- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-16 00:41:19+12:00
- Desc:
- Updating Noble 1962 model:
* Exposing the membrane potential to the top-level model;
* adding SED-ML for the paced and pacemaker variants of the model.
Using OpenCOR Snapshot release 2021-09-14.
- Permanent Source URI:
- https://models.fieldml.org/workspace/a1/rawfile/f954e59183314cd37f86c8832dc81317d01c8ec5/dojo-presentation/js/andre/ContentItemDisplay.js
/* ***** BEGIN LICENSE BLOCK *****
* Version: MPL 1.1/GPL 2.0/LGPL 2.1
*
* The contents of this file are subject to the Mozilla Public License Version
* 1.1 (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
* http://www.mozilla.org/MPL/
*
* Software distributed under the License is distributed on an "AS IS" basis,
* WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
* for the specific language governing rights and limitations under the
* License.
*
* The Original Code is "Andre's Reference Description Framework".
*
* The Initial Developer of the Original Code is
* David Nickerson <nickerso@users.sourceforge.net>.
* Portions created by the Initial Developer are Copyright (C) 2007-2008
* the Initial Developer. All Rights Reserved.
*
* Contributor(s):
*
* Alternatively, the contents of this file may be used under the terms of
* either the GNU General Public License Version 2 or later (the "GPL"), or
* the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
* in which case the provisions of the GPL or the LGPL are applicable instead
* of those above. If you wish to allow use of your version of this file only
* under the terms of either the GPL or the LGPL, and not to allow others to
* use your version of this file under the terms of the MPL, indicate your
* decision by deleting the provisions above and replace them with the notice
* and other provisions required by the GPL or the LGPL. If you do not delete
* the provisions above, a recipient may use your version of this file under
* the terms of any one of the MPL, the GPL or the LGPL.
*
* ***** END LICENSE BLOCK ***** */
/* a widget used to contain a content item */
dojo.provide("andre.ContentItemDisplay");
dojo.require("dojo.fx");
dojo.require("dojox.layout.ContentPane");
dojo.require("andre.CitationData");
dojo.require("andre.CreationData");
dojo.require("andre.ModificationData");
dojo.require("andre.InlineTitlePane");
dojo.require("andre.ClosablePane");
dojo.require("andre.Chart");
dojo.declare("andre.ContentItemDisplay", andre.ClosablePane, {
store: null,
item: null,
srcBaseURL: null,
// chart: andre.Chart
// Will be the chart object if this is a graph content item.
chart: null,
// chartContainer: DomNode
// Inserted into the page to hold the chart, if any, as a place holder for when we are ready to position the chart to the correct location within the page flow.
chartContainer: null,
postMixInProperties: function () {
// make sure the id is set correctly, we want the ensure that we can always refer to this dijit via it's data store identity.
this.id = this.store.getIdentity(this.item);
// and set the (initial?) title
if (this.store.hasAttribute(this.item,"title")) {
this.heading = this.store.getValue(this.item,"title");
} else {
this.showHeading = false;
if (this.heading == "") this.heading = "Untitled content item";
}
// and set up the type
if (this.store.hasAttribute(this.item,"type")) this.type = this.store.getValue(this.item,"type");
else {
console.debug("ERROR: missing type on content item");
this.type = "unknown";
}
// and the type specific icon
this.iconClass = andre.utils.getIconClass(this.type);
this.iconClass += " contentItemIcon";
},
postCreate: function() {
// Populate the containerNode of the closable pane
console.log("andre.ContentItemDisplay.postCreate() called for: " + this.id);
this.inherited(arguments);
// First add the standard annotations
if (this.type != "component") {
this._appendCommonAnnotations(this.item,this.containerNode,true);
} else {
// for components we want to use the ultimate import parent component
var imports = andre.utils.getComponentImportList(this.store,this.item);
var c = imports.pop();
this._appendCommonAnnotations(c,this.containerNode,true);
}
// and now type specific
if ((this.type == "root") || (this.type == "task")) {
this._appendTaskContent();
} else if (this.type == "graph") {
this._appendGraphContent();
} else if (this.type == "simulation") {
this._appendSimulationContent();
} else if (this.type == "model") {
this._appendModelContent();
} else if (this.type == "component") {
this._appendComponentContent();
} else if (this.type == "variable") {
this._appendVariableContent();
}
},
/* we need this as the tabContainer.startup() method must be called after the tab container has been inserted into the page body. */
addToDocument: function(refNode,position) {
console.debug("adding to document in position: " + position);
dojo.style(this.domNode,"opacity","0");
dojo.place(this.domNode,refNode,position);
// move the chart, if any, to the correct location
if (this.chart) {
this.chart.place(this.chartContainer,"first");
}
dojo.fadeIn({node: this.domNode, duration: 500}).play();
},
_appendCommonAnnotations: function(/*StoreItem*/item, /*DomNode*/parent, /*Bool*/updateHeader) {
// summary: append the common annotations to the current content item
// item: the data store item to use to look for commom annotations; we provide this here as we may not always want to use the content item's 'item' attribute (i.e., in the case of components).
