grnsight 4.0.0 → 6.0.0

package/test/import-graphml-tests.js

@@ -5,8 +5,9 @@ var UTF8 = { encoding: "utf-8" };
 
 var importController = require(__dirname + "/../server/controllers" + "/import-controller")();
 var constants = require(__dirname + "/../server/controllers" + "/constants");
+var initWorkbook = require(__dirname + "/../server/controllers" + "/helpers.js").initWorkbook;
 
-var expectedUnweightedNetwork = {
+var expectedUnweightedWorkbook = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -24,10 +25,12 @@ var expectedUnweightedNetwork = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "unweighted"
-};
+    sheetType: "unweighted",
+    meta: {},
+    expression:{}
+});
 
-var expectedWeightedNetwork = {
+var expectedWeightedWorkbook = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -45,10 +48,12 @@ var expectedWeightedNetwork = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "weighted"
-};
+    sheetType: "weighted",
+    meta: {},
+    expression:{}
+});
 
-var expectedUnweightedNetworkWithCycle = {
+var expectedUnweightedWorkbookWithCycle = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -69,10 +74,12 @@ var expectedUnweightedNetworkWithCycle = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "unweighted"
-};
+    sheetType: "unweighted",
+    meta: {},
+    expression:{}
+});
 
-var expectedWeightedNetworkWithCycle = {
+var expectedWeightedWorkbookWithCycle = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -93,8 +100,10 @@ var expectedWeightedNetworkWithCycle = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "weighted"
-};
+    sheetType: "weighted",
+    meta: {},
+    expression:{}
+});
 
 /* eslint-disable quotes */
 // Temporarily disabling double-quote rule because graphML has a lot of double quotes.
@@ -268,8 +277,8 @@ var misspelledGraphTagTestGraphMl = [
 ].join("\n");
 
 
-// Added networks and GraphML documents
-var newExpectedWeightedNetwork = {
+// Added workbooks and GraphML documents
+var newExpectedWeightedWorkbook = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -288,8 +297,10 @@ var newExpectedWeightedNetwork = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "weighted"
-};
+    sheetType: "weighted",
+    meta: {},
+    expression:{}
+});
 
 var templateGraphmlFileForNewTests = [
     '<?xml version="1.0" encoding="UTF-8"?>',
@@ -566,28 +577,28 @@ var missingOpeningQuote = [
 ].join("\n");
 
 describe("Import from GraphML", function () {
-    it("should import unweighted networks from GraphML correctly", function () {
+    it("should import unweighted workbooks from GraphML correctly", function () {
         expect(
           importController.graphMlToGrnsight(unweightedTestGraphMl)
-        ).to.deep.equal(expectedUnweightedNetwork);
+        ).to.deep.equal(expectedUnweightedWorkbook);
     });
 
-    it("should import weighted networks from GraphML correctly", function () {
+    it("should import weighted workbooks from GraphML correctly", function () {
         expect(
           importController.graphMlToGrnsight(weightedTestGraphMl)
-        ).to.deep.equal(expectedWeightedNetwork);
+        ).to.deep.equal(expectedWeightedWorkbook);
     });
 
-    it("should import unweighted networks with cycles from GraphML correctly", function () {
+    it("should import unweighted workbooks with cycles from GraphML correctly", function () {
         expect(
           importController.graphMlToGrnsight(unweightedTestGraphMlWithCycle)
-        ).to.deep.equal(expectedUnweightedNetworkWithCycle);
+        ).to.deep.equal(expectedUnweightedWorkbookWithCycle);
     });
 
