grnsight 6.0.7 → 7.2.0

package/server/controllers/export-constants.js

@@ -37,8 +37,9 @@ module.exports = {
             warningCode: "INCORRECT_NETWORK_SHEET_EXPORT_WARNING",
             errorDescription: "GRNsight has detected that the 'network' sheet or the 'network_optimized_weights'" +
                 " sheet is improperly formattedPlease look over your exported workbook and ensure that network" +
-                " sheets have cell A1 as 'cols regulators/rows targets' exactly, and all gene are using the  naming" +
-                " conventions listed at: \nhttps://dondi.github.io/GRNsight/documentation.html."
+                " sheets have cell A1 as 'cols regulators/rows targets' or 'cols protein1/ rows protein2' exactly" +
+                " and all gene are using the  naming conventions listed at:" +
+                " \nhttps://dondi.github.io/GRNsight/documentation.html."
         },
         // Missing Source Genes
         MISSING_SOURCE_GENES_EXPORT_WARNING: {

package/server/controllers/exporters/sif.js

@@ -7,7 +7,12 @@ var exportEdges = function (workbook, gene, geneIndex) {
         if (link.source === geneIndex) {
             result += [
                 gene.name,
-                workbook.sheetType === constants.UNWEIGHTED ? "pd" : link.value,
+                workbook.sheetType === constants.WEIGHTED ?
+                    link.value : (workbook.meta) ?
+                    (workbook.meta.data.workbookType === constants.NETWORK_PPI_MODE ?
+                        "pp" : "pd") :
+                    workbook.workbookType === constants.NETWORK_PPI_MODE ?
+                    "pp" : "pd",
                 workbook.genes[link.target].name
             ].join("\t") + "\n";
         }

package/server/controllers/exporters/xlsx.js

@@ -1,5 +1,6 @@
 // const { meta } = require("eslint/lib/rules/*");
 const xlsx = require("node-xlsx");
+const { CELL_A1_GRN, CELL_A1_PPI, NETWORK_GRN_MODE } = require("../constants");
 
 const buildGeneNameArray = function (genes) {
     const geneNameArray = genes.map(gene => gene["name"]);
@@ -10,7 +11,7 @@ const createArrayWithZeroes = function (length) {
     return Array.apply(null, Array(length)).map(() => 0);
 };
 
-const buildNetworkSheet = function (genes, links) {
+const buildNetworkSheet = function (genes, links, workbookType) {
     const geneNameArray = buildGeneNameArray(genes);
     // The +1 to length is because we ALSO add the gene name to each of the network sheet arrays.
     const networkSheet = genes.map(() => createArrayWithZeroes(genes.length + 1));
@@ -18,7 +19,11 @@ const buildNetworkSheet = function (genes, links) {
     // Place the gene name in the beginning of the network sheet array.
     // EX: ["CIN5", 0, 0, 1]
     Object.keys(geneNameArray).forEach(index => networkSheet[index][0] = geneNameArray[index]);
-    geneNameArray.unshift("cols regulators/rows targets");
+    if (workbookType === NETWORK_GRN_MODE) {
+        geneNameArray.unshift(CELL_A1_GRN);
+    } else {
+        geneNameArray.unshift(CELL_A1_PPI);
+    }
 
     links.forEach((link) => {
         networkSheet[link.target][link.source + 1] = link.value;
@@ -115,7 +120,7 @@ const buildXlsxSheet = function (workbook) {
                         {
                             "name": network,
                             "data": buildNetworkSheet(workbook.exportSheets.networks[network].genes,
-                                workbook.exportSheets.networks[network].links)
+                                workbook.exportSheets.networks[network].links, workbook.meta.data.workbookType)
                         }
                     );
                 }

package/server/controllers/expression-sheet-parser.js

@@ -154,17 +154,11 @@ module.exports = function (workbook) {
         warnings: [],
         errors: []
     };
-    var expCount = 0;
 
     workbook.forEach(function (sheet) {
         if (isExpressionSheet(sheet.name)) {
             output["expression"][sheet.name] = parseExpressionSheet(sheet);
-            expCount++;
         }
     });
-
-    if (expCount <= 0) {
-        addExpWarning(output, constants.warnings.missingExpressionWarning());
-    }
     return output;
 };

