diff --git a/client/galaxy/scripts/galaxy.pages.js b/client/galaxy/scripts/galaxy.pages.js index d5cca10e0cb..1188ded5dd2 100644 --- a/client/galaxy/scripts/galaxy.pages.js +++ b/client/galaxy/scripts/galaxy.pages.js @@ -444,10 +444,11 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm if ($("#make-importable:checked").val() != null) make_importable = true; grid.$("input[name=id]:checked").each(function() { + var elt = $(this); // Get item ID and name. - var item_id = $(this).val(); + var item_id = elt.val(); // Use ':first' because there are many labels in table; the first one is the item name. - var item_name = $(`label[for='${item_id}']:first`).text(); + var item_name = elt.closest('td').next('td').find('label').text(); if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular); diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 943dd0da10f..0ee76ece236 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -72,6 +72,23 @@ _cp1252 = { } +PAGE_MAXRAW = 10**15 + + +def _get_page_identifiers(item_id, app): + # Assume if item id is integer and less than 10**15, it's unencoded. + try: + decoded_id = int(item_id) + if decoded_id >= PAGE_MAXRAW: + raise ValueError("Identifier larger than maximum expected raw int, must be already encoded.") + encoded_id = app.security.encode_id(item_id) + except ValueError: + # It's an encoded id. + encoded_id = item_id + decoded_id = app.security.decode_id(item_id) + return (encoded_id, decoded_id) + + def format_bool(b): if b: return "yes" @@ -620,7 +637,11 @@ class PageController(BaseUIController, SharableMixin, id = self.decode_id(id) page = trans.sa_session.query(model.Page).get(id) assert page.user == trans.user - return trans.fill_template("page/editor.mako", page=page) + content = page.latest_revision.content + processor = _PageContentProcessor(trans, _placeholderRenderForEdit) + processor.feed(content) + content = unicodify(processor.output(), 'utf-8') + return trans.fill_template("page/editor.mako", page=page, content=content) @web.expose @web.require_login("use Galaxy pages") @@ -707,6 +728,10 @@ class PageController(BaseUIController, SharableMixin, # Sanitize content content = sanitize_html(content) + processor = _PageContentProcessor(trans, _placeholderRenderForSave) + processor.feed(content) + # Output is string, so convert to unicode for saving. + content = unicodify(processor.output(), 'utf-8') # Add a new revision to the page with the provided content. page_revision = model.PageRevision() @@ -901,12 +926,10 @@ class PageController(BaseUIController, SharableMixin, def get_item(self, trans, id): return self.get_page(trans, id) - def _get_embedded_history_html(self, trans, id): + def _get_embedded_history_html(self, trans, decoded_id): """ Returns html suitable for embedding in another page. """ - # TODO: should be moved to history controller and/or called via ajax from the template - decoded_id = self.decode_id(id) # histories embedded in pages are set to importable when embedded, check for access here history = self.history_manager.get_accessible(decoded_id, trans.user, current_history=trans.history) @@ -929,11 +952,11 @@ class PageController(BaseUIController, SharableMixin, content_dicts=contents) return filled - def _get_embedded_visualization_html(self, trans, id): + def _get_embedded_visualization_html(self, trans, encoded_id): """ Returns html suitable for embedding visualizations in another page. """ - visualization = self.get_visualization(trans, id, False, True) + visualization = self.get_visualization(trans, encoded_id, False, True) visualization.annotation = self.get_item_annotation_str(trans.sa_session, visualization.user, visualization) if not visualization: return None @@ -955,11 +978,11 @@ class PageController(BaseUIController, SharableMixin, def _get_embed_html(self, trans, item_class, item_id): """ Returns HTML for embedding an item in a page. """ item_class = self.get_class(item_class) + encoded_id, decoded_id = _get_page_identifiers(item_id, trans.app) if item_class == model.History: - return self._get_embedded_history_html(trans, item_id) + return self._get_embedded_history_html(trans, decoded_id) elif item_class == model.HistoryDatasetAssociation: - decoded_id = self.decode_id(item_id) dataset = self.hda_manager.get_accessible(decoded_id, trans.user) dataset = self.hda_manager.error_if_uploading(dataset) @@ -969,14 +992,62 @@ class PageController(BaseUIController, SharableMixin, return trans.fill_template("dataset/embed.mako", item=dataset, item_data=data) elif item_class == model.StoredWorkflow: - workflow = self.get_stored_workflow(trans, item_id, False, True) + workflow = self.get_stored_workflow(trans, encoded_id, False, True) workflow.annotation = self.get_item_annotation_str(trans.sa_session, workflow.user, workflow) if workflow: self.get_stored_workflow_steps(trans, workflow) return trans.fill_template("workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps) elif item_class == model.Visualization: - return self._get_embedded_visualization_html(trans, item_id) + return self._get_embedded_visualization_html(trans, encoded_id) elif item_class == model.Page: pass + + +PLACEHOLDER_TEMPLATE = '''

Embedded Galaxy {class_shorthand} - '{item_name}'

[Do not edit this block; Galaxy will fill it in with the annotated {class_shorthand} when it is displayed]