-    it("should import weighted networks with cycles from GraphML correctly", function () {
+    it("should import weighted workbooks with cycles from GraphML correctly", function () {
         expect(
           importController.graphMlToGrnsight(weightedTestGraphMlWithCycle)
-        ).to.deep.equal(expectedWeightedNetworkWithCycle);
+        ).to.deep.equal(expectedWeightedWorkbookWithCycle);
     });
 
     it("should issue an general graphML syntax error because there is a missing end tag", function () {
@@ -649,7 +660,7 @@ describe("Import from GraphML", function () {
         fs.readFile(__dirname + "/../test-files/import-samples/hyper.graphml", UTF8, function (error, data) {
             expect(
                 importController.graphMlToGrnsight(data)
-            ).to.deep.equal({
+            ).to.deep.equal(initWorkbook({
                 genes: [
                     { name: "n0" },
                     { name: "n1" },
@@ -669,13 +680,13 @@ describe("Import from GraphML", function () {
                 positiveWeights: [],
                 negativeWeights: [],
                 sheetType: "unweighted"
-            }); // Look ma, no hyperedges.
+            })); // Look ma, no hyperedges.
         });
 
         fs.readFile(__dirname + "/../test-files/import-samples/nested.graphml", UTF8, function (error, data) {
             expect(
                 importController.graphMlToGrnsight(data)
-            ).to.deep.equal({
+            ).to.deep.equal(initWorkbook({
                 genes: [
                     { name: "n0" },
                     { name: "n1" },
@@ -698,8 +709,10 @@ describe("Import from GraphML", function () {
                 warnings: [],
                 positiveWeights: [],
                 negativeWeights: [],
-                sheetType: "unweighted"
-            }); // Look ma, no nested graphs (nor edges that refer to them).
+                sheetType: "unweighted",
+                meta: {},
+                expression:{}
+            })); // Look ma, no nested graphs (nor edges that refer to them).
         });
     });
 
@@ -707,7 +720,7 @@ describe("Import from GraphML", function () {
         fs.readFile(__dirname + "/../test-files/import-samples/4-gene_4-edge_Manual-Cytoscape_test-naming.graphml", UTF8, function (error, data) {
             expect(
                 importController.graphMlToGrnsight(data)
-            ).to.deep.equal({
+            ).to.deep.equal(initWorkbook({
                 genes: [
                     { name: "Gene4_name" },
                     { name: "Gene3_name" },
@@ -726,8 +739,10 @@ describe("Import from GraphML", function () {
                 warnings: [],
                 positiveWeights: [],
                 negativeWeights: [],
-                sheetType: "unweighted"
-            });
+                sheetType: "unweighted",
+                meta: {},
+                expression:{}
+            }));
         });
     });
 
@@ -735,7 +750,7 @@ describe("Import from GraphML", function () {
         fs.readFile(__dirname + "/../test-files/import-samples/graph-with-yed-tags.graphml", UTF8, function (error, data) {
             expect(
                 importController.graphMlToGrnsight(data)
-            ).to.deep.equal({
+            ).to.deep.equal(initWorkbook({
                 genes: [
                     { name: "January" },
                     { name: "n1" }
@@ -749,8 +764,10 @@ describe("Import from GraphML", function () {
                 warnings: [],
                 positiveWeights: [],
                 negativeWeights: [],
-                sheetType: "unweighted"
-            });
+                sheetType: "unweighted",
+                meta: {},
+                expression:{}
+            }));
         });
     });
 
@@ -758,7 +775,7 @@ describe("Import from GraphML", function () {
         fs.readFile(__dirname + "/../test-files/import-samples/4-node_4-edge_manual-yED.graphml", UTF8, function (error, data) {
             expect(
                 importController.graphMlToGrnsight(data)
-            ).to.deep.equal({
+            ).to.deep.equal(initWorkbook({
                 genes: [
                     { name: "A" },
                     { name: "B" },
@@ -775,16 +792,18 @@ describe("Import from GraphML", function () {
 
                 errors: [],
                 warnings: [],
-                sheetType: "unweighted"
-            });
+                sheetType: "unweighted",
+                meta: {},
+                expression:{}
+            }));
         });
     });
 
