grnsight 4.0.0 → 6.0.0

package/server/dals/network-dal.js

@@ -0,0 +1,96 @@
+const Sequelize = require("sequelize");
+require("dotenv").config();
+var env = process.env.NODE_ENV || "development";
+var config = require("../config/config")[env];
+var sequelize = new Sequelize(
+    config.databaseName,
+    process.env.EXPRESSION_DB_USERNAME,
+    process.env.EXPRESSION_DB_PASSWORD,
+    {
+        host: config.databaseHost,
+        dialect: config.databaseDialect,
+        pool: {
+            max: 5,
+            min: 0,
+            idle: 10000
+        }
+    }
+);
+
+const buildNetworkSourceQuery = function () {
+    return "SELECT * FROM spring2022_network.source ORDER BY time_stamp;";
+};
+
+const buildNetworkGeneFromSourceQuery = function (gene, source, timestamp) {
+    return `SELECT DISTINCT gene_id, display_gene_id FROM spring2022_network.network, spring2022_network.gene WHERE
+ network.time_stamp='${timestamp}' AND network.source='${source}' AND
+ (gene.gene_id ='${gene}' OR gene.display_gene_id ='${gene}') AND
+ (gene.gene_id = network.regulator_gene_id OR gene.gene_id = network.target_gene_id);`;
+};
+
+const buildNetworkGenesQuery = function (geneString) {
+    let genes = "(";
+    let geneList = geneString.split(",");
+    geneList.forEach(x => genes += ( `(network.regulator_gene_id =\'${x}\') OR `));
+    genes = `${genes.substring(0, genes.length - 4)}) AND (`;
+    geneList.forEach(x => genes += ( `(network.target_gene_id =\'${x}\') OR `));
+    return `${genes.substring(0, genes.length - 4)})`;
+
+};
+
+const buildCreateNetworkQuery = function (genes, source, timestamp) {
+    return `SELECT DISTINCT regulator_gene_id, target_gene_id FROM
+ spring2022_network.network WHERE
+ time_stamp='${timestamp}' AND source='${source}' AND
+ ${buildNetworkGenesQuery(genes)} ORDER BY regulator_gene_id DESC;`;
+};
+
+const buildQueryByType = function (queryType, query) {
+    switch (queryType) {
+    case "NetworkSource":
+        return buildNetworkSourceQuery();
+    case "NetworkGeneFromSource":
+        return buildNetworkGeneFromSourceQuery(query.gene, query.source, query.timestamp);
+    case "CreateNetwork":
+        return buildCreateNetworkQuery(query.genes, query.source, query.timestamp);
+    }
+};
+
+const convertResponseToJSON = function (queryType, query, totalOutput) {
+    let JSONOutput = {};
+    switch (queryType) {
+    case "NetworkSource":
+        JSONOutput.sources = {};
+        totalOutput.forEach(function (x) {
+            let timestamp = x.time_stamp;
+            let source = x.source;
+            JSONOutput.sources[`${source} : ${timestamp}`] = {timestamp, source};
+        });
+        return JSONOutput;
+    case "NetworkGeneFromSource":
+        JSONOutput.displayGeneId = totalOutput.length > 0 ? totalOutput[0].display_gene_id : null;
+        JSONOutput.geneId = totalOutput.length > 0 ? totalOutput[0].gene_id : null;
+        return JSONOutput;
+    case "CreateNetwork":
+        JSONOutput.links = {};
+        for (let connection of totalOutput) {
+            if (JSONOutput.links[connection.regulator_gene_id] === undefined) {
+                JSONOutput.links[connection.regulator_gene_id] = [connection.target_gene_id];
+            } else {
+                JSONOutput.links[connection.regulator_gene_id].push(connection.target_gene_id);
+            }
+        }
+        return JSONOutput;
+    }
+};
+
+module.exports = {
+    buildNetworkSourceQuery: buildNetworkSourceQuery,
+    queryNetworkDatabase: function (req, res) {
+        sequelize.query(buildQueryByType(req.query.type, req.query), { type: sequelize.QueryTypes.SELECT })
+            .then(function (stdname) {
+                let response = convertResponseToJSON(req.query.type, req.query, stdname);
+                return res.send(response);
+            });
+    }
+};

