Merge branch 'develop' into Bugfix/DEVSU-2931-updated_by-is-not-getting-populated

Author: sshugsc

app/models/reports/report.js

@@ -76,20 +76,6 @@ module.exports = (sequelize, Sq) => {
       },
       allowNull: false,
     },
-    seqQc: {
-      name: 'seqQc',
-      field: 'seq_qc',
-      type: Sq.JSONB,
-      jsonSchema: {
-        schema: {
-          type: 'array',
-          items: {
-            type: 'object',
-          },
-          example: [{Reads: '2534M', bioQC: 'passed'}],
-        },
-      },
-    },
     config: {
       type: Sq.TEXT,
     },

app/models/reports/smallMutations.js

@@ -134,6 +134,9 @@ module.exports = (sequelize, Sq) => {
       field: 'tumour_ref_copies',
       type: Sq.INTEGER,
     },
+    exon: {
+      type: Sq.TEXT,
+    },
     library: {
       type: Sq.TEXT,
     },

app/routes/report/appendices.js

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

migrations/latest/20260513214647-DEVSU-2914-add-exon-column-to-small-mutations.js

@@ -0,0 +1,13 @@
+const TABLE = 'reports_small_mutations';
+
+module.exports = {
+  async up(queryInterface, Sequelize) {
+    await queryInterface.addColumn(TABLE, 'exon', {
+      type: Sequelize.TEXT,
+    });
+  },
+
+  async down(queryInterface) {
+    await queryInterface.removeColumn(TABLE, 'exon');
+  },
+};

migrations/latest/20260519215459-DEVSU-2928-datafix-seqqc.js

@@ -0,0 +1,92 @@
+const {v4: uuidv4} = require('uuid');
+
+module.exports = {
+  up: async (queryInterface) => {
+    await queryInterface.sequelize.transaction(async (transaction) => {
+      const reports = await queryInterface.sequelize.query(
+        `
+          SELECT id, seq_qc
+          FROM reports
+          WHERE seq_qc IS NOT NULL;
+        `,
+        {
+          type: queryInterface.sequelize.QueryTypes.SELECT,
+          transaction,
+        },
+      );
+
+      const now = new Date();
+      const rows = [];
+
+      for (const report of reports) {
+        for (const seqQCItem of report.seq_qc) {
+          rows.push({
+            ident: uuidv4(),
+            created_at: now,
+            updated_at: now,
+            report_id: report.id,
+            reads: seqQCItem.Reads,
+            bio_qc: seqQCItem.bioQC,
+            lab_qc: seqQCItem.labQC,
+            sample: seqQCItem.Sample,
+            library: seqQCItem.Library,
+            coverage: seqQCItem.Coverage,
+            input_ng: seqQCItem.Input_ng,
+            input_ug: seqQCItem.Input_ug,
+            protocol: seqQCItem.Protocol,
+            sample_name: seqQCItem['Sample Name'],
+            duplicate_reads_perc: seqQCItem.Duplicate_Reads_Perc,
+          });
+        }
+      }
+
+      if (rows.length !== 0) {
+        await queryInterface.bulkInsert('reports_seqqc', rows, {transaction});
+      }
+
+      await queryInterface.removeColumn('reports', 'seq_qc', {transaction});
+    });
+  },
+
+  down: async (queryInterface, Sq) => {
+    await queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.addColumn('reports', 'seq_qc', {
+        type: Sq.JSONB,
+        defaultValue: null,
+      }, {transaction});
+
+      await queryInterface.sequelize.query(`
+        WITH restored_seq_qc AS (
+          SELECT
+            report_id,
+            jsonb_agg(jsonb_build_object(
+              'Reads', reads,
+              'bioQC', bio_qc,
+              'labQC', lab_qc,
+              'Sample', sample,
+              'Library', library,
+              'Coverage', coverage,
+              'Input_ng', input_ng,
+              'Input_ug', input_ug,
+              'Protocol', protocol,
+              'Sample Name', sample_name,
+              'Duplicate_Reads_Perc', duplicate_reads_perc
+            )) AS seq_qc
+          FROM reports_seqqc
+          GROUP BY report_id
+        )
+        UPDATE reports r
+        SET seq_qc = restored_seq_qc.seq_qc
+        FROM restored_seq_qc
+        WHERE r.id = restored_seq_qc.report_id;
+      `, {transaction});
+
+      await queryInterface.sequelize.query(`
+        DELETE FROM reports_seqqc rs
+        USING reports r
+        WHERE rs.report_id = r.id
+          AND r.seq_qc IS NOT NULL;
+      `, {transaction});
+    });
+  },
+};