package/server/controllers/grnsettings-database-controller.js

@@ -0,0 +1,17 @@
+
+var grnsettingDal = require(__dirname + "/../dals/grnsetting-dal");
+
+
+module.exports = function (app) {
+
+    app.get("/grnsettingsdb", function (req, res) {
+        try {
+            return grnsettingDal.queryDefaultDataset(req, res);
+        } catch (e) {
+            res.json({error: e.stack});
+            res.json({error: e.name});
+            res.json({error: e.message});
+
+        }
+    });
+};

package/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 +54,25 @@ module.exports = function (sif) {
             }
         });
 
+        let hasNumbers = relationships.some(isNumber);
+        let allNumbers = relationships.every(isNumber);
+
+        let workbookType;
+        if (allNumbers) {
+            workbookType = constants.NETWORK_GRN_MODE;
+        } else {
+            let stringRelationships = relationships.filter(function (relationship) {
+                return !isNumber(relationship);
+            });
+            if (stringRelationships.every(rel => rel === "pp")) {
+                workbookType = constants.NETWORK_PPI_MODE;
+            } else if (stringRelationships.every(rel => rel === "pd")) {
+                workbookType = constants.NETWORK_GRN_MODE;
+            } else if (stringRelationships.every(rel => rel === "pp" || rel === "pd")) {
+                errors.push(sifConstants.errors.SIF_MIXED_RELATIONSHIP_TYPE_ERROR);
+            }
+        }
+
         if (unweightedRelationshipTypeErrorDetected) {
             errors.push(sifConstants.errors.SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR);
         }
@@ -62,9 +81,8 @@ module.exports = function (sif) {
             errors.push(sifConstants.errors.SIF_MISSING_DATA_ERROR);
         }
 
-        var hasNumbers = relationships.some(isNumber);
-        var allNumbers = relationships.every(isNumber);
         return {
+            workbookType: workbookType,
             sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED,
             warnings: hasNumbers && !allNumbers ? constants.warnings.EDGES_WITHOUT_WEIGHTS : null,
             errors: errors
@@ -77,7 +95,7 @@ module.exports = function (sif) {
 
     var genes = [];
     var links = [];
-    var workbookType = "unweighted";
+    var workbookMeta = "unweighted";
 
     var nullEntries = entries.filter(function (entry) {
         return entry === null;
@@ -92,13 +110,13 @@ module.exports = function (sif) {
             }
         });
 
-        workbookType = sifWorkbookType(entries);
-        if (workbookType.warnings) {
-            warnings.push(workbookType.warnings);
+        workbookMeta = sifWorkbookType(entries);
+        if (workbookMeta.warnings) {
+            warnings.push(workbookMeta.warnings);
         }
 
-        if (workbookType.errors) {
-            workbookType.errors.forEach(function (error) {
+        if (workbookMeta.errors) {
+            workbookMeta.errors.forEach(function (error) {
                 errors.push(error);
             });
         }
@@ -117,7 +135,7 @@ module.exports = function (sif) {
                         source: sourceIndex,
                         target: targetIndex
                     };
-                    if (workbookType.sheetType === constants.WEIGHTED) {
+                    if (workbookMeta.sheetType === constants.WEIGHTED) {
                         link.value = +entry[RELATIONSHIP];
                     }
                     links.push(link);
@@ -133,7 +151,8 @@ module.exports = function (sif) {
         links: links,
         errors: errors,
         warnings: warnings,
-        sheetType: workbookType.sheetType,
+        sheetType: workbookMeta.sheetType,
+        workbookType: workbookMeta.workbookType,
         positiveWeights: [],
         negativeWeights: [],
         meta: {},

package/server/controllers/network-database-controller.js

@@ -1,12 +1,12 @@
 
-var expressionDal = require(__dirname + "/../dals/network-dal");
+var networkDal = require(__dirname + "/../dals/network-dal");
 
 
 module.exports = function (app) {
 
     app.get("/networkdb", function (req, res) {
         try {
-            return expressionDal.queryNetworkDatabase(req, res);
+            return networkDal.queryNetworkDatabase(req, res);
         } catch (e) {
             res.json({error: e.stack});
             res.json({error: e.name});

package/server/controllers/network-sheet-parser.js

@@ -2,13 +2,13 @@
 // var path = require("path");
 // var demoWorkbooks = require(__dirname + "/demo-workbooks");
 