     // Added Tests
-    it("should import this weighted network from GraphML correctly", function () {
+    it("should import this weighted workbook from GraphML correctly", function () {
         expect(
             importController.graphMlToGrnsight(templateGraphmlFileForNewTests)
-        ).to.deep.equal(newExpectedWeightedNetwork);
+        ).to.deep.equal(newExpectedWeightedWorkbook);
     });
 
     it("should issue an invalid attribute name graphML syntax error because there is a missing source tag name", function () {

package/test/import-sif-tests.js

@@ -5,8 +5,9 @@ var extend = require("jquery-extend");
 
 var importController = require(__dirname + "/../server/controllers" + "/import-controller")();
 var constants = require(__dirname + "/../server/controllers" + "/constants");
+var initWorkbook = require(__dirname + "/../server/controllers" + "/helpers.js").initWorkbook;
 
-var expectedUnweightedNetwork = {
+var expectedUnweightedWorkbook = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -24,10 +25,12 @@ var expectedUnweightedNetwork = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "unweighted"
-};
+    sheetType: "unweighted",
+    meta: {},
+    expression:{}
+});
 
-var expectedWeightedNetwork = {
+var expectedWeightedWorkbook = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -45,10 +48,12 @@ var expectedWeightedNetwork = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "weighted"
-};
+    sheetType: "weighted",
+    meta: {},
+    expression:{}
+});
 
-var expectedUnweightedNetworkWithCycle = {
+var expectedUnweightedWorkbookWithCycle = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -69,10 +74,12 @@ var expectedUnweightedNetworkWithCycle = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "unweighted"
-};
+    sheetType: "unweighted",
+    meta: {},
+    expression:{}
+});
 
-var expectedWeightedNetworkWithCycle = {
+var expectedWeightedWorkbookWithCycle = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -93,8 +100,10 @@ var expectedWeightedNetworkWithCycle = {
     warnings: [],
     positiveWeights: [],
     negativeWeights: [],
-    sheetType: "weighted"
-};
+    sheetType: "weighted",
+    meta: {},
+    expression:{}
+});
 
 // Unweighted SIF
 
@@ -242,7 +251,7 @@ var strayDataInMultiColumnFormat = [
     "E"
 ].join("\r\n");
 
-var triviallyTabbedUnweightedNetwork = [
+var triviallyTabbedUnweightedWorkbook = [
     "A",
     [ "B", "pd", "A", "C" ].join("\t"),
     [ "C", "pd", "B" ].join("\t"),
@@ -272,44 +281,44 @@ var sifWithSemanticErrorOnly = [
 ].join("\r\n");
 
 describe("Import from SIF", function () {
-    it("should import unweighted networks from SIF correctly", function () {
+    it("should import unweighted workbooks from SIF correctly", function () {
         expect(
             importController.sifToGrnsight(unweightedTestSif)
-        ).to.deep.equal(expectedUnweightedNetwork);
+        ).to.deep.equal(expectedUnweightedWorkbook);
     });
 
-    it("should import weighted networks from SIF correctly", function () {
+    it("should import weighted workbooks from SIF correctly", function () {
         expect(
             importController.sifToGrnsight(weightedTestSif)
-        ).to.deep.equal(expectedWeightedNetwork);
+        ).to.deep.equal(expectedWeightedWorkbook);
     });
 
-    it("should import inconsistently weighted networks from SIF as unweighted", function () {
+    it("should import inconsistently weighted workbooks from SIF as unweighted", function () {
         expect(
             importController.sifToGrnsight(inconsistentlyWeightedTestSif)
-        ).to.deep.equal(extend(true, {}, expectedUnweightedNetwork, {
+        ).to.deep.equal(extend(true, {}, expectedUnweightedWorkbook, {
             warnings: [
                 constants.warnings.EDGES_WITHOUT_WEIGHTS
             ]
         }));
     });
 