''' + +# This is a mapping of the id portion of page contents to the cssclass/shortname. +PAGE_CLASS_MAPPING = { + 'History': 'History', + 'HistoryDatasetAssociation': 'Dataset', + 'StoredWorkflow': 'Workflow', + 'Visualization': 'Visualization' +} + + +def _placeholderRenderForEdit(trans, item_class, item_id): + return _placeholderRenderForSave(trans, item_class, item_id, encode=True) + + +def _placeholderRenderForSave(trans, item_class, item_id, encode=False): + encoded_item_id, decoded_item_id = _get_page_identifiers(item_id, trans.app) + item_name = '' + if item_class == 'History': + history = trans.sa_session.query(trans.model.History).get(decoded_item_id) + history = managers.base.security_check(trans, history, False, True) + item_name = history.name + elif item_class == 'HistoryDatasetAssociation': + hda = trans.sa_session.query(trans.model.HistoryDatasetAssociation).get(decoded_item_id) + hda = managers.base.security_check(trans, hda , False, True) + item_name = hda.name + elif item_class == 'StoredWorkflow': + wf = trans.sa_session.query(trans.model.StoredWorkflow).get(decoded_item_id) + wf = managers.base.security_check(trans, wf, False, True) + item_name = wf.name + elif item_class == 'Visualization': + visualization = trans.sa_session.query(trans.model.Visualization).get(decoded_item_id) + visualization = managers.base.security_check(trans, visualization, False, True) + item_name = visualization.title + class_shorthand = PAGE_CLASS_MAPPING[item_class] + if encode: + item_id = encoded_item_id + else: + item_id = decoded_item_id + return PLACEHOLDER_TEMPLATE.format( + item_class=item_class, + class_shorthand=class_shorthand, + class_shorthand_lower=class_shorthand.lower(), + item_id=item_id, + item_name=item_name + ) diff --git a/scripts/pages_identifier_conversion.py b/scripts/pages_identifier_conversion.py new file mode 100644 index 00000000000..b7139e8e77d --- /dev/null +++ b/scripts/pages_identifier_conversion.py @@ -0,0 +1,57 @@ +import argparse +import difflib +import logging +import os +import sys + +sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))) + +import galaxy +import galaxy.app +import galaxy.config +from galaxy.objectstore import build_object_store_from_config +from galaxy.util import unicodify +from galaxy.util.bunch import Bunch +from galaxy.util.script import app_properties_from_args, populate_config_args +from galaxy.web.security import SecurityHelper +from galaxy.webapps.galaxy.controllers.page import _PageContentProcessor, _placeholderRenderForSave + + +def main(argv): + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument('-k', '--secret-key', help='Key to convert pages with', default='') + parser.add_argument('-d', '--dry-run', help='No changes, just test it.', action='store_true') + populate_config_args(parser) + args = parser.parse_args() + properties = app_properties_from_args(args) + config = galaxy.config.Configuration(**properties) + secret = args.secret_key or config.id_secret + security_helper = SecurityHelper(id_secret=secret) + object_store = build_object_store_from_config(config) + if not config.database_connection: + print("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml") + + model = galaxy.config.init_models_from_config(config, object_store=object_store) + session = model.context.current + pagerevs = session.query(model.PageRevision).all() + mock_trans = Bunch(app=Bunch(security=security_helper), model=model, user_is_admin=lambda: True, sa_session=session) + for p in pagerevs: + try: + processor = _PageContentProcessor(mock_trans, _placeholderRenderForSave) + processor.feed(p.content) + newcontent = unicodify(processor.output(), 'utf-8') + if p.content != newcontent: + if not args.dry_run: + p.content = unicodify(processor.output(), 'utf-8') + session.add(p) + session.flush() + else: + print("Modifying revision %s." % p.id) + print(difflib.unified_diff(p.content, newcontent)) + except Exception: + logging.exception("Error parsing page, rolling changes back and skipping revision %s. Please report this error." % p.id) + session.rollback() + + +if __name__ == '__main__': + main(sys.argv) diff --git a/static/scripts/bundled/extended.bundled.js b/static/scripts/bundled/extended.bundled.js index 88a63efb325..f0dbdad9562 100644 --- a/static/scripts/bundled/extended.bundled.js +++ b/static/scripts/bundled/extended.bundled.js @@ -46,5 +46,5 @@ s=n,l=t("
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t=this;document.addEventListener("copy",function(e){""===window.getSelection().toString()&&(t.app.workflow.active_node&&"subworkflow"!==t.app.workflow.active_node.type&&e.clipboardData.setData("application/json",JSON.stringify({nodeId:t.app.workflow.active_node.id})),e.preventDefault())}),document.addEventListener("paste",function(e){if(document.activeElement&&"textarea"!==document.activeElement.type&&"text"!==document.activeElement.type){var n;try{n=JSON.parse(e.clipboardData.getData("application/json")).nodeId}catch(t){}n&&t.app.workflow.nodes.hasOwnProperty(n)&&t.app.workflow.nodes[n].clone(),e.preventDefault()}})},update_viewport_overlay:function(){var t=this.cc,e=this.cv,n=this.oc,i=this.ov,r=t.width(),a=t.height(),o=n.width(),s=n.height(),l=t.position();i.css({left:-l.left/r*o,top:-l.top/a*s,width:e.width()/r*o-2,height:e.height()/a*s-2})},draw_overview:function(){var 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t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(5),s=a(o),l=n(720),c=a(l),d=t.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return i.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);){var e=this.getWorkflowOutput(t);this.workflow_outputs.splice(i.indexOf(this.workflow_outputs,e),1)}},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var n={output_name:t};return e&&(n.label=e),this.workflow_outputs.push(n),!0}return!1},labelWorkflowOutput:function(t,e){var n=!1,i=null;if(this.isWorkflowOutput(t)){var r=this.getWorkflowOutput(t);i=r.label,r.label=e,n=i!=e}else n=this.addWorkflowOutput(t,e);return 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r=Object.assign({},i,e);n.init_field_data(r),n.update_field_data(r),t.app.workflow.activate_node(n)}})},destroy:function(){r.each(this.input_terminals,function(t,e){e.destroy()}),r.