// the base ID to use on all items
var baseID = this.store.getIdentity(item);
if (updateHeader) {
// update the title (in case item is different to this.item)
if (this.store.hasAttribute(item,"title")) {
this.setHeading(this.store.getValue(item,"title"));
}
}
// put the common annotations into their own container
var annotation = parent.appendChild(dojo.doc.createElement("div"));
dojo.addClass(annotation,"content-item-common-annotation");
// then the citation inline title pane
if (this.store.hasAttribute(item,"citations")) {
e = new andre.CitationData(this.store, this.store.getValues(item,"citations"));
if (e) {
var references = annotation.appendChild(dojo.doc.createElement("div"));
references.appendChild(e.toNode());
// and create the dijit
var itp = new andre.InlineTitlePane({title: e.toStringShort(), open: false, id: baseID + "-references-dijit"},references);
} else {
console.debug("Error getting the citations data in a DOM node");
}
}
// followed by the history title pane
var historyTitle = "";
var history = null;
if (this.store.hasAttribute(item,"created")) {
e = new andre.CreationData(this.store, this.store.getValue(item,"created"));
if (e) {
history = annotation.appendChild(dojo.doc.createElement("div"));
history.appendChild(e.toNode());
historyTitle = e.toStringShort();
} else {
console.debug("Error getting the created data in a DOM node");
}
}
if (this.store.hasAttribute(item,"modifications")) {
e = new andre.ModificationData(this.store, this.store.getValues(item,"modifications"));
if (e) {
if (!history) history = annotation.appendChild(dojo.doc.createElement("div"));
history.appendChild(e.toNode());
historyTitle = e.toStringShort() + " (" + historyTitle + ")";
} else {
console.debug("Error getting the modifications data in a DOM node");
}
}
if (history) {
var itp = new andre.InlineTitlePane({title: historyTitle, open: false, id: baseID + "-history-dijit"}, history);
}
// other relevant data?
if (this.store.hasAttribute(item,"species")) {
e = parent.appendChild(dojo.doc.createElement("div"));
dojo.addClass(e,"content-item-species-annotation");
e.appendChild(dojo.doc.createElement("span")).innerHTML = "Species: ";
e.appendChild(dojo.doc.createElement("i")).innerHTML = this.store.getValue(item,"species");
}
if (this.store.hasAttribute(item,"bio_entity")) {
e = parent.appendChild(dojo.doc.createElement("div"));
dojo.addClass(e,"content-item-bioe_entity-annotation");
e.appendChild(dojo.doc.createElement("span")).innerHTML = "Biological Entity: ";
e.appendChild(dojo.doc.createElement("span")).innerHTML = this.store.getValue(item,"bio_entity");
}
// an abstract?
if (this.store.hasAttribute(item,"abstract")) {
e = parent.appendChild(dojo.doc.createElement("div"));
dojo.addClass(e,"content-item-abstract");
e.innerHTML = this.store.getValue(item,"abstract");
}
// any description?
