grnsight 5.1.0 → 6.0.4

package/server/controllers/database-controller.js

@@ -1,129 +0,0 @@
-
-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});
-
-        }
-    });
-
-};