-    it("should import unweighted networks with cycles from SIF correctly", function () {
+    it("should import unweighted workbooks with cycles from SIF correctly", function () {
         expect(
             importController.sifToGrnsight(unweightedTestSifWithCycle)
-        ).to.deep.equal(expectedUnweightedNetworkWithCycle);
+        ).to.deep.equal(expectedUnweightedWorkbookWithCycle);
     });
 
-    it("should import weighted networks with cycles from SIF correctly", function () {
+    it("should import weighted workbooks with cycles from SIF correctly", function () {
         expect(
             importController.sifToGrnsight(weightedTestSifWithCycle)
-        ).to.deep.equal(expectedWeightedNetworkWithCycle);
+        ).to.deep.equal(expectedWeightedWorkbookWithCycle);
     });
 
-    it("should import inconsistently weighted networks with cycles from SIF as unweighted", function () {
+    it("should import inconsistently weighted workbooks with cycles from SIF as unweighted", function () {
         expect(
             importController.sifToGrnsight(inconsistentlyWeightedTestSifWithCycle)
-        ).to.deep.equal(extend(true, {}, expectedUnweightedNetworkWithCycle, {
+        ).to.deep.equal(extend(true, {}, expectedUnweightedWorkbookWithCycle, {
             warnings: [
                 constants.warnings.EDGES_WITHOUT_WEIGHTS
             ]
@@ -319,7 +328,7 @@ describe("Import from SIF", function () {
     it("should import nodes mentioned only in edges (i.e., targeted but targetless)", function () {
         expect(
             importController.sifToGrnsight(unweightedTestSifWithUntargeted)
-        ).to.deep.equal({
+        ).to.deep.equal(initWorkbook({
             genes: [
                 { name: "A" },
                 { name: "B" },
@@ -339,14 +348,16 @@ describe("Import from SIF", function () {
             warnings: [],
             positiveWeights: [],
             negativeWeights: [],
-            sheetType: "unweighted"
-        });
+            sheetType: "unweighted",
+            meta: {},
+            expression:{}
+        }));
     });
 
-    it("should import a network with a single node correctly", function () {
+    it("should import a workbook with a single node correctly", function () {
         expect(
             importController.sifToGrnsight(sifWithOneNode)
-        ).to.deep.equal({
+        ).to.deep.equal(initWorkbook({
             genes: [
                 { name: "A" }
             ],
@@ -355,8 +366,10 @@ describe("Import from SIF", function () {
             warnings: [],
             positiveWeights: [],
             negativeWeights: [],
-            sheetType: "weighted"
-        });
+            sheetType: "weighted",
+            meta: {},
+            expression:{}
+        }));
     });
 
 });
@@ -442,22 +455,22 @@ describe("Import from SIF syntactic checker", function () {
         ).to.equal("SIF_STRAY_DATA_ERROR");
     });
 
-    it("should throw an error if there is stray data for unweighted networks", function () {
+    it("should throw an error if there is stray data for unweighted workbooks", function () {
         expect(
             importController.sifToGrnsight(unweightedTestSifWithStrayData).errors[0].errorCode
         ).to.equal("SIF_STRAY_DATA_ERROR");
     });
 
-    it("should throw an error if there is stray data at the bottom of an unweighted network", function () {
+    it("should throw an error if there is stray data at the bottom of an unweighted workbook", function () {
         expect(
             importController.sifToGrnsight(unweightedTestSifWithStrayDataAtBottom).errors[0].errorCode
         ).to.equal("SIF_STRAY_DATA_ERROR");
     });
 
-    it("should accept trivially tabbed networks", function () {
+    it("should accept trivially tabbed workbooks", function () {
         expect(
-            importController.sifToGrnsight(triviallyTabbedUnweightedNetwork)
-        ).to.deep.equal(expectedUnweightedNetwork);
+            importController.sifToGrnsight(triviallyTabbedUnweightedWorkbook)
+        ).to.deep.equal(expectedUnweightedWorkbook);
     });
 
 });