if (this.store.hasAttribute(item,"description")) {
e = parent.appendChild(dojo.doc.createElement("div"));
dojo.addClass(e,"content-item-description");
e.innerHTML = this.store.getValue(item,"description");
}
},
_appendTaskContent: function() {
// summary: add task specific content to the content item display
console.debug("_appendTaskContent called");
var childrenTypes = ["tasks","graphs"];
var childrenHeadings = ["Tasks:","Defined Graphs:"];
for (var t = 0;t<childrenTypes.length;t++) {
if (this.store.hasAttribute(this.item,childrenTypes[t])) {
var tasks = this.store.getValues(this.item,childrenTypes[t]);
if (tasks.length > 0) {
var element = this.containerNode.appendChild(dojo.doc.createElement("div"));
dojo.addClass(element,"content-item-sub-content-container");
var e = element.appendChild(dojo.doc.createElement("h3"));
dojo.addClass(e,"content-item-sub-header");
e.innerHTML = childrenHeadings[t];
var ul = element.appendChild(dojo.doc.createElement("ul"));
for (var i=0;i<tasks.length;i++) {
e = ul.appendChild(dojo.doc.createElement("li"));
var text = "Anonymous";
if (this.store.hasAttribute(tasks[i],"title")) {
text = this.store.getValue(tasks[i],"title");
}
e.appendChild(andre.utils.makeContentItemLink( this.store.getIdentity(tasks[i]), this.id, text, childrenTypes[t] == "tasks" ? "task" : "graph"));
}
}
}
}
},
_appendGraphContent: function() {
// summary: add graph specific content to the content item display
console.debug("_appendGraphContent called with srcBaseURL set to: " + this.srcBaseURL);
// create a container to hold the graph information
this.chartContainer = this.containerNode.appendChild(dojo.doc.createElement("div"));
dojo.addClass(this.chartContainer,"graph-container");
// assemble the style object for the graph
var style = {};
style.width = "400px";
style.height = "400px";
if (this.store.hasAttribute(this.item,"background")) {
style.backgroundColor = this.store.getValue(this.item,"background");
}
if (this.store.hasAttribute(this.item,"colour")) {
style.color = this.store.getValue(this.item,"colour");
}
if (this.store.hasAttribute(this.item,"csvSource")) {
var titles = {};
if (this.store.hasAttribute(this.item,"title")) titles.title = this.store.getValue(this.item,"title");
if (this.store.hasAttribute(this.item,"xLabel")) titles.x = this.store.getValue(this.item,"xLabel");
if (this.store.hasAttribute(this.item,"yLabel")) titles.y = this.store.getValue(this.item,"yLabel");
/* FIXME: should encode the generated CSV file URL into the JSON source for the reference description */
var csvURL = this.srcBaseURL + this.store.getValue(this.item,"csvSource");
this.chart = new andre.Chart(this.id, csvURL, style, titles);
if (this.store.hasAttribute(this.item,"traces")) {
var traces = this.store.getValues(this.item,"traces");
dojo.forEach(traces, function(trace,i) {
var style = {};
if (this.store.hasAttribute(trace,"colour")) {
style.stroke = this.store.getValue(trace,"colour");
}
if (this.store.hasAttribute(trace,"label")) {
this.chart.addSeriesByLabel(this.store,trace,style);
} else {
this.chart.addSeriesByPosition((i+1).toString(),style);
}
}, this);
} else {
console.log("ERROR: No traces in graph?");
}
} else {
console.log("ERROR: No data for graph?");
}
},
_appendSimulationContent: function() {
// summary: add simulation specific content to the content item display
console.debug("_appendSimulationContent called");
// create a container to hold the simulation information
var container = this.containerNode.appendChild(dojo.doc.createElement("div"));
dojo.addClass(container,"simulation-container");
// a simple header?
container.appendChild(dojo.doc.createElement("h3")).appendChild(dojo.doc.createTextNode("Simulation definition"));
// put the definition in a definition list
var dl = container.appendChild(dojo.doc.createElement("dl"));
dojo.addClass(dl,"simulation-definition");
// must have a model reference
dl.appendChild(dojo.doc.createElement("dt")).appendChild(dojo.doc.createTextNode("Model"));
var model = this.store.getValue(this.item,"model");
// and the model should have a title?
var title = "Untitled";
if (this.store.hasAttribute(model,"title")) title = this.store.getValue(model,"title");
var id = this.store.getIdentity(model);
dl.appendChild(andre.utils.makeContentItemLink(id, this.id, title, "model"));
// and a bound interval
dl.appendChild(dojo.doc.createElement("dt")).appendChild( dojo.doc.createTextNode("Bound Interval"));
var interval = this.store.getValue(this.item,"boundInterval");
// which will have a variable reference
var variable = this.store.getValue(interval,"variable");
dl.appendChild(dojo.doc.createElement("dd")).appendChild( andre.utils.makeContentItemLinkFromURI(this.store, variable, this.id));
// the integration parameters
dl.appendChild(dojo.doc.createElement("dd")).innerHTML = "Starting value: " + this.store.getValue(interval,"start");
dl.appendChild(dojo.doc.createElement("dd")).innerHTML = "Ending value: " + this.store.getValue(interval,"end");
dl.appendChild(dojo.doc.createElement("dd")).innerHTML = "Maximum step size: " + this.store.getValue(interval,"maximumStepSize");
dl.appendChild(dojo.doc.createElement("dd")).innerHTML = "Tabulation step size: " + this.store.getValue(interval,"tabulationStepSize");
// and finally the numerical methods
dl.appendChild(dojo.doc.createElement("dt")).appendChild( dojo.doc.createTextNode("Numerical Methods"));
var numericalMethods = this.store.getValue(this.item,"numericalMethods");
dl.appendChild(dojo.doc.createElement("dd")).innerHTML = "Multistep method: " + this.store.getValue(numericalMethods,"multistepMethod");
dl.appendChild(dojo.doc.createElement("dd")).innerHTML = "Iteration method: " + this.store.getValue(numericalMethods,"iterationMethod");
dl.appendChild(dojo.doc.createElement("dd")).innerHTML = "Linear solver: " + this.store.getValue(numericalMethods,"linearSolver");
},
_appendModelContent: function() {
// summary: add model specific content to the content item display
console.debug("_appendModelContent called");
// create a container to hold the model information
var container = this.containerNode.appendChild(dojo.doc.createElement("div"));
dojo.addClass(container,"model-container");
// the only model content is a list of components?
