grnsight 3.0.0 → 5.1.0

package/test/export-tests.js

@@ -1,10 +1,12 @@
 var expect = require("chai").expect;
 var extend = require("jquery-extend");
+var xlsx = require("node-xlsx");
+var test = require("./test");
 
 var exportController = require(__dirname + "/../server/controllers/export-controller")();
 var constants = require(__dirname + "/../server/controllers/constants");
 
-var unweightedTestNetwork = {
+var unweightedTestWorkbook = {
     genes: [
         { name: "A" },
         { name: "B" },
@@ -21,7 +23,7 @@ var unweightedTestNetwork = {
     sheetType: "unweighted"
 };
 
-var weightedTestNetwork = {
+var weightedTestWorkbook = {
     genes: [
         { name: "A" },
         { name: "B" },
@@ -38,7 +40,7 @@ var weightedTestNetwork = {
     sheetType: "weighted"
 };
 
-var unweightedTestNetworkWithCycle = {
+var unweightedTestWorkbookWithCycle = {
     genes: [
         { name: "A" },
         { name: "B" },
@@ -58,7 +60,7 @@ var unweightedTestNetworkWithCycle = {
     sheetType: "unweighted"
 };
 
-var weightedTestNetworkWithCycle = {
+var weightedTestWorkbookWithCycle = {
     genes: [
         { name: "A" },
         { name: "B" },
@@ -79,8 +81,8 @@ var weightedTestNetworkWithCycle = {
 };
 
 describe("Export to SIF", function () {
-    it("should export unweighted networks to SIF correctly", function () {
-        var lines = exportController.grnsightToSif(unweightedTestNetwork).split("\n");
+    it("should export unweighted workbooks to SIF correctly", function () {
+        var lines = exportController.grnsightToSif(unweightedTestWorkbook).split("\n");
         expect(lines[0].split("\t")).to.deep.equal([ "A", "", "" ]);
         expect(lines[1].split("\t")).to.deep.equal([ "B", "pd", "A" ]);
         expect(lines[2].split("\t")).to.deep.equal([ "B", "pd", "C" ]);
@@ -88,8 +90,8 @@ describe("Export to SIF", function () {
         expect(lines[4].split("\t")).to.deep.equal([ "D", "", "" ]);
     });
 
-    it("should export weighted networks to SIF correctly", function () {
-        var lines = exportController.grnsightToSif(weightedTestNetwork).split("\n");
+    it("should export weighted workbooks to SIF correctly", function () {
+        var lines = exportController.grnsightToSif(weightedTestWorkbook).split("\n");
         expect(lines[0].split("\t")).to.deep.equal([ "A", "", "" ]);
         expect(lines[1].split("\t")).to.deep.equal([ "B", "-0.75", "A" ]);
         expect(lines[2].split("\t")).to.deep.equal([ "B", "0.25", "C" ]);
@@ -97,8 +99,8 @@ describe("Export to SIF", function () {
         expect(lines[4].split("\t")).to.deep.equal([ "D", "", "" ]);
     });
 
-    it("should export unweighted networks with cycles to SIF correctly", function () {
-        var lines = exportController.grnsightToSif(unweightedTestNetworkWithCycle).split("\n");
+    it("should export unweighted workbooks with cycles to SIF correctly", function () {
+        var lines = exportController.grnsightToSif(unweightedTestWorkbookWithCycle).split("\n");
         expect(lines[0].split("\t")).to.deep.equal([ "A", "pd", "A" ]);
         expect(lines[1].split("\t")).to.deep.equal([ "B", "pd", "A" ]);
         expect(lines[2].split("\t")).to.deep.equal([ "B", "pd", "C" ]);
@@ -107,8 +109,8 @@ describe("Export to SIF", function () {
         expect(lines[5].split("\t")).to.deep.equal([ "E", "", "" ]);
     });
 