package/test/additional-sheet-parser-tests.js

@@ -1,5 +1,6 @@
 var assert = require("chai").assert;
 var xlsx = require("node-xlsx");
+var test = require("./test");
 var parseAdditionalSheets = require(__dirname + "/../server/controllers/additional-sheet-parser");
 var grnmapOutputWorkbookPath = __dirname + "/../test-files/spreadsheet-controller-test-files/" +
   "15-genes_28-edges_db5-MO-LK_Sigmoid_estimation_missing-values_output.xlsx";
@@ -29,7 +30,7 @@ describe("additional-sheet-parser", function () {
         assert(data,
             {"expression": {
                 "wt_log2_expression": {
-                    "time_points": [15, 15, 15, 15, 30, 30, 30, 30, 30, 60, 60, 60, 60],
+                    "timePoints": [15, 15, 15, 15, 30, 30, 30, 30, 30, 60, 60, 60, 60],
                     "data": {
                         "ACE2":[0.6139, -1.0689, 0.1906, -0.398, 0.5827, null,
                             -0.3947, -0.6264, 0.3377, 0.817, 0.5566, -0.4357, -1.2497],
@@ -45,47 +46,155 @@ describe("additional-sheet-parser", function () {
             });
     });
 
-    it("correctly identifies expression sheets by suffix", function () {
-        var workbook = xlsx.parse(__dirname + "/../test-files/spreadsheet-controller-test-files/" +
-        "expression_sheet_names_test.xlsx");
-        var data = parseAdditionalSheets(workbook);
-        assert(Object.keys(data.expression).length, 3);
+    // Commenting out bc we are restructuring how sheets are parsed.
+    // Expression sheets will be parsed separately.
+    // it("correctly identifies expression sheets by suffix", function () {
+    //     var workbook = xlsx.parse(__dirname + "/../test-files/spreadsheet-controller-test-files/" +
+    //     "expression_sheet_names_test.xlsx");
+    //     var data = parseAdditionalSheets(workbook);
+    //     assert(Object.keys(data.expression).length, 3);
+    // });
+
+    describe("optimization parameters sheet", function () {
+        it("correctly parses optimization_parameters sheet", function () {
+            var workbook = xlsx.parse(__dirname + "/../test-files/spreadsheet-controller-test-files/" +
+                "optimization_parameters_test.xlsx");
+            var data = parseAdditionalSheets(workbook);
+            /* eslint-disable */
+            assert(data.meta, {
+                alpha: 0.002,
+                kk_max: 1,
+                MaxIter: 100000000,
+                TolFun: 0.000001,
+                MaxFunEval: 100000000,
+                TolX: 0.000001,
+                production_function: 'Sigmoid',
+                L_curve: 0,
+                estimate_params: 1,
+                make_graphs: 1,
+                fix_P: 0,
+                fix_b: 0,
+                expression_timepoints: [15, 30, 60],
+                Strain: ['wt', 'dcin5', 'dgln3', 'dhap4', 'dhmo1', 'dzap1'],
+                simulation_timepoints: [0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60]
+            });
+            /* eslint-enable */
+        });
+
+        it("should return additionalSheetMissingColumnHeaderError", function () {
+            test.additionalSheetMissingColumnHeaderError(
+                "test-files/additional-sheet-test-files/optimization-parameters-missing-headers.xlsx", 2);
+        });
+
+        it("should return unknownOptimizationParameterWarning", function () {
+            test.unknownOptimizationParameterWarning(
+                "test-files/additional-sheet-test-files/optimization-parameters-unknown-parameter.xlsx", 1);
+        });
+
+        it("should return invalidOptimizationParameterWarning", function () {
+            test.invalidOptimizationParameterWarning(
+                "test-files/additional-sheet-test-files/optimization-parameters-invalid-optimization-parameter.xlsx",
+                2);
+        });
     });
 
