Merge pull request #1085 from dondi/maika-1079

Fixing issue #1072.

server/controllers/importers/sif.js

@@ -44,7 +44,7 @@ module.exports = function (sif) {
         sifEntries.forEach(function (entry) {
             if (entry.length > TARGET) {
                 if (!isNumber(entry[RELATIONSHIP])) {
-                    if (entry[RELATIONSHIP] !== "pd") {
+                    if (entry[RELATIONSHIP] !== "pd" && entry[RELATIONSHIP] !== "pp") {
                         unweightedRelationshipTypeErrorDetected = true;
                     }
                 }
@@ -54,6 +54,24 @@ module.exports = function (sif) {
             }
         });
 
+        let hasNumbers = relationships.some(isNumber);
+        let allNumbers = relationships.every(isNumber);
+
+        let networkMode;
+        if (allNumbers) {
+            networkMode = "grn";
+        } else {
+            for (const relationship of relationships) {
+                if (relationship === "pp") {
+                    networkMode = "protein-protein-physical-interaction";
+                    break;
+                } else if (relationship === "pd") {
+                    networkMode = "grn";
+                    break;
+                }
+            }
+        }
+
         if (unweightedRelationshipTypeErrorDetected) {
             errors.push(sifConstants.errors.SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR);
         }
@@ -62,9 +80,8 @@ module.exports = function (sif) {
             errors.push(sifConstants.errors.SIF_MISSING_DATA_ERROR);
         }
 
-        var hasNumbers = relationships.some(isNumber);
-        var allNumbers = relationships.every(isNumber);
         return {
+            networkMode: networkMode,
             sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED,
             warnings: hasNumbers && !allNumbers ? constants.warnings.EDGES_WITHOUT_WEIGHTS : null,
             errors: errors
@@ -134,6 +151,7 @@ module.exports = function (sif) {
         errors: errors,
         warnings: warnings,
         sheetType: workbookType.sheetType,
+        networkMode: workbookType.networkMode,
         positiveWeights: [],
         negativeWeights: [],
         meta: {},

server/controllers/network-sheet-parser.js

@@ -94,7 +94,15 @@ var parseNetworkSheet = function (sheet, network) {
     var rowData = [];
 
     // check for “cols regulators/rows targets” in cell A1
-    const cellA1 = sheet.data[0][0];
+    let cellA1 = "";
+    try {
+        cellA1 = sheet.data[0][0];
+    } catch (err) {
+        const row = 0;
+        const column = 0;
+        addError(network, constants.errors.missingValueError(row, column));
+        return network;
+    }
 
     // TODO There are now 2 valid values for cellA1. One indicates GRN, the other is PPI.
     // If neither, then we continue with the warning.

server/controllers/sif-constants.js

@@ -13,10 +13,10 @@ module.exports = {
         SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR: {
             errorCode: "SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR",
             possibleCause: "The SIF importer detects an unweighted network with an unsupported relationship type.",
-            suggestedFix: "SIF files accepted by GRNsight must use 'pd' as the text string for the relationship" +
-                " type in unweighted networks. Please review the SIF input documentation. Additionally, this" +
-                " error may be have been caused by missing data in your file, which caused the importer to" +
-                " incorrectly interpret a source or target as the relationship."
+            suggestedFix: "SIF files accepted by GRNsight must use 'pd' or 'pp' as the text string for the" +
+                " relationship type in unweighted networks. Please review the SIF input documentation." +
+                " Additionally, this error may be have been caused by missing data in your file, which caused " +
+                "the importer to incorrectly interpret a source or target as the relationship."
         },
 
         SIF_MISSING_DATA_ERROR: {

test/import-sif-tests.js

@@ -7,7 +7,7 @@ var importController = require(__dirname + "/../server/controllers" + "/import-c
 var constants = require(__dirname + "/../server/controllers" + "/constants");
 var initWorkbook = require(__dirname + "/../server/controllers" + "/helpers.js").initWorkbook;
 
-var expectedUnweightedWorkbook = initWorkbook({
+let expectedUnweightedGRNWorkbook = initWorkbook({
     genes: [
         { name: "A" },
         { name: "B" },
@@ -27,9 +27,35 @@ var expectedUnweightedWorkbook = initWorkbook({
     negativeWeights: [],
     sheetType: "unweighted",
     meta: {},
-    expression:{}
+    expression:{},
+    networkMode: "grn"
+});
+
+let expectedUnweightedPPIWorkbook = initWorkbook({
+    genes: [
+        { name: "A" },
+        { name: "B" },
+        { name: "C" },
+        { name: "D" }
+    ],
+
+    links: [
+        { source: 1, target: 0 },
+        { source: 1, target: 2 },
+        { source: 2, target: 1 }
+    ],
+
+    errors: [],
+    warnings: [],
+    positiveWeights: [],
+    negativeWeights: [],
+    sheetType: "unweighted",
+    meta: {},
+    expression:{},
+    networkMode: "protein-protein-physical-interaction"
 });
 
+
 var expectedWeightedWorkbook = initWorkbook({
     genes: [
         { name: "A" },
@@ -50,6 +76,7 @@ var expectedWeightedWorkbook = initWorkbook({
     negativeWeights: [],
     sheetType: "weighted",
     meta: {},
+    networkMode: "grn",
     expression:{}
 });
 