-    it("should export weighted networks with cycles to SIF correctly", function () {
-        var lines = exportController.grnsightToSif(weightedTestNetworkWithCycle).split("\n");
+    it("should export weighted workbooks with cycles to SIF correctly", function () {
+        var lines = exportController.grnsightToSif(weightedTestWorkbookWithCycle).split("\n");
         expect(lines[0].split("\t")).to.deep.equal([ "A", "0.875", "A" ]);
         expect(lines[1].split("\t")).to.deep.equal([ "B", "-0.75", "A" ]);
         expect(lines[2].split("\t")).to.deep.equal([ "B", "0.25", "C" ]);
@@ -126,8 +128,8 @@ var EXPORT_COMMENT = "<!-- Exported by GRNsight v" + constants.VERSION + "  " +
 // We'll allow single quotes here because graphMl has a lot of double quotes in it
 // and it's easier to not escape them all.
 describe("Export to GraphML", function () {
-    it("should export unweighted networks to GraphML correctly", function () {
-        var lines = exportController.grnsightToGraphMl(unweightedTestNetwork).split("\n").map(function (line) {
+    it("should export unweighted workbooks to GraphML correctly", function () {
+        var lines = exportController.grnsightToGraphMl(unweightedTestWorkbook).split("\n").map(function (line) {
             return line.trim();
         });
 
@@ -175,8 +177,8 @@ describe("Export to GraphML", function () {
         });
     });
 
-    it("should export weighted networks to GraphML correctly", function () {
-        var lines = exportController.grnsightToGraphMl(weightedTestNetwork).split("\n").map(function (line) {
+    it("should export weighted workbooks to GraphML correctly", function () {
+        var lines = exportController.grnsightToGraphMl(weightedTestWorkbook).split("\n").map(function (line) {
             return line.trim();
         });
 
@@ -228,8 +230,9 @@ describe("Export to GraphML", function () {
         });
     });
 
-    it("should export unweighted networks with cycles to GraphML correctly", function () {
-        var lines = exportController.grnsightToGraphMl(unweightedTestNetworkWithCycle).split("\n").map(function (line) {
+    it("should export unweighted workbooks with cycles to GraphML correctly", function () {
+        var lines = exportController.grnsightToGraphMl(unweightedTestWorkbookWithCycle).split("\n")
+        .map(function (line) {
             return line.trim();
         });
 
@@ -288,8 +291,8 @@ describe("Export to GraphML", function () {
         });
     });
 
-    it("should export weighted networks with cycles to GraphML correctly", function () {
-        var lines = exportController.grnsightToGraphMl(weightedTestNetworkWithCycle).split("\n").map(function (line) {
+    it("should export weighted workbooks with cycles to GraphML correctly", function () {
+        var lines = exportController.grnsightToGraphMl(weightedTestWorkbookWithCycle).split("\n").map(function (line) {
             return line.trim();
         });
 
@@ -354,12 +357,11 @@ describe("Export to GraphML", function () {
         });
     });
 