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),r(this.element).remove()},make_active:function(){r(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),r(t).removeClass("toolForm-active")},set_tool_version:function(){"tool"===this.type&&this.config_form&&(this.tool_version=this.config_form.version,this.content_id=this.config_form.id)},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.set_tool_version(),this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,n=new c.default({el:this.element[0],node:e});e.nodeView=n,r.each(t.data_inputs,function(t,e){n.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&n.addRule(),r.each(t.data_outputs,function(t,e){n.addDataOutput(e)}),n.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,n=e.nodeView,a=[];if(r.each(n.outputViews,function(e,n){var r=n.output.name,o=t.data_outputs,s=!1;i.each(o,function(t){t.name==r&&(s=!0)}),!1===s&&a.push(r)}),i.each(a,function(t){i.each(n.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),n.outputViews[t].remove(),delete n.outputViews[t],delete e.output_terminals[t]}),r.each(e.workflow_outputs,function(t,n){n&&!e.output_terminals[n.output_name]&&e.workflow_outputs.splice(t,1)}),r.each(t.data_outputs,function(t,i){n.outputViews[i.name]?(e.output_terminals[i.name].datatypes=i.extensions,e.output_terminals[i.name].destroyInvalidConnections()):n.addDataOutput(i)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.set_tool_version(),this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var o=t.post_job_actions;this.post_job_actions=o||{}}e.nodeView.renderToolErrors();var s=n.$("div.inputs"),l=n.newInputsDiv(),c={};i.each(t.data_inputs,function(t){var n=e.nodeView.addDataInput(t,l);c[t.name]=n}),i.each(i.difference(i.values(n.terminalViews),i.values(c)),function(t){t.el.terminal.destroy()}),n.terminalViews=c,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&n.updateDataOutput(t.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=r(this.element).find(".toolFormBody");e.find("div").remove();var n="
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    ";this.config_form=n,e.html(n),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});e.default=d}).call(e,n(2),n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(1),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=n(721),l=r(s),c=n(723),d=r(c);e.default=t.View.extend({initialize:function(t){this.node=t.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name),this.$el.attr("node-label",this.node.label)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return i("
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s.default.OutputCollectionTerminal({element:this.el,collection_type:e,collection_type_source:n,datatypes:t.extensions})}});e.default={InputTerminalView:p,OutputTerminalView:m,InputCollectionTerminalView:_,OutputCollectionTerminalView:v}}).call(e,n(2),n(1),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){this.collectionType=t,this.isCollection=!0,this.rank=t.split(":").length}Object.defineProperty(e,"__esModule",{value:!0});var o=n(20),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(o);window.workflow_globals=window.workflow_globals||{};var l={isCollection:!1,canMatch:function(){return!1},canMapOver:function(){return!1},toString:function(){return"NullCollectionType[]"},append:function(t){return t},equal:function(t){return t===this}},c={isCollection:!0,canMatch:function(t){return l!==t},canMapOver:function(){return!1},toString:function(){return"AnyCollectionType[]"},append:function(){return c},equal:function(t){return t===this}};t.extend(a.prototype,{append:function(t){return t===l?this:t===c?t:new a(this.collectionType+":"+t.collectionType)},canMatch:function(t){return t!==l&&(t===c||t.collectionType==this.collectionType)},canMapOver:function(t){if(t===l)return!1;if(t===c)return!1;if(this.rank<=t.rank)return!1;var e=t.collectionType;return this._endsWith(this.collectionType,e)},effectiveMapOver:function(t){var e=t.collectionType;return new a(this.collectionType.substring(0,this.collectionType.length-e.length-1))},equal:function(t){return t.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(t,e){return-1!==t.indexOf(e,t.length-e.length)}});var d=i.Model.extend({initialize:function(t){this.mapOver=t.mapOver||l,this.terminal=t.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(l)},setMapOver:function(t){this.mapOver=t,this.trigger("change")}}),u=i.Model.extend({initialize:function(t){this.element=t.element,this.connectors=[]},connect:function(t){this.connectors.push(t),this.node&&this.node.markChanged()},disconnect:function(e){this.connectors.splice(t.inArray(e,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){t.each(this.connectors,function(t,e){e.redraw()})},destroy:function(){t.each(this.connectors.slice(),function(t,e){e.destroy()})},destroyInvalidConnections:function(){r.each(this.connectors,function(t){t&&t.destroyIfInvalid()})},setMapOver:function(t){this.multiple||this.mapOver().equal(t)||(this.terminalMapping.setMapOver(t),r.each(this.node.output_terminals,function(e){e.setMapOver(t)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:l},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),h=u.extend({initialize:function(t){u.prototype.initialize.call(this,t),this.datatypes=t.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||r.each(this.node.mappedInputTerminals(),function(t){t.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),r.each(this.connectors,function(t){var e=t.handle2;e&&(e.resetMappingIfNeeded(),t.destroyIfInvalid())})}}),f=u.extend({initialize:function(t){u.prototype.initialize.call(this,t),this.update(t.input)},canAccept:function(t){return!this._inputFilled()&&this.attachable(t)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||r.each(this.node.output_terminals,function(t){t.