cgds - npm Package Compare versions

Comparing version 0.1.2 to 0.1.3

lib/cgds.js

@@ -36,9 +36,9 @@ "use strict";
 
-toJSON = function (data) {
-    var lines, columns;
+toJSON = function (data, callback) {
+    var lines, errorTerms, errorOccured, columns;
  // Split lines.
     lines = data.split(/\r?\n/);
- // Drop comments.
+ // Drop comments and empty lines.
     lines = lines.filter(function (line) {
-        if (line.charAt(0) === "#") {
+        if (line.charAt(0) === "#" || line === "") {
             return false;
@@ -49,13 +49,29 @@ } else {
     });
- // Convert to JSON.
-    columns = lines.shift().split(/\t/);
-    lines = lines.map(function (line) {
-        var obj;
-        obj = {};
-        line.split(/\t/).forEach(function (column, idx) {
-            obj[columns[idx]] = column;
+ // If the first line starts with "Error: " or in some buggy cases with the whole
+ // error string after dropping the comments, then it is likely to be an error.
+    errorTerms = ["Error: ", "No genetic profile available for genetic_profile_id: "];
+    errorOccured = errorTerms.some(function (errorTerm) {
+        if (lines[0].lastIndexOf(errorTerm, 0) === 0) {
+            return true;
+        } else {
+            return false;
+        }
+    });
+    if (errorOccured === true) {
+        callback({
+            message: lines[0]
+        }, null);
+    } else {
+     // Convert to JSON.
+        columns = lines.shift().split(/\t/);
+        lines = lines.map(function (line) {
+            var obj;
+            obj = {};
+            line.split(/\t/).forEach(function (column, idx) {
+                obj[columns[idx]] = column;
+            });
+            return obj;
         });
-        return obj;
-    });
-    return lines;
+        callback(null, lines);
+    }
 };
@@ -81,3 +97,3 @@
     get(this.url + "?cmd=getTypesOfCancer", this.proxy, function (err, res) {
-        callback(null, toJSON(res));
+        toJSON(res, callback);
     });
@@ -91,3 +107,3 @@ };
     get(this.url + "?cmd=getCancerStudies", this.proxy, function (err, res) {
-        callback(null, toJSON(res));
+        toJSON(res, callback);
     });
@@ -104,3 +120,3 @@ };
     get(this.url + "?cmd=getGeneticProfiles&cancer_study_id=" + cancerStudyId, this.proxy, function (err, res) {
-        callback(null, toJSON(res));
+        toJSON(res, callback);
     });
@@ -117,3 +133,3 @@ };
     get(this.url + "?cmd=getCaseLists&cancer_study_id=" + cancerStudyId, this.proxy, function (err, res) {
-        callback(null, toJSON(res));
+        toJSON(res, callback);
     });
@@ -147,3 +163,3 @@ };
     get(this.url + "?cmd=getProfileData&case_set_id=" + caseSetId + "&genetic_profile_id=" + geneticProfileId + "&gene_list=" + geneList, this.proxy, function (err, res) {
-        callback(null, toJSON(res));
+        toJSON(res, callback);
     });
@@ -180,3 +196,3 @@ };
     get(url, this.proxy, function (err, res) {
-        callback(null, toJSON(res));
+        toJSON(res, callback);
     });
@@ -193,3 +209,3 @@ };
     get(this.url + "?cmd=getClinicalData&case_set_id=" + caseSetId, this.proxy, function (err, res) {
-        callback(null, toJSON(res));
+        toJSON(res, callback);
     });
@@ -196,0 +212,0 @@ };

package.json

 {
     "name": "cgds",
     "description": "A module for querying the Cancer Genomics Data Server (CGDS).",
-    "version": "0.1.2",
+    "version": "0.1.3",
     "author": {
@@ -6,0 +6,0 @@ "name": "Alexander Grüneberg",

