grnsight 4.0.0 → 6.0.0

package/server/controllers/workbook-constants.js

@@ -0,0 +1,521 @@
+// Currently only going to number 76 because currently the workbook errors out at 75+ genes.
+var numbersToLetters = {
+    0: "A", 1: "B", 2: "C", 3: "D", 4: "E", 5: "F", 6: "G", 7: "H", 8: "I", 9: "J", 10: "K", 11: "L", 12: "M",
+    13: "N", 14: "O", 15: "P", 16: "Q", 17: "R", 18: "S", 19: "T", 20: "U", 21: "V", 22: "W", 23: "X", 24: "Y",
+    25: "Z", 26: "AA", 27: "AB", 28: "AC", 29: "AD", 30: "AE", 31: "AF", 32: "AG", 33: "AH", 34: "AI", 35: "AJ",
+    36: "AK", 37: "AL", 38: "AM", 39: "AN", 40: "AO", 41: "AP", 42: "AQ", 43: "AR", 44: "AS", 45: "AT", 46: "AU",
+    47: "AV", 48: "AW", 49: "AX", 50: "AY", 51: "AZ", 52: "BA", 53: "BB", 54: "BC", 55: "BD", 56: "BE", 57: "BF",
+    58: "BG", 59: "BH", 60: "BI", 61: "BJ", 62: "BK", 63: "BL", 64: "BM", 65: "BN", 66: "BO", 67: "BP", 68: "BQ",
+    69: "BR", 70: "BS", 71: "BT", 72: "BU", 73: "BV", 74: "BW", 75: "BX", 76: "BY"
+};
+
+module.exports = {
+    numbersToLetters,
+
+    warnings: {
+
+        extraneousDataWarning: function (sheetName, row) {
+            return {
+                warningCode: "EXTRANEOUS_DATA",
+                errorDescription: `There is extraneous data outside of the set rows and columns of the 
+                ${sheetName} sheet in row ${row}.`
+            };
+        },
+
+        invalidOptimizationParameter: function (sheetName, param, paramType) {
+            return {
+                warningCode: "INVALID_OPTIMIZATION_PARAMETER",
+                errorDescription: `The optimization parameter '${param}' in the ${sheetName} sheet, is invalid. ` +
+                    `Please ensure that the optimization parameter's value is a ${paramType}.`
+            };
+        },
+
+        unknownOptimizationParameter: function (sheetName, param) {
+            return {
+                warningCode: "UNKNOWN_OPTIMIZATION_PARAMETER",
+                errorDescription: `The optimization parameter '${param}' in the ${sheetName} sheet, is unknown. ` +
+                    "Please ensure that the spelling of all optimization_parameters is correct, and " +
+                    "make sure that you are using only supported optimization parameters."
+            };
+        },
+
+        unknownOptimizationDiagnosticsParameter: function (sheetName, param) {
+            return {
+                warningCode: "UNKNOWN_OPTIMIZATION_DIAGNOSTICS_PARAMETER",
+                errorDescription: `The optimization parameter '${param}' in the ${sheetName} sheet, is unknown. ` +
+                    "Please ensure that the spelling of all optimization_parameters is correct, and " +
+                    "make sure that you are using only supported optimization parameters."
+            };
+        },
+
+        invalidOptimizationDiagnosticsValue: function (sheetName, param) {
+            return {
+                warningCode: "INVALID_OPTIMIZATION_DIAGNOSTICS_VALUE",
+                errorDescription: `The optimization parameter '${param}' in the ${sheetName} sheet, is invalid. ` +
+                    "Please ensure that the optimization parameter's value is a number."
+            };
+        },
+
+        incorrectMSEGeneHeaderWarning: function (sheetName, row) {
+            return {
+                warningCode: "INCORRECT_MSE_GENE_HEADER",
+                errorDescription: `The Gene Header in row ${row} of the ${sheetName} sheet, is incorrect. ` +
+                    `Please ensure that you have an empty row only before Row ${row}, ` +
+                    `and that Row ${row} Column A is spelled 'Gene' exactly.`
+            };
+        },
+
+        incorrectMSEHeaderWarning: function (sheetName, header, row, columnLetter) {
+            return {
+                warningCode: "INCORRECT_MSE_HEADER",
+                errorDescription: `The header ${header} in row ${row} column ${columnLetter} of the ` +
+                    `${sheetName} sheet, does not contain 'MSE' Please ensure that you have the correct column header.`
+            };
+        },
+
+        missingMSEDataWarning: function (sheetName, row, columnLetter) {
+            return {
+                warningCode: "MISSING_MSE_DATA",
+                errorDescription: `The MSE data in row ${row} column ${columnLetter} of the ${sheetName} sheet, ` +
+                    "is missing. Please ensure that your data is correct and complete."