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){return!!this.connected()&&(!this.multiple||!!this._collectionAttached())},_collectionAttached:function(){if(this.connected()){var t=this.connectors[0].handle1;return!!t&&!!(t.isCollection||t.isMappedOver()||t.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var t=this.mapOver();if(t.isCollection)return[t];var e=[];return this.node.hasConnectedOutputTerminals()?e.push(r.first(r.values(this.node.output_terminals)).mapOver()):r.each(this.node.connectedMappedInputTerminals(),function(t){e.push(t.mapOver())}),e},_producesAcceptableDatatype:function(t){for(var e in this.datatypes){var n=this.datatypes[e];if("input"==n)return!0;var i=[];if(i=i.concat(t.datatypes),t.node.post_job_actions)for(var r in t.node.post_job_actions){var a=t.node.post_job_actions[r];"ChangeDatatypeAction"!=a.action_type||""!==a.output_name&&a.output_name!=t.name||!a.action_arguments||i.push(a.action_arguments.newtype)}for(var o in i){var s=i[o];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(i[o],n))return!0}}return!1},_otherCollectionType:function(t){var e=l;t.isCollection&&(e=t.collectionType);var n=t.mapOver();return n.isCollection&&(e=n.append(e)),e}}),p=f.extend({update:function(t){this.datatypes=t.extensions,this.multiple=t.multiple,this.collection=!1},connect:function(t){f.prototype.connect.call(this,t);var e=t.handle1;if(e){var n=this._otherCollectionType(e);n.isCollection&&this.setMapOver(n)}},attachable:function(t){var e=this._otherCollectionType(t),n=this.mapOver();if(e.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==e.rank&&this._producesAcceptableDatatype(t));if(n.isCollection&&n.canMatch(e))return this._producesAcceptableDatatype(t);return!!this._mappingConstraints().every(r.bind(e.canMatch,e))&&this._producesAcceptableDatatype(t)}return!n.isCollection&&this._producesAcceptableDatatype(t)}}),_=f.extend({update:function(t){this.multiple=!1,this.collection=!0,this.datatypes=t.extensions;var e=[];t.collection_types?r.each(t.collection_types,function(t){e.push(new a(t))}):e.push(c),this.collectionTypes=e},connect:function(t){f.prototype.connect.call(this,t);var e=t.handle1;if(e){var n=this._effectiveMapOver(e);this.setMapOver(n)}},_effectiveMapOver:function(t){var e=this.collectionTypes,n=this._otherCollectionType(t);if(!r.some(e,function(t){return t.canMatch(n)}))for(var i in e){var a=e[i];if(n.canMapOver(a)){var o=n.effectiveMapOver(a);if(o!=l)return o}}return l},_effectiveCollectionTypes:function(){var t=this.mapOver();return r.map(this.collectionTypes,function(e){return t.append(e)})},attachable:function(t){var e=this._otherCollectionType(t);if(e.isCollection){var n=this._effectiveCollectionTypes(),i=this.mapOver();if(r.some(n,function(t){return t.canMatch(e)}))return this._producesAcceptableDatatype(t);if(i.isCollection)return!1;if(r.some(this.collectionTypes,function(t){return e.canMapOver(t)})){var a=this._effectiveMapOver(t);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(t)}}return!1}}),g=u.extend({initialize:function(t){if(u.prototype.initialize.call(this,t),this.datatypes=t.datatypes,t.collection_type)this.collectionType=new a(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=c}this.isCollection=!0},update:function(t){var e;if(t.collection_type)e=new a(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),e=c}e.collectionType!=this.collectionType.collectionType&&r.each(this.connectors,function(t){s.warning("Destroying a connection because collection type has changed."),t.destroy()}),this.collectionType=e}});e.default={InputTerminal:p,OutputTerminal:h,InputCollectionTerminal:_,OutputCollectionTerminal:g,TerminalMapping:d,CollectionTypeDescription:a,NULL_COLLECTION_TYPE_DESCRIPTION:l,ANY_COLLECTION_TYPE_DESCRIPTION:c}}).call(e,n(0),n(2),n(1))},function(t,e,n){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var i=t.View.extend({className:"form-row dataRow input-data-row",initialize:function(t){this.input=t.input,this.nodeView=t.nodeView,this.terminalElement=t.terminalElement,this.$el.attr("name",this.input.name).html(this.input.label),t.skipResize||(this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()),this.$el.css({position:"",left:"",top:"",display:""}),this.$el.remove())}}),r=t.View.extend({className:"form-row dataRow",initialize:function(t){this.output=t.output,this.terminalElement=t.terminalElement,this.nodeView=t.nodeView;var e=this.output,i=e.name,r=this.nodeView.node;if(e.extensions.indexOf("input")>=0||e.extensions.indexOf("input_collection")>=0||(i=i+" ("+e.extensions.join(", ")+")"),this.$el.html(i),this.calloutView=null,["tool","subworkflow"].indexOf(r.type)>=0){var o=new a({label:i,output:e,node:r});this.calloutView=o,this.$el.append(o.el),this.$el.hover(function(){o.hoverImage()},function(){o.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=t.View.extend({tagName:"div",initialize:function(t){this.label=t.label,this.node=t.node,this.output=t.output;var e=this,i=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(n("
