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ComponentsInitialization.js
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ComponentsInitialization.js
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define(function (require) {
return function (GEPPETTO) {
var link = document.createElement("link");
link.type = "text/css";
link.rel = "stylesheet";
link.href = "geppetto/extensions/geppetto-vfb/css/VFB.css";
document.getElementsByTagName("head")[0].appendChild(link);
// any required stuff
var Query = require('./../../js/geppettoModel/model/Query');
var ImportType = require('./../../js/geppettoModel/model/ImportType');
var Bloodhound = require("typeahead.js/dist/bloodhound.min.js");
var vfbTutorial = require('./tutorials/controlPanelTutorial.json');
var markdown = require( "markdown" ).markdown;
var stackMD = window.origin+"/extensions/geppetto-vfb/mdHelpFiles/stack.md";
var termMD = window.origin+"/extensions/geppetto-vfb/mdHelpFiles/term.md";
//Retrieve
function getMDText(urlLocation){
var result = null;
$.ajax( { url: urlLocation,
type: 'get',
dataType: 'html',
async: false,
success: function(data) { result = data; }
}
);
return result;
}
//retrieve MD files text output and stores it into local variables
var termHelpInfo = getMDText(termMD);
var stackHelpInfo = getMDText(stackMD);
/*ADD COMPONENTS*/
//Logo initialization
GEPPETTO.ComponentFactory.addComponent('LOGO', {logo: 'gpt-fly'}, document.getElementById("geppettologo"));
//Tutorial component initialization
GEPPETTO.ComponentFactory.addWidget('TUTORIAL', {
name: 'VFB Tutorial',
tutorialData: vfbTutorial,
isStateless: true,
closeByDefault : true
}, function() {
//temporary until sessions allow to customise the tutorial component
GEPPETTO.Tutorial.addTutorial("https://raw.githubusercontent.com/jrmartin/vfb-extension/vfb-8/17/tutorials/queryTutorial.json");
GEPPETTO.Tutorial.addTutorial("https://raw.githubusercontent.com/jrmartin/vfb-extension/vfb-8/17/tutorials/spotlightTutorial.json");
GEPPETTO.Tutorial.addTutorial("https://raw.githubusercontent.com/jrmartin/vfb-extension/vfb-8/17/tutorials/termTutorial.json");
GEPPETTO.Tutorial.addTutorial("https://raw.githubusercontent.com/jrmartin/vfb-extension/vfb-8/17/tutorials/stackTutorial.json");
});
//Control panel initialization
GEPPETTO.ComponentFactory.addComponent('CONTROLPANEL', {enableInfiniteScroll: true}, document.getElementById("controlpanel"), function () {
// CONTROLPANEL configuration
// set column meta - which custom controls to use, source configuration for data, custom actions
var controlPanelColMeta = [
{
"columnName": "path",
"order": 1,
"locked": false,
"displayName": "Path",
"source": "$entity$.getPath()"
},
{
"columnName": "name",
"order": 2,
"locked": false,
"customComponent": GEPPETTO.LinkComponent,
"displayName": "Name",
"source": "$entity$.getName()",
"actions": "setTermInfo($entity$['$entity$' + '_meta'], $entity$.getName());"
},
{
"columnName": "type",
"order": 3,
"locked": false,
"customComponent": GEPPETTO.LinkArrayComponent,
"displayName": "Type",
"source": "$entity$.$entity$_meta.getTypes().map(function (t) {return t.type.getInitialValue().value})",
"actions": "window.fetchVariableThenRun('$entity$', window.setTermInfoCallback);",
},
{
"columnName": "controls",
"order": 4,
"locked": false,
"customComponent": GEPPETTO.ControlsComponent,
"displayName": "Controls",
"cssClassName": "controlpanel-controls-column",
"source": "",
"actions": "GEPPETTO.ControlPanel.refresh();"
},
{
"columnName": "image",
"order": 5,
"locked": false,
"customComponent": GEPPETTO.ImageComponent,
"displayName": "Image",
"cssClassName": "img-column",
"source": "GEPPETTO.ModelFactory.getAllVariablesOfMetaType($entity$.$entity$_meta.getType(), 'ImageType')[0].getInitialValues()[0].value.data"
}
];
GEPPETTO.ControlPanel.setColumnMeta(controlPanelColMeta);
// which columns to display
GEPPETTO.ControlPanel.setColumns(['name', 'type', 'controls', 'image']);
// which instances to display in the control panel
GEPPETTO.ControlPanel.setDataFilter(function (entities) {
var visualInstances = GEPPETTO.ModelFactory.getAllInstancesWithCapability(GEPPETTO.Resources.VISUAL_CAPABILITY, entities);
var visualParents = [];
for (var i = 0; i < visualInstances.length; i++) {
if (visualInstances[i].getParent() != null){