+const { NETWORK_PPI_MODE, NETWORK_GRN_MODE, CELL_A1_GRN, CELL_A1_PPI } = require("./constants");
 const { initWorkbook } = require("./helpers");
 
 var semanticChecker = require(__dirname + "/semantic-checker");
 
 var constants = require(__dirname + "/workbook-constants");
 
-
 // const NETWORK_SHEET_NAMES = ["network", "network_optimized_weights"];
 
 // const isNetworkSheet = (sheetName) => {
@@ -94,9 +94,26 @@ var parseNetworkSheet = function (sheet, network) {
     var rowData = [];
 
     // check for “cols regulators/rows targets” in cell A1
-    const cellA1 = sheet.data[0][0];
-    if (cellA1 !== "cols regulators/rows targets") {
-        addWarning(network, constants.warnings.incorrectCellA1WorkbookWarning(sheet.name));
+    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.
+
+    // Depending on the value of cellA1, we want to make a new property `networkType` which
+    // will indicate the network type. THe web app then reads this to decide what to do next.
+    if (cellA1 !== CELL_A1_GRN && cellA1 !== CELL_A1_PPI) {
+        addWarning(
+            network,
+            constants.warnings.incorrectCellA1WorkbookWarning(sheet.name)
+        );
     }
 
     // Get Source Genes
@@ -275,27 +292,52 @@ var parseNetworkSheet = function (sheet, network) {
     return semanticChecker(network);
 };
 
+/*
+ * This method detect the network type of the workbook file either grn or protein-protein-physical-interactions
+ * If cellA1 = "cols regulators/ row targets" -> workbookType = grn
+ * If cellA1 = "cols protein1/ rows protein2" -> workbookType = "protein-protein-physical-interaction"
+ * else undefined
+*/
+
+exports.workbookType = function (workbookFile) {
+    let workbookType;
+    for (const sheet of workbookFile) {
+        if (sheet.name.toLowerCase() === "network") {
+            const cellA1 = sheet.data[0][0];
+
+            if (cellA1 === CELL_A1_GRN) {
+                workbookType = NETWORK_GRN_MODE;
+            } else if (cellA1 === CELL_A1_PPI) {
+                workbookType = NETWORK_PPI_MODE;
+            } else {
+                workbookType = undefined;
+            }
+            break;
+        }
+    }
+    return workbookType;
+};
 
-module.exports = function (workbookFile) {
+exports.networks = function (workbookFile) {
     const networks = {
         network: {},
         networkOptimizedWeights: {},
         networkWeights: {},
     };
 
-    for (let i = 0; i < workbookFile.length; i++) {
+    for (const element of workbookFile) {
         // === 'network' for backwards compatibility of test files
-        if (workbookFile[i].name.toLowerCase() === "network") {
+        if (element.name.toLowerCase() === "network") {
             // Here we have found a network sheet containing simple data. We keep looking
             // in case there is also a network sheet with optimized weights
-            networks.network = parseNetworkSheet(workbookFile[i], initWorkbook({ sheetType: "unweighted" }));
-        } else if (workbookFile[i].name.toLowerCase() === "network_optimized_weights" ) {
+            networks.network = parseNetworkSheet(element, initWorkbook({ sheetType: "unweighted" }));
+        } else if (element.name.toLowerCase() === "network_optimized_weights" ) {
             // We found a network sheet with optimized weights, which is the ideal data source.
-            networks.networkOptimizedWeights = parseNetworkSheet(workbookFile[i],
+            networks.networkOptimizedWeights = parseNetworkSheet(element,
                 initWorkbook({ sheetType: "weighted" }));
-        } else if (workbookFile[i].name.toLowerCase() === "network_weights") {
+        } else if (element.name.toLowerCase() === "network_weights") {
             // We found a network_weights sheet to preserve existing network type sheet data
-            networks.networkWeights = parseNetworkSheet(workbookFile[i], initWorkbook({ sheetType: "weighted" }));
+            networks.networkWeights = parseNetworkSheet(element, initWorkbook({ sheetType: "weighted" }));
         }
     }
 