+            };
+        },
+
+        invalidMSEDataWarning: function (sheetName, row, columnLetter) {
+            return {
+                warningCode: "INVALID_MSE_DATA",
+                errorDescription: `The data in row ${row} column ${columnLetter} of the ${sheetName} sheet, ` +
+                    "is not a number. Please ensure that your MSE data is correct and only contains numbers."
+            };
+        },
+
+        missingSourceGeneWarning: function (row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                warningCode: "MISSING_SOURCE",
+                errorDescription: "A source gene name is missing in cell " + colLetter + rowNum + "."
+            };
+        },
+
+        incorrectCellA1WorkbookWarning: function (sheetName) {
+            return {
+                warningCode: "MISLABELED_NETWORK_CELL_A1",
+                errorDescription: `The top left cell of the ${sheetName} sheet is mislabeled.
+                Replace the incorrect label with \'cols regulators/rows targets\' exactly.`
+            };
+        },
+
+        missingTargetGeneWarning: function (row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                warningCode: "MISSING_TARGET",
+                errorDescription: "A target gene name is missing in cell " + colLetter + rowNum + "."
+            };
+        },
+
+        invalidMatrixDataWarning: function (row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                warningCode: "INVALID_DATA",
+                errorDescription: "The value in cell " + colLetter + rowNum + ", is undefined."
+            };
+        },
+
+        randomDataWarning: function (type, row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                warningCode: "RANDOM_DATA",
+                errorDescription: "The value in cell " + colLetter + rowNum + ", has a corresponding source" +
+                " and/or target gene that is detected as " + type + "."
+            };
+        },
+
+        emptyRowWarning: function (row) {
+            var rowNum = row + 1;
+            return {
+                warningCode: "EMPTY_ROW",
+                errorDescription: "Row " + rowNum + " was found to contain no data."
+            };
+        },
+
+        workbookSizeWarning: function (genesLength, edgesLength) {
+            return {
+                warningCode: "INVALID_NETWORK_SIZE",
+                errorDescription: "Your workbook has " + genesLength + " genes, and " + edgesLength +
+                " edges. Please note that workbooks are recommended to have less than 50 genes and 100 edges."
+            };
+        },
+
+        networkSizeWarning: function (genesLength, edgesLength) {
+            return {
+                warningCode: "INVALID_NETWORK_SIZE",
+                errorDescription: `Your network has ${genesLength} genes, and ${edgesLength} 
+                    edges. Please note that networks are recommended to have less than 50 genes and 100 edges.`
+            };
+        },
+
+        incorrectlyNamedSheetWarning: {
+            warningCode: "INCORRECTLY_NAMED_SHEET",
+            errorDescription: "The uploaded file appears to contain a weighted network, but contains no \
+                 'network_optimized_weights' sheet. A weighted network must be contained in a sheet called \
+                 'network_optimized_weights' in order to be drawn as a weighted graph. \
+                 Please check if the sheet(s) in the uploaded spreadsheet have been named properly."
+        },
+
+        missingExpressionSheetWarning: {
+            warningCode: "MISSING_EXPRESSION_SHEET",
+            errorDescription: "_log2_expression or _log2_optimized_expression worksheet was \
+            not detected. The network graph will display without node coloring. If you want \
+            the nodes to be colored with expression data, you can upload your own expression \
+            data by adding one or more of those worksheets to your Excel workbook or select \
+            from data in GRNsight's Expression Database, found in the Node menu or panel."
+        },
+
+        noSpeciesInformationDetected: {
+            warningCode: "MISSING_SPECIES_INFORMATION",
+            errorDescription: "No species information was detected in your input file." +
+                " GRNsight defaults to Saccharomyces cerevisiae. You can change the species" +
+                " selection in the Species menu or panel."
+        },
+
+        unknownSpeciesDetected: function (workbookSpecies, workbookTaxon) {
+            return {
+                warningCode: "UNKNOWN_SPECIES_DETECTED",
+                errorDescription: "GRNsight detected the species " + workbookSpecies +
+                    " and the taxon " + workbookTaxon + " in your input file." +
+                    " This is not one of the supported species, or was formatted incorrectly" +
+                    " You can change the species selection in the Species menu or panel."