-    it("should export networks with a filename as the graph element id", function () {
-        var networkWithFilename = extend(true, unweightedTestNetwork, { filename: "hello.graphml" });
-        var lines = exportController.grnsightToGraphMl(networkWithFilename).split("\n").map(function (line) {
+    it("should export workbooks with a filename as the graph element id", function () {
+        var workbookWithFilename = extend(true, unweightedTestWorkbook, { filename: "hello.graphml" });
+        var lines = exportController.grnsightToGraphMl(workbookWithFilename).split("\n").map(function (line) {
             return line.trim();
         });
-
         var expectedGraphMlLines = [
             '<?xml version="1.0" encoding="UTF-8"?>',
             '<graphml xmlns="http://graphml.graphdrawing.org/xmlns" ' +
@@ -404,3 +406,408 @@ describe("Export to GraphML", function () {
         });
     });
 });
+
+const inputWorkbook = {
+    "genes": [
+        { "name": "ACE2" },
+        { "name": "AFT2" },
+        { "name": "CIN5" },
+    ],
+
+    "links": [
+        {
+            "source": 0,
+            "target": 0,
+            "value": 1,
+            type: "arrowhead",
+            stroke: "black"
+        },
+
+        {
+            source: 1,
+            target: 1,
+            value: 1,
+            type: "arrowhead",
+            stroke: "black"
+        },
+
+        {
+            source: 2,
+            target: 1,
+            value: 1,
+            type: "arrowhead",
+            stroke: "black"
+        },
+
+        {
+            source: 2,
+            target: 2,
+            value: 1,
+            type: "arrowhead",
+            stroke: "black"
+        }
+    ],
+
+    network: {
+        "genes": [
+            { "name": "ACE2" },
+            { "name": "AFT2" },
+            { "name": "CIN5" },
+        ],
+
+        "links": [
+            {
+                "source": 0,
+                "target": 0,
+                "value": 1,
+                type: "arrowhead",
+                stroke: "black"
+            },
+
+            {
+                source: 1,
+                target: 1,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black"
+            },
+
+            {
+                source: 2,
+                target: 1,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black"
+            },
+
+            {
+                source: 2,
+                target: 2,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black"
+            }
+        ],
+    },
+
+    networkWeights: {
+        "genes": [
+            { "name": "ACE2" },
+            { "name": "AFT2" },
+            { "name": "CIN5" },
+        ],
+
+        "links": [
+            {
+                "source": 0,
+                "target": 0,
+                "value": 1,
+                type: "arrowhead",
+                stroke: "black"
+            },
+
+            {
+                source: 1,
+                target: 1,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black"
+            },
+
+            {
+                source: 2,
+                target: 1,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black"
+            },
+
+            {
+                source: 2,
+                target: 2,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black"
+            }
+        ],
+    },
+
+    "meta": {
+        data: {
+            "L_curve": 0,
+            "MaxFunEval": 1000000,
+            "MaxIter": 1000000,
+            "Strain": ["wt", "dcin5"],
+            "TolFun": 0.00001,
+            "TolX": 0.00001,
+            "alpha": 0.001,
+            "estimate_params": 1,
+            "expression_timepoints": [0.4, 0.8, 1.2],
+            "fix_P": 1,
+            "fix_b": 0,
+            "kk_max": 1,
+            "make_graphs": 1,
+            "production_function": "testMM",
+            "simulation_timepoints": [0, 0.1, 0.2],
+            "species": "Saccharomyces cerevisiae",
+            "taxon_id": 559292
+        }
+    },
+
+    "test": {
+        "production_rates": {
+            data: {
+                "ACE2": 0.5,
+                "AFT2": 1,
+                "CIN5": 2
+            }
+        },
+
+        "degradation_rates": {
+            data: {
+                "ACE2": 1,
+                "AFT2": 1,
+                "CIN5": 1
+            }
+        },
+
+        "threshold_b": {
+            data: {
+                "ACE2": 0,
+                "AFT2": 0,
+                "CIN5": 0
+            }
+        }
+    },
+
+
+    "exportExpression": {
+        "wt_log2_expression": {
+            "timePoints": [
+                0.4,
+                0.8,
+                1.2
+            ],
+            "data": {
+                "id": [
+                    0.4,
+                    0.8,
+                    1.2
+                ],
+                "ACE2": [
+                    1,
+                    2,
+                    3
+                ],
+
+                "AFT2": [
+                    4,
+                    5,
+                    6
+                ],
+
+                "CIN5": [
+                    7,
+                    8,
+                    9
+                ]
+            }
+        },
+
+        "dcin5_log2_expression": {
+            "timePoints": [
+                0.4,
+                0.8,
+                1.2
+            ],
+            "data": {
+                "id": [
+                    0.4,
+                    0.8,
+                    1.2
+                ],
+                "ACE2": [
+                    10,
+                    11,
+                    12
+                ],
+
+                "AFT2": [
+                    13,
