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Conflicts: README.md citation.txt
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‎README.md‎

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@@ -27,7 +27,7 @@ We love receiving patches for bug fixes and new features. Please follow these si
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## Citations
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To cite OPS.js in publications please see [the zenodo record](https://zenodo.org/record/21396#.VbJPs_lVhBc "OPS.js zenodo record").
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>Ian Dunlop et al.. (2015). ops.js: OPS.js 6.0.2 for Open PHACTS 1.5 API. Zenodo. 10.5281/zenodo.21396
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>Ian Dunlop et al.. (2015). ops.js: OPS.js 6.1.2 for Open PHACTS 1.5 API. Zenodo. 10.5281/zenodo.21008
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For Bibtex use:
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@@ -38,8 +38,8 @@ For Bibtex use:
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> andrawaag and
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> Stian Soiland-Reyes and
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> PANDORINO},
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> title = {ops.js: OPS.js 6.0.2 for Open PHACTS 1.5 API},
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> month = jul,
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> title = {ops.js: OPS.js 6.1.2 for Open PHACTS 1.5 API},
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> month = aug,
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> year = 2015,
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> doi = {10.5281/zenodo.21396},
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> url = {http://dx.doi.org/10.5281/zenodo.21396}

‎citation.txt‎

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@@ -5,9 +5,9 @@ author = {Ian Dunlop and
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andrawaag and
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Stian Soiland-Reyes and
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PANDORINO},
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title = {ops.js: OPS.js 6.0.2 for Open PHACTS 1.5 API},
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month = jul,
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title = {ops.js: OPS.js 6.1.2 for Open PHACTS 1.5 API},
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month = aug,
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year = 2015,
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doi = {10.5281/zenodo.21396},
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url = {http://dx.doi.org/10.5281/zenodo.21396}
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doi = {10.5281/zenodo.21008},
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url = {http://dx.doi.org/10.5281/zenodo.21008}
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}

‎package.json‎

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@@ -1,6 +1,6 @@
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{
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"name": "ops.js",
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"version": "6.0.2",
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"version": "6.1.2",
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"description": "Javascript based library to access the Open PHACTS API and discover bio-chemical and life sciences data",
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"main": "./src/OPS.js",
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"directories": {

‎src/DiseaseSearch.js‎

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@@ -515,14 +515,19 @@ DiseaseSearch.prototype.parseDiseasesByTargetResponse = function(response) {
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URI = item[constants.ABOUT];
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gene = {};
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gene["URI"] = item.forGene[constants.ABOUT];
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gene["encodes"] = item.forGene.encodes[constants.ABOUT];
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if (item.forGene.encodes.exactMatch != null) {
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gene["encodesProvenance"] = item.forGene.encodes.exactMatch[constants.ABOUT] != null ? item.forGene.encodes.exactMatch[constants.ABOUT] : null;
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gene["encodesLabel"] = item.forGene.encodes.exactMatch.prefLabel != null ? item.forGene.encodes.exactMatch.prefLabel : null;
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gene["encodes"] = [];
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Utils.arrayify(item.forGene.encodes).forEach(function(encode, i) {
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var about = encode[constants.ABOUT];
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if (encode.exactMatch != null) {
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var provenance = encode.exactMatch[constants.ABOUT] != null ? item.forGene.encodes.exactMatch[constants.ABOUT] : null;
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var label = encode.exactMatch.prefLabel != null ? item.forGene.encodes.exactMatch.prefLabel : null;
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gene["encodes"].push({"uri": about, "provenance": provenance, "label": label});
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} else {
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gene["encodesProvenance"] = null;
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gene["encodesLabel"] = null;
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gene["encodes"].push({"uri": about});
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gene["provenance"] = null;
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gene["label"] = null;
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}
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});
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diseases.push({
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"name": name,
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"URI": URI,

‎src/OPS.js‎

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@@ -206,7 +206,7 @@ module.exports = Openphacts;
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* @typedef {Array.<Object>} DiseasesByTargetResponse
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* @property {string} URI - URI
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* @property {string} name - name
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* @property {Array.<object>} gene - containing URI for the gene, link to the gene it encodes, encodesLabel and encodesProvenance link to where the label came from
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* @property {Array.<object>} gene - containing URI for the gene and an array of encoded genes with link to the gene it encodes, label and provenance link to where the label came from
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*/
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/**
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* Contains list of targets for a particular disease fetched with {@link DiseaseSearch#targetsByDisease}