visualParents.push(visualInstances[i].getParent());
}
}
visualInstances = visualInstances.concat(visualParents);
var compositeInstances = [];
for (var i = 0; i < visualInstances.length; i++) {
if (visualInstances[i].getType().getMetaType() == GEPPETTO.Resources.COMPOSITE_TYPE_NODE) {
compositeInstances.push(visualInstances[i]);
}
}
return compositeInstances;
});
// custom controls configuration in the controls column
GEPPETTO.ControlPanel.setControlsConfig({
"VisualCapability": {
"select": {
"id": "select",
"condition": "GEPPETTO.SceneController.isSelected($instance$.$instance$_obj != undefined ? [$instance$.$instance$_obj] : []) || GEPPETTO.SceneController.isSelected($instance$.$instance$_swc != undefined ? [$instance$.$instance$_swc] : [])",
"false": {
"actions": ["$instance$.select()"],
"icon": "fa-hand-stop-o",
"label": "Unselected",
"tooltip": "Select",
"id": "select",
},
"true": {
"actions": ["$instance$.deselect()"],
"icon": "fa-hand-rock-o",
"label": "Selected",
"tooltip": "Deselect",
"id": "deselect",
}
},
"color": {
"id": "color",
"actions": ["$instance$.setColor('$param$');"],
"icon": "fa-tint",
"label": "Color",
"tooltip": "Color"
},
"zoom": {
"id": "zoom",
"actions": ["GEPPETTO.SceneController.zoomTo($instances$)"],
"icon": "fa-search-plus",
"label": "Zoom",
"tooltip": "Zoom"
},
"visibility_obj": {
"showCondition": "$instance$.getType().hasVariable($instance$.getId() + '_obj')",
"condition": "(function() { var visible = false; if ($instance$.getType().$instance$_obj != undefined && $instance$.getType().$instance$_obj.getType().getMetaType() != GEPPETTO.Resources.IMPORT_TYPE && $instance$.$instance$_obj != undefined) { visible = GEPPETTO.SceneController.isVisible([$instance$.$instance$_obj]); } return visible; })()",
"false": {
"id": "visibility_obj",
"actions": ["(function(){var instance = Instances.getInstance('$instance$.$instance$_obj'); if (instance.getType().getMetaType() == GEPPETTO.Resources.IMPORT_TYPE) { var col = instance.getParent().getColor(); instance.getType().resolve(function() { instance.setColor(col); GEPPETTO.trigger('experiment:visibility_changed', instance); GEPPETTO.ControlPanel.refresh(); }); } else { GEPPETTO.SceneController.show([instance]); }})()"],
"icon": "fa-eye-slash",
"label": "Hidden",
"tooltip": "Show 3D Volume"
},
"true": {
"id": "visibility_obj",
"actions": ["GEPPETTO.SceneController.hide([$instance$.$instance$_obj])"],
"icon": "fa-eye",
"label": "Visible",
"tooltip": "Hide 3D Volume"
}
},
"visibility_swc": {
"showCondition": "$instance$.getType().hasVariable($instance$.getId() + '_swc')",
"condition": "(function() { var visible = false; if ($instance$.getType().$instance$_swc != undefined && $instance$.getType().$instance$_swc.getType().getMetaType() != GEPPETTO.Resources.IMPORT_TYPE && $instance$.$instance$_swc != undefined) { visible = GEPPETTO.SceneController.isVisible([$instance$.$instance$_swc]); } return visible; })()",
"false": {
"id": "visibility_swc",
"actions": ["(function(){var instance = Instances.getInstance('$instance$.$instance$_swc'); if (instance.getType().getMetaType() == GEPPETTO.Resources.IMPORT_TYPE) { var col = instance.getParent().getColor(); instance.getType().resolve(function() { instance.setColor(col); GEPPETTO.trigger('experiment:visibility_changed', instance); GEPPETTO.ControlPanel.refresh(); }); } else { GEPPETTO.SceneController.show([instance]); }})()"],
"icon": "fa-eye-slash",
"label": "Hidden",
"tooltip": "Show 3D Skeleton"
},
"true": {
"id": "visibility_swc",
"actions": ["GEPPETTO.SceneController.hide([$instance$.$instance$_swc])"],
"icon": "fa-eye",
"label": "Visible",
"tooltip": "Hide 3D Skeleton"
}
},
},
"Common": {
"info": {
"id": "info",
"actions": ["var displayTxt = '$instance$'.split('.')['$instance$'.split('.').length - 1]; setTermInfo($instance$[displayTxt + '_meta'], displayTxt);"],
"icon": "fa-info-circle",
"label": "Info",
"tooltip": "Info"
},
"delete": {
"showCondition": "$instance$.getId()!=window.templateID",
"id": "delete",
"actions": ["if($instance$.getPath() == ((window.termInfoPopup.data != undefined) ? eval(window.termInfoPopup.data).getParent().getPath() : undefined)) { setTermInfo(window[window.templateID][window.templateID+'_meta'], window[window.templateID][window.templateID+'_meta'].getParent().getId());} $instance$.deselect(); $instance$.delete();"],