+            };
+        },
+
+        missingExpressionWarning: function () {
+            return {
+                warningCode: "MISSING_EXPRESSION_SHEET",
+                errorDescription: "_log2_expression or _log2_optimized_expression worksheet was \
+                not detected. The network graph will display without node coloring. If you want \
+                the nodes to be colored with expression data, you can upload your own expression \
+                data by adding one or more of those worksheets to your Excel network or select \
+                from data in GRNsight's Expression Database, found in the Node menu or panel."
+            };
+        },
+    },
+
+    errors: {
+        errorsCountError: {
+            errorCode: "ERRORS_OVERLOAD",
+            possibleCause: "This workbook has over 20 errors.",
+            suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
+            "Documentation page and try again. If you fix these errors and try to upload again, there may be " +
+            "further errors detected. As a general approach for fixing the errors, consider copying and " +
+            "pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
+        },
+
+        warningsCountError: {
+            errorCode: "WARNINGS_OVERLOAD",
+            possibleCause: "This workbook has over 75 warnings.",
+            suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
+            "Documentation page and try again. If you fix these errors and try to upload again, there may be " +
+            "further errors detected. As a general approach for fixing the errors, consider copying and " +
+            "pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
+        },
+
+        unknownError: {
+            errorCode: "UNKNOWN_ERROR",
+            possibleCause: "An unexpected error occurred.",
+            suggestedFix: "Please contact the GRNsight team at kdahlquist@lmu.edu, and attach the spreadsheet you" +
+            " attempted to upload."
+        },
+
+        idLabelError: function (sheetName) {
+            return {
+                errorCode: "MISLABELED_ID_CELL",
+                possibleCause: `The top left cell of the ${sheetName} sheet is mislabeled.`,
+                suggestedFix: "Replace the incorrect label with \'id\' exactly."
+            };
+        },
+
+        invalidGeneLengthError: function (sheetName, gene, row) {
+            return {
+                errorCode: "INVALID_GENE_LENGTH",
+                possibleCause: `Gene '${gene}' in row ${row}, column A in the ${sheetName} sheet is too long.`,
+                suggestedFix: "Please make your gene names be less than 13 characters."
+            };
+        },
+
+        specialCharacterError: function (sheetName, gene, row) {
+            return {
+                errorCode: "INVALID_CHARACTER",
+                possibleCause: `The value under gene name ${gene} at row ${row} in the ${sheetName} sheet, 
+                contains an invalid character.`,
+                suggestedFix: "Please ensure all genes in the data are formatted properly with no" +
+                    " special characters except for '-' and '_'."
+            };
+        },
+
+        incorrectColumnHeaderError: function (sheetName, columnLetter, header) {
+            return {
+                errorCode: "INCORRECT_COLUMN_HEADER",
+                possibleCause: `Column ${columnLetter} in the ${sheetName} sheet has an incorrect header.`,
+                suggestedFix: `Replace the incorrect label with '${header}' exactly.`
+            };
+        },
+
+        missingColumnHeaderError: function (sheetName, columnLetter, header) {
+            if (sheetName && columnLetter && header) {
+                return {
+                    errorCode: "MISSING_COLUMN_HEADER",
+                    possibleCause: `Column ${columnLetter} in the ${sheetName}` +
+                        ` sheet is missing the header '${header}'.`,
+                    suggestedFix: `Set the missing label to '${header}' exactly.`
+                };
+            } else {
+                return {
+                    errorCode: "MISSING_COLUMN_HEADER",
+                    possibleCause: `A column in the ${sheetName} sheet is missing a header.`,
+                    suggestedFix: "Add headers to all columns."
+                };
+            }
+        },
+
+        invalidGeneTypeError: function (sheetName, gene, row) {
+            return {
+                errorCode: "INVALID_GENE_TYPE",
+                possibleCause: `Gene '${gene}' in row ${row}, column A in the ${sheetName} sheet is not a string.`,
+                suggestedFix: "Please make your gene name a string starting with a letter."
+            };
+        },
+
+        invalidValueError: function (sheetName, value, row, valueType) {
+            return {
+                errorCode: "INVALID_VALUE",
+                possibleCause: `${valueType} '${value}' in row ${row},` +
+                    ` column B in the ${sheetName} sheet is not a number.`,
+                suggestedFix: `Please ensure that all ${valueType} values are numbers.`
+            };
+        },
+
+        emptyWorkbookError: function () {
+            return {
+                errorCode: "EMPTY_NETWORK_ERROR",
+                possibleCause: "GRNsight detects that the file you uploaded is empty and \
+                does not contain any network information.",
+                suggestedFix: "Please review the file and ensure that it specifies a workbook."