    ").append(n("").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var t=e.output.name;i.isWorkflowOutput(t)?(i.removeWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")):(i.addWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png")),window.workflow_globals.workflow.has_changes=!0,window.workflow_globals.canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."}),this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8}),this.$el.show(),this.resetImage()},resetImage:function(){this.node.isWorkflowOutput(this.output.name)?this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"):this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")},hoverImage:function(){this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-yellow.png")}});e.default={DataInputView:i,DataOutputView:r}}).call(e,n(2),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t){var e=t.model.attributes,n=e.workflow,i=e.node;e.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:i.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),e.inputs.unshift({type:"text",name:"__label",label:"Label",value:i.label,help:(0,d.default)("Add a step label."),fixed:!0,onchange:function(e){var r=!1;for(var a in n.nodes){var o=n.nodes[a];if(o.label&&o.label==e&&o.id!=i.id){r=!0;break}}var s=t.data.match("__label");t.element_list[s].model.set("error_text",r&&"Duplicate label. Please fix this before saving the workflow."),t.trigger("change")}})}function o(t,e,n,i){var r=i.node.post_job_actions;e=e||[],e.push(t);for(var a in t.inputs){var s=t.inputs[a];if(s.action){if(s.name="pja__"+n+"__"+s.action,s.pja_arg&&(s.name+="__"+s.pja_arg),s.payload)for(var l in s.payload)s.payload[s.name+"__"+l]=s.payload[l],delete s.payload[l];var c=r[s.action+n];if(c){for(var d in e)e[d].expanded=!0;s.pja_arg?s.value=c.action_arguments&&c.action_arguments[s.pja_arg]||s.value:s.value="true"}}s.inputs&&o(s,e.slice(0),n,i)}}function s(t,e){var n=[],i=[],r=e.datatypes,a=e.node,s=e.workflow;for(var l in r)n.push({0:r[l],1:r[l]});for(l in a.input_terminals)i.push(a.input_terminals[l].name);n.sort(function(t,e){return t.label>e.label?1:t.labelhere     for more information. Valid inputs are: '+i.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:n,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:(0,d.default)("Assign columns"),type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return o(u,[],t,e),u}function l(t){var e=t.model.attributes,n=e.inputs,i=e.node,r=i.post_job_actions,a=i.output_terminals&&Object.keys(i.output_terminals)[0];if(a){n.push({name:"pja__"+a+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(r["EmailAction"+a])),ignore:"false",help:(0,d.default)("An email notification will be sent when the job has completed."),payload:{host:window.location.host}}),n.push({name:"pja__"+a+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(r["DeleteIntermediatesAction"+a])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var o in i.output_terminals)n.push(s(o,e))}}Object.defineProperty(e,"__esModule",{value:!0});var c=n(3),d=r(c),u=n(5),h=r(u),f=n(26),p=r(f),_=n(55),g=r(_),m=t.View.extend({initialize:function(t){var e=this,n=t.node;this.form=new p.default(h.default.merge(t,{onchange:function(){h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:n.id,type:n.type,content_id:n.content_id,inputs:e.form.data.create()},success:function(t){n.update_field_data(t)}})}})),a(this.form),this.form.render()}}),v=t.View.extend({initialize:function(t){var e=this,n=t.node;this.form=new g.default(h.default.merge(t,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(t,n){e._customize(n),t.resolve()},buildmodel:function(t,e){e.model.get("postchange")(t,e)},postchange:function(t,r){var a=r.model.attributes,o={tool_id:a.id,tool_version:a.version,type:"tool",inputs:i.extend(!0,{},r.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",o),h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:o,success:function(i){r.model.set(i.config_form),e._customize(r),r.update(i.config_form),r.errors(i.config_form),n.update_field_data(i),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",i),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",e),t.reject()}})}}))},_customize:function(t){var e=t.model.attributes;h.default.deepeach(e.inputs,function(t){t.type&&(-1!=["data","data_collection"].indexOf(t.type)?(t.type="hidden",t.info="Data input '"+t.name+"' ("+h.default.textify(t.extensions)+")",t.value={__class__:"RuntimeValue"}):t.fixed||(t.collapsible_value={__class__:"RuntimeValue"},t.is_workflow=t.options&&0===t.options.length||-1!=["integer","float"].indexOf(t.type)))}),h.default.deepeach(e.inputs,function(t){"conditional"===t.type&&(t.test_param.collapsible_value=void 0)}),l(t),a(t)}});e.default={Default:m,Tool:v}}).call(e,n(2),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(1),c=r(l),d=n(224),u=r(d),h=n(15),f=a(h),p=n(5),_=a(p),g=n(33),m=a(g),v=n(31),y=a(v);n(150);var b=t.Model.extend({is_visible:function(t,e){var n=t.getBoundingClientRect(),r=i("svg")[0].getBoundingClientRect();return!(n.right<0||n.left>r.right||n.bottom<0||n.top>r.bottom)}}),w={drawTicks:function(t,e,n,i,r){var a=t.append("g").selectAll("g").data(e).enter().append("g").selectAll("g").data(n).enter().append("g").attr("class","tick").attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"}),o=[],s=[],l=function(t){return t.angle>Math.PI?"end":null};return r?(o=[0,0,0,-4],s=[4,0,"",".35em"],l=null):(o=[1,0,4,0],s=[0,4,".35em",""]),a.append("line").attr("x1",o[0]).attr("y1",o[1]).attr("x2",o[2]).attr("y1",o[3]).style("stroke","#000"),a.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",l).attr("transform",i).text(function(t){return t.label})},formatNum:function(t,e){if(void 0===e&&(e=2),null===t)return null;var n=null;if(Math.abs(t)<1)n=t.toPrecision(e);else{var i=Math.round(t.toPrecision(e));t=Math.abs(t),t<1e3?n=i:t<1e6?n=Math.round((i/1e3).toPrecision(3)).toFixed(0)+"K":t<1e9&&(n=Math.round((i/1e6).toPrecision(3)).toFixed(0)+"M")}return n}},x=t.Model.extend({}),k=t.View.extend({className:"circster",initialize:function(t){this.genome=t.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var e=this.model.get("config");e.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),e.