"icon": "fa-trash-o",
"label": "Delete",
"tooltip": "Delete"
}
}
});
// which controls will be rendered, strings need to match ids in the controls configuration
GEPPETTO.ControlPanel.setControls({
"Common": ['info', 'delete'],
"VisualCapability": ['select', 'color', 'visibility', 'zoom', 'visibility_obj', 'visibility_swc']
});
});
//Spotlight initialization
GEPPETTO.ComponentFactory.addComponent('SPOTLIGHT', {indexInstances: false}, document.getElementById("spotlight"), function () {
// SPOTLIGHT configuration
var spotlightConfig = {
"SpotlightBar": {
"DataSources": {},
"CompositeType": {
"type": {
"actions": [
"setTermInfo($variableid$['$variableid$' + '_meta'],'$variableid$');GEPPETTO.Spotlight.close();",
],
"icon": "fa-info-circle",
"label": "Show info",
"tooltip": "Show info"
},
"query": {
actions: [
"window.fetchVariableThenRun('$variableid$', window.addToQueryCallback);"
],
icon: "fa-quora",
label: "Add to query",
tooltip: "Add to query"
},
},
"VisualCapability": {
"buttonOne": {
"condition": "GEPPETTO.SceneController.isSelected($instances$)",
"false": {
"actions": ["GEPPETTO.SceneController.select($instances$)"],
"icon": "fa-hand-stop-o",
"label": "Unselected",
"tooltip": "Select"
},
"true": {
"actions": ["GEPPETTO.SceneController.deselect($instances$)"],
"icon": "fa-hand-rock-o",
"label": "Selected",
"tooltip": "Deselect"
},
},
"buttonTwo": {
"condition": "GEPPETTO.SceneController.isVisible($instances$)",
"false": {
"actions": [
"GEPPETTO.SceneController.show($instances$)"
],
"icon": "fa-eye-slash",
"label": "Hidden",
"tooltip": "Show"
},
"true": {
"actions": [
"GEPPETTO.SceneController.hide($instances$)"
],
"icon": "fa-eye",
"label": "Visible",
"tooltip": "Hide"
}
},
"buttonThree": {
"actions": [
"GEPPETTO.SceneController.zoomTo($instances$);GEPPETTO.Spotlight.close();"
],
"icon": "fa-search-plus",
"label": "Zoom",
"tooltip": "Zoom"
},
}
}
};
GEPPETTO.Spotlight.setButtonBarConfiguration(spotlightConfig);
// external datasource configuration
var spotlightDataSourceConfig = {
VFB: {
url: "https://www.virtualflybrain.org/search/select?fl=short_form,label,synonym,id,type,has_narrow_synonym_annotation,has_broad_synonym_annotation&start=0&fq=ontology_name:(fbbt)&fq=is_obsolete:false&fq=shortform_autosuggest:VFB_*%20OR%20shortform_autosuggest:FB*&rows=250&bq=is_defining_ontology:true%5E100.0%20label_s:%22%22%5E2%20synonym_s:%22%22%20in_subset_annotation:BRAINNAME%5E3%20short_form:FBbt_00003982%5E2&q=*$SEARCH_TERM$*%20OR%20$SEARCH_TERM$&defType=edismax&qf=label%20synonym%20label_autosuggest_ws%20label_autosuggest_e%20label_autosuggest%20synonym_autosuggest_ws%20synonym_autosuggest_e%20synonym_autosuggest%20shortform_autosuggest%20has_narrow_synonym_annotation%20has_broad_synonym_annotation&wt=json&indent=true",
crossDomain: true,
id: "short_form",
label: {field: "label", formatting: "$VALUE$"},
explode_fields: [{field: "short_form", formatting: "$VALUE$ ($LABEL$)"}],
explode_arrays: [{field: "synonym", formatting: "$VALUE$ ($LABEL$)"}],
type: {
class: {
icon: "fa-file-text-o",
buttons: {
buttonOne: {
actions: ["window.fetchVariableThenRun('$ID$', window.setTermInfoCallback);"],
icon: "fa-info-circle",
label: "Show info",
tooltip: "Show info"
},
buttonTwo: {
actions: ["window.fetchVariableThenRun('$ID$', window.addToQueryCallback, '$LABEL$');"],
icon: "fa-quora",
label: "Add to query",
tooltip: "Add to query"
}
}
},
individual: {
icon: "fa-file-image-o",
buttons: {
buttonOne: {
actions: ["window.fetchVariableThenRun('$ID$', window.setTermInfoCallback);"],
icon: "fa-info-circle",
label: "Show info",
tooltip: "Show info"
},
buttonTwo: {
actions: ["window.fetchVariableThenRun('$ID$', window.addToSceneCallback);"],
icon: "fa-file-image-o",
label: "Add to scene",
tooltip: "Add to scene"
},
buttonThree: {
actions: ["window.fetchVariableThenRun('$ID$', window.addToQueryCallback, '$LABEL$');"],
icon: "fa-quora",
label: "Add to query",
tooltip: "Add to query"
}
}
}
},
bloodhoundConfig: {
datumTokenizer: function (d) {
return Bloodhound.tokenizers.nonword(d.label.replace('_', ' '));
},
queryTokenizer: function (q) {
return Bloodhound.tokenizers.nonword(q.replace('_', ' '));
},
sorter: function (a, b) {
var term = $('#typeahead').val();
return customSorter(a, b, term);