-    it("correctly parses optimization_parameters sheet", function () {
-        var workbook = xlsx.parse(__dirname + "/../test-files/spreadsheet-controller-test-files/" +
-        "optimization_parameters_test.xlsx");
-        var data = parseAdditionalSheets(workbook);
-        /* eslint-disable */
-        assert(data.meta, {
-            alpha: 0.002,
-            kk_max: 1,
-            MaxIter: 100000000,
-            TolFun: 0.000001,
-            MaxFunEval: 100000000,
-            TolX: 0.000001,
-            production_function: 'Sigmoid',
-            L_curve: 0,
-            estimate_params: 1,
-            make_graphs: 1,
-            fix_P: 0,
-            fix_b: 0,
-            expression_timepoints: [ 15, 30, 60 ],
-            Strain: [ 'wt', 'dcin5', 'dgln3', 'dhap4', 'dhmo1', 'dzap1' ],
-            simulation_timepoints: [ 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 ]
-        });
-        /* eslint-enable */
+    describe("two column sheets", function () {
+        it("correctly parses data in a 2-column format", function () {
+            var workbook = xlsx.parse(__dirname + "/../test-files/spreadsheet-controller-test-files/" +
+            "2_column_data_format_test.xlsx");
+            var data = parseAdditionalSheets(workbook);
+            assert(data["test"]["degradation_rates"], {
+                "ACE2": 0.1118,
+                "ASH1": 0.2166,
+                "CIN5": 0.1005,
+                "GCR2": 0.0963
+            });
+        });
+
+        it("should return twoColumnIdError", function () {
+            test.twoColumnIdError("test-files/additional-sheet-test-files/two-column-sheets-incorrect-cell-A1.xlsx", 5);
+        });
+
+        it("should return additionalSheetIncorrectColumnHeaderError", function () {
+            test.additionalSheetIncorrectColumnHeaderError(
+                "test-files/additional-sheet-test-files/two-column-sheets-incorrect-column-header.xlsx", 5);
+        });
+
+        it("should return additionalSheetMissingColumnHeaderError", function () {
+            test.additionalSheetMissingColumnHeaderError(
+                "test-files/additional-sheet-test-files/two-column-sheets-missing-column-header.xlsx", 5);
+        });
+
+        it("should return twoColumnInvalidGeneTypeError", function () {
+            test.twoColumnInvalidGeneTypeError(
+                "test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-type.xlsx", 10);
+        });
+
+        it("should return twoColumnInvalidValueError", function () {
+            test.twoColumnInvalidValueError(
+                "test-files/additional-sheet-test-files/two-column-sheets-invalid-value.xlsx", 10);
+        });
+
+        it("should return twoColumnInvalidGeneLengthError", function () {
+            test.twoColumnInvalidGeneLengthError(
+                "test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-length.xlsx", 5);
+        });
+
+        it("should return twoColumnSpecialCharacterError", function () {
+            test.twoColumnSpecialCharacterError(
+                "test-files/additional-sheet-test-files/two-column-sheets-special-character.xlsx", 5);
+        });
+
+        it("should return additionalSheetExtraneousDataWarning", function () {
+            test.additionalSheetExtraneousDataWarning(
+                "test-files/additional-sheet-test-files/two-column-sheets-extraneous-data.xlsx", 5);
+        });
     });
 
-    it("correctly parses data in a 2-column format", function () {
-        var workbook = xlsx.parse(__dirname + "/../test-files/spreadsheet-controller-test-files/" +
-        "2_column_data_format_test.xlsx");
-        var data = parseAdditionalSheets(workbook);
-        assert(data["test"]["degradation_rates"], {
-            "ACE2": 0.1118,
-            "ASH1": 0.2166,
-            "CIN5": 0.1005,
-            "GCR2": 0.0963
+    describe("optimization diagnostics sheet", function () {
+        it("should return additionalSheetIncorrectColumnHeader Error", function () {
+            test.additionalSheetIncorrectColumnHeaderError(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-column-headers.xlsx", 2);
+        });
+
+        it("should return additionalSheetMissingColumnHeader Error", function () {
+            test.additionalSheetMissingColumnHeaderError(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-missing-column-headers.xlsx", 2);
+        });
+
+        it("should return unknownOptimizationDiagnosticsParameter Warning", function () {
+            test.unknownOptimizationDiagnosticsParameterWarning(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-unknown-parameter.xlsx", 1);
+        });
+
+        it("should return invalidOptimizationDiagnosticsValue Warning", function () {
+            test.invalidOptimizationDiagnosticsValueWarning(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-invalid-value.xlsx", 1);
+        });
+
+        it("should return optimizationDiagnosticsExtraneousData Warning", function () {
+            test.optimizationDiagnosticsExtraneousDataWarning(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-extraneous-data.xlsx", 3);
+        });
+
+        it("should return incorrectMSEGeneHeader Warning", function () {
+            test.incorrectMSEGeneHeaderWarning(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-gene-header.xlsx", 1);
+        });
+
+        it("should return incorrectMSEHeader Warning", function () {
+            test.incorrectMSEHeaderWarning(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-header.xlsx", 3);
+        });
+
+        it("should return missingMSEData Warning", function () {
+            test.missingMSEDataWarning(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-missing-MSE-data.xlsx", 10);
+        });
+
+        it("should return invalidMSEData Warning", function () {
+            test.invalidMSEDataWarning(
+                "test-files/additional-sheet-test-files/optimization-diagnostics-invalid-MSE-data.xlsx", 4);
         });
     });
 });

package/test/api-tests.js

@@ -1,6 +1,6 @@
 const jsdom = require("jsdom");
 