+                    14,
+                    15
+                ],
+
+                "CIN5": [
+                    16,
+                    17,
+                    18
+                ]
+            }
+        }
+    }
+};
+
+describe("Export to spreadsheet", function () {
+    it("should export a workbook to a spreadsheet object properly", function () {
+        const expectedSheet = [
+            {
+                name: "network",
+                data: [
+                    ["cols regulators/rows targets", "ACE2", "AFT2", "CIN5"],
+                    ["ACE2", 1, 0, 0],
+                    ["AFT2", 0, 1, 1],
+                    ["CIN5", 0, 0, 1]
+                ]
+            },
+
+            {
+                name: "network_weights",
+                data: [
+                    ["cols regulators/rows targets", "ACE2", "AFT2", "CIN5"],
+                    ["ACE2", 1, 0, 0],
+                    ["AFT2", 0, 1, 1],
+                    ["CIN5", 0, 0, 1]
+                ]
+            },
+
+            {
+                name: "optimization_parameters",
+                data: [
+                    ["optimization_parameter", "value"],
+                    ["L_curve", 0],
+                    ["MaxFunEval", 1000000],
+                    ["MaxIter", 1000000],
+                    ["Strain", "wt", "dcin5"],
+                    ["TolFun", 0.00001],
+                    ["TolX", 0.00001],
+                    ["alpha", 0.001],
+                    ["estimate_params", 1],
+                    ["expression_timepoints", 0.4, 0.8, 1.2],
+                    ["fix_P", 1],
+                    ["fix_b", 0],
+                    ["kk_max", 1],
+                    ["make_graphs", 1],
+                    ["production_function", "testMM"],
+                    ["simulation_timepoints", 0, 0.1, 0.2],
+                    ["species", "Saccharomyces cerevisiae"],
+                    ["taxon_id", 559292]
+                ]
+            },
+
+            {
+                name: "production_rates",
+                data: [
+                    ["id", "production_rate"],
+                    ["ACE2", 0.5],
+                    ["AFT2", 1],
+                    ["CIN5", 2],
+                ]
+            },
+
+            {
+                name: "degradation_rates",
+                data: [
+                    ["id", "degradation_rate"],
+                    ["ACE2", 1],
+                    ["AFT2", 1],
+                    ["CIN5", 1]
+                ]
+            },
+
+            {
+                name: "threshold_b",
+                data: [
+                    ["id", "threshold_b"],
+                    ["ACE2", 0],
+                    ["AFT2", 0],
+                    ["CIN5", 0]
+                ]
+            },
+
+            {
+                name: "wt_log2_expression",
+                data:
+                [
+                    ["id", 0.4, 0.8, 1.2],
+                    [
+                        "ACE2",
+                        1,
+                        2,
+                        3
+                    ],
+                    [
+                        "AFT2",
+                        4,
+                        5,
+                        6
+                    ],
+                    [
+                        "CIN5",
+                        7,
+                        8,
+                        9
+                    ]
+                ]
+            },
+
+            {
+                name: "dcin5_log2_expression",
+                data: [
+                    ["id", 0.4, 0.8, 1.2],
+                    [
+                        "ACE2",
+                        10,
+                        11,
+                        12
+                    ],
+                    [
+                        "AFT2",
+                        13,
+                        14,
+                        15
+                    ],
+                    [
+                        "CIN5",
+                        16,
+                        17,
+                        18
+                    ]
+                ]
+            }
+        ];
+
+        const actualSheet = exportController.grnsightToXlsx(inputWorkbook);
+        expect(actualSheet).to.deep.equal(xlsx.build(expectedSheet));
+    });
+
+    it("should export a workbook exactly as the import",
+        function () {
+            test.importFileSameAsExportFile(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx");
+            test.importFileSameAsExportFile(
+                "test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx");
+            test.importFileSameAsExportFile(
+                "test-files/additional-sheet-test-files/optimization-parameters-default.xlsx");
+        }
+    );
+
+    it("should import a workbook with minor additional sheet warnings," +
+    " export the workbook, and import the exported workbook properly",
+        function () {
+            test.importExportReImportNoErrorsOrWarnings(
+                "test-files/additional-sheet-test-files/optimization-parameters-incorrect-headers.xlsx");
+            test.importExportReImportNoErrorsOrWarnings(
+                "test-files/additional-sheet-test-files/two-column-sheets-missing-column-header.xlsx");
+            test.importExportReImportNoErrorsOrWarnings(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-gene-header.xlsx");
+        }
+    );
+
+    it("should import a workbook with no warnings, export the workbook, and import the exported workbook properly",
+        function () {
+            test.importExportReImportNoErrorsOrWarnings(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx");
+        }
+    );
+});

