js.ontology-tree-view.js Maven / Gradle / Ivy
(function($, molgenis) {
"use strict";
var restApi = new molgenis.RestClient();
var standardModal = new molgenis.StandardModal();
var TREE_LABEL = "label";
var ROOT = "root";
var LAST = "isLast";
var ENTITY_TYPE = "entity_type";
var ONTOLOGY_IRI = "ontologyIRI";
var ONTOLOGY_ID = "id";
var ONTOLOGY_NAME = "ontologyName";
var ONTOLOGY_TERM = "ontologyTerm";
var ONTOLOGY_TERM_IRI = "ontologyTermIRI";
var SYNONYMS = "ontologyTermSynonym";
var ONTOLOGY_TERM_DEFINITION = "definition";
var NODE_PATH = "nodePath";
var PARENT_NODE_PATH = "parentNodePath";
var PARENT_ONTOLOGY_TERM_IRI = "parentOntologyTermIRI";
var treeDict = null;
var container = null;
molgenis.OntologyTree = function OntologyTree(treeContainerId){
container = $('#' + treeContainerId);
};
molgenis.OntologyTree.prototype.updateOntologyTree = function(ontologyIRI){
var ontologyIndex = getOntologyTermByIri(ontologyIRI);
if(ontologyIndex && ontologyIndex.items.length > 0){
var topNode = ontologyIndex.items[0];
topNode.attributes = removeDuplicate(getRootOntologyTerms(topNode));
createEntityMetaTree(topNode, null);
}
function getRootOntologyTerms(ontology){
var rootOntologyTerms = restApi.get('/api/v1/' + ontology[ONTOLOGY_NAME], {'expand' : ['attributes'], 'q' : {
'q' : [{
'field' : ROOT,
'operator' : 'EQUALS',
'value' : true
},{
'operator' : 'AND'
},{
'field' : ONTOLOGY_IRI,
'operator' : 'EQUALS',
'value' : ontology[ONTOLOGY_IRI]
},{
'operator' : 'AND'
},{
'field' : LAST,
'operator' : 'EQUALS',
'value' : false
}]
}});
return rootOntologyTerms.items;
}
};
molgenis.OntologyTree.prototype.queryTree = function(ontologyIRI, query){
if(query !== undefined && query !== ''){
var molgenisTree = container.tree('getTree');
treeDict = treeDict ? treeDict : molgenisTree.rootNode.toDict(true);
molgenisTree.reload();
var ontologyIndex = getOntologyTermByIri(ontologyIRI);
if(ontologyIndex.items.length > 0){
var ontology = ontologyIndex.items[0];
var ontologyTerms = removeDuplicate(searchByQuery(ontology, query)).sort(function(a, b){
return molgenis.naturalSort(b.nodePath.split('.').length, a.nodePath.split('.').length);
});
if(ontologyTerms.length > 0){
$.each(ontologyTerms, function(index, ontologyTerm){
getParentNode(molgenisTree, ontologyTerm);
});
}else{
molgenis.createAlert([{'message' : 'No ontology terms are found for query "' + query + '".'}], 'error');
}
}
}
function searchByQuery(ontology, query){
var ontologyTermResult = restApi.get('/api/v1/' + ontology[ONTOLOGY_ID], {'expand' : ['attributes'], 'q' : {
'q' : [{
'field' : SYNONYMS,
'operator' : 'EQUALS',
'value' : query
}]
}}, null);
return ontologyTermResult.items;
}
};
molgenis.OntologyTree.prototype.restoreTree = function(){
if(treeDict){
var molgenisTree = container.tree('getTree');
molgenisTree.rootNode.fromDict(treeDict);
treeDict = null;
}
};
molgenis.OntologyTree.prototype.locateTerm = function(ontologyTerm){
var molgenisTree = container.tree('getTree');
molgenisTree.reload();
ontologyTerm = getOntologyTerm(ontologyTerm);
var currentNode = getParentNode(molgenisTree, ontologyTerm, true);
currentNode.setFocus();
var middlePosition = container.offset().top + container.height()/2;
var scrolledDis = Math.abs($(molgenisTree.rootNode.ul).offset().top - container.offset().top);
if($(currentNode.li).offset().top > middlePosition){
container.scrollTop($(currentNode.li).offset().top - middlePosition + scrolledDis);
}else{
container.scrollTop(scrolledDis - middlePosition + $(currentNode.li).offset().top);
}
};
function getParentNode(molgenisTree, ontologyTerm, showSibling){
var currentNode = null;
if(ontologyTerm){
var nodeKey = ontologyTerm.href;
//Check if the node exists in the tree already
if(!molgenisTree.getNodeByKey(nodeKey)){
//Recursively add parent nodes to the tree first
var parentOntologyTerm = getParentOntologyTerm(ontologyTerm);
var parentNode = getParentNode(molgenisTree, getParentOntologyTerm(ontologyTerm), showSibling);
//Add current node the tree
if(parentNode){
container.tree('appendChildNodes', parentNode, showSibling ? removeDuplicate(parentOntologyTerm.attributes.items) : removeDuplicate([ontologyTerm]));
}else{
console.log('error parent node cannot but null!');
}
}
currentNode = molgenisTree.getNodeByKey(nodeKey);
}
return currentNode;
}
function removeDuplicate (listOfNodes){