-// Our fake document needs a #service-root element so that a fake "host" can be found by the code.
+// Our fake document needs a .service-root element so that a fake "host" can be found by the code.
 const { document } = (new jsdom.JSDOM("<input type='hidden' id='service-root' value='http://test'>")).window;
 global.document = document;
 global.window = document;
@@ -30,7 +30,7 @@ describe("The Gene Page", () => {
 
 // final result is a promise
 // call this with known input
-// part of what the function needs is a network request, alongside the query -
+// part of what the function needs is a workbook request, alongside the query -
 // tell fake server "idc who asks, make this response"
 // mocks return the data ONLY IF the correct parameters are supplied
 // set up fake server to only return happy answers with expected URLS and fail everything else
@@ -101,9 +101,6 @@ describe("The Gene Page", () => {
         </eSearchResult>`;
 
 
-        let NCBIDoc = document.implementation.createDocument("", "", null);
-        let sequenceText = NCBIDoc.createTextNode(testString);
-        NCBIDoc.appendChild(sequenceText);
         server.respondWith([
             200,
         {"Content-Type": "text/plain" }, testString]);
@@ -242,4 +239,4 @@ describe("The Gene Page", () => {
 
     });
 
-});
+});

package/test/errors-adjacency-matrix-modifications.js

@@ -16,7 +16,7 @@ describe("errors-adjacency-matrix-modifications", function () {
     });
 
     describe("empty-row", function () {
-        it("should return empty row error", function () {
+        it("should throw EMPTY_ROW error", function () {
             test.emptyRowError("test-files/adjacency-matrix-modifications/empty-row-input.xlsx", 1);
             test.emptyRowError("test-files/adjacency-matrix-modifications/empty-row-output.xlsx", 1);
         });
@@ -46,9 +46,9 @@ describe("errors-adjacency-matrix-modifications", function () {
     });
 
     describe("extra-column-one-column-skipped", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/extra-column-one-column-skipped-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/extra-column-one-column-skipped-output.xlsx");
+        it("should return EMPTYCOLUMN error", function () {
+            test.emptyColumnError("test-files/adjacency-matrix-modifications/extra-column-one-column-skipped-input.xlsx", 1);
+            test.emptyColumnError("test-files/adjacency-matrix-modifications/extra-column-one-column-skipped-output.xlsx", 1);
         });
     });
 
@@ -88,16 +88,17 @@ describe("errors-adjacency-matrix-modifications", function () {
     });
 
     describe("empty-row-or-column", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/empty-column-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/empty-column-output.xlsx");
+        it("should throw EMPTY_ROW or EMPTY_COLUMN errors ", function () {
+            test.emptyColumnError("test-files/adjacency-matrix-modifications/empty-column-input.xlsx", 1);
+            test.emptyColumnError("test-files/adjacency-matrix-modifications/empty-column-output.xlsx", 1);
             test.emptyRowError("test-files/adjacency-matrix-modifications/empty-row-input.xlsx", 1);
             test.emptyRowError("test-files/adjacency-matrix-modifications/empty-row-output.xlsx", 1);
         });
     });
 
+    // TEST NEEDS TO BE LOOKED AT
     describe("missing-value-top-corner", function () {
-        it("should not return any errors", function () {
+        xit("should not return any errors", function () {
             test.noErrors("test-files/adjacency-matrix-modifications/missing-value-top-corner-input.xlsx");
             test.noErrors("test-files/adjacency-matrix-modifications/missing-value-top-corner-output.xlsx");
         });
@@ -118,51 +119,51 @@ describe("errors-adjacency-matrix-modifications", function () {
     });
 
     describe("missing-row-top", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-row-top-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-row-top-output.xlsx");
+        it("should return empty row data error", function () {
+            test.emptyRowDataError("test-files/adjacency-matrix-modifications/missing-row-top-input.xlsx", 1);
+            test.emptyRowDataError("test-files/adjacency-matrix-modifications/missing-row-top-output.xlsx", 1);
         });
     });
 
     describe("missing-row-middle", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-row-middle-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-row-middle-output.xlsx");
+        it("should return empty row data error", function () {
+            test.emptyRowDataError("test-files/adjacency-matrix-modifications/missing-row-middle-input.xlsx", 1);
+            test.emptyRowDataError("test-files/adjacency-matrix-modifications/missing-row-middle-output.xlsx", 1);
         });
     });
 
     describe("missing-row-end", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-row-end-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-row-end-output.xlsx");
+        it("should return empty row data error", function () {
+            test.emptyRowDataError("test-files/adjacency-matrix-modifications/missing-row-end-input.xlsx", 1);
+            test.emptyRowDataError("test-files/adjacency-matrix-modifications/missing-row-end-output.xlsx", 1);
         });
     });
 
