#1030 change EXPRESSION_DB_USERNAME -> DB_USERNAME and EXPRESSION_DB_…

…PASSWORD -> DB_PASSWORD
dondi · Nov 27, 2024 · d44b7d3 · d44b7d3
1 parent 0acca88
commit d44b7d3
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Showing 4 changed files with 247 additions and 162 deletions.
diff --git a/server/dals/expression-dal.js b/server/dals/expression-dal.js
@@ -4,85 +4,110 @@ 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,
         pool: {
             max: 5,
             min: 0,
-            idle: 10000
-        }
+            idle: 10000,
+        },
     }
 );
 
-const buildExpressionGenesQuery = function (geneString) {
+const buildExpressionGenesQuery = function(geneString) {
     let genes = "";
     let geneList = geneString.split(",");
-    geneList.forEach(x => genes += ( `(LOWER(gene_expression.gene.display_gene_id) = LOWER(\'${x}\')) OR `));
+    geneList.forEach(
+        (x) =>
+            (genes += `(LOWER(gene_expression.gene.display_gene_id) = LOWER(\'${x}\')) OR `)
+    );
     return genes.substring(0, genes.length - 4);
 };
 
-const buildExpressionProductionDegradationRatesQuery = function (rateType, genes) {
+const buildExpressionProductionDegradationRatesQuery = function(
+    rateType,
+    genes
+) {
     return `
     SELECT gene.display_gene_id, ${rateType}  FROM gene_expression.${rateType}, gene_expression.gene WHERE
     ((${buildExpressionGenesQuery(genes)}) 
     AND gene_expression.gene.gene_id = gene_expression.${rateType}.gene_id) ORDER BY display_gene_id;`;
 };
 
-const buildExpressionTimepointsFromDatasetQuery = function (dataset) {
+const buildExpressionTimepointsFromDatasetQuery = function(dataset) {
     return `
     SELECT DISTINCT time_point, sample_id FROM gene_expression.expression WHERE
     dataset = '${dataset}' ORDER BY time_point ASC;`;
 };
 
-const buildExpressionDataQuery = function (dataset, genes) {
+const buildExpressionDataQuery = function(dataset, genes) {
     return `SELECT * FROM gene_expression.expression, gene_expression.gene 
     WHERE gene_expression.expression.dataset='${dataset}'
     AND ((${buildExpressionGenesQuery(genes)}) 
     AND gene_expression.gene.gene_id = gene_expression.expression.gene_id) ORDER BY sort_index;`;
 };
 
-
-
-const buildExpressionQuery = function (query) {
+const buildExpressionQuery = function(query) {
     const expressionQueries = {
-        "DegradationRates": () => buildExpressionProductionDegradationRatesQuery("degradation_rate", query.genes),
-        "ProductionRates" : () => buildExpressionProductionDegradationRatesQuery("production_rate", query.genes),
-        "ExpressionData" : () => buildExpressionDataQuery(query.dataset, query.genes),
-        "ExpressionDatasets" : () => "SELECT DISTINCT dataset FROM gene_expression.expression ORDER BY dataset ASC;",
-        "ExpressionTimePoints": () => buildExpressionTimepointsFromDatasetQuery(query.dataset)
+        DegradationRates: () =>
+            buildExpressionProductionDegradationRatesQuery(
+                "degradation_rate",
+                query.genes
+            ),
+        ProductionRates: () =>
+            buildExpressionProductionDegradationRatesQuery(
+                "production_rate",
+                query.genes
+            ),
+        ExpressionData: () =>
+            buildExpressionDataQuery(query.dataset, query.genes),
+        ExpressionDatasets: () =>
+            "SELECT DISTINCT dataset FROM gene_expression.expression ORDER BY dataset ASC;",
+        ExpressionTimePoints: () =>
+            buildExpressionTimepointsFromDatasetQuery(query.dataset),
     };
     if (Object.keys(expressionQueries).includes(query.type)) {
         return expressionQueries[query.type]();
     }
 };
 
-const listExpressionGeneData = function (gene, totalOutput) {
+const listExpressionGeneData = function(gene, totalOutput) {
     let listOfData = [];
-    totalOutput.forEach(function (x) {
+    totalOutput.forEach(function(x) {
         if (x.display_gene_id.toLowerCase() === gene.toLowerCase()) {
             listOfData.push(Number(x.expression));
         }
     });
     return listOfData;
 };
 