package/test/expression-data-import-tests.js

@@ -0,0 +1,113 @@
+/* eslint-disable max-len */
+
+var test = require("./test");
+
+describe("expression-data-import-tests", function () {
+
+    describe("MISSING_EXPRESSION_SHEET", function () {
+        it.skip("_log2_expression or _log2_optimized_expression worksheet was not detected.",
+        "The network graph will display without node coloring. If you wish for the workbook to be colored",
+        "you can upload your own expression data by adding one or more of those worksheets to your Excel",
+        "workbook or select, or select from data in GRNsight's Expression Database, found in the Node menu or panel.", function () {
+            test.missingExpressionWarning("test-files/expression-data-test-sheets/expression_sheet_not_existing.xlsx", 1);
+        });
+    });
+
+    describe("MISLABELED_ID_CELL", function () {
+        it("Top left cell must contain \'id\' exactly.", function () {
+            test.idLabelError("test-files/expression-data-test-sheets/expression_sheet_wrong_id_label.xlsx", 1);
+        });
+    });
+
+    describe("GENE_MISMATCH", function () {
+        it("Gene names in column A do not match the order of those in network sheet.", function () {
+            test.geneMismatchError("test-files/expression-data-test-sheets/expression_sheet_wrong_order_gene_names.xlsx", 1);
+        });
+    });
+
+    describe("wrong_case_gene_names", function () {
+        it.skip("Gene names in column A do not match the case of those in network sheet.", function () {
+            test.labelError("test-files/expression-data-test-sheets/expression_sheet_mismatched_case_gene_names.xlsx", 1);
+        });
+    });
+
+    describe("MISSING_GENE_NAME", function () {
+        it("Gene names in column A are missing a gene name listed in the network sheet.", function () {
+            test.missingGeneNameError("test-files/expression-data-test-sheets/expression_sheet_missing_gene_name.xlsx", 1);
+        });
+    });
+
+    describe("EXTRA_GENE_NAME", function () {
+        it("Gene names in column A have an extra gene name than those listed in the network sheet.", function () {
+            test.extraGeneNameError("test-files/expression-data-test-sheets/expression_sheet_extra_gene_name.xlsx", 1);
+        });
+    });
+
+    describe("MISSING_COLUMN_HEADER", function () {
+        it("All columns in expression sheet must have a header or label.", function () {
+            test.missingColumnHeaderError("test-files/expression-data-test-sheets/expression_sheet_missing_column_header.xlsx", 1);
+        });
+    });
+
+    describe("empty_column", function () {
+        it("Column in expression sheet contains no data.", function () {
+            test.emptyExpressionColumnError("test-files/expression-data-test-sheets/expression_sheet_empty_column.xlsx", 1);
+        });
+    });
+
+    describe("EMPTY_ROW", function () {
+        it("Row in expression sheet contains no data.", function () {
+            test.emptyExpressionRowError("test-files/expression-data-test-sheets/expression_sheet_empty_row.xlsx", 1);
+        });
+    });
+
+    describe("EXTRANEOUS_DATA", function () {
+        it("There is erroneous data in the expression sheet.", function () {
+            test.extraneousDataWarning("test-files/expression-data-test-sheets/expression_sheet_erroneous_data.xlsx", 1);
+        });
+    });
+
+    describe("NEGATIVE_TIME_POINT", function () {
+        it("There are one or more negative time points in the expression sheet.", function () {
+            test.negativeTimePointError("test-files/expression-data-test-sheets/expression_sheet_negative_time_points.xlsx", 2);
+        });
+    });
+
+    describe("NON_MONOTONIC_TIME_POINTS", function () {
+        it("There are duplicate time points in the expression sheet.", function () {
+            test.nonMonotonicTimePointsError(
+                "test-files/expression-data-test-sheets/expression_sheet_incorrectly_ordered_time_points.xlsx", 1);
+        });
+    });
+    describe("NON_NUMERICAL_TIME_POINT", function () {
+        it("There are non-numerical time points in the expression sheet.", function () {
+            test.nonNumericalTimePointError(
+                "test-files/expression-data-test-sheets/expression_sheet_non_numerical_time_points.xlsx", 1);
+        });
+    });
+
+    describe("DUPLICATE_TIME_POINTS", function () {
+        it("should return no error", function () {
+            test.noErrors("test-files/expression-data-test-sheets/expression_sheet_correct_numbering.xlsx", 1);
+        });
+    });
+
+    describe("wrong-exp-sheet-name-due-to-convention", function () {
+        it.skip("Incorrect expression sheet naming convention", function () {
+            test.incorrectlyNamedExpressionSheetWarning("test-files/expression-data-test-sheets/expression_sheet_wrong_sheet_name_convention.xlsx", 1);
+        });
+    });
+
+    describe("resolvable-missing-data", function () {
+        it.skip("should return no error", function () {
+            test.noErrors("test-files/expression-data-test-sheets/expression_sheet_missing_data_ok.xlsx", 1);
+        });
+    });
+
+    describe("different-number-of-columns", function () {
+        it.skip("should not return any errors", function () {
+            test.noErrors("test-files/expression-data-test-sheets/expression_sheet_different_number_of_columns.xlsx", 0);
+        });
+    });
+
+});

