+ # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository.
+ # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict.
+ action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict )
+ perl_packages = []
for env_elem in action_elem:
if env_elem.tag == 'package':
- """
- A valid package definition can be:
- XML::Parser
- http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz
- Unfortunately, CPAN does not support versioning. If you want real Reproducibility,
- you need to specify the tarball path and the right order of different tarballs manually.
- """
+ # A valid package definition can be:
+ # XML::Parser
+ # http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz
+ # Unfortunately CPAN does not support versioning, so if you want real reproducibility you need to specify
+ # the tarball path and the right order of different tarballs manually.
perl_packages.append( env_elem.text.strip() )
if perl_packages:
action_dict[ 'perl_packages' ] = perl_packages
@@ -782,7 +818,8 @@
# run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=package_name )
raise Exception( 'Tool dependency installation using proprietary fabric scripts is not yet supported.' )
else:
- install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
+ tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
+ return tool_dependency
def parse_env_shell_entry( action, name, value, line ):
new_value = value
@@ -814,7 +851,7 @@
actions_dict = dict( install_dir=dependent_install_dir )
if package_name:
actions_dict[ 'package_name' ] = package_name
- tool_dependency = None
+ tool_dependencies = []
action_dict = {}
if tool_dependencies_config:
required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config )
@@ -827,17 +864,17 @@
required_td_package_name = required_td_elem.get( 'name', None )
required_td_package_version = required_td_elem.get( 'version', None )
if required_td_package_name==package_name and required_td_package_version==package_version:
- tool_dependency, actions = handle_set_environment_entry_for_package( app=app,
- install_dir=required_install_dir,
- tool_shed_repository=tool_shed_repository,
- package_name=package_name,
- package_version=package_version,
- elem=required_td_elem,
- required_repository=required_repository )
+ tool_dependencies, actions = handle_set_environment_entry_for_package( app=app,
+ install_dir=required_install_dir,
+ tool_shed_repository=tool_shed_repository,
+ package_name=package_name,
+ package_version=package_version,
+ elem=required_td_elem,
+ required_repository=required_repository )
if actions:
actions_dict[ 'actions' ] = actions
break
- return tool_dependency, actions_dict
+ return tool_dependencies, actions_dict
def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ):
"""
@@ -950,13 +987,22 @@
# Handle setting environment variables using a fabric method.
fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True )
sa_session.refresh( tool_dependency )
- if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
- tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED
- sa_session.add( tool_dependency )
- sa_session.flush()
- print 'Environment variable ', env_var_name, 'set in', install_dir
+ if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR,
+ app.model.ToolDependency.installation_status.INSTALLED ]:
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=app.model.ToolDependency.installation_status.INSTALLED,
+ error_message=None,
+ remove_from_disk=False )
+ log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \
+ ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) )
else:
- raise NotImplementedError( 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' )
+ error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).'
+ tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=app.model.ToolDependency.installation_status.ERROR,
+ error_message=error_message,
+ remove_from_disk=False )
return tool_dependency
def strip_path( fpath ):
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py
@@ -257,6 +257,33 @@
log.debug( error_message )
return env_shell_file_paths
+def get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, elem, action_dict ):
+ """
+ Parse an XML tag set to discover all child repository dependency tags and define the path to an env.sh file associated
+ with the repository (this requires the repository dependency to be in an installed state). The received action_dict
+ will be updated with these discovered paths and returned to the caller. This method handles tool dependency definition
+ tag sets <setup_r_environment>, <setup_ruby_environment> and <setup_perl_environment>.
+ """
+ # An example elem is:
+ # <action type="setup_perl_environment">
+ # <repository name="package_perl_5_18" owner="iuc">
+ # <package name="perl" version="5.18.1" />
+ # </repository>
+ # <repository name="package_expat_2_1" owner="iuc" prior_installation_required="True">
+ # <package name="expat" version="2.1.0" />
+ # </repository>
+ # <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
+ # <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
+ # </action>
+ for action_elem in elem:
+ if action_elem.tag == 'repository':
+ env_shell_file_paths = get_env_shell_file_paths( app, action_elem )
+ all_env_shell_file_paths.extend( env_shell_file_paths )
+ if all_env_shell_file_paths:
+ action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths
+ action_dict[ 'action_shell_file_paths' ] = env_shell_file_paths
+ return action_dict
+
def get_env_var_values( install_dir ):
env_var_dict = {}
env_var_dict[ 'INSTALL_DIR' ] = install_dir
@@ -415,16 +442,6 @@
continue
return actions_elem_tuples
-
-def parse_setup_environment_repositories( app, all_env_shell_file_paths, action_elem, action_dict ):
- env_shell_file_paths = get_env_shell_file_paths( app, action_elem.find('repository') )
-
- all_env_shell_file_paths.extend( env_shell_file_paths )
- if all_env_shell_file_paths:
- action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths
- action_dict[ 'action_shell_file_paths' ] = env_shell_file_paths
-
-
def url_download( install_dir, downloaded_file_name, download_url, extract=True ):
file_path = os.path.join( install_dir, downloaded_file_name )
src = None
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -85,12 +85,11 @@
includes_tool_dependencies = True
# Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies. We don't add to installed_td