+            };
+        },
+
+        semanticDuplicateGeneError: function (geneName) {
+            return {
+                errorCode: "SEMANTIC_DUPLICATE_GENE",
+                possibleCause: "There exists a duplicate for " + geneName + ".",
+                suggestedFix: "Please remove the duplicate gene and submit again."
+            };
+        },
+
+        geneLengthError: function (geneName) {
+            return {
+                errorCode: "INVALID_GENE_LENGTH",
+                possibleCause: "Gene " + geneName + " is more than 12 characters in length.",
+                suggestedFix: "Genes may only be between 1 and 12 characters in length. Please" +
+                    " shorten the name and submit again."
+            };
+        },
+
+        workbookSizeError: function (genesLength, edgesLength) {
+            return {
+                errorCode: "INVALID_NETWORK_SIZE",
+                possibleCause: "This network has " + genesLength + " genes, and " + edgesLength + " edges.",
+                suggestedFix: "networks may not have more than 75 genes or 150 edges. Please reduce the size" +
+                " of your network and try again."
+            };
+        },
+
+        missingNetworkError: {
+            errorCode: "MISSING_NETWORK",
+            possibleCause: "This file does not have a 'network' sheet or a 'network_optimized_weights' sheet.",
+            suggestedFix: "Please select another file, or rename the sheet containing the adjacency matrix \
+            accordingly. Please refer to the " +
+            "<a href='http://dondi.github.io/GRNsight/documentation.html#section1' \
+            target='_blank'>Documentation page</a> for more information."
+        },
+
+        corruptGeneError: function (row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                errorCode: "CORRUPT_GENE",
+                possibleCause: `The gene name in cell ${colLetter} ${rowNum} appears to be invalid.`,
+                suggestedFix: "Please fix the error and try uploading again."
+            };
+        },
+
+        missingValueError: function (row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                errorCode: "MISSING_VALUE",
+                possibleCause: `The value in the cell ${colLetter} ${rowNum} 
+                in the adjacency matrix appears to have a missing value.`,
+                suggestedFix: "Please ensure that all cells have a value, then upload the file again."
+            };
+        },
+
+        duplicateGeneError: function (geneType, geneName) {
+            return {
+                errorCode: "DUPLICATE_GENE",
+                possibleCause: `There exists a duplicate for ${geneType} gene ${geneName}.`,
+                suggestedFix: "Please remove the duplicate gene and submit again."
+            };
+        },
+
+        dataTypeError: function (row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                errorCode: "INVALID_CELL_DATA_TYPE",
+                possibleCause: `The value in cell ${colLetter} ${rowNum} is not a number.`,
+                suggestedFix: "Please ensure all values in the data matrix are numbers and try again."
+            };
+        },
+
+        emptyRowError: function (row) {
+            var rowNum = row + 1;
+            return {
+                errorCode: "EMPTY_ROW",
+                possibleCause: `Row ${rowNum} does not contain any data.`,
+                suggestedFix: `Please ensure all rows contain data and all empty rows are removed. 
+                Also, please ensure that no extraneous data is outside of the matrix, 
+                as this may cause this error.`
+            };
+        },
+
+        emptyRowDataError: function (row, sheetName) {
+            var rowNum = row + 1;
+            return {
+                errorCode: "EMPTY_ROW_DATA",
+                possibleCause: `Row ${rowNum}, in the ${sheetName} sheet, was found to contain no data.`,
+                suggestedFix: "Populate empty row with data."
+            };
+        },
+
+        emptyMatrixDataError: function (sheetName) {
+            return {
+                errorCode: "EMPTY_MATRIX_DATA",
+                possibleCause: `The ${sheetName} sheet was found to contain no data in the adjacency matrix.`,
+                suggestedFix: "Populate empty matrix with data."
+            };
+        },
+
+        emptyColumnError: function (column, sheetName) {
+            var columnLetter = numbersToLetters[column];
+            return {
+                errorCode: "EMPTY_COLUMN",
+                possibleCause: `Column ${columnLetter}, in the ${sheetName} sheet, is empty.`,
+                suggestedFix: "Delete empty column, or populate with data."
