grnsight 3.0.0 → 5.1.0

package/server/controllers/constants.js

@@ -11,48 +11,15 @@ module.exports = {
         EDGES_WITHOUT_WEIGHTS: {
             warningCode: "EDGES_WITHOUT_WEIGHTS",
             errorDescription: "GRNsight has detected that one or more edges in your network are missing numerical" +
-            " weight values. Because the algorithm GRNsight uses for determining the arrowhead type and the color and" +
-            " thickness of the edges requires numerical weight values, your graph will display as an unweighted graph" +
-            " with black edges and pointed arrowheads. If you want to display the network as a weighted graph, please" +
-            " modify your input file to include weight values for all edges."
+                " weight values. Because the algorithm GRNsight uses for determining the arrowhead type and the" +
+                " color and  thickness of the edges requires numerical weight values, your graph will display as" +
+                " an unweighted graph with black edges and pointed arrowheads. If you want to display the network" +
+                " as a weighted graph, please modify your input file to include weight values for all edges."
         },
 
         EDGE_DEFAULT_NOT_DIRECTED: {
             warningCode: "EDGE_DEFAULT_NOT_DIRECTED",
             errorDescription: "GRNsight interprets the graph as directed unconditionally."
         },
-
-        SIF_FORMAT_WARNING: {
-            warningCode: "SIF_FORMAT_WARNING",
-            errorDescription: " GRNsight has detected that there are no tabs in your file. The GRNsight specification" +
-            " for SIF files states that data must be delimited by tabs. Please review your data. This warning may" +
-            " suggest that your SIF file has comma separated data or contains no data at all. Additionally, valid" +
-            " networks which consist of single source nodes may also trigger this warning."
-        }
     },
-
-    errors: {
-        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."
-        },
-
-        SIF_MISSING_DATA_ERROR: {
-            errorCode: "SIF_MISSING_DATA_ERROR",
-            possibleCause: "GRNsight has detected that your SIF file contains missing data. ",
-            suggestedFix: "Please review the data. In a SIF file, each entry must have a source node, relationship" +
-            " type, and at least one target node, separated by tabs. An entry with a single source node is also" +
-            " allowed."
-        },
-
-        SIF_STRAY_DATA_ERROR: {
-            errorCode: "SIF_STRAY_DATA_ERROR",
-            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."
-        }
-    }
 };

package/server/controllers/database-controller.js

@@ -0,0 +1,129 @@
+
+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 timepointsSources = [
+    {
+        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 timepointsByDataset = {};
+timepointsSources.forEach(source => timepointsByDataset[source.key] = source.value);
+
+let buildTimepointsQuery = function (selection) {
+    let timepoints = "";
+    selection.forEach(x => timepoints += ("fall2021.expression.time_point=" + x + " OR "));
+    return timepoints.substring(0, timepoints.length - 4);
+};
+
+let buildGenesQuery = function (geneString) {
+    let genes = "";
+    let geneList = geneString.split(",");
+    geneList.forEach(x => genes += ( `(fall2021.gene.display_gene_id =\'${x}\') OR `));
+    return genes.substring(0, genes.length - 4);
+};
+
+let buildQuery = function (dataset, timepoints, genes) {
+    return timepoints ?
+    `SELECT *  FROM fall2021.expression, fall2021.gene WHERE fall2021.expression.dataset='${dataset}' AND
+    (${buildTimepointsQuery(timepoints)}) AND
+    ((${buildGenesQuery(genes)}) AND fall2021.gene.gene_id = fall2021.expression.gene_id) ORDER BY sort_index;`
+    : `SELECT * FROM fall2021.expression, fall2021.gene WHERE fall2021.expression.dataset='${dataset}'
+    AND ((${buildGenesQuery(genes)}) AND fall2021.gene.gene_id = fall2021.expression.gene_id) ORDER BY sort_index;`;
+};
+
+let listGeneData = function (gene, totalOutput) {
+    let listOfData = [];
+    totalOutput.forEach(function (x) {
+        if (x.display_gene_id === gene) {
+            listOfData.push(Number(x.expression));
+        }
+    });
+    return listOfData;
+};
+
+let convertToJSON = function (totalOutput, dataset, timePoints, allGenes) {
+    let JSONOutput = {
+        timePoints,
+        data: {
+            id: timePoints
+        }
+    };
+    allGenes.forEach(x => JSONOutput.data[x.toString()] = listGeneData(x, totalOutput));
+    return JSONOutput;
+};
+
+module.exports = function (app) {
+
+    app.get("/expressiondb", function (req, res) {
+        try {
+            return sequelize.query(buildQuery(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 = convertToJSON(stdname, dataset, timepointsByDataset[dataset], geneList);
+                    return res.send(response);
+                });
+        } catch (e) {
+            res.json({error: e.stack});
+            res.json({error: e.name});
+            res.json({error: e.message});
+
+        }
+    });
+
+};