if (this.store.hasAttribute(this.item,"components")) {
var components = this.store.getValues(this.item,"components");
if (components.length > 0) {
var e = container.appendChild(dojo.doc.createElement("h3"));
dojo.addClass(e,"content-item-sub-header");
e.innerHTML = "Math Containers";
var ul = container.appendChild(dojo.doc.createElement("ul"));
dojo.forEach(components, function(component,i) {
e = ul.appendChild(dojo.doc.createElement("li"));
// component is the actual unique component we want to link to, but we want to display the title of the ultimate import parent as a more meaningful link text to display to the user
var imports = andre.utils.getComponentImportList(this.store,component);
var c = imports.pop();
var title = "Anonymous";
if (this.store.hasAttribute(c,"title")) title = this.store.getValue(c,"title");
e.appendChild(andre.utils.makeContentItemLink(this.store.getIdentity(component), this.id, title, "component"));
}, this);
}
}
},
_appendComponentContent: function() {
// summary: append component specific content
// if this is a component that has been imported we want to provide access to any data associated with any of the imported instances
if (this.store.hasAttribute(this.item,"importedAs")) {
var container = this.containerNode.appendChild(dojo.doc.createElement("div"));
dojo.addClass(container,"imported-as-container");
var imports = andre.utils.getComponentImportList(this.store,this.item);
// we already have the annotations from the ultimate parent component so we can disregard that one
imports.pop();
// now we walk our way back to this component
this._appendComponentImportedAsContent(imports,container);
}
// and output the math from this component
if (this.store.hasAttribute(this.item,"math")) {
var math = dojo.doc.createElement("object");
dojo.addClass(math,"math-container");
var mathURL = this.srcBaseURL + this.store.getValue(this.item,"math");
math.setAttribute("data",mathURL);
math.setAttribute("type","application/xhtml+xml");
this.containerNode.appendChild(math);
}
},
_appendComponentImportedAsContent: function(/*Array*/imports, /*DomNode*/node) {
// summary: walk back through the imported-as components adding the annotations as children of the given
while (imports.length > 0) {
var c = imports.pop();
var container = node.appendChild(dojo.doc.createElement("div"));
dojo.addClass(container,"imported-as-component");
//var e = container.appendChild(dojo.doc.createElement("div"));
//dojo.addClass(e,"imported-as-component-header");
var title = "Untitled";
if (this.store.hasAttribute(c,"title")) title = this.store.getValue(c,"title");
//e.innerHTML = "Imported from: " + title;
this._appendCommonAnnotations(c,container,false);
var itp = new andre.InlineTitlePane({title: "Imported from: " + title, open: false},container);
}
},
_appendVariableContent: function() {
// summary: append variable specific data to the content item display
console.log("appending variable content");
var div = this.containerNode.appendChild(dojo.doc.createElement("div"));
if (this.store.hasAttribute(this.item,"initialValueVariable")) {
div.appendChild(dojo.doc.createElement("b")).innerHTML = "Initial value: ";
var ivV = this.store.getValue(this.item,"initialValueVariable");
var title = "initial value variable";
if (this.store.hasAttribute(ivV,"title")) title = this.store.getValue(ivV, "title");
div.appendChild(andre.utils.makeContentItemLink(this.store.getIdentity(ivV), this.id, title, "variable"));
} else if (this.store.hasAttribute(this.item,"initialValue")) {
div.appendChild(dojo.doc.createElement("b")).innerHTML = "Initial value: ";
div.appendChild(dojo.doc.createElement("span")).innerHTML = this.store.getValue(this.item,"initialValue");
}
div = this.containerNode.appendChild(dojo.doc.createElement("div"));
div.appendChild(dojo.doc.createElement("b")).innerHTML = "Units: ";
if (this.store.hasAttribute(this.item,"units")) {
div.appendChild(dojo.doc.createElement("span")).innerHTML = this.store.getValue(this.item,"units");
} else {
div.appendChild(dojo.doc.createElement("span")).innerHTML = "unknown";
}
if (this.store.hasAttribute(this.item,"definedIn")) {
var id = this.store.getValue(this.item,"definedIn");
var div = this.containerNode.appendChild(dojo.doc.createElement("div"));