}
}
}
};
GEPPETTO.Spotlight.addDataSource(spotlightDataSourceConfig);
});
//Foreground initialization
GEPPETTO.ComponentFactory.addComponent('FOREGROUND', {addToForegroundControls : false}, document.getElementById("foreground-toolbar"));
//Query control initialization
GEPPETTO.ComponentFactory.addComponent('QUERY', {enableInfiniteScroll: true}, document.getElementById("querybuilder"), function () {
// QUERY configuration
var queryResultsColMeta = [
{
"columnName": "id",
"order": 1,
"locked": false,
"visible": true,
"displayName": "ID",
},
{
"columnName": "name",
"order": 2,
"locked": false,
"visible": true,
"customComponent": GEPPETTO.QueryLinkComponent,
"actions": "window.fetchVariableThenRun('$entity$', function(){ var instance = Instances.getInstance('$entity$.$entity$_meta'); setTermInfo(instance, instance.getParent().getName());});",
"displayName": "Name",
"cssClassName": "query-results-name-column",
},
{
"columnName": "description",
"order": 3,
"locked": false,
"visible": true,
"displayName": "Definition",
"cssClassName": "query-results-description-column"
},
{
"columnName": "type",
"order": 4,
"locked": false,
"visible": true,
"displayName": "Type",
"cssClassName": "query-results-type-column"
},
{
"columnName": "controls",
"order": 5,
"locked": false,
"visible": false,
"customComponent": GEPPETTO.QueryResultsControlsComponent,
"displayName": "Controls",
"actions": "",
"cssClassName": "query-results-controls-column"
},
{
"columnName": "images",
"order": 6,
"locked": false,
"visible": true,
"customComponent": GEPPETTO.SlideshowImageComponent,
"displayName": "Images",
"actions": "window.fetchVariableThenRun('$entity$', function () { var meta = '$entity$' + '.' + '$entity$' + '_meta'; var inst = Instances.getInstance(meta); setTermInfo(inst, $entity$.getName()); resolve3D('$entity$'); });",
"cssClassName": "query-results-images-column"
}
];
GEPPETTO.QueryBuilder.setResultsColumnMeta(queryResultsColMeta);
// which columns to display in the results
GEPPETTO.QueryBuilder.setResultsColumns(['name', 'description', 'type', 'images']);
var queryResultsControlConfig = {
"Common": {
"info": {
"id": "info",
"actions": [
"window.fetchVariableThenRun('$ID$', window.setTermInfoCallback);"
],
"icon": "fa-info-circle",
"label": "Info",
"tooltip": "Info"
},
"flybase": {
"showCondition": "'$ID$'.startsWith('FBbt')",
"id": "flybase",
"actions": [
"window.open('http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=' + '$ID$'.replace(/_/g, ':'), '_blank').focus()"
],
"icon": "gpt-fly",
"label": "FlyBase",
"tooltip": "FlyBase Term"
},
"flybase": {
"showCondition": "('$ID$'.startsWith('FB') && !'$ID$'.startsWith('FBbt'))",
"id": "flybase",
"actions": [
"window.open('http://flybase.org/reports/' + '$ID$'.replace(/_/g, ':'), '_blank').focus()"
],
"icon": "gpt-fly",
"label": "FlyBase",
"tooltip": "FlyBase Report"
}
}
};
GEPPETTO.QueryBuilder.setResultsControlsConfig(queryResultsControlConfig);
// add datasource config to query control
var queryBuilderDatasourceConfig = {
VFB: {
url: "https://www.virtualflybrain.org/search/select?fl=short_form,label,synonym,id,type,has_narrow_synonym_annotation,has_broad_synonym_annotation&start=0&fq=ontology_name:(fbbt)&fq=is_obsolete:false&fq=shortform_autosuggest:VFB_*%20OR%20shortform_autosuggest:FBbt_*&rows=250&bq=is_defining_ontology:true%5E100.0%20label_s:%22%22%5E2%20synonym_s:%22%22%20in_subset_annotation:BRAINNAME%5E3%20short_form:FBbt_00003982%5E2&q=*$SEARCH_TERM$*%20OR%20$SEARCH_TERM$&defType=edismax&qf=label%20synonym%20label_autosuggest_ws%20label_autosuggest_e%20label_autosuggest%20synonym_autosuggest_ws%20synonym_autosuggest_e%20synonym_autosuggest%20shortform_autosuggest%20has_narrow_synonym_annotation%20has_broad_synonym_annotation&wt=json&indent=true",
crossDomain: true,
id: "short_form",
label: {field: "label", formatting: "$VALUE$"},
explode_fields: [{field: "short_form", formatting: "$VALUE$ ($LABEL$)"}],
explode_arrays: [{field: "synonym", formatting: "$VALUE$ ($LABEL$)"}],
type: {
class: {
actions: ["window.fetchVariableThenRun('$ID$', function(){ GEPPETTO.QueryBuilder.addQueryItem({ term: '$LABEL$', id: '$ID$'}); });"],
icon: "fa-dot-circle-o"
},
individual: {
actions: ["window.fetchVariableThenRun('$ID$', function(){ GEPPETTO.QueryBuilder.addQueryItem({ term: '$LABEL$', id: '$ID$'}); });"],