# and missing_td here because at this point they are empty.
- installed_td, missing_td = get_installed_and_missing_tool_dependencies( trans, tool_shed_url, tool_dependencies )
+ installed_td, missing_td = get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies )
# In cases where a repository dependency is required only for compiling a dependent repository's tool dependency, the value of
# repository_dependencies will be an empty dictionary here.
if repository_dependencies:
# We have a repository with one or more defined repository dependencies.
- missing_td = {}
if not repository:
repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision )
if repository and repository.metadata:
@@ -118,9 +117,8 @@
required_tool_dependencies[ td_key ] = td_dict
if required_tool_dependencies:
# Discover and categorize all tool dependencies defined for this repository's repository dependencies.
- required_installed_td, required_missing_td = get_installed_and_missing_tool_dependencies( trans,
- tool_shed_url,
- required_tool_dependencies )
+ required_installed_td, required_missing_td = \
+ get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, required_tool_dependencies )
if required_installed_td:
if not includes_tool_dependencies:
includes_tool_dependencies = True
@@ -291,7 +289,7 @@
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
-def get_installed_and_missing_tool_dependencies( trans, tool_shed_url, tool_dependencies_dict ):
+def get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies_dict ):
"""Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories being installed into Galaxy."""
installed_tool_dependencies = {}
missing_tool_dependencies = {}
@@ -460,15 +458,18 @@
try:
dependencies_ignored = app.toolbox.dependency_manager and not app.toolbox.dependency_manager.uses_tool_shed_dependencies()
if dependencies_ignored:
- log.info("Skipping package %s, tool shed dependency resolver not enabled." % package_name)
- # Tool dependency resolves have been configured and they do not
- # include the tool shed. Do not install package.
- status = app.model.ToolDependency.installation_status.ERROR
+ log.debug( "Skipping package %s because tool shed dependency resolver not enabled." % str( package_name ) )
+ # Tool dependency resolves have been configured and they do not include the tool shed. Do not install package.
if app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY:
## TODO: Do something here such as marking it installed or
## configured externally.
pass
- tool_dependency.status = status
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=app.model.ToolDependency.installation_status.ERROR,
+ error_message=None,
+ remove_from_disk=False )
else:
tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies )
except Exception, e:
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da lib/tool_shed/util/tool_dependency_util.py
--- a/lib/tool_shed/util/tool_dependency_util.py
+++ b/lib/tool_shed/util/tool_dependency_util.py
@@ -221,7 +221,8 @@
return url_template
return None
-def get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ):
+def get_installed_and_missing_tool_dependencies_for_installed_repository( trans, repository, all_tool_dependencies ):
+ """Return the lists of installed tool dependencies and missing tool dependencies for a Tool Shed repository that has been installed into Galaxy."""