package/test/grnstate-tests.js

@@ -0,0 +1,29 @@
+import "chai/register-should";
+import { grnState } from "../web-client/public/js/grnstate";
+
+describe("The grnState model object", () => {
+    it("should update the reset normalization maximum correctly", () => {
+        grnState.workbook = {
+            positiveWeights: [0.7715106466403678, 5.212343052095555, 0.826365326790911, 1.5180198066137216,
+                0.27964603867183396, 2.9870960868914778, 0.7743557796125339, 0.6701684007311992, 0.22069064019031245,
+                0.2841810246722045, 0.08852330457981578, 0.5563132195423768],
+            negativeWeights: [-1.1672013354497313, -2.4438462486461163, -1.485274408559026, -0.7371671668856121,
+                -2.9527940988546217, -3.3875125167057103, -0.0735729607899455, -0.12373154839822605,
+                -0.5487650216350863, -0.442904423529279, -0.8662459811465724, -2.850006860838391, -1.5733259134754158,
+                -0.02279063304065471, -1.9832439149172112, -0.25954746744906587],
+        };
+        grnState.resetNormalizationMax.should.equal(5.212343052095555);
+
+        grnState.workbook = {
+            positiveWeights: [1, 2, 3, 4, 5, 6, 7, 8],
+            negativeWeights: [-1, -2, -3, -4, -5, -6, -7, -8],
+        };
+        grnState.resetNormalizationMax.should.equal(8);
+    });
+
+    it("should update, store, and return the species and taxon ID", () => {
+        grnState.genePageData.species.should.equal("Saccharomyces_cerevisiae");
+        grnState.genePageData.taxonJaspar.should.equal("4932");
+        grnState.genePageData.taxonUniprot.should.equal("559292");
+    });
+});