icon: "fa-square-o"
}
},
queryNameToken: '$NAME',
resultsFilters: {
getId: function (record) {
return record[0]
},
getName: function (record) {
return record[1]
},
getDescription: function (record) {
return record[2]
},
getType: function (record) {
return record[3]
},
getImageData: function (record) {
return record[4]
},
getRecords: function (payload) {
return payload.results.map(function (item) {
return item.values
})
}
},
bloodhoundConfig: {
datumTokenizer: function (d) {
return Bloodhound.tokenizers.nonword(d.label.replace('_', ' '));
},
queryTokenizer: function (q) {
return Bloodhound.tokenizers.nonword(q.replace('_', ' '));
},
sorter: function (a, b) {
var term = $("#query-typeahead").val();
return customSorter(a, b, term);
}
}
}
};
GEPPETTO.QueryBuilder.addDataSource(queryBuilderDatasourceConfig);
});
//Canvas initialisation
window.vfbCanvas = undefined;
GEPPETTO.ComponentFactory.addComponent('CANVAS', {}, document.getElementById("sim"), function () {
this.flipCameraY();
this.flipCameraZ();
this.setWireframe(true);
this.displayAllInstances();
window.vfbCanvas = this;
if(window.StackViewer1 != undefined){
window.StackViewer1.setCanvasRef(this);
}
});
//Loading spinner initialization
GEPPETTO.Spinner.setLogo("gpt-fly");
// VFB initialization routines
window.initVFB = function () {
window.templateID = undefined;
window.redirectURL = '$PROTOCOL$//$HOST$/?i=$TEMPLATE$,$VFB_ID$&id=$VFB_ID$';
// widgets default dimensions and positions
var getStackViewerDefaultWidth = function() { return Math.ceil(window.innerWidth / 4); };
var getStackViewerDefaultHeight = function() { return Math.ceil(window.innerHeight/4) - 10; };
var getTermInfoDefaultWidth = function() { return Math.ceil(window.innerWidth / 4); };
var getTermInfoDefaultHeight = function() { return ((window.innerHeight - Math.ceil(window.innerHeight/4))-20); };
var getTermInfoDefaultX = function() { return (window.innerWidth - (Math.ceil(window.innerWidth / 4) + 10)); };
var getStackViewerDefaultX = function() { return (window.innerWidth - (Math.ceil(window.innerWidth / 4) + 10)); };
var getStackViewerDefaultY = function() { return (window.innerHeight - Math.ceil(window.innerHeight/4)); };
var getTermInfoDefaultY = function() {return 10;};
var getButtonBarDefaultX = function() { return (Math.ceil(window.innerWidth / 2) - 125); };
var getButtonBarDefaultY = function() { return 10; };
// logic to assign colours to elements in the scene
window.colours = ["0x5b5b5b", "0x00ff00", "0xff0000", "0x0000ff", "0x0084f6", "0x008d46", "0xa7613e", "0x4f006a", "0x00fff6", "0x3e7b8d", "0xeda7ff", "0xd3ff95", "0xb94fff", "0xe51a58", "0x848400", "0x00ff95", "0x61002c", "0xf68412", "0xcaff00", "0x2c3e00", "0x0035c1", "0xffca84", "0x002c61", "0x9e728d", "0x4fb912", "0x9ec1ff", "0x959e7b", "0xff7bb0", "0x9e0900", "0xffb9b9", "0x8461ca", "0x9e0072", "0x84dca7", "0xff00f6", "0x00d3ff", "0xff7258", "0x583e35", "0x003e35", "0xdc61dc", "0x6172b0", "0xb9ca2c", "0x12b0a7", "0x611200", "0x2c002c", "0x5800ca", "0x95c1ca", "0xd39e23", "0x84b058", "0xe5edb9", "0xf6d3ff", "0xb94f61", "0x8d09a7", "0x6a4f00", "0x003e9e", "0x7b3e7b", "0x3e7b61", "0xa7ff61", "0x0095d3", "0x3e7200", "0xb05800", "0xdc007b", "0x9e9eff", "0x4f4661", "0xa7fff6", "0xe5002c", "0x72dc72", "0xffed7b", "0xb08d46", "0x6172ff", "0xdc4600", "0x000072", "0x090046", "0x35ed4f", "0x2c0000", "0xa700ff", "0x00f6c1", "0x9e002c", "0x003eff", "0xf69e7b", "0x6a7235", "0xffff46", "0xc1b0b0", "0x727272", "0xc16aa7", "0x005823", "0xff848d", "0xb08472", "0x004661", "0x8dff12", "0xb08dca", "0x724ff6", "0x729e00", "0xd309c1", "0x9e004f", "0xc17bff", "0x8d95b9", "0xf6a7d3", "0x232309", "0xff6aca", "0x008d12", "0xffa758", "0xe5c19e", "0x00122c", "0xc1b958", "0x00c17b", "0x462c00", "0x7b3e58", "0x9e46a7", "0x4f583e", "0x6a35b9", "0x72b095", "0xffb000", "0x4f3584", "0xb94635", "0x61a7ff", "0xd38495", "0x7b613e", "0x6a004f", "0xed58ff", "0x95d300", "0x35a7c1", "0x00009e", "0x7b3535", "0xdcff6a", "0x95d34f", "0x84ffb0", "0x843500", "0x4fdce5", "0x462335", "0x002c09", "0xb9dcc1", "0x588d4f", "0x9e7200", "0xca4684", "0x00c146", "0xca09ed", "0xcadcff", "0x0058a7", "0x2ca77b", "0x8ddcff", "0x232c35", "0xc1ffb9", "0x006a9e", "0x0058ff", "0xf65884", "0xdc7b46", "0xca35a7", "0xa7ca8d", "0x4fdcc1", "0x6172d3", "0x6a23ff", "0x8d09ca", "0xdcc12c", "0xc1b97b", "0x3e2358", "0x7b6195", "0xb97bdc", "0xffdcd3", "0xed5861", "0xcab9ff", "0x3e5858", "0x729595", "0x7bff7b", "0x95356a", "0xca9eb9", "0x723e1a", "0x95098d", "0xf68ddc", "0x61b03e", "0xffca61", "0xd37b72", "0xffed9e", "0xcaf6ff", "0x58c1ff", "0x8d61ed", "0x61b972", "0x8d6161", "0x46467b", "0x0058d3", "0x58dc09", "0x001a72", "0xd33e2c", "0x959546", "0xca7b00", "0x4f6a8d", "0x9584ff", "0x46238d", "0x008484", "0xf67235", "0x9edc84", "0xcadc6a", "0xb04fdc", "0x4f0912", "0xff1a7b", "0x7bb0d3", "0x1a001a", "0x8d35f6", "0x5800a7", "0xed8dff", "0x969696", "0xffd300"];