if all_tool_dependencies:
tool_dependencies = {}
missing_tool_dependencies = {}
@@ -429,7 +430,7 @@
required_repository, installed_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple )
if required_repository:
required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
- get_installed_and_missing_tool_dependencies( trans, required_repository, tool_dependencies )
+ get_installed_and_missing_tool_dependencies_for_installed_repository( trans, required_repository, tool_dependencies )
if required_repository_installed_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_installed_tool_dependencies = \
@@ -479,14 +480,16 @@
error_message = ''
return removed, error_message
-def set_tool_dependency_attributes( trans, tool_dependency, status, error_message, remove_from_disk=False ):
+def set_tool_dependency_attributes( app, tool_dependency, status, error_message=None, remove_from_disk=False ):
+ sa_session = app.model.context.current
if remove_from_disk:
- installation_directory = tool_dependency.installation_directory( trans.app )
+ installation_directory = tool_dependency.installation_directory( app )
removed, err_msg = remove_tool_dependency_installation_directory( installation_directory )
tool_dependency.error_message = error_message
tool_dependency.status = status
- trans.sa_session.add( tool_dependency )
- trans.sa_session.flush()
+ sa_session.add( tool_dependency )
+ sa_session.flush()
+ return tool_dependency
def tool_dependency_is_orphan( type, name, version, tools ):
"""
diff -r d0ac928b3c1d529e32793a0fc27710e4a1585346 -r f78dcb9eb2897c452c3475d21bd601c0a91b63da test/unit/tool_shed/test_td_common_util.py
--- a/test/unit/tool_shed/test_td_common_util.py
+++ b/test/unit/tool_shed/test_td_common_util.py
@@ -33,8 +33,7 @@
assert path == join( TEST_INSTALL_DIR, "env.sh" )
assert line == ". /usr/share/R/libs"
-
-def test_parse_setup_environment_repositories( ):
+def test_get_env_shell_file_paths_from_setup_environment_elem( ):
xml = """<action name="setup_r_environment"><repository name="package_r_3_0_1" owner="bgruening" toolshed="toolshed.g2.bx.psu.edu" changeset_revision="1234567"><package name="R" version="3.0.1" />
@@ -49,26 +48,25 @@
r_env_sh = '/path/to/go/env.sh'
- def mock_get_env_shell_file_paths( app, elem):
+ def mock_get_env_shell_file_paths( app, elem ):
assert app == mock_app
assert elem.get( 'name' ) == "package_r_3_0_1"
return [ r_env_sh ]
- with __mock_common_util_method("get_env_shell_file_paths", mock_get_env_shell_file_paths):
- td_common_util.parse_setup_environment_repositories( mock_app, all_env_paths, action_elem, action_dict )
+ with __mock_common_util_method( "get_env_shell_file_paths", mock_get_env_shell_file_paths ):
+ td_common_util.get_env_shell_file_paths_from_setup_environment_elem( mock_app, all_env_paths, action_elem, action_dict )
## Verify old env files weren't deleted.
assert required_for_install_env_sh in all_env_paths
## Verify new ones added.
assert r_env_sh in all_env_paths
## env_shell_file_paths includes everything
- assert all( [env in action_dict[ 'env_shell_file_paths' ] for env in all_env_paths] )
+ assert all( [ env in action_dict[ 'env_shell_file_paths' ] for env in all_env_paths ] )
## action_shell_file_paths includes only env files defined in
## inside the setup_ action element.
assert required_for_install_env_sh not in action_dict[ 'action_shell_file_paths' ]
assert r_env_sh in action_dict[ 'action_shell_file_paths' ]
-
## Poor man's mocking. Need to get a real mocking library as real Galaxy development
## dependnecy.
@contextmanager
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commit/galaxy-central: Dave Bouvier: Script to check the contents of an S3 bucket for tool dependency installation paths that have no contents, or that contain only the installation log. Optionally delete any found paths.
by commits-noreply＠bitbucket.org 19 Nov '13
by commits-noreply＠bitbucket.org 19 Nov '13
19 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d0ac928b3c1d/
Changeset: d0ac928b3c1d
User: Dave Bouvier
Date: 2013-11-19 22:37:11
Summary: Script to check the contents of an S3 bucket for tool dependency installation paths that have no contents, or that contain only the installation log. Optionally delete any found paths.
Affected #: 1 file
diff -r 5b91b8e9e71b037478dd76b105f34a775b7279dc -r d0ac928b3c1d529e32793a0fc27710e4a1585346 lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
--- /dev/null
+++ b/lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
@@ -0,0 +1,155 @@
+import argparse
+import os
+import sys
+
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] )
+sys.path = new_path
+
+from galaxy.util import asbool
+from galaxy import eggs
+eggs.require( 'boto' )
+
+import boto
+
+from tool_shed.galaxy_install.tool_dependencies.fabric_util import INSTALLATION_LOG
+
+
+class BucketList( object ):
+
+ def __init__( self, amazon_id, amazon_secret, bucket ):
+ # Connect to S3 using the provided Amazon access key and secret identifier.
+ self.s3 = boto.connect_s3( amazon_id, amazon_secret )
+ self.bucket_name = bucket
+ # Connect to S3 using the received bucket name.
+ self.bucket = boto.s3.bucket.Bucket( self.s3, bucket )
+ self.install_dirs = self.get_tool_dependency_install_paths()
+ self.empty_installation_paths = self.check_for_empty_tool_dependency_installation_paths()
+
+ def display_empty_installation_paths( self ):
+ for empty_installation_path in self.empty_installation_paths:
+ print empty_installation_path
+
+ def delete_empty_installation_paths( self ):
+ print 'Deleting empty installation paths.'