test/cgds-spec.js

@@ -50,3 +50,4 @@ var expect, CGDS;
                 cgds.getTypesOfCancer(function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -70,3 +71,4 @@ expect(Object.keys(res[0])).to.eql(["type_of_cancer_id", "name"]);
                 cgds.getCancerStudies(function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -96,5 +98,6 @@ expect(Object.keys(res[0])).to.eql(["cancer_study_id", "name", "description"]);
             });
-            it("should return a JSON representation of a tab-delimited file with six columns", function (done) {
+            it("should return a JSON representation of a tab-delimited file with six columns for an existing cancer study", function (done) {
                 cgds.getGeneticProfiles("brca_tcga", function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -105,2 +108,10 @@ expect(Object.keys(res[0])).to.eql(["genetic_profile_id", "genetic_profile_name", "genetic_profile_description", "cancer_study_id", "genetic_alteration_type", "show_profile_in_analysis_tab"]);
             });
+            it("should return an error if the cancer study does not exist", function (done) {
+                cgds.getGeneticProfiles("foo", function (err, res) {
+                    expect(err).to.not.be(null);
+                    expect(err.message).to.be("Error: Problem when identifying a cancer study for the request.");
+                    expect(res).to.be(null);
+                    done();
+                });
+            });
         });
@@ -125,5 +136,6 @@
             });
-            it("should return a JSON representation of a tab-delimited file with five columns", function (done) {
+            it("should return a JSON representation of a tab-delimited file with five columns if cancer study exists", function (done) {
                 cgds.getCaseLists("brca_tcga", function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -134,2 +146,10 @@ expect(Object.keys(res[0])).to.eql(["case_list_id", "case_list_name", "case_list_description", "cancer_study_id", "case_ids"]);
             });
+            it("should return an error if the cancer study does not exist", function (done) {
+                cgds.getGeneticProfiles("foo", function (err, res) {
+                    expect(err).to.not.be(null);
+                    expect(err.message).to.be("Error: Problem when identifying a cancer study for the request.");
+                    expect(res).to.be(null);
+                    done();
+                });
+            });
         });
@@ -176,3 +196,4 @@
                     cgds.getProfileData("brca_tcga_3way_complete", "brca_tcga_mutations", "TP53", function (err, res) {
-                        expect(res).to.be.a(Array);
+                        expect(err).to.be(null);
+                        expect(res).to.be.an(Array);
                         expect(res.length).to.be.greaterThan(0);
@@ -192,3 +213,4 @@ expect(Object.keys(res[0])).to.contain("GENE_ID");
                     cgds.getProfileData("brca_tcga_3way_complete", "brca_tcga_mutations", ["TP53", "GATA3"], function (err, res) {
-                        expect(res).to.be.a(Array);
+                        expect(err).to.be(null);
+                        expect(res).to.be.an(Array);
                         expect(res.length).to.be.greaterThan(0);
@@ -208,3 +230,4 @@ expect(Object.keys(res[0])).to.contain("GENE_ID");
                     cgds.getProfileData("brca_tcga_3way_complete", ["brca_tcga_mutations", "brca_tcga_log2CNA"], "TP53", function (err, res) {
-                        expect(res).to.be.a(Array);
+                        expect(err).to.be(null);
+                        expect(res).to.be.an(Array);
                         expect(res.length).to.be.greaterThan(0);
@@ -228,3 +251,26 @@ expect(Object.keys(res[0])).to.contain("GENETIC_PROFILE_ID");
             });
-
+            it("should return an error if the case set does not exist", function (done) {
+                cgds.getProfileData("foo", "brca_tcga_mutations", "TP53", function (err, res) {
+                    expect(err).to.not.be(null);
+                    expect(err.message).to.be("Error: Invalid case_set_id:  foo.");
+                    expect(res).to.be(null);
+                    done();
+                });
+            });
+            it("should return an error if the genetic profile does not exist", function (done) {
+                cgds.getProfileData("brca_tcga_3way_complete", "foo", "TP53", function (err, res) {
+                    expect(err).to.not.be(null);
+                    expect(err.message).to.be("No genetic profile available for genetic_profile_id:  foo.");
+                    expect(res).to.be(null);
+                    done();
+                });
+            });
+            it("should return an empty result if the gene does not exist", function (done) {
+                cgds.getProfileData("brca_tcga_3way_complete", "brca_tcga_mutations", "foo", function (err, res) {
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
+                    expect(res.length).to.be(0);
+                    done();
+                });
+            });
         });
@@ -259,3 +305,4 @@
                 cgds.getMutationData("brca_tcga_mutations", "TP53", function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -268,3 +315,4 @@ 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"]);
                 cgds.getMutationData("brca_tcga_mutations", ["TP53", "GATA3"], function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -277,3 +325,4 @@ 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"]);
                 cgds.getMutationData(["brca_tcga_mutations", "brca_tcga_log2CNA"], "TP53", function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -286,3 +335,4 @@ 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"]);
                 cgds.getMutationData(["brca_tcga_mutations", "brca_tcga_log2CNA"], ["TP53", "GATA3"], function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -295,3 +345,4 @@ 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"]);
                 cgds.getMutationData("brca_tcga_mutations", "TP53", "brca_tcga_3way_complete", function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -302,2 +353,18 @@ 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"]);
             });
+            it("should return an error if the genetic profile id does not exist", function (done) {
+                cgds.getMutationData("foo", "TP53", function (err, res) {
+                    expect(err).to.not.be(null);
+                    expect(err.message).to.be("Error: Problem when identifying a cancer study for the request.");
+                    expect(res).to.be(null);
+                    done();
+                });
+            });
+            it("should return an empty result if the gene does not exist", function (done) {
+                cgds.getMutationData("brca_tcga_mutations", "foo", function (err, res) {
+                    expect(err).to.be(null);
+                    expect(res).to.be.an(Array);
+                    expect(res.length).to.be(0);
+                    done();
+                });
+            });
         });
@@ -324,3 +391,3 @@
                 cgds.getClinicalData("brca_tcga_3way_complete", function (err, res) {
-                    expect(res).to.be.a(Array);
+                    expect(res).to.be.an(Array);
                     expect(res.length).to.be.greaterThan(0);
@@ -331,2 +398,10 @@ 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"]);
             });
+            it("should return an error if the case set does not exist", function (done) {
+                cgds.getClinicalData("foo", function (err, res) {
+                    expect(err).to.not.be(null);
+                    expect(err.message).to.be("Error: Problem when identifying a cancer study for the request.");
+                    expect(res).to.be(null);
+                    done();
+                });
+            });
         });
@@ -333,0 +408,0 @@

No alert changes

Improved metrics

Total package byte prevSize

34538

increased by15.76%

Lines of code

601

increased by18.07%

No dependency changes