+            };
+        },
+        emptyColumnDataError: function (column, sheetName) {
+            var columnLetter = numbersToLetters[column];
+            return {
+                errorCode: "EMPTY_COLUMN_DATA",
+                possibleCause: `Column ${columnLetter}, in the ${sheetName} sheet, was found to contain no data.`,
+                suggestedFix: "Populate empty column with data."
+            };
+        },
+
+        outsideCellError: function (row, column) {
+            var colLetter = numbersToLetters[column];
+            var rowNum = row + 1;
+            return {
+                errorCode: "EMPTY_CELL",
+                possibleCause: `The cell at ${colLetter} ${rowNum} contains data that is outside the matrix.`,
+                suggestedFix: "Please remove all extraneous data from outside the matrix and ensure matrix is correct"
+            };
+        },
+
+        geneMismatchError: function (sheetName) {
+            return {
+                errorCode: "GENE_MISMATCH",
+                possibleCause: `Gene names in column A of the "${sheetName}" sheet do not 
+                match the order of those in the network sheet.`,
+                suggestedFix: `Please ensure that the gene names are in the same order 
+                as those in both the "network" sheet and the 
+                "network_optimized_weights" sheet.`
+            };
+        },
+
+        extraGeneNamesError: function (sheetName) {
+            return {
+                errorCode: "EXTRA_GENE_NAME",
+                possibleCause: `Gene names in column A of the "${sheetName}" sheet have 
+                one or more extra genes than those listed in the network sheet.`,
+                suggestedFix: `Please ensure that the genes in the "${sheetName}" sheet are
+                the same as the genes in the "network" sheet and the "network_optimized_weights" sheet.`
+            };
+        },
+
+        missingGeneNamesError: function (sheetName) {
+            return {
+                errorCode: "MISSING_GENE_NAME",
+                possibleCause: `Gene names in column A of the "${sheetName}"
+                    sheet are missing one or more genes from the network sheet.`,
+                suggestedFix: `Please ensure that the genes in the "${sheetName}"
+                     are the same as the genes in the "network" sheet and the 
+                    "network_optimized_weights" sheet.`
+            };
+        },
+
+        emptyExpressionRowError: function (row, sheetName) {
+            return {
+                errorCode: "EMPTY_ROW",
+                possibleCause: `There is an empty row in the ${sheetName} sheet. It is located at row ${row}.`,
+                suggestedFix: "Delete empty row, or populate with data."
+            };
+        },
+
+        emptyExpressionColumnError: function (column, sheetName ) {
+            var columnLetter = numbersToLetters[column];
+            return {
+                errorCode: "EMPTY_COLUMN",
+                possibleCause: `There is an empty column in the ${sheetName} sheet. It is located at column
+                ${columnLetter}.`,
+                suggestedFix: "Delete empty column, or populate with data."
+            };
+        },
+
+        negativeTimePointError: function (column, sheetName) {
+            var columnLetter = numbersToLetters[column];
+            return {
+                errorCode: "NEGATIVE_TIME_POINT",
+                possibleCause: `There is a negative time point in the ${sheetName} sheet. It is located at
+                column ${columnLetter}.`,
+                suggestedFix: "Change the negative time point to a positive and ensure expression data is correct."
+            };
+        },
+
+        nonMonotonicTimePointsError: function (column, sheetName) {
+            var columnLetter = numbersToLetters[column];
+            return {
+                errorCode: "NON_MONOTONIC_TIME_POINTS",
+                possibleCause: `The time points located in the ${sheetName} sheet are not sequenced in an increasing 
+                fashion. The first instance of this is at column ${columnLetter}.`,
+                suggestedFix: `Please ensure that the time points are ordered in an increasing fashion, and ensure 
+                expression data is correct.`
+            };
+        },
+
+        nonNumericalTimePointsError: function (column, sheetName) {
+            var columnLetter = numbersToLetters[column];
+            return {
+                errorCode: "NON_NUMERICAL_TIME_POINT",
+                possibleCause: `There is a non-numerical time point in the ${sheetName} sheet. It is located at
+                column ${columnLetter}.`,
+                suggestedFix: "Change the non-numerical time point to a positive number and ensure expression data \
+                is correct."