+ for empty_installation_path in self.empty_installation_paths:
+ # Get all keys in the S3 bucket that start with the installation path, and delete each one.
+ for path_to_delete in self.bucket.list( prefix=empty_installation_path ):
+ self.bucket.delete_key( path_to_delete.key )
+ print 'Deleted empty path %s' % str( empty_installation_path )
+
+ def get_tool_dependency_install_paths( self ):
+ found_paths = []
+ for item in self.bucket.list():
+ name = str( item.name )
+ # Skip environment_settings and __virtualenv_src, since these directories do not contain package tool dependencies.
+ if name.startswith( 'environment_settings' ) or name.startswith( '__virtualenv_src' ):
+ continue
+ paths = name.rstrip('/').split( '/' )
+ # Paths are in the format name/version/owner/repository/changeset_revision. If the changeset revision is
+ # present, we need to check the contents of that path. If not, then the tool dependency was completely
+ # uninstalled.
+ if len( paths ) >= 5:
+ td_install_dir = '/'.join( paths[ :5 ] ) + '/'
+ if td_install_dir not in found_paths:
+ found_paths.append( name )
+ return found_paths
+
+ def check_for_empty_tool_dependency_installation_paths( self ):
+ empty_directories = []
+ for item in self.install_dirs:
+ # Get all entries under the path for this tool dependency.
+ contents = self.bucket.list( prefix=item )
+ tool_dependency_path_contents = []
+ # Find out if there are two or less items in the path. The first entry will be the installation path itself.
+ # If only one other item exists, and the full path ends with the installation log, this is an incorrectly installed
+ # tool dependency.
+ for item in contents:
+ tool_dependency_path_contents.append( item )
+ # If there are more than two items in the path, we cannot safely assume that the dependency failed to
+ # install correctly.
+ if len( tool_dependency_path_contents ) > 2:
+ break
+ # If the root directory is the only entry in the path, we have an empty tool dependency installation path.
+ if len( tool_dependency_path_contents ) == 1:
+ empty_directories.append( tool_dependency_path_contents[ 0 ] )
+ # Otherwise, if the only other entry is the installation log, we have an installation path that should be deleted.
+ # This would not be the case in a Galaxy instance, since the Galaxy admin will need to verify the contents of
+ # the installation path in order to determine which action should be taken.
+ elif len( tool_dependency_path_contents ) == 2 and tool_dependency_path_contents[1].name.endswith( INSTALLATION_LOG ):
+ empty_directories.append( tool_dependency_path_contents[ 0 ] )
+ return [ item.name for item in empty_directories ]
+
+def main( args ):
+ '''
+ Amazon credentials can be provided in one of three ways:
+ 1. By specifying them on the command line with the --id and --secret arguments.
+ 2. By specifying a path to a file that contains the credentials in the form ACCESS_KEY:SECRET_KEY
+ using the --s3passwd argument.
+ 3. By specifying the above path in the 's3passwd' environment variable.
+ Each listed option will override the ones below it, if present.
+ '''
+ if None in [ args.id, args.secret ]:
+ if args.s3passwd is None:
+ args.s3passwd = os.environ.get( 's3passwd', None )
+ if args.s3passwd is not None and os.path.exists( args.s3passwd ):
+ awsid, secret = file( args.s3passwd, 'r' ).read().rstrip( '\n' ).split( ':' )
+ else:
+ print 'Amazon ID and secret not provided, and no s3passwd file found.'
+ return 1
+ else:
+ awsid = args.id
+ secret = args.secret
+ dependency_cleaner = BucketList( awsid, secret, args.bucket )
+ if len( dependency_cleaner.empty_installation_paths ) == 0:
+ print 'No empty installation paths found, exiting.'
+ return 0
+ print 'The following %d tool dependency installation paths were found to be empty or contain only the file %s.' % \
+ ( len( dependency_cleaner.empty_installation_paths ), INSTALLATION_LOG )
+ if asbool( args.delete ):
+ dependency_cleaner.delete_empty_installation_paths()
+ else:
+ for empty_installation_path in dependency_cleaner.empty_installation_paths:
+ print empty_installation_path
+ return 0
+
+if __name__ == '__main__':
+ description = 'Determine if there are any tool dependency installation paths that should be removed. Remove them if '
+ description += 'the --delete command line argument is provided with a true value.'