window.coli = 0;
window.setSepCol = function (entityPath) {
var c = coli;
coli++;
if (coli > 199) {
coli = 0;
}
if (Instances.getInstance(entityPath).setColor != undefined){
Instances.getInstance(entityPath).setColor(colours[c], true).setOpacity(0.3, true);
try {
Instances.getInstance(entityPath)[entityPath + '_swc'].setOpacity(1.0);
} catch (ignore) {
}
if (c = 0) {
Instances.getInstance(entityPath).setOpacity(0.2, true);
}
}else{
console.log('Issue setting colour for ' + entityPath);
}
};
// custom handler for resolving 3d geometries
window.resolve3D = function (path, callback) {
var rootInstance = Instances.getInstance(path);
window.updateHistory(rootInstance.getName());
GEPPETTO.SceneController.deselectAll();
// check if we can set templateID (first template loaded will be kept as templateID)
if(window.templateID == undefined){
var superTypes = rootInstance.getType().getSuperType();
for(var i=0; i<superTypes.length; i++){
if(superTypes[i].getId() == 'Template'){
window.templateID = rootInstance.getId();
}
}
} else {
// check if the user is adding to the scene something belonging to another template
var superTypes = rootInstance.getType().getSuperType();
var templateID = "unknown";
for(var i=0; i<superTypes.length; i++){
if(superTypes[i].getId() == window.templateID){
templateID = superTypes[i].getId()
}
if(superTypes[i].getId() == 'Class'){
templateID = window.templateID;
return; // Exit if Class - Class doesn't have image types.
}
}
var meta = rootInstance[rootInstance.getId() + '_meta'];
if(meta != undefined){
if (typeof meta.getType().template != "undefined"){
var templateMarkup = meta.getType().template.getValue().wrappedObj.value.html;
var domObj = $(templateMarkup);
var anchorElement = domObj.filter('a');
// extract ID
var templateID = anchorElement.attr('instancepath');
if (window.EMBEDDED){
var curHost = parent.document.location.host;
var curProto = parent.document.location.protocol;
}else{
var curHost = document.location.host;
var curProto = document.location.protocol;
}
if(templateID != window.templateID){
// open new window with the new template and the instance ID
var targetWindow = '_blank';
var newUrl = window.redirectURL.replace(/\$VFB_ID\$/gi, rootInstance.getId()).replace(/\$TEMPLATE\$/gi, templateID).replace(/\$HOST\$/gi, curHost).replace(/\$PROTOCOL\$/gi, curProto);
window.open(newUrl, targetWindow);
// stop flow here, we don't want to add to scene something with a different template
return;
}
}
}
}
var instance = undefined;
// check if we have swc
try {
instance = Instances.getInstance(path + "." + path + "_swc");
} catch (ignore) {
}
// if no swc check if we have obj
if (instance == undefined) {
try {
instance = Instances.getInstance(path + "." + path + "_obj");
} catch (ignore) {
}
}
// if anything was found resolve type (will add to scene)
if (instance != undefined) {
var postResolve = function () {
setSepCol(path);
if (callback != undefined) {
callback();
}
};
if(instance.getType() instanceof ImportType) {
instance.getType().resolve(postResolve);
} else {
// add instance to scene
vfbCanvas.display([instance]);
// trigger update for components that are listening
GEPPETTO.trigger(GEPPETTO.Events.Instances_created, [instance]);
postResolve();
}
}
// independently from the above, check if we have slices for the instance
try {
instance = Instances.getInstance(path + "." + path + "_slices");
if(instance.getType() instanceof ImportType){
instance.getType().resolve();
}
} catch (ignore) {
// any alternative handling goes here
}
};
window.fetchVariableThenRun = function(variableId, callback, label){
GEPPETTO.SceneController.deselectAll(); // signal something is happening!