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"!==t.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"===t.get("track_type")})},get_tracks_bounds:function(){var t=this.get_circular_tracks(),e=this.model.get("config").get_value("arc_dataset_height"),n=this.model.get("config").get_value("track_gap"),i=Math.min(this.$el.width(),this.$el.height())-20,r=i/2-t.length*(e+n)+n-this.label_arc_height,a=u.range(r,i/2,e+n);return c.map(a,function(t){return[t,t+e]})},render:function(){var t=this,e=t.$el.width(),n=t.$el.height(),i=this.get_circular_tracks(),r=this.get_chord_tracks(),a=t.model.get("config").get_value("total_gap"),o=this.get_tracks_bounds(),s=u.select(t.$el[0]).append("svg").attr("width",e).attr("height",n).attr("pointer-events","all").append("svg:g").call(u.behavior.zoom().on("zoom",function(){var e=d.event.scale;s.attr("transform","translate("+d.event.translate+") scale("+e+")"),t.scale!==e&&(t.zoom_drag_timeout&&clearTimeout(t.zoom_drag_timeout),t.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+e/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(e,n){var i=new T({el:s.append("g")[0],track:e,radius_bounds:o[n],genome:t.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(e){var n=new A({el:s.append("g")[0],track:e,radius_bounds:o[0],genome:t.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],c=[l,l+this.label_arc_height];this.label_track_view=new C({el:s.append("g")[0],track:new x,radius_bounds:c,genome:t.genome,total_gap:a}),this.label_track_view.render()},add_track:function(t){var e=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===t.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new A({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:n,genome:this.genome,total_gap:e});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();c.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])}),c.each(this.chords_views,function(t){t.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new T({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:r[a],genome:this.genome,total_gap:e});o.render(),this.circular_views.push(o)}},remove_track:function(t,e,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();c.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])})},update_track_bounds:function(){var t=this.get_tracks_bounds();c.each(this.circular_views,function(e,n){e.update_radius_bounds(t[n])}),c.each(this.chords_views,function(e){e.update_radius_bounds(t[0])})}}),M=t.View.extend({tagName:"g",initialize:function(t){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=t.total_gap,this.track=t.track,this.radius_bounds=t.radius_bounds,this.genome=t.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=u.select(this.$el[0])},get_fill_color:function(){var t=this.track.get("config").get_value("block_color");return t||(t=this.track.get("config").get_value("color")),t},render:function(){var t=this.parent_elt,e=this.chroms_layout,n=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=t.selectAll("g").data(e).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(t){return t.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(t)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(t){this.radius_bounds=t;var e=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",e),this._transition_chrom_data(),this._transition_labels()},update_scale:function(t){var e=this.scale;if(this.scale=t,!(t<=e)){var n=this,r=new b;return this.parent_elt.selectAll("path.chrom-data").filter(function(t,e){return r.is_visible(this)}).each(function(e,r){var a,o=u.select(this),s=o.attr("chrom"),l=n.genome.get_chrom_region(s),d=n.track.get("data_manager");d.can_get_more_detailed_data(l)&&(a=n.track.get("data_manager").get_more_detailed_data(l,"Coverage",0,t),i.when(a).then(function(t){o.remove(),n._update_data_bounds();var e=c.find(n.chroms_layout,function(t){return t.data.chrom===s}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,e,t).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var t=this.track,e=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(t.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=c.reject(c.map(i,function(t,n){var i=null,a=r._get_path_function(e[n],t);return a&&(i=a(t.data)),i}),function(t){return null===t}),o=t.get("config").get_value("color");n.each(function(t,e){u.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[e])})})}},_transition_labels:function(){},_update_data_bounds:function(t){this.data_bounds=t||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(t){var e=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){e.data_bounds=e.get_data_bounds(i),r.get("config").set_value("min_value",e.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",e.data_bounds[1],{silent:!0});var o=c.zip(n,i);c.each(o,function(n){var i=n[0],r=n[1];return e._render_chrom_data(t,i,r)});var s=e.get_fill_color();e.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s),a.resolve(t)}),a},_render_chrom_data:function(t,e,n){},_get_path_function:function(t,e){},_chroms_layout:function(){var t=this.genome.get_chroms_info(),e=u.layout.pie().value(function(t){return t.len}).sort(null),n=e(t),i=2*Math.PI*this.total_gap/t.length;return c.map(n,function(t,e){var n=t.endAngle-i;return t.endAngle=n>t.startAngle?n:t.startAngle,t})}}),C=M.extend({initialize:function(t){M.prototype.initialize.call(this,t),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(t){var e=this,n=t.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom}),n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>e.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").text(function(t){return t.data.chrom});var i=function(t){var n=(t.endAngle-t.startAngle)/t.value,i=u.range(0,t.value,25e6).map(function(i,r){return{radius:e.innerRadius,angle:i*n+t.startAngle,label:0===r?0:r%3?null:e.formatNum(i)}});return i.length<4&&(i[i.length-1].label=e.formatNum(Math.round((i[i.length-1].angle-t.startAngle)/n))),i},r=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null},a=c.