package/server/controllers/protein-database-controller.js

@@ -0,0 +1,18 @@
+
+var proteinDal = require(__dirname + "/../dals/protein-dal");
+
+
+module.exports = function (app) {
+
+    app.get("/proteindb", function (req, res) {
+        try {
+            return proteinDal.queryProteinDatabase(req, res);
+        } catch (e) {
+            res.json({error: e.stack});
+            res.json({error: e.name});
+            res.json({error: e.message});
+
+        }
+    });
+
+};

package/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: {
@@ -32,5 +32,12 @@ module.exports = {
             possibleCause: "GRNsight has detected stray data and/or extraneous blank rows in your SIF file. ",
             suggestedFix: "Please review the data and delete extraneous data from the file."
         },
+
+        SIF_MIXED_RELATIONSHIP_TYPE_ERROR: {
+            errorCode: "SIF_MIXED_RELATIONSHIP_TYPE_ERROR",
+            possibleCause: "The SIF importer detects a SIF file with mixed relationship types.",
+            suggestedFix: ["GRNsight only supports networks with a single relationship type.",
+                "Please review the relationships for consistency."].join(" ")
+        },
     },
 };

package/server/controllers/spreadsheet-controller.js

@@ -1,6 +1,7 @@
 var multiparty = require("multiparty");
 var xlsx = require("node-xlsx");
 var path = require("path");
+const { NETWORK_GRN_MODE, NETWORK_PPI_MODE } = require("./constants");
 var parseAdditionalSheets = require(__dirname + "/additional-sheet-parser");
 var parseExpressionSheets = require(__dirname + "/expression-sheet-parser");
 var parseNetworkSheet = require(__dirname + "/network-sheet-parser");
@@ -21,6 +22,11 @@ var SPECIES = [
     "Saccharomyces cerevisiae",
 ];
 
+const WORKBOOK_TYPES = [
+    NETWORK_GRN_MODE,
+    NETWORK_PPI_MODE
+];
+
 var TAXON_ID = ["3702", "6293", "7227", "9606", "10090", "4932", "559292"];
 
 var isExpressionSheet = function (sheetName) {
@@ -43,6 +49,15 @@ var doesSpeciesExist = function (speciesInfo) {
     return false;
 };
 
+var supportWorkbookType = function (type) {
+    for (var t in WORKBOOK_TYPES) {
+        if (WORKBOOK_TYPES[t] === type) {
+            return true;
+        }
+    }
+    return false;
+};
+
 var addMessageToArray = function (messageArray, message) {
     messageArray.push(message);
 };
@@ -106,7 +121,8 @@ var crossSheetInteractions = function (workbookFile) {
 
     // Refactored the parseNetworkSheet function to preserve all network type sheets including "network",
     // "network_optimized_weights",and "network_weights" restructuring workbook object as a result
-    var networks = parseNetworkSheet(workbookFile);
+
+    var networks = parseNetworkSheet.networks(workbookFile);
 
     // Parse expression and 2-column data, then add to workbook object
     // Eventually, will split this up into parsing for each type of sheet.
@@ -180,6 +196,20 @@ var crossSheetInteractions = function (workbookFile) {
         }
     }
 