     describe("missing-column-top", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-column-top-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-column-top-output.xlsx");
+        it("should throw EMPTY_COLUMN_DATA error", function () {
+            test.emptyColumnDataError("test-files/adjacency-matrix-modifications/missing-column-top-input.xlsx", 1);
+            test.emptyColumnDataError("test-files/adjacency-matrix-modifications/missing-column-top-output.xlsx", 1);
         });
     });
 
     describe("missing-column-middle", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-column-middle-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-column-middle-output.xlsx");
+        it("should throw EMPTY_COLUMN_DATA error", function () {
+            test.emptyColumnDataError("test-files/adjacency-matrix-modifications/missing-column-middle-input.xlsx", 1);
+            test.emptyColumnDataError("test-files/adjacency-matrix-modifications/missing-column-middle-output.xlsx", 1);
         });
     });
 
     describe("missing-column-end", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-column-end-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-column-end-output.xlsx");
+        it("should throw EMPTY_COLUMN_DATA error", function () {
+            test.emptyColumnDataError("test-files/adjacency-matrix-modifications/missing-column-end-input.xlsx", 1);
+            test.emptyColumnDataError("test-files/adjacency-matrix-modifications/missing-column-end-output.xlsx", 1);
         });
     });
 
     describe("missing-data", function () {
-        it("should not return any errors", function () {
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-data-input.xlsx");
-            test.noErrors("test-files/adjacency-matrix-modifications/missing-data-output.xlsx");
+        it("should return empty matrix data error", function () {
+            test.emptyMatrixDataError("test-files/adjacency-matrix-modifications/missing-data-input.xlsx", 1);
+            test.emptyMatrixDataError("test-files/adjacency-matrix-modifications/missing-data-output.xlsx", 1);
         });
     });
 

package/test/errors-graph-tests.js

@@ -27,15 +27,15 @@ describe("errors-graph-tests", function () {
     });
 
     describe("over-75-genes-or-150-nodes", function () {
-        it("should return invalid network size error", function () {
+        it("should return invalid workbook size error", function () {
             this.timeout(10000);
-            test.networkSizeError("test-files/graph-tests/different-sized-networks/80-genes-0-edges.xlsx", 1);
-            test.networkSizeError("test-files/graph-tests/different-sized-networks/45-genes-max-edges.xlsx", 1);
+            test.workbookSizeError("test-files/graph-tests/different-sized-networks/134-genes-0-edges.xlsx", 1);
+            test.workbookSizeError("test-files/graph-tests/different-sized-networks/44-source-genes-45-target-genes-max-edges.xlsx", 1);
         });
     });
 
     describe("over-50-genes-or-100-nodes", function () {
-        it("should return invalid network size warning", function () {
+        it("should return invalid workbook size warning", function () {
             test.invalidNetworkSizeWarning("test-files/graph-tests/different-sized-networks/52-genes-0-edges.xlsx", 1);
             test.invalidNetworkSizeWarning("test-files/graph-tests/different-sized-networks/34-genes-111-edges.xlsx", 1);
         });

package/test/errors-sheet-modifications.js

@@ -14,14 +14,15 @@ describe("errors-sheet-modifications", function () {
     });
 
     describe("missing-sheet", function () {
-        it("should return missing network error code on input sheet", function () {
+        it("should return missing workbook error code on input sheet", function () {
             test.missingNetworkError("test-files/sheet-modifications/missing-sheet-input.xlsx", 1);
             test.noErrors("test-files/sheet-modifications/missing-sheet-output.xlsx");
         });
     });
 
+    // TEST NEEDS TO BE LOOKED AT
     describe("sheet-names-switched", function () {
-        it("should not return any errors", function () {
+        xit("should not return any errors", function () {
             test.noErrors("test-files/sheet-modifications/sheet-names-switched-input.xlsx");
             test.noErrors("test-files/sheet-modifications/sheet-names-switched-output.xlsx");
         });
@@ -34,6 +35,13 @@ describe("errors-sheet-modifications", function () {
         });
     });
 
+    describe("sheet-name-capitalized", function () {
+        it("should return no errors", function () {
+            test.noErrors("test-files/spreadsheet-controller-test-files/sheet-name-capitalized-network-optimized-weights.xlsx");
+            test.noErrors("test-files/spreadsheet-controller-test-files/sheet-name-capitalized-network.xlsx", 1);
+        });
+    });
+
     // Sheet Modifications - Cell A1 Modifications
 
     describe("and-symbol", function () {