var variables = GEPPETTO.ModelFactory.getTopLevelVariablesById([variableId]);
if (!variables.length>0) {
Model.getDatasources()[0].fetchVariable(variableId, function() {
callback(variableId, label);
});
} else {
callback(variableId, label);
}
};
window.addToSceneCallback = function(variableId){
var instance = Instances.getInstance(variableId);
var meta = Instances.getInstance(variableId + '.' + variableId + '_meta');
resolve3D(variableId, function() {
GEPPETTO.SceneController.deselectAll();
instance.select();
//GEPPETTO.Spotlight.openToInstance(instance);
setTermInfo(meta, meta.getParent().getId());
});
};
window.addToQueryCallback = function(variableId, label) {
window.clearQS();
GEPPETTO.QueryBuilder.clearAllQueryItems();
GEPPETTO.QueryBuilder.switchView(false);
GEPPETTO.QueryBuilder.addQueryItem({
term: (label != undefined) ? label : eval(variableId).getName(),
id: variableId
});
GEPPETTO.QueryBuilder.open();
};
window.setTermInfoCallback = function(variableId){
var instance = Instances.getInstance(variableId + '.' + variableId + '_meta');
setTermInfo(instance, instance.getParent().getId());
};
// custom handler for term info clicks
window.customHandler = function (node, path, widget) {
var n;
var otherId;
var otherName;
try {
n = eval(path);
} catch (ex) {
node = undefined;
}
var meta = path + "." + path + "_meta";
var target = widget;
// if (GEPPETTO.isKeyPressed("meta")) {
// target = G.addWidget(1, {isStateless: true}).addCustomNodeHandler(customHandler, 'click');
//}
if (n != undefined) {
var metanode = Instances.getInstance(meta);
if (target.data == metanode){
window.resolve3D(path);
}else{
target.setData(metanode).setName(n.getName());
}
} else {
// check for passed ID:
if (path.indexOf(',')>-1){
otherId = path.split(',')[1];
otherName = path.split(',')[2];
path = path.split(',')[0];
}
// try to evaluate as path in Model
var entity = Model[path];
if(entity instanceof Query){
GEPPETTO.trigger('spin_logo');
$("body").css("cursor", "progress");
// clear query builder
GEPPETTO.QueryBuilder.clearAllQueryItems();
var callback = function(){
// check if any results with count flag
if(GEPPETTO.QueryBuilder.props.model.count > 0){
// runQuery if any results
GEPPETTO.QueryBuilder.runQuery();
} else {
GEPPETTO.QueryBuilder.switchView(false);
}
// show query component
GEPPETTO.QueryBuilder.open();
$("body").css("cursor", "default");
GEPPETTO.trigger('stop_spin_logo');
};
// add query item + selection
if (otherId == undefined) {
GEPPETTO.QueryBuilder.addQueryItem({ term: widget.name, id: widget.data.getParent().getId(), queryObj: entity}, callback);
}else{
if (window[otherId] == undefined){
window.fetchVariableThenRun(otherId, function(){GEPPETTO.QueryBuilder.addQueryItem({ term: otherName, id: otherId, queryObj: entity}, callback)});
}else{
GEPPETTO.QueryBuilder.addQueryItem({ term: otherName, id: otherId, queryObj: entity}, callback);
}
}
} else {
Model.getDatasources()[0].fetchVariable(path, function () {
Instances.getInstance(meta);
target.setData(eval(meta)).setName(eval(path).getName());
resolve3D(path);
});
}
}
};
// set term info on selection
GEPPETTO.on(GEPPETTO.Events.Select, function (instance) {
var selection = GEPPETTO.SceneController.getSelection();
if (selection.length > 0 && instance.isSelected()) {
var latestSelection = instance;
var currentSelectionName = getTermInfoWidget().name;
if(latestSelection.getChildren().length > 0){
// it's a wrapper object - if name is different from current selection set term info
if(currentSelectionName != latestSelection.getName()) {
setTermInfo(latestSelection[latestSelection.getId() + "_meta"], latestSelection[latestSelection.getId() + "_meta"].getName());
}
} else {
// it's a leaf (no children) / grab parent if name is different from current selection set term info
var parent = latestSelection.getParent();
if(parent != null && currentSelectionName != parent.getName()){
setTermInfo(parent[parent.getId() + "_meta"], parent[parent.getId() + "_meta"].getName());
}
}
}
if (window.StackViewer1 != undefined){
updateStackWidget();
}
});
// stack widget helper methods
var getSliceInstances = function(){
var potentialInstances = GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith('_slices');
var sliceInstances = [];
var instance;
for(var i=0; i<potentialInstances.length; i++){
instance = Instances.getInstance(potentialInstances[i],false);
if (instance){
sliceInstances.push(instance);
}
}
return sliceInstances;
};
var updateStackWidget = function(){
window.checkConnection();
console.log('Updating stack...');
window.StackViewer1.setData({
instances: getSliceInstances()
});
};
window.addStackWidget = function(){
var sliceInstances = getSliceInstances();
if (window.StackViewer1 == undefined){
var config;
var domainId = [];
var domainName = [];
if (typeof sliceInstances[0] !== "undefined"){
config = JSON.parse(sliceInstances[0].getValue().wrappedObj.value.data);
}
if (config == undefined || typeof config !== "undefined"){
config = {
serverUrl: 'http://www.virtualflybrain.org/fcgi/wlziipsrv.fcgi',
templateId: 'NOTSET'
};
}
G.addWidget(8, {isStateless: true}).setConfig(config).setData({
instances: sliceInstances
});
// set canvas if it's already there
if(window.vfbCanvas != undefined){
window.StackViewer1.setCanvasRef(window.vfbCanvas);
}
// set initial position:
window.StackViewer1.setPosition(getStackViewerDefaultX(), getStackViewerDefaultY());