+    additionalData.meta.data.workbookType = parseNetworkSheet.workbookType(workbookFile);
+    if (additionalData.meta.data.workbookType === undefined) {
+        addWarning(workbook, constants.warnings.noWorkbookTypeDetected);
+        additionalData.meta.data.workbookType = NETWORK_GRN_MODE;
+    } else if (!supportWorkbookType(additionalData.meta.data.workbookType)) {
+        addWarning(
+            workbook,
+            constants.warnings.unsupportedWorkbookTypeDetected(
+                additionalData.meta.data.workbookType
+            )
+        );
+        additionalData.meta.data.workbookType = NETWORK_GRN_MODE;
+    }
+
     if (additionalData.meta.data.species === undefined && additionalData.meta.data.taxon_id === undefined) {
         addWarning(workbook, constants.warnings.noSpeciesInformationDetected);
         additionalData.meta.data.species = "Saccharomyces cerevisiae";
@@ -203,6 +233,11 @@ var crossSheetInteractions = function (workbookFile) {
     // FUTURE IMPROVEMENT: not all expression sheets are specifically named 'wt_log2_expression.'
     // We need to account for all the different possible expression sheet names.
     if (expressionData) {
+        if (additionalData.meta.data.workbookType === constants.NETWORK_GRN_MODE) {
+            if (expressionData["expression"] && Object.keys(expressionData["expression"]).length === 0) {
+                addWarning(expressionData, constants.warnings.missingExpressionWarning());
+            }
+        }
         if (expressionData.errors !== undefined) {
             expressionData.errors.forEach(data => workbook.errors.push(data));
         }
@@ -411,6 +446,14 @@ module.exports = function (app) {
                 app
             );
         });
+
+        app.get("/demo/ppi", function (req, res) {
+            return demoWorkbooks(
+                "test-files/demo-files/18_proteins_81_edges_PPI.xlsx",
+                res,
+                app
+            );
+        });
     }
 
     // exporting parseNetworkSheet for use in testing. Do not remove!

package/server/controllers/workbook-constants.js

@@ -102,7 +102,8 @@ module.exports = {
             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.`
+                Replace the incorrect label with \'cols regulators/ rows targets\' or \'cols 
+                protein1/ rows protein2'\ exactly.`
             };
         },
 
@@ -178,8 +179,7 @@ module.exports = {
         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."
+                " GRNsight defaults to Saccharomyces cerevisiae."
         },
 
         unknownSpeciesDetected: function (workbookSpecies, workbookTaxon) {
@@ -188,7 +188,24 @@ module.exports = {
                 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."
+                    " GRNsight defaults to Saccharomyces cerevisiae."
+            };
+        },
+
+        noWorkbookTypeDetected : {
+            warningCode: "MISSING_WORKBOOK_TYPE_INFORMATION",
+            errorDescription: "No workbook type was detected in your input file." +
+                " GRNsight defaults to a gene regulatory network. You can change the workbook type" +
+                " selection in the Network menu or panel."
+        },
+
+        unsupportedWorkbookTypeDetected: function (workbookType) {
+            return {
+                warningCode: "UNKNOWN_WORKBOOK_TYPE_DETECTED",
+                errorDescription: "GRNsight detected the workbook type " + workbookType +
+                    " in your input file. This is not one of the supported workbook types, or was formatted" +
+                    " incorrectly. GRNsight defaults to a gene regulatory network. You can change the workbook type" +
+                    " selection in the Network menu or panel."
             };
         },
 

package/server/dals/expression-dal.js

@@ -4,8 +4,8 @@ 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,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
@@ -20,7 +20,7 @@ var sequelize = new Sequelize(
 const buildExpressionGenesQuery = function (geneString) {
     let genes = "";
     let geneList = geneString.split(",");
-    geneList.forEach(x => genes += ( `(gene_expression.gene.display_gene_id =\'${x}\') OR `));
+    geneList.forEach(x => genes += ( `(LOWER(gene_expression.gene.display_gene_id) = LOWER(\'${x}\')) OR `));
     return genes.substring(0, genes.length - 4);
 };
 