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>e.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});c.extend(C.prototype,w);var S=M.extend({initialize:function(t){M.prototype.initialize.call(this,t);var e=this.track.get("config");e.get("min_value").on("change:value",this._update_min_max,this),e.get("max_value").on("change:value",this._update_min_max,this),e.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var t=this.track.get("config"),e=[t.get_value("min_value"),t.get_value("max_value")];this._update_data_bounds(e),this.parent_elt.selectAll(".min_max").text(function(t,n){return e[n]})},_quantile:function(t,e){return t.sort(u.ascending),u.quantile(t,e)},_render_chrom_data:function(t,e,n){var i=this._get_path_function(e,n);return i?t.datum(n.data).append("path").attr("class","chrom-data").attr("chrom",e.data.chrom).attr("d",i):null},_get_path_function:function(t,e){if("string"==typeof e||!e.data||0===e.data.length)return null;var n=u.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),i=u.scale.linear().domain([0,e.data.length]).range([t.startAngle,t.endAngle]),r=u.svg.line.radial().interpolate("linear").radius(function(t){return n(t[1])}).angle(function(t,e){return i(e)});return u.svg.area.radial().interpolate(r.interpolate()).innerRadius(n(0)).outerRadius(r.radius()).angle(r.angle())},render_labels:function(){var t=this,e=function(){return"rotate(90)"},n=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),e,!0).classed("min_max",!0);c.each(n,function(e){i(e).click(function(){new m.default.ConfigSettingCollectionView({collection:t.track.get("config")}).render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var t=this,e=c.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>.08}),n=c.filter(e,function(t,e){return e%3==0}),i=c.flatten(c.map(n,function(e){return t._data_bounds_ticks_fn()(e)}));this.parent_elt.selectAll("g.tick").data(i).transition().attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"})}},_data_bounds_ticks_fn:function(){var t=this;return function(e){return[{radius:t.radius_bounds[0],angle:e.startAngle,label:t.formatNum(t.data_bounds[0])},{radius:t.radius_bounds[1],angle:e.startAngle,label:t.formatNum(t.data_bounds[1])}]}},get_data_bounds:function(t){}});c.extend(S.prototype,w);var T=S.extend({get_data_bounds:function(t){var e=c.flatten(c.map(t,function(t){return t?c.map(t.data,function(t){return parseInt(t[1],10)||0}):0}));return[c.min(e),this._quantile(e,.98)||c.max(e)]}}),A=M.extend({render:function(){var t=this;i.when(t.track.get("data_manager").data_is_ready()).then(function(){i.when(t.track.get("data_manager").get_genome_wide_data(t.genome)).then(function(e){var n=[],i=t.genome.get_chroms_info();c.each(e,function(e,r){var a=i[r].chrom,o=c.map(e.data,function(e){var n=t._get_region_angle(a,e[1]),i=t._get_region_angle(e[3],e[4]);return{source:{startAngle:n,endAngle:n+.01},target:{startAngle:i,endAngle:i+.01}}});n=n.concat(o)}),t.parent_elt.append("g").attr("class","chord").selectAll("path").data(n).enter().append("path").style("fill",t.get_fill_color()).attr("d",u.svg.chord().radius(t.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(t){this.radius_bounds=t,this.parent_elt.selectAll("path").transition().attr("d",u.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(t,e){var n=c.find(this.chroms_layout,function(e){return e.data.chrom===t});return n.endAngle-(n.endAngle-n.startAngle)*(n.data.len-e)/n.data.len}}),j=t.View.extend({initialize:function(){_.default.cssLoadFile("static/style/circster.css");var t=new f.default.Genome(window.galaxy_config.app.genome),e=new f.default.GenomeVisualization(window.galaxy_config.app.viz_config);e.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset 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t=this;r("#PhyloViz").empty(),t.mainSVG=d.select("#PhyloViz").append("svg:svg").attr("width",t.width).attr("height",t.height).attr("pointer-events","all").call(t.zoomFunc.on("zoom",function(){t.zoomAndPan()})),t.boundingRect=t.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",t.width).attr("height",t.height).attr("stroke","black").attr("fill","white"),t.vis=t.mainSVG.append("svg:g").attr("class","vis"),t.layoutOptions={model:t.phyloTree,width:t.width,height:t.height,vis:t.vis,margins:t.margins},r("#title").text("Phylogenetic Tree from "+t.phyloTree.get("title")+":");new b(t.layoutOptions)},zoomAndPan:function(t){var e,n;void 0!==t&&(e=t.zoom,n=t.translate);var i=this,r=i.zoomFunc.scale(),a=i.zoomFunc.translate(),o="",s="";switch(e){case"reset":r=1,a=[0,0];break;case"+":r*=1.1;break;case"-":r*=.9;break;default:"number"==typeof e?r=e:null!==d.event&&(r=d.event.scale)}if(!(ri.MAX_SCALE)){if(i.zoomFunc.scale(r),o="translate("+i.margins[3]+","+i.margins[0]+") 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t=this;r.each(t.phyloTree.defaults,function(e,n){t.phyloTree.set(e,n)}),t.updateUI()},render:function(){}}),M=m.extend({className:"Settings",initialize:function(t){var e=this;e.el=r("#nodeSelectionView"),e.phyloTree=t.phyloTree,e.UI={enableEdit:r("#phylovizEditNodesCheck"),saveChanges:r("#phylovizNodeSaveChanges"),cancelChanges:r("#phylovizNodeCancelChanges"),name:r("#phyloVizSelectedNodeName"),dist:r("#phyloVizSelectedNodeDist"),annotation:r("#phyloVizSelectedNodeAnnotation")},e.valuesOfConcern={name:null,dist:null,annotation:null},r("#nodeSelCloseBtn").off().on("click",function(){e.el.hide()}),e.UI.saveChanges.off().on("click",function(){e.updateNodes()}),e.UI.cancelChanges.off().on("click",function(){e.cancelChanges()}),function(t){t.fn.enable=function(e){return t(this).each(function(){e?t(this).removeAttr("disabled"):t(this).attr("disabled","disabled")})}}(i),e.UI.enableEdit.off().on("click",function(){e.toggleUI()})},toggleUI:function(){var t=this,e=t.UI.enableEdit.is(":checked");e||t.cancelChanges(),r.each(t.valuesOfConcern,function(n,i){t.UI[n].enable(e)}),e?