-const convertExpressionToJSON = function (totalOutput, dataset, timePoints, allGenes) {
+const convertExpressionToJSON = function(
+    totalOutput,
+    dataset,
+    timePoints,
+    allGenes
+) {
     let JSONOutput = {
         timePoints,
         data: {
-            id: timePoints
-        }
+            id: timePoints,
+        },
     };
-    allGenes.forEach(x => JSONOutput.data[x.toString()] = listExpressionGeneData(x, totalOutput));
+    allGenes.forEach(
+        (x) =>
+            (JSONOutput.data[x.toString()] = listExpressionGeneData(
+                x,
+                totalOutput
+            ))
+    );
     return JSONOutput;
 };
 
 const ProductionDegradationRateToJSON = (totalOutput, rateType) => {
-    const JSONOutput = {
-    };
+    const JSONOutput = {};
     for (let gene of totalOutput) {
         JSONOutput[gene.display_gene_id] = gene[rateType];
     }
@@ -91,7 +116,7 @@ const ProductionDegradationRateToJSON = (totalOutput, rateType) => {
 
 const DatasetToJSON = (totalOutput) => {
     const JSONOutput = {
-        expressionDatasets : []
+        expressionDatasets: [],
     };
     for (let dataset of totalOutput) {
         JSONOutput.expressionDatasets.push(dataset.dataset);
@@ -109,24 +134,40 @@ const TimePointsToJSON = (totalOutput, dataset) => {
 };
 
 module.exports = {
-    queryExpressionDatabase: function (req, res) {
-        return sequelize.query(buildExpressionQuery(req.query),
-                { type: sequelize.QueryTypes.SELECT })
-                    .then(function (stdname) {
-                        const convertToJSON = {
-                            "DegradationRates" : () => ProductionDegradationRateToJSON(stdname, "degradation_rate"),
-                            "ProductionRates" : () => ProductionDegradationRateToJSON(stdname, "production_rate"),
-                            "ExpressionData" : () => convertExpressionToJSON(
-                                        stdname,
-                                        req.query.dataset,
-                                        req.query.timepoints.split(",").map(x => Number(x)),
-                                        req.query.genes.split(",")),
-                            "ExpressionDatasets": () => DatasetToJSON(stdname),
-                            "ExpressionTimePoints": () => TimePointsToJSON(stdname, req.query.dataset)
-                        };
-                        const type = req.query.type;
-                        return (Object.keys(convertToJSON).includes(type)) ? res.send(convertToJSON[type]()) :
-                            res.send(500, { errors: "Something went wrong."});
-                    });
-    }
-};
+    queryExpressionDatabase: function(req, res) {
+        return sequelize
+            .query(buildExpressionQuery(req.query), {
+                type: sequelize.QueryTypes.SELECT,
+            })
+            .then(function(stdname) {
+                const convertToJSON = {
+                    DegradationRates: () =>
+                        ProductionDegradationRateToJSON(
+                            stdname,
+                            "degradation_rate"
+                        ),
+                    ProductionRates: () =>
+                        ProductionDegradationRateToJSON(
+                            stdname,
+                            "production_rate"
+                        ),
+                    ExpressionData: () =>
+                        convertExpressionToJSON(
+                            stdname,
+                            req.query.dataset,
+                            req.query.timepoints
+                                .split(",")
+                                .map((x) => Number(x)),
+                            req.query.genes.split(",")
+                        ),
+                    ExpressionDatasets: () => DatasetToJSON(stdname),
+                    ExpressionTimePoints: () =>
+                        TimePointsToJSON(stdname, req.query.dataset),
+                };
+                const type = req.query.type;
+                return Object.keys(convertToJSON).includes(type)
+                    ? res.send(convertToJSON[type]())
+                    : res.send(500, { errors: "Something went wrong." });
+            });
+    },
+};
diff --git a/server/dals/grnsetting-dal.js b/server/dals/grnsetting-dal.js
@@ -4,46 +4,48 @@ 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,
         pool: {
             max: 5,
             min: 0,
-            idle: 10000
-        }
+            idle: 10000,
+        },
     }
 );
 
-const buildGetDefaultDataset = function () {
+const buildGetDefaultDataset = function() {
     return `
     SELECT grnsettings.expression_dataset FROM settings.grnsettings;`;
 };
 
 const DefaultDatasetToJSON = (totalOutput) => {
     const JSONOutput = {
-        defaultDataset : []
+        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) {
+    queryDefaultDataset: function(req, res) {
+        return sequelize
+            .query(buildGetDefaultDataset(), {
+                type: sequelize.QueryTypes.SELECT,
+            })
+            .then(function(stdname) {
                 const convertToJSON = {
-                    "DefaultDataset" : () => DefaultDatasetToJSON(stdname)
+                    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." });
+                return Object.keys(convertToJSON).includes(type)
+                    ? res.send(convertToJSON[type]())
+                    : res.status(500).send({ errors: "Something went wrong." });
             });
-    }
-};
+    },
+};