var uniqueNodes = [];
if(listOfNodes.length > 0){
var nodeMap = {};
$.each(listOfNodes, function(index, eachNode){
var name = eachNode[ONTOLOGY_TERM_IRI];
if(nodeMap[name]){
if(eachNode[SYNONYMS] !== eachNode[ONTOLOGY_TERM]){
var existingNode = nodeMap[name];
existingNode.synonyms.push(eachNode[SYNONYMS]);
nodeMap[name] = existingNode;
}
}else{
eachNode.synonyms = [];
if(eachNode[SYNONYMS] !== eachNode[ONTOLOGY_TERM]){
eachNode.synonyms.push(eachNode[SYNONYMS]);
}
nodeMap[name] = eachNode;
}
});
//Add tree label to the node data
$.map(nodeMap, function(value, key){
if(value[ONTOLOGY_TERM]){
value[TREE_LABEL] = value[ONTOLOGY_TERM];
}
else if(value[ONTOLOGY_NAME]){
value[TREE_LABEL] = value[ONTOLOGY_NAME];
}
uniqueNodes.push(value);
});
}
return uniqueNodes.sort(function(a, b){
return molgenis.naturalSort(a[TREE_LABEL], b[TREE_LABEL]);
});
}
function getOntologyTermByIri(ontologyIRI){
if(ontologyIRI){
var request = {
'q' : [{
'field' : ONTOLOGY_IRI,
'operator' : 'EQUALS',
'value' : ontologyIRI
}]
};
return restApi.get("/api/v1/ontologyindex/", {'q' : request}, null);
}
return null;
}
function getOntologyTerm(option){
var ontologyTerms = restApi.get('/api/v1/' + option[ONTOLOGY_NAME], {'expand' : ['attributes'], 'q' : {
'q' : [{
'field' : ONTOLOGY_TERM_IRI,
'operator' : 'EQUALS',
'value' : option[ONTOLOGY_TERM_IRI]
},{
'operator' : 'AND'
},{
'field' : NODE_PATH,
'operator' : 'EQUALS',
'value' : option[NODE_PATH]
}]
}});
return ontologyTerms.items.length > 0 ? ontologyTerms.items[0] : null;
}
function getParentOntologyTerm(option){
var parentOntologyTerms = restApi.get('/api/v1/' + option[ONTOLOGY_NAME], {'expand' : ['attributes'], 'q' : {
'q' : [{
'field' : ONTOLOGY_TERM_IRI,
'operator' : 'EQUALS',
'value' : option[PARENT_ONTOLOGY_TERM_IRI]
},{
'operator' : 'AND'
},{
'field' : NODE_PATH,
'operator' : 'EQUALS',
'value' : option[PARENT_NODE_PATH]
}]
}});
return parentOntologyTerms.items.length > 0 ? parentOntologyTerms.items[0] : null;
}
function createEntityMetaTree(entityMetaData, attributes) {
container.css({
'height' : '500px',
'overflow' : 'auto'
}).tree({
'entityMetaData' : entityMetaData,
'selectedAttributes' : attributes,
'onAttributesSelect' : function(selects) {
console.log(selects);
},
'onAttributeClick' : function(attribute) {
$('#ontology-term-info').empty().append(ontologyTermInfo(attribute));
},
'lazyload' : function(data, createChildren){
var href = data.node.data.attribute.href;
var ontologyTerm = restApi.get(href, {'expand' : ['attributes']});
data.result = createChildren(removeDuplicate(ontologyTerm.attributes.items));
}
});
container.on('hover', 'span.fancytree-title', function(event){
var node = $.ui.fancytree.getNode(event);
var selectorElement = node.li ? $(node.li) : $(node.ul);
var data = gatherSynonyms(node.data.attribute);
if(data.synonyms.length > 0){
var listOfSynonyms = $('');
$.each(data.synonyms, function(index, synonym){
listOfSynonyms.append('* ' + synonym + '
');
});
$(node.li).children('span:eq(0)').popover({
'title' : 'Synonyms',
'trigger' : 'hover',
'placement' : 'bottom',
'html' : true,
'content' : listOfSynonyms
}).popover('show');
}
});
}
function gatherSynonyms(attribute){
var data = {};
var ontologyTerm = restApi.get(attribute.href, {'expand' : ['attributes']}, null);
var baseUrl = ontologyTerm.href.substring(0, ontologyTerm.href.lastIndexOf('/') + 1)
var relatedOntologyTerms = restApi.get(baseUrl, {'expand' : ['attributes'], 'q' : {
'q' : [{
'field' : ONTOLOGY_TERM_IRI,
'operator' : 'EQUALS',
'value' : ontologyTerm[ONTOLOGY_TERM_IRI]
}]
}}, null);
if(relatedOntologyTerms.items.length > 0){
data = removeDuplicate(relatedOntologyTerms.items)[0];
}
return data;
}
function ontologyTermInfo(attribute){
var table = $('
').addClass('table').width('500px');
var data = gatherSynonyms(attribute);
table.append('Ontology ' + data[ONTOLOGY_IRI] + ' OntologyTerm ' + data[ONTOLOGY_TERM_IRI] + ' Name ' + data[ONTOLOGY_TERM] + ' Definition ' + data[ONTOLOGY_TERM_DEFINITION] + '
');
$.each(data.synonyms, function(index, synonym){
listOfSynonyms.append('' + synonym + ' ');
});
var synonymContainer = $('Synonyms ').append(synonymContainer).appendTo(table);
}
table.find('th').width('30%');
return table;
}
}($, window.top.molgenis = window.top.molgenis || {}));© 2015 - 2025 Weber Informatics LLC | Privacy Policy