var myself = this;
this.store.fetchItemByIdentity({
identity: id,
onItem: function(item,request) {
div.appendChild(dojo.doc.createElement("b")).innerHTML = "Defined in math container: ";
div.appendChild(andre.utils.makeContentItemLinkFromItem(myself.store, item, myself.id));
},
onError: function(error,request) {
var e = dojo.doc.createElement("div");
dojo.addClass(e,"error-message");
e.innerHTML = "Error getting math container link: " + error;
}
});
}
if (this.store.hasAttribute(this.item,"usedIn")) {
console.log("Appending usedIn components");
div = this.containerNode.appendChild(dojo.doc.createElement("div"));
div.appendChild(dojo.doc.createElement("b")).innerHTML = "Used in math containers:";
var ul = div.appendChild(dojo.doc.createElement("ul"));
var usedInComponents = this.store.getValues(this.item,"usedIn");
dojo.forEach(usedInComponents, function(usedIn,i) {
var cID = usedIn[0];
var vID = usedIn[1];
var li = ul.appendChild(dojo.doc.createElement("li"));
// the basic structure of the list element
var componentSpan = li.appendChild(dojo.doc.createElement("span"));
li.appendChild(dojo.doc.createTextNode(" as variable:"));
var variableSpan = li.appendChild(dojo.doc.createElement("div"));
var myself = this;
// link to the math container where this variable is used
this.store.fetchItemByIdentity({
identity: cID,
onItem: function(item,request) {
componentSpan.appendChild(andre.utils.makeContentItemLinkFromItem(myself.store, item, myself.id));
},
onError: function(error,request) {
var e = dojo.doc.createElement("div");
dojo.addClass(e,"error-message");
e.innerHTML = "Error getting math container link: " + error;
}
});
// and the reference to the variable in that math container
this.store.fetchItemByIdentity({
identity: vID,
onItem: function(item,request) {
var title = "Unknown";
if (myself.store.hasAttribute(item,"title")) title = myself.store.getValue(item,"title");
myself._appendCommonAnnotations(item,variableSpan,false);
var itp = new andre.InlineTitlePane({title: title, open: false}, variableSpan);
},
onError: function(error,request) {
var e = dojo.doc.createElement("div");
dojo.addClass(e,"error-message");
e.innerHTML = "Error getting math container link: " + error;
}
});
/*if (this.store.hasAttribute(this.item,"connectedVariables")) {
var connectedVariables = this.store.getValues(this.item,"connectedVariables");
var container = this.containerNode.appendChild(dojo.doc.createElement("div"));
dojo.addClass(container,"variable-alias-container");
container.appendChild(dojo.doc.createElement("h3")).innerHTML = "Also known as:";
dojo.forEach(connectedVariables, function(variable) {
var c = container.appendChild(dojo.doc.createElement("div"));
dojo.addClass(c,"variable-alias");
var title = "Unknown";
if (this.store.hasAttribute(variable,"title")) title = this.store.getValue(variable,"title");
this._appendCommonAnnotations(variable,c,false);
var itp = new andre.InlineTitlePane({title: title, open: false}, c);
}, this);
}*/
}, this);
}
},
onClickCloseButton: function(event) {
//console.dir(this);
console.debug("onClickCloseButton: closing content item: " + this.id);
// first fade out and set display to none - wipeOut will set display none
var fadeTime = 500;
var fade = dojo.fadeOut({node: this.domNode, duration: fadeTime});
var wipe = dojo.fx.wipeOut({node: this.domNode, duration: fadeTime});
dojo.fx.combine([fade, wipe]).play();
// need to give the animation time to play out
// FIXME: scope changes to window within here, so need to set what we need into local variables?
var myself = this;
setTimeout(function() {
console.debug("onClickCloseButton: destroying content item: " + myself.id);
// destroy the chart?
if (this.chart) this.chart.destroy();
// destroy all the dijit's first?
myself.destroyRecursive();
console.debug("onClickCloseButton: destroyed content item: " + myself.id);
}, fadeTime);
},
onClickSourceButton: function(event) {
console.debug("onClickSourceButton: view source of content item: " + this.id);
if (this.store.hasAttribute(this.item,"uri")) {
var uri = this.store.getValue(this.item,"uri");
console.debug("view source at uri: " + uri);
window.open(uri);
} else {
alert("Sorry, no source defined for this content item");
}
},
});