@@ -76,7 +103,8 @@ var expectedUnweightedWorkbookWithCycle = initWorkbook({
     negativeWeights: [],
     sheetType: "unweighted",
     meta: {},
-    expression:{}
+    expression:{},
+    networkMode: "grn"
 });
 
 var expectedWeightedWorkbookWithCycle = initWorkbook({
@@ -102,18 +130,26 @@ var expectedWeightedWorkbookWithCycle = initWorkbook({
     negativeWeights: [],
     sheetType: "weighted",
     meta: {},
-    expression:{}
+    expression:{},
+    networkMode: "grn"
 });
 
 // Unweighted SIF
 
-var unweightedTestSif = [
+var unweightedGRNTestSif = [
     "A",
     [ "B", "pd", "A", "C" ].join("\t"),
     [ "C", "pd", "B" ].join("\t"),
     "D"
 ].join("\r\n"); // Mix up linebreak types to test normalization.
 
+var unweightedPPITestSif = [
+    "A",
+    [ "B", "pp", "A", "C" ].join("\t"),
+    [ "C", "pp", "B" ].join("\t"),
+    "D"
+].join("\r\n"); // Mix up linebreak types to test normalization.
+
 var unweightedTestSifWithCycle = [
     [ "A", "pd", "A" ].join("\t"),
     [ "B", "pd", "A", "C" ].join("\t"),
@@ -283,8 +319,11 @@ var sifWithSemanticErrorOnly = [
 describe("Import from SIF", function () {
     it("should import unweighted workbooks from SIF correctly", function () {
         expect(
-            importController.sifToGrnsight(unweightedTestSif)
-        ).to.deep.equal(expectedUnweightedWorkbook);
+            importController.sifToGrnsight(unweightedGRNTestSif)
+        ).to.deep.equal(expectedUnweightedGRNWorkbook);
+        expect(
+            importController.sifToGrnsight(unweightedPPITestSif)
+        ).to.deep.equal(expectedUnweightedPPIWorkbook);
     });
 
     it("should import weighted workbooks from SIF correctly", function () {
@@ -296,7 +335,7 @@ describe("Import from SIF", function () {
     it("should import inconsistently weighted workbooks from SIF as unweighted", function () {
         expect(
             importController.sifToGrnsight(inconsistentlyWeightedTestSif)
-        ).to.deep.equal(extend(true, {}, expectedUnweightedWorkbook, {
+        ).to.deep.equal(extend(true, {}, expectedUnweightedGRNWorkbook, {
             warnings: [
                 constants.warnings.EDGES_WITHOUT_WEIGHTS
             ]
@@ -350,7 +389,8 @@ describe("Import from SIF", function () {
             negativeWeights: [],
             sheetType: "unweighted",
             meta: {},
-            expression:{}
+            expression:{},
+            networkMode: "grn"
         }));
     });
 
@@ -368,7 +408,8 @@ describe("Import from SIF", function () {
             negativeWeights: [],
             sheetType: "weighted",
             meta: {},
-            expression:{}
+            expression:{},
+            networkMode: "grn"
         }));
     });
 
@@ -399,11 +440,11 @@ describe("Import from SIF syntactic checker", function () {
 
     it("should produce no warnings or errors for correct data", function () {
         expect(
-            importController.sifToGrnsight(unweightedTestSif).errors.length
+            importController.sifToGrnsight(unweightedGRNTestSif).errors.length
         ).to.equal(0);
     });
 
-    it("should throw an error for unweighted graphs with relationship types other than 'pd'", function () {
+    it("should throw an error for unweighted graphs with relationship types other than 'pd' and 'pp", function () {
         expect(
             importController.sifToGrnsight(unweightedTestSifWithIncorrectRelationshipType).errors.length
         ).to.equal(1);
@@ -470,7 +511,7 @@ describe("Import from SIF syntactic checker", function () {
     it("should accept trivially tabbed workbooks", function () {
         expect(
             importController.sifToGrnsight(triviallyTabbedUnweightedWorkbook)
-        ).to.deep.equal(expectedUnweightedWorkbook);
+        ).to.deep.equal(expectedUnweightedGRNWorkbook);
     });
 
 });

web-client/public/js/setup-load-and-import-handlers.js

@@ -143,10 +143,15 @@ export const setupLoadAndImportHandlers = (grnState) => {
                         break;
                     }
                 }
-                // TODO 👆🏼 The back end will add a `networkType` property to this object.
-                //     The web app can then adjust various things based on that.
                 grnState.workbook = workbook;
-                grnState.mode = workbook.meta.data.workbookType;
+
+                if (grnState.name.includes(".sif")) {
+                    grnState.mode = workbook.networkMode;
+                } else if (grnState.name.includes(".graphml")) {
+                    grnState.mode = "grn";
+                } else {
+                    grnState.mode = workbook.meta.data.workbookType;
+                }
                 grnState.workbook.expressionNames = Object.keys(workbook.expression);
                 if (uploadRoute !== "upload") {
                     grnState.annotateLinks();