(t.UI.saveChanges.show(),t.UI.cancelChanges.show()):(t.UI.saveChanges.hide(),t.UI.cancelChanges.hide())},cancelChanges:function(){var t=this,e=t.phyloTree.get("selectedNode");e&&r.each(t.valuesOfConcern,function(n,i){t.UI[n].val(e[n])})},updateNodes:function(){var t=this,e=t.phyloTree.get("selectedNode");if(e){if(!t.isAcceptableValue(t.UI.dist,0,1)||t.hasIllegalJsonCharacters(t.UI.name)||t.hasIllegalJsonCharacters(t.UI.annotation))return;r.each(t.valuesOfConcern,function(n,i){e[n]=t.UI[n].val()}),t.phyloTree.set("nodeAttrChangedTime",new Date)}else alert("No node selected")}}),C=m.extend({initialize:function(){var t=this;r("#phyloVizSearchBtn").on("click",function(){var e=r("#phyloVizSearchTerm"),n=r("#phyloVizSearchCondition").val().split("-"),i=n[0],a=n[1];t.hasIllegalJsonCharacters(e),"dist"===i&&t.isAcceptableValue(e,0,1),t.searchTree(i,a,e.val())})},searchTree:function(t,e,n){d.selectAll("g.node").classed("searchHighlight",function(i){var r=i[t];if(void 0!==r&&null!==r)if("dist"===t)switch(e){case"greaterEqual":return r>=+n;case"lesserEqual":return r<=+n;default:return}else if("name"===t||"annotation"===t)return-1!==r.toLowerCase().indexOf(n.toLowerCase())})}});e.default={PhylovizView:w}}).call(e,n(2),n(0),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var 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e=this.get("settings"),n=t.get("settings");for(var i in e)if(!n[i]||e[i]!==n[i])return!1;return!0},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}}),A=t.Collection.extend({model:T}),j=p.default.Visualization.extend({defaults:c.extend({},p.default.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),initialize:function(t){this.set("dataset",new b.default.Dataset(t.dataset)),this.set("tool",new v.default.Tool(t.tool)),this.set("regions",new p.default.GenomeRegionCollection(t.regions)),this.set("tracks",new A(t.tracks));var e=this.get("tool");this.set("tool_with_samplable_inputs",e),e.remove_inputs(["data","hidden_data","conditional","text"]),this.set("parameter_tree",new S({tool:e,config:t.tree_config}))},add_track:function(t){this.get("tracks").add(t)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset 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e=this.templatePaginator();r("body").find(".folder-paginator").html(e({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(t){this.options=i.extend(this.options,t),!0===this.options.can_add_library_item?r(".add-library-items").show():r(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(r(".dataset-manipulation").show(),r(".logged-dataset-manipulation").hide()):(r(".logged-dataset-manipulation").show(),r(".dataset-manipulation").show()):(r(".logged-dataset-manipulation").hide(),r(".dataset-manipulation").hide()),this.$el.find('[data-toggle="tooltip"]').tooltip({trigger:"hover"})},createFolderFromModal:function(t){var e=this;t.preventDefault(),t.stopPropagation();var n=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:(0,l.default)("Create New Folder"),body:n(),buttons:{Create:function(){e.createNewFolderEvent()},Close:function(){Galaxy.modal.hide()}}})},createNewFolderEvent:function(){var e=this.serializeNewFolder();if(this.validateNewFolder(e)){var n,i=new p.default.FolderAsModel,r=t.history.fragment.split("/");n=r.indexOf("page")>-1?r[r.length-3]:r[r.length-1],i.url=i.urlRoot+n,i.save(e,{success:function(t){Galaxy.modal.hide(),h.default.success("Folder created."),t.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(t)},error:function(t,e){Galaxy.modal.hide(),void 0!==e.responseJSON?h.default.error(e.responseJSON.err_msg):h.default.error("An error occurred.")}})}else h.default.error("Folder's name is 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e=this.modal.$("input[name=history_name]").val();if(""!==e)this.createNewHistory(e).done(function(e){t.processImportToHistory(e.id,e.name)}).fail(function(t,e,n){h.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var n=r("select[name=import_to_history] option:selected").val(),i=r("select[name=import_to_history] option:selected").text();this.processImportToHistory(n,i),this.modal.enableButton("Import")}},createNewHistory:function(t){return r.post(Galaxy.root+"api/histories",{name:t})},processImportToHistory:function(t,e){for(var n=this.findCheckedItems(),i=[],r=n.dataset_ids.length-1;r>=0;r--){var o=n.dataset_ids[r],s=new p.default.HistoryItem;s.url=s.urlRoot+t+"/contents",s.content=o,s.source="library",i.push(s)}for(var l=n.folder_ids.length-1;l>=0;l--){var c=n.folder_ids[l],s=new p.default.HistoryItem;s.url=s.urlRoot+t+"/contents",s.content=c,s.source="library_folder",i.push(s)}this.initChainCallControl({length:i.length,action:"to_history",history_name:e}),a.getJSON(Galaxy.root+"history/set_as_current?id="+t),this.chainCallImportingIntoHistory(i,e)},updateProgress:function(){this.progress+=this.progressStep,r(".progress-bar-import").width(Math.round(this.progress)+"%");var t=Math.round(this.progress)+"% Complete";r(".completion_span").text(t)},download:function(t){var e=this.findCheckedItems(),n=Galaxy.root+"api/libraries/datasets/download/"+t,i={ld_ids:e.dataset_ids,folder_ids:e.folder_ids};this.processDownload(n,i,"get")},processDownload:function(t,e,n){if(t&&e){e="string"==typeof e?e:r.param(e);var i="";r.each(e.split("&"),function(){var t=this.split("=");i+=''}),r('
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