window.StackViewer1.setSize(getStackViewerDefaultHeight(), getStackViewerDefaultWidth());
window.StackViewer1.setName('Slice Viewer');
window.StackViewer1.setTrasparentBackground(true);
window.StackViewer1.showHistoryIcon(false);
window.StackViewer1.setHelpInfo(stackHelpInfo);
window.StackViewer1.$el.bind('restored', function(event,id) {
if(id == window.StackViewer1.getId()){
if(window.StackViewer1 != undefined) {
window.StackViewer1.setSize(getStackViewerDefaultHeight(), getStackViewerDefaultWidth());
window.StackViewer1.setPosition(getStackViewerDefaultX(), getStackViewerDefaultY());
}
}
});
// on change to instances reload stack:
GEPPETTO.on(GEPPETTO.Events.Instance_deleted, function(path){
console.log(path.split('.')[0] + ' deleted...');
if (window.StackViewer1 != undefined){
if(path!=undefined && path.length > 0){
window.StackViewer1.removeSlice(path);
}else{
console.log('Removing instance issue: ' + path);
}
}
});
GEPPETTO.on(GEPPETTO.Events.Instances_created, function(instances){
console.log('Instance created...');
if (window.StackViewer1 != undefined){
if(instances!=undefined && instances.length > 0){
var config = {
serverUrl: 'http://www.virtualflybrain.org/fcgi/wlziipsrv.fcgi',
templateId: window.templateID
};
instances.forEach(function (parentInstance){
parentInstance.parent.getChildren().forEach(function (instance){
if (instance.getName() == 'Stack Viewer Slices'){
window.StackViewer1.addSlices(instance);
if (instance.parent.getId() == window.templateID){
try{
config=JSON.parse(instance.getValue().wrappedObj.value.data);
window.StackViewer1.setConfig(config);
}catch (err){
console.log(err.message);
window.StackViewer1.setConfig(config);
}
}
console.log('Passing instance: ' + instance.getId());
}
})
});
}
}
});
// on colour change update:
GEPPETTO.on(GEPPETTO.Events.Color_set, function(instances){
console.log('Colour change...');
if (window.StackViewer1 != undefined){
if(instances!=undefined && instances.instance){
if (instances.instance.getType().getMetaType() == 'CompositeType'){
instances.instance.getChildren().forEach(function (instance){if (instance.getName() == 'Stack Viewer Slices'){window.StackViewer1.addSlices(instance)}});
}else if (instances.instance.parent && instances.instance.parent.getType().getMetaType() == 'CompositeType'){
instances.instance.parent.getChildren().forEach(function (instance){if (instance.getName() == 'Stack Viewer Slices'){window.StackViewer1.addSlices(instance)}});
}else{
console.log('Colour setting issue: ' + instances);
}
}else{
console.log('Colour setting issue! ' + instances);
}
}
});
$('.ui-dialog-titlebar-minimize').hide(); //hide all minimize buttons
} else {
window.vfbWindowResize();
$('#' + window.StackViewer1.getId()).parent().effect('shake', {distance:5, times: 3}, 500);
}
};
// custom sorter for bloodhound
window.customSorter = function (a, b, InputString) {
//move exact matches to top
if (InputString == a.label) {
return -1;
}
if (InputString == b.label) {
return 1;
}
//close match without case matching
if (InputString.toLowerCase() == a.label.toLowerCase()) {
return -1;
}
if (InputString.toLowerCase() == b.label.toLowerCase()) {
return 1;
}
//match ignoring joinging nonwords
Bloodhound.tokenizers.nonword("test thing-here12 34f").join(' ');
if (Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ') == Bloodhound.tokenizers.nonword(a.label.toLowerCase()).join(' ')) {
return -1;
}
if (Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ') == Bloodhound.tokenizers.nonword(b.label.toLowerCase()).join(' ')) {
return 1;
}
//match against id
if (InputString.toLowerCase() == a.id.toLowerCase()) {
return -1;
}
if (InputString.toLowerCase() == b.id.toLowerCase()) {
return 1;
}
//pick up any match without nonword join character match
if (Bloodhound.tokenizers.nonword(a.label.toLowerCase()).join(' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ')) < 0 && Bloodhound.tokenizers.nonword(b.label.toLowerCase()).join(' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ')) > -1) {
return 1;
}
if (Bloodhound.tokenizers.nonword(b.label.toLowerCase()).join(' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ')) < 0 && Bloodhound.tokenizers.nonword(a.label.toLowerCase()).join(' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ')) > -1) {
return -1;
}
//also with underscores ignored
if (Bloodhound.tokenizers.nonword(a.label.toLowerCase()).join(' ').replace('_', ' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ').replace('_', ' ')) < 0 && Bloodhound.tokenizers.nonword(b.label.toLowerCase()).join(' ').replace('_', ' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ').replace('_', ' ')) > -1) {
return 1;
}
if (Bloodhound.tokenizers.nonword(b.label.toLowerCase()).join(' ').replace('_', ' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ').replace('_', ' ')) < 0 && Bloodhound.tokenizers.nonword(a.label.toLowerCase()).join(' ').replace('_', ' ').indexOf(Bloodhound.tokenizers.nonword(InputString.toLowerCase()).join(' ').replace('_', ' ')) > -1) {
return -1;
}
//if not found in one then advance the other
if (a.label.toLowerCase().indexOf(InputString.toLowerCase()) < 0 && b.label.toLowerCase().indexOf(InputString.toLowerCase()) > -1) {
return 1;
}
if (b.label.toLowerCase().indexOf(InputString.toLowerCase()) < 0 && a.label.toLowerCase().indexOf(InputString.toLowerCase()) > -1) {
return -1;