Merge pull request #180 from bcgsc/release/v7.7.0

v7.7.0

app/models/germlineSmallMutation/variants.js

@@ -194,6 +194,12 @@ module.exports = (sequelize, Sq) => {
       type: Sq.TEXT,
       allowNull: true,
     },
+    previouslyReported: {
+      name: 'previously_reported',
+      field: 'previously_reported',
+      type: Sq.TEXT,
+      allowNull: true,
+    },
   }, {
     ...DEFAULT_OPTIONS,
     tableName: 'germline_small_mutations_variant',

app/models/index.js

@@ -474,14 +474,22 @@ template.hasMany(analysisReports, {
 // Template Appendix
 const templateAppendix = require('./template/templateAppendix')(sequelize, Sq);
 
-template.hasOne(templateAppendix, {
+template.hasMany(templateAppendix, {
   as: 'appendix', foreignKey: 'templateId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
 });
 
 templateAppendix.belongsTo(template, {
   as: 'template', foreignKey: 'templateId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
 });
 
+project.hasMany(templateAppendix, {
+  as: 'appendix', foreignKey: 'projectId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
+});
+
+templateAppendix.belongsTo(project, {
+  as: 'project', foreignKey: 'projectId', targetKey: 'id', onDelete: 'CASCADE', constraints: true,
+});
+
 // Germline Small Mutations
 require('./germlineSmallMutation')(sequelize, Sq);
 

app/models/template/templateAppendix.js

@@ -14,6 +14,17 @@ module.exports = (sequelize, Sq) => {
         key: 'id',
       },
     },
+    projectId: {
+      name: 'projectId',
+      field: 'project_id',
+      type: Sq.INTEGER,
+      unique: false,
+      allowNull: true,
+      references: {
+        model: 'projects',
+        key: 'id',
+      },
+    },
     text: {
       type: Sq.TEXT,
     },
@@ -30,7 +41,7 @@ module.exports = (sequelize, Sq) => {
   // set instance methods
   templateAppendix.prototype.view = function (scope) {
     if (scope === 'public') {
-      const {id, templateId, deletedAt, updatedBy, ...publicView} = this.dataValues;
+      const {id, projectId, templateId, deletedAt, updatedBy, ...publicView} = this.dataValues;
       return publicView;
     }
     return this;

app/routes/report/images.js

@@ -135,9 +135,33 @@ const IMAGES_CONFIG = [
     format: 'PNG',
   },
   {
-    pattern: 'expression.spearman\\.(tcga|gtex|cser|hartwig|pediatric)',
+    pattern: 'expression.spearman.tcga',
     width: 1100,
-    height: 1360,
+    height: 3000,
+    format: 'PNG',
+  },
+  {
+    pattern: 'expression.spearman.gtex',
+    width: 1100,
+    height: 4050,
+    format: 'PNG',
+  },
+  {
+    pattern: 'expression.spearman.cser',
+    width: 1100,
+    height: 1125,
+    format: 'PNG',
+  },
+  {
+    pattern: 'expression.spearman.hartwig',
+    width: 1100,
+    height: 1500,
+    format: 'PNG',
+  },
+  {
+    pattern: 'expression.spearman.pediatric',
+    width: 1100,
+    height: 2775,
     format: 'PNG',
   },
   {

app/routes/template/templateAppendix.js

@@ -1,5 +1,6 @@
 const HTTP_STATUS = require('http-status-codes');
 const express = require('express');
+const {Op} = require('sequelize');
 
 const router = express.Router({mergeParams: true});
 
@@ -22,8 +23,33 @@ const updateSchema = schemaGenerator(db.models.templateAppendix, {
 // Add middleware to get template appendix
 router.use('/', async (req, res, next) => {
   try {
+    if (req.body.projectId) {
+      req.project = await db.models.project.findOne({
+        where:
+          {ident: req.body.projectId},
+      });
+    } else {
+      req.project = null;
+    }
+
+    let projectId;
+    if (req.project) {
+      req.body.projectId = req.project.id;
+      projectId = req.project.id;
+    } else {
+      projectId = null;
+    }
+
     req.templateAppendix = await db.models.templateAppendix.findOne({
-      where: {templateId: req.template.id},
+      where:
+      {
+        [Op.and]: [
+          {templateId: req.template.id},
+          {projectId},
+        ],
+      },
+      include:
+      [{model: db.models.project.scope('public'), as: 'project'}],
     });
   } catch (error) {
     logger.error(`Unable to get template appendix ${error}`);
@@ -32,6 +58,19 @@ router.use('/', async (req, res, next) => {
     });
   }
 
+  // Convert Project ID to ident in GET endpoint
+  if (req.project && req.templateAppendix && req.method === 'GET') {
+    req.templateAppendix.projectId = req.project.ident;
+  }
+
+  // Throw an error if Project ident is provided but not existent
+  if (!req.project && req.body.projectId) {
+    logger.error(`Invalid project ID for template appendix: ${req.body.projectId}`);
+    return res.status(HTTP_STATUS.NOT_FOUND).json({
+      error: {message: `Invalid project ID for template appendix: ${req.body.projectId}`},
+    });
+  }
+
   // Throw an error for a POST when a template appendix already exists
   if (req.templateAppendix && req.method === 'POST') {
     logger.error(`Template appendix already exists for ${req.template.name}`);

migrations/20220725194105-DEVSU-1830-add-germline-variant-previously-reported-field.js

@@ -0,0 +1,15 @@
+const GERMLINE_SMALL_VARIANTS_TABLE = 'germline_small_mutations_variant';
+
+module.exports = {
+  up: async (queryInterface, Sq) => {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      return Promise.all([
+        queryInterface.addColumn(GERMLINE_SMALL_VARIANTS_TABLE, 'previously_reported', Sq.TEXT, {transaction}),
+      ]);
+    });
+  },
+
+  down: async () => {
+    throw new Error('Not Implemented!');
+  },
+};

migrations/20220725201352-DEVSU-1668-add-project_id-to-template-appendix.js

@@ -0,0 +1,27 @@
+const TEMPLATES_TABLE = 'templates_appendix';
+
+module.exports = {
+  up: (queryInterface, Sq) => {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.addColumn(TEMPLATES_TABLE, 'project_id', {
+        name: 'projectId',
+        field: 'project_id',
+        type: Sq.INTEGER,
+        unique: false,
+        allowNull: true,
+        references: {
+          model: 'projects',
+          key: 'id',
+        },
+      }, {transaction});
+      await queryInterface.sequelize.query(
+        'DROP INDEX templates_appendix_template_id_index;',
+        {transaction},
+      );
+    });
+  },
+
+  down: () => {
+    throw new Error('Not Implemented!');
+  },
+};

package.json

@@ -1,7 +1,7 @@
 {
   "private": true,
   "name": "ipr-api",
-  "version": "7.6.0",
+  "version": "7.7.0",
   "description": "Integrated Pipeline Reports API",
   "main": "bin/server.js",
   "scripts": {