@@ -62,7 +62,7 @@ const buildExpressionQuery = function (query) {
 const listExpressionGeneData = function (gene, totalOutput) {
     let listOfData = [];
     totalOutput.forEach(function (x) {
-        if (x.display_gene_id === gene) {
+        if (x.display_gene_id.toLowerCase() === gene.toLowerCase()) {
             listOfData.push(Number(x.expression));
         }
     });

package/server/dals/grnsetting-dal.js

@@ -0,0 +1,49 @@
+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.DB_USERNAME,
+    process.env.DB_PASSWORD,
+    {
+        host: config.databaseHost,
+        dialect: config.databaseDialect,
+        pool: {
+            max: 5,
+            min: 0,
+            idle: 10000
+        }
+    }
+);
+
+const buildGetDefaultDataset = function () {
+    return `
+    SELECT grnsettings.expression_dataset FROM settings.grnsettings;`;
+};
+
+const DefaultDatasetToJSON = (totalOutput) => {
+    const JSONOutput = {
+        defaultDataset : []
+    };
+    for (let dataset of totalOutput) {
+        JSONOutput.defaultDataset.push(dataset.expression_dataset);
+    }
+    return JSONOutput;
+};
+
+
+module.exports = {
+    queryDefaultDataset: function (req, res) {
+        return sequelize.query(buildGetDefaultDataset(),
+            { type: sequelize.QueryTypes.SELECT })
+            .then(function (stdname) {
+                const convertToJSON = {
+                    "DefaultDataset" : () => DefaultDatasetToJSON(stdname)
+                };
+                const type = req.query.type;
+                return (Object.keys(convertToJSON).includes(type)) ? res.send(convertToJSON[type]()) :
+                    res.status(500).send({ errors: "Something went wrong." });
+            });
+    }
+};

package/server/dals/network-dal.js

@@ -1,12 +1,11 @@
-/* eslint-disable max-len */
 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,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
@@ -19,14 +18,13 @@ var sequelize = new Sequelize(
 );
 
 const buildNetworkSourceQuery = function () {
-    return "SELECT * FROM gene_regulatory_network.source ORDER BY time_stamp;";
+    return "SELECT * FROM gene_regulatory_network.source ORDER BY time_stamp DESC;";
 };
 
-const buildNetworkGeneFromSourceQuery = function (gene, source, timestamp) {
-    return `SELECT DISTINCT gene_id, display_gene_id FROM gene_regulatory_network.network, gene_regulatory_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 buildNetworkGeneFromSourceQuery = function (gene) {
+    return `SELECT DISTINCT gene_id, display_gene_id FROM 
+    gene_regulatory_network.gene WHERE (gene.gene_id ='${gene}'
+    OR gene.display_gene_id ='${gene}')`;
 };
 
 const buildNetworkGenesQuery = function (geneString) {
@@ -49,7 +47,7 @@ const buildGenerateNetworkQuery = function (genes, source, timestamp) {
 const buildQueryByType = function (queryType, query) {
     const networkQueries = {
         "NetworkSource": () => buildNetworkSourceQuery(),
-        "NetworkGeneFromSource": () => buildNetworkGeneFromSourceQuery(query.gene, query.source, query.timestamp),
+        "NetworkGeneFromSource": () => buildNetworkGeneFromSourceQuery(query.gene),
         "GenerateNetwork": () => buildGenerateNetworkQuery(query.genes, query.source, query.timestamp)
     };
     if (Object.keys(networkQueries).includes(query.type)) {
@@ -57,16 +55,17 @@ const buildQueryByType = function (queryType, query) {
     }
 };
 
+// const response = convertResponseToJSON(req.query.type, req.query, stdname);
 const convertResponseToJSON = function (queryType, query, totalOutput) {
     let JSONOutput = {};
     switch (queryType) {
     case "NetworkSource":
         JSONOutput.sources = {};
-        totalOutput.forEach(function (x) {
-            const timestamp = x.time_stamp;
-            const source = x.source;
-            const displayName = x.display_name;
-            JSONOutput.sources[`${displayName} : ${timestamp.toISOString().split("T")[0]}`] = {timestamp, source};
+        totalOutput.forEach(function (connection) {
+            const timestamp = connection.time_stamp;
+            const source = connection.source;
+            const displayName = connection.display_name;
+            JSONOutput.sources[`${displayName}: ${timestamp.toISOString().split("T")[0]}`] = {timestamp, source};
         });
         return JSONOutput;
     case "NetworkGeneFromSource":