+ parser = argparse.ArgumentParser( description=description )
+ parser.add_argument( '--delete',
+ dest='delete',
+ required=True,
+ action='store',
+ default=False,
+ type=asbool,
+ help='Whether to delete empty folders or list them on exit.' )
+ parser.add_argument( '--bucket',
+ dest='bucket',
+ required=True,
+ action='store',
+ metavar='name',
+ help='The S3 bucket where tool dependencies are installed.' )
+ parser.add_argument( '--id',
+ dest='id',
+ required=False,
+ action='store',
+ default=None,
+ metavar='ACCESS_KEY',
+ help='The identifier for an amazon account that has read access to the bucket.' )
+ parser.add_argument( '--secret',
+ dest='secret',
+ required=False,
+ action='store',
+ default=None,
+ metavar='SECRET_KEY',
+ help='The secret key for an amazon account that has upload/delete access to the bucket.' )
+ parser.add_argument( '--s3passwd',
+ dest='s3passwd',
+ required=False,
+ action='store',
+ default=None,
+ metavar='path/file',
+ help='The path to a file containing Amazon access credentials, in the format KEY:SECRET.' )
+ args = parser.parse_args()
+ sys.exit( main( args ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Upload: Transfer first genome selection to unselected genome selectors
by commits-noreply＠bitbucket.org 19 Nov '13
by commits-noreply＠bitbucket.org 19 Nov '13
19 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5b91b8e9e71b/
Changeset: 5b91b8e9e71b
User: guerler
Date: 2013-11-19 22:30:55
Summary: Upload: Transfer first genome selection to unselected genome selectors
Affected #: 2 files
diff -r eb071eaf633899f235babae41240975ab98551a1 -r 5b91b8e9e71b037478dd76b105f34a775b7279dc static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -151,13 +151,26 @@
// update info
it.find('#size').html(this.size_to_string (file.size));
- // add functionality to remove button
+ // add functionality to new row elements
var self = this;
it.find('#symbol').on('click', function() { self.event_remove (index) });
it.find('#text-content').on('keyup', function() {
var count = it.find('#text-content').val().length;
it.find('#size').html(self.size_to_string (count));
});
+ it.find('#genome').on('change', function(e) {
+ // identify target
+ var $target = $(e.target);
+ var selected_genome = $target.val();
+
+ // identify other genome selectors
+ var genomes = (self.$el).find('.genome');
+ genomes.each(function() {
+ var $select = $(this);
+ if ($select.val() == '?')
+ $select.val(selected_genome);
+ });
+ });
// initialize progress
this.event_progress(index, file, 0);
diff -r eb071eaf633899f235babae41240975ab98551a1 -r 5b91b8e9e71b037478dd76b105f34a775b7279dc static/scripts/utils/galaxy.uploadbox.js
--- a/static/scripts/utils/galaxy.uploadbox.js
+++ b/static/scripts/utils/galaxy.uploadbox.js
@@ -24,7 +24,6 @@
error_filesize : "File exceeds 2GB. Please use an FTP client.",
error_default : "Please make sure the file is available.",
error_server : "Upload request failed.",
- error_toomany : "You can only queue <20 files per upload session.",
error_login : "Uploads require you to log in.",
error_missing : "No upload content available."
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Upload: Do not use root when nginx_upload_path is defined
by commits-noreply＠bitbucket.org 19 Nov '13
by commits-noreply＠bitbucket.org 19 Nov '13
19 Nov '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/eb071eaf6338/
Changeset: eb071eaf6338
User: guerler
Date: 2013-11-19 21:45:49
Summary: Upload: Do not use root when nginx_upload_path is defined
Affected #: 2 files
diff -r c3f3523b6580c23feab1ca90d1333ca05dc3abaa -r eb071eaf633899f235babae41240975ab98551a1 static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -216,7 +216,7 @@
return null;
// configure uploadbox
- this.uploadbox.configure({url : galaxy_config.root + this.options.nginx_upload_path, paramname : "files_0|file_data"});
+ this.uploadbox.configure({url : this.options.nginx_upload_path, paramname : "files_0|file_data"});
// configure tool
tool_input = {};
diff -r c3f3523b6580c23feab1ca90d1333ca05dc3abaa -r eb071eaf633899f235babae41240975ab98551a1 templates/webapps/galaxy/galaxy.masthead.mako
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -34,7 +34,7 @@
masthead_config = {
## inject configuration
'brand' : app.config.get("brand", ""),
- 'nginx_upload_path' : app.config.get("nginx_upload_path", "api/tools"),
+ 'nginx_upload_path' : app.config.get("nginx_upload_path", h.url_for(controller='api', action='tools')),
'use_remote_user' : app.config.use_remote_user,
'remote_user_logout_href' : app.config.remote_user_logout_href,
'enable_cloud_launch' : app.config.get_bool('enable_cloud_launch', False),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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