rename seqQC column to seqQc; add new table reports_seqqc

Author: sshugsc

app/middleware/report.js

@@ -38,6 +38,10 @@ module.exports = async (req, res, next, ident) => {
       model: db.models.signatures.scope('public'),
       as: 'signatures',
     },
+    {
+      model: db.models.seqQC.scope('public'),
+      as: 'seqQC',
+    },
   ];
 
   let result;

app/models/index.js

@@ -113,6 +113,16 @@ patientInformation.belongsTo(analysisReports, {
   as: 'report', foreignKey: 'reportId', onDelete: 'CASCADE', onUpdate: 'CASCADE', constraints: true,
 });
 
+// seqqc
+const seqQC = require('./reports/seqqc')(sequelize, Sq);
+
+seqQC.belongsTo(analysisReports, {
+  as: 'report', foreignKey: 'reportId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
+});
+analysisReports.hasMany(seqQC, {
+  as: 'seqQC', foreignKey: 'reportId', onDelete: 'CASCADE', constraints: true,
+});
+
 // Summary
 const summary = {};
 summary.variantCounts = require('./reports/genomic/summary/variantCounts')(sequelize, Sq);

app/models/reports/report.js

@@ -76,7 +76,9 @@ module.exports = (sequelize, Sq) => {
       },
       allowNull: false,
     },
-    seqQC: {
+    seqQc: {
+      name: 'seqQc',
+      field: 'seq_qc',
       type: Sq.JSONB,
       jsonSchema: {
         schema: {

app/models/reports/seqqc.js

@@ -0,0 +1,92 @@
+const {DEFAULT_COLUMNS, DEFAULT_REPORT_OPTIONS} = require('../base');
+
+module.exports = (sequelize, Sq) => {
+  const seqQC = sequelize.define('seqQC', {
+    ...DEFAULT_COLUMNS,
+    reportId: {
+      name: 'reportId',
+      field: 'report_id',
+      type: Sq.INTEGER,
+      references: {
+        model: 'reports',
+        key: 'id',
+      },
+    },
+    reads: {
+      name: 'Reads',
+      field: 'reads',
+      type: Sq.TEXT,
+    },
+    bioQC: {
+      name: 'bioQC',
+      field: 'bio_qc',
+      type: Sq.TEXT,
+    },
+    labQC: {
+      name: 'labQC',
+      field: 'lab_qc',
+      type: Sq.TEXT,
+    },
+    sample: {
+      name: 'Sample',
+      field: 'sample',
+      type: Sq.TEXT,
+    },
+    library: {
+      name: 'Library',
+      field: 'library',
+      type: Sq.TEXT,
+    },
+    coverage: {
+      name: 'Coverage',
+      field: 'coverage',
+      type: Sq.TEXT,
+    },
+    inputNg: {
+      name: 'InputNg',
+      field: 'input_ng',
+      type: Sq.TEXT,
+    },
+    inputUg: {
+      name: 'InputUg',
+      field: 'input_ug',
+      type: Sq.TEXT,
+    },
+    protocol: {
+      name: 'Protocol',
+      field: 'protocol',
+      type: Sq.TEXT,
+    },
+    sampleName: {
+      name: 'SampleName',
+      field: 'sample_name',
+      type: Sq.TEXT,
+    },
+    duplicateReadsPerc: {
+      name: 'DuplicateReadsPerc',
+      field: 'duplicate_reads_perc',
+      type: Sq.TEXT,
+    },
+  }, {
+    ...DEFAULT_REPORT_OPTIONS,
+    tableName: 'reports_seqqc',
+    scopes: {
+      public: {
+        attributes: {exclude: ['id', 'reportId', 'deletedAt', 'updatedBy']},
+      },
+    },
+  });
+
+  // set instance methods
+  seqQC.prototype.view = function (scope) {
+    if (scope === 'public') {
+      const {
+        id, reportId, deletedAt, updatedBy, ...publicView
+      } = this.dataValues;
+      return publicView;
+    }
+    return this;
+  };
+
+  return seqQC;
+};

app/routes/report/appendices.js

@@ -13,7 +13,8 @@ router.route('/')
     try {
       const result = await db.models.report.findOne({
         where: {ident: req.report.ident},
-        attributes: ['seqQC', 'config'],
+        attributes: ['seqQc', 'config'],
+        include: ['seqQC'],
       });
       return res.json(result);
     } catch (error) {

migrations/latest/20260330184401-DEVSU-2848-create-seqqc-table.js

@@ -0,0 +1,85 @@
+const TABLE = 'reports_seqqc';
+const {DEFAULT_COLUMNS} = require('../../app/models/base');
+
+module.exports = {
+  up: (queryInterface, Sq) => {
+    // Create new notifications tables
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.renameColumn('reports', 'seqQC', 'seq_qc', {transaction});
+      await queryInterface.createTable(TABLE, {
+        ...DEFAULT_COLUMNS,
+        reportId: {
+          name: 'reportId',
+          field: 'report_id',
+          type: Sq.INTEGER,
+          references: {
+            model: 'reports',
+            key: 'id',
+          },
+          onDelete: 'CASCADE',
+          onUpdate: 'CASCADE',
+          allowNull: false,
+        },
+        reads: {
+          name: 'Reads',
+          field: 'reads',
+          type: Sq.TEXT,
+        },
+        bioQC: {
+          name: 'bioQC',
+          field: 'bio_qc',
+          type: Sq.TEXT,
+        },
+        labQC: {
+          name: 'labQC',
+          field: 'lab_qc',
+          type: Sq.TEXT,
+        },
+        sample: {
+          name: 'Sample',
+          field: 'sample',
+          type: Sq.TEXT,
+        },
+        library: {
+          name: 'Library',
+          field: 'library',
+          type: Sq.TEXT,
+        },
+        coverage: {
+          name: 'Coverage',
+          field: 'coverage',
+          type: Sq.TEXT,
+        },
+        inputNg: {
+          name: 'InputNg',
+          field: 'input_ng',
+          type: Sq.TEXT,
+        },
+        inputUg: {
+          name: 'InputUg',
+          field: 'input_ug',
+          type: Sq.TEXT,
+        },
+        protocol: {
+          name: 'Protocol',
+          field: 'protocol',
+          type: Sq.TEXT,
+        },
+        sampleName: {
+          name: 'SampleName',
+          field: 'sample_name',
+          type: Sq.TEXT,
+        },
+        duplicateReadsPerc: {
+          name: 'DuplicateReadsPerc',
+          field: 'duplicate_reads_perc',
+          type: Sq.TEXT,
+        },
+      }, {transaction});
+    });
+  },
+
+  down: () => {
+    throw new Error('Not Implemented!');
+  },
+};