cgds - npm Package Compare versions

Comparing version 0.1.3 to 0.1.4

Gruntfile.js

@@ -10,3 +10,3 @@ module.exports = function (grunt) {
                 options: {
-                    alias: "lib/<%= pkg.name %>.js:<%= pkg.name %>"
+                    alias: ["lib/<%= pkg.name %>.js:<%= pkg.name %>"]
                 }
@@ -13,0 +13,0 @@ }

lib/cgds.js

 "use strict";
 
-var http, url, get, toJSON, CGDS;
+var http, https, url, get, toJSON, CGDS;
 
 http = require("http");
+https = require("https");
 url = require("url");
 
 get = function (uri, proxy, callback) {
-    var options;
+    var options, responseHandler, req;
     if (typeof proxy === "function") {
@@ -19,6 +20,3 @@ callback = proxy;
     }
- // Browserify does not default to port 80 if the page
- // is served from a port other than 80.
-    options.port = 80;
-    http.get(options, function (res) {
+    responseHandler = function (res) {
         var body;
@@ -34,3 +32,17 @@ // Browserify does not seem to work well with buffers ("no method copy"),
         });
-    });
+    };
+    // Don't use http.get until https://github.com/substack/https-browserify/pull/1
+    // is fixed.
+    options.method = "GET";
+    // Setting withCredentials to false is required until
+    // https://github.com/substack/http-browserify/pull/47 is fixed.
+    options.withCredentials = false;
+    if (options.protocol === "https:") {
+        options.port = 443;
+        req = https.request(options, responseHandler);
+    } else {
+        options.port = 80;
+        req = http.request(options, responseHandler);
+    }
+    req.end();
 };
@@ -37,0 +49,0 @@

package.json

 {
     "name": "cgds",
+    "version": "0.1.4",
     "description": "A module for querying the Cancer Genomics Data Server (CGDS).",
-    "version": "0.1.3",
-    "author": {
-        "name": "Alexander Grüneberg",
-        "email": "[e-mail]"
-    },
+    "keywords": ["cbio", "cancer", "genomics", "tcga", "mskcc"],
+    "bugs": "https://github.com/agrueneberg/CGDS-JS/issues",
+    "license": "MIT",
+    "author": "Alexander Grüneberg <[e-mail]>",
+    "main": "./lib/cgds.js",
     "repository": {
         "type": "git",
-        "url": "https://github.com/agrueneberg/CGDS-JS"
+        "url": "https://github.com/agrueneberg/CGDS-JS.git"
     },
-    "licenses": [{
-        "type": "The MIT License",
-        "url": "http://www.opensource.org/licenses/mit-license.php"
-    }],
-    "main": "./lib/cgds.js",
+    "scripts": {
+        "test": "./node_modules/.bin/mocha"
+    },
     "devDependencies": {
-        "grunt": "~0.4.1",
-        "grunt-browserify": "~1.2.1",
-        "grunt-contrib-uglify": "~0.2.2",
-        "browserify": "~2.25.0",
-        "mocha": "~1.12.0",
-        "expect.js": "~0.2.0"
+        "grunt": "~0.4.4",
+        "grunt-browserify": "~2.0.7",
+        "grunt-contrib-uglify": "~0.4.0",
+        "browserify": "~3.41.0",
+        "mocha": "~1.18.2",
+        "expect.js": "~0.3.1"
     },
     "engines": {
         "node": ">= 0.10.0"
-    },
-    "scripts": {
-        "test": "./node_modules/.bin/mocha"
     }
 }

test/cgds-spec.js

@@ -35,2 +35,4 @@ var expect, CGDS;
 
+        this.timeout(5000);
+
         beforeEach(function () {
@@ -254,3 +256,3 @@ cgds = new CGDS("http://www.cbioportal.org/public-portal/webservice.do");
                     expect(err).to.not.be(null);
-                    expect(err.message).to.be("No genetic profile available for genetic_profile_id:  foo.");
+                    expect(err.message).to.be("Error: Problem when identifying a cancer study for the request.");
                     expect(res).to.be(null);
@@ -300,3 +302,3 @@ done();
                     expect(res.length).to.be.greaterThan(0);
-                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "genetic_profile_id"]);
+                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "reference_read_count_tumor", "variant_read_count_tumor", "reference_read_count_normal", "variant_read_count_normal", "genetic_profile_id"]);
                     done();
@@ -310,3 +312,3 @@ });
                     expect(res.length).to.be.greaterThan(0);
-                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "genetic_profile_id"]);
+                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "reference_read_count_tumor", "variant_read_count_tumor", "reference_read_count_normal", "variant_read_count_normal", "genetic_profile_id"]);
                     done();
@@ -320,3 +322,3 @@ });
                     expect(res.length).to.be.greaterThan(0);
-                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "genetic_profile_id"]);
+                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "reference_read_count_tumor", "variant_read_count_tumor", "reference_read_count_normal", "variant_read_count_normal", "genetic_profile_id"]);
                     done();
@@ -330,3 +332,3 @@ });
                     expect(res.length).to.be.greaterThan(0);
-                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "genetic_profile_id"]);
+                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "reference_read_count_tumor", "variant_read_count_tumor", "reference_read_count_normal", "variant_read_count_normal", "genetic_profile_id"]);
                     done();
@@ -340,3 +342,3 @@ });
                     expect(res.length).to.be.greaterThan(0);
-                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "genetic_profile_id"]);
+                    expect(Object.keys(res[0])).to.eql(["entrez_gene_id", "gene_symbol", "case_id", "sequencing_center", "mutation_status", "mutation_type", "validation_status", "amino_acid_change", "functional_impact_score", "xvar_link", "xvar_link_pdb", "xvar_link_msa", "chr", "start_position", "end_position", "reference_allele", "variant_allele", "reference_read_count_tumor", "variant_read_count_tumor", "reference_read_count_normal", "variant_read_count_normal", "genetic_profile_id"]);
                     done();
@@ -384,3 +386,3 @@ });
                     expect(res.length).to.be.greaterThan(0);
-                    expect(Object.keys(res[0])).to.eql(["case_id", "overall_survival_months", "overall_survival_status", "disease_free_survival_months", "disease_free_survival_status", "age_at_diagnosis"]);
+                    expect(Object.keys(res[0])).to.eql(["CASE_ID", "DFS_MONTHS", "DFS_STATUS", "OS_MONTHS", "OS_STATUS"]);
                     done();
@@ -387,0 +389,0 @@ });

New alerts

Network access

Supply chain risk

This module accesses the network.

Found 1 instance in 1 package

Fixed alerts

No bug tracker

Maintenance

Package does not have a linked bug tracker in package.json.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

35624

increased by3.14%

Number of package files

8

increased by14.29%

Lines of code

614

increased by2.16%

Worsened metrics

Number of medium supply chain risk alerts

2

increased by100%

No dependency changes