‎src/Version.js‎

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@@ -17,7 +17,7 @@ Version = function Version() {
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*/
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Version.prototype.information = function() {
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return {
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"version": "6.0.2",
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"version": "6.1.2",
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"author": "Ian Dunlop",
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"ORCID": "http://orcid.org/0000-0001-7066-3350",
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"title": "OPS.js",
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"organization": "School of Computer Science",
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"address": "University of Manchester, UK",
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"year": "2015",
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"month": "July",
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"month": "August",
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"url": "http://github.com/openphacts/ops.js",
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"LDA-version": "1.5"
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};

‎src/combined.js‎

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@@ -1933,10 +1933,11 @@ function createXHR(options, callback) {
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// IE must die
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}
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xhr.ontimeout = errorFunc
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xhr.open(method, uri, !sync)
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xhr.open(method, uri, !sync, options.username, options.password)
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//has to be after open
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xhr.withCredentials = !!options.withCredentials
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if(!sync) {
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xhr.withCredentials = !!options.withCredentials
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}
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// Cannot set timeout with sync request
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// not setting timeout on the xhr object, because of old webkits etc. not handling that correctly
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// both npm's request and jquery 1.x use this kind of timeout, so this is being consistent
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URI = item[constants.ABOUT];
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gene = {};
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gene["URI"] = item.forGene[constants.ABOUT];
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gene["encodes"] = item.forGene.encodes[constants.ABOUT];
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if (item.forGene.encodes.exactMatch != null) {
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gene["encodesProvenance"] = item.forGene.encodes.exactMatch[constants.ABOUT] != null ? item.forGene.encodes.exactMatch[constants.ABOUT] : null;
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gene["encodesLabel"] = item.forGene.encodes.exactMatch.prefLabel != null ? item.forGene.encodes.exactMatch.prefLabel : null;
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gene["encodes"] = [];
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Utils.arrayify(item.forGene.encodes).forEach(function(encode, i) {
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var about = encode[constants.ABOUT];
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if (encode.exactMatch != null) {
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var provenance = encode.exactMatch[constants.ABOUT] != null ? item.forGene.encodes.exactMatch[constants.ABOUT] : null;
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var label = encode.exactMatch.prefLabel != null ? item.forGene.encodes.exactMatch.prefLabel : null;
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gene["encodes"].push({"uri": about, "provenance": provenance, "label": label});
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} else {
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gene["encodesProvenance"] = null;
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gene["encodesLabel"] = null;
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gene["encodes"].push({"uri": about});
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gene["provenance"] = null;
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gene["label"] = null;
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}
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});
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diseases.push({
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"name": name,
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"URI": URI,
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* @typedef {Array.<Object>} DiseasesByTargetResponse
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* @property {string} URI - URI
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* @property {string} name - name
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* @property {Array.<object>} gene - containing URI for the gene, link to the gene it encodes, encodesLabel and encodesProvenance link to where the label came from
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* @property {Array.<object>} gene - containing URI for the gene and an array of encoded genes with link to the gene it encodes, label and provenance link to where the label came from
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*/
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/**
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* Contains list of targets for a particular disease fetched with {@link DiseaseSearch#targetsByDisease}
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*/
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Version.prototype.information = function() {
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return {
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"version": "6.0.0",
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"version": "6.1.2",
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"author": "Ian Dunlop",
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"ORCID": "http://orcid.org/0000-0001-7066-3350",
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"title": "OPS.js",
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"organization": "School of Computer Science",
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"address": "University of Manchester, UK",
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"year": "2015",
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"month": "July",
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"month": "August",
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"url": "http://github.com/openphacts/ops.js",
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"LDA-version": "1.5"
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};

‎test/spec/integration/DiseaseIntegrationSpec.js‎

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runs(function() {
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expect(this_success).toBe(true);
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expect(this_status).toBe(200);
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// API contract states that these will be present
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expect(this_result).toBeDefined();
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expect(this_result.length).toBeGreaterThan(0);
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expect(this_result[0].name).not.toBeNull();
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expect(this_result[0].URI).not.toBeNull();
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expect(this_result[0].gene).not.toBeNull();
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expect(this_result[0].gene.URI).not.toBeNull();
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expect(this_result[0].gene.encodes).not.toBeNull();
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expect(this_result[0].gene.encodes[0]).not.toBeNull();
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expect(this_result[0].gene.encodes[0].uri).not.toBeNull();
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// encodesProvenance & encodesLabel are optional
222-
expect(this_result[0].gene.encodesProvenance).toBeDefined();
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expect(this_result[0].gene.encodesLabel).toBeDefined();
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expect(this_result[0].gene.encodes[0].label).toBeDefined();
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expect(this_result[0].gene.encodes[0].provenance).toBeDefined();
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});
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searcher.diseasesByTarget('http://purl.uniprot.org/uniprot/Q9Y5Y9', null, null, null, null, callback);
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});

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