+            };
+        },
+    }
+};

package/server/dals/expression-dal.js

@@ -0,0 +1,122 @@
+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 expressionTimepointsSources = [
+    {
+        key: "Barreto_2012_wt",
+        value: [10, 10, 20, 20, 20, 20, 40, 40, 40, 40, 60, 60, 60, 60, 120, 120, 120, 120]
+    },
+
+    {
+        key: "Dahlquist_2018_dcin5",
+        value: [15, 15, 15, 15, 30, 30, 30, 30, 60, 60, 60, 60, 90, 90, 90, 90, 120, 120, 120, 120]
+    },
+
+    {
+        key: "Dahlquist_2018_dgln3",
+        value: [15, 15, 15, 15, 30, 30, 30, 30, 60, 60, 60, 60, 90, 90, 90, 90, 120, 120, 120, 120]
+    },
+
+    {
+        key: "Dahlquist_2018_dhap4",
+        value: [15, 15, 15, 15, 30, 30, 30, 30, 60, 60, 60, 60, 90, 90, 90, 120, 120, 120]
+    },
+
+    {
+        key: "Dahlquist_2018_dzap1",
+        value: [15, 15, 15, 15, 30, 30, 30, 30, 60, 60, 60, 60, 90, 90, 90, 90, 120, 120, 120, 120]
+    },
+
+    {
+        key: "Dahlquist_2018_wt",
+        value: [15, 15, 15, 15, 30, 30, 30, 30, 30, 60, 60, 60, 60, 90, 90, 90, 90, 90, 120, 120, 120, 120, 120]
+    },
+
+    {
+        key: "Kitagawa_2002_wt",
+        value: [15, 15, 15, 30, 30, 30, 120, 120, 120]
+    },
+
+    {
+        key: "Thorsen_2007_wt",
+        value: [15, 15, 15, 30, 30, 30, 60, 60, 60, 60, 60, 60, 1080, 1080, 1080]
+    }
+];
+
+const expressionTimepointsByDataset = {};
+expressionTimepointsSources.forEach(source => expressionTimepointsByDataset[source.key] = source.value);
+
+let buildExpressionTimepointsQuery = function (selection) {
+    let timepoints = "";
+    selection.forEach(x => timepoints += ("fall2021.expression.time_point=" + x + " OR "));
+    return timepoints.substring(0, timepoints.length - 4);
+};
+
+let buildExpressionGenesQuery = function (geneString) {
+    let genes = "";
+    let geneList = geneString.split(",");
+    geneList.forEach(x => genes += ( `(fall2021.gene.display_gene_id =\'${x}\') OR `));
+    return genes.substring(0, genes.length - 4);
+};
+
+let buildExpressionQuery = function (dataset, timepoints, genes) {
+    return timepoints ?
+    `SELECT *  FROM fall2021.expression, fall2021.gene WHERE fall2021.expression.dataset='${dataset}' AND
+    (${buildExpressionTimepointsQuery(timepoints)}) AND
+    ((${buildExpressionGenesQuery(genes)}) 
+    AND fall2021.gene.gene_id = fall2021.expression.gene_id) ORDER BY sort_index;`
+    : `SELECT * FROM fall2021.expression, fall2021.gene WHERE fall2021.expression.dataset='${dataset}'
+    AND ((${buildExpressionGenesQuery(genes)}) 
+    AND fall2021.gene.gene_id = fall2021.expression.gene_id) ORDER BY sort_index;`;
+};
+
+let listExpressionGeneData = function (gene, totalOutput) {
+    let listOfData = [];
+    totalOutput.forEach(function (x) {
+        if (x.display_gene_id === gene) {
+            listOfData.push(Number(x.expression));
+        }
+    });
+    return listOfData;
+};
+
+let convertExpressionToJSON = function (totalOutput, dataset, timePoints, allGenes) {
+    let JSONOutput = {
+        timePoints,
+        data: {
+            id: timePoints
+        }
+    };
+    allGenes.forEach(x => JSONOutput.data[x.toString()] = listExpressionGeneData(x, totalOutput));
+    return JSONOutput;
+};
+
+module.exports = {
+    queryExpressionDatabase: function (req, res) {
+        return sequelize.query(buildExpressionQuery(req.query.dataset, req.query.timepoints, req.query.genes),
+                { type: sequelize.QueryTypes.SELECT })
+                    .then(function (stdname) {
+                        let dataset = req.query.dataset;
+                        let geneList = req.query.genes.split(",");
+                        let response = convertExpressionToJSON(
+                            stdname, dataset, expressionTimepointsByDataset[dataset], geneList);
+                        return res.send(response);
+                    });
+    }
+};