feature/DEVSU-2543-auto-image-sizing

README.md

@@ -152,14 +152,6 @@ sequence by running this SQL command after the insert:
 Otherwise, you will get a unique constraint error when inserting via the API because Sequelize will try use an id
 that is now taken.
 
-## Adding new image types
-
-Steps to add a new image type:
-1. Open file app/routes/report/images.js
-2. Add new object to IMAGES_CONFIG. Pattern will be the regex for the image key being uploaded
-3. Open file app/constants.js
-4. Add new entry to VALID_IMAGE_KEY_PATTERN based on the IMAGES_CONFIG pattern
-
 ## Process Manager
 
 The production installation of IPR is run & managed by [pm2](http://pm2.keymetrics.io/)

app/constants.js

@@ -23,26 +23,6 @@ module.exports = {
     'probeResults',
     'proteinVariants',
   ],
-  VALID_IMAGE_KEY_PATTERN: `^${[
-    'mutSignature\\.(corPcors|barplot)\\.(dbs|indels|sbs)',
-    'subtypePlot\\.\\S+',
-    '(cnv|loh)\\.[12345]',
-    'cnvLoh.circos',
-    'mutationBurden\\.(barplot|density|legend)_(sv|snv|indel|snv_indel)\\.(primary|secondary|tertiary|quaternary)',
-    'circosSv\\.(genome|transcriptome)',
-    'expDensity\\.(histogram|violin\\.(tcga|gtex|cser|hartwig|pediatric))\\.\\S+',
-    'expression\\.(chart|legend|spearman\\.(tcga|gtex|cser|hartwig|target|pediatric|brca\\.(molecular|receptor)))',
-    'microbial\\.circos\\.(genome|transcriptome)',
-    'cibersort\\.(cd8_positive|combined)_t-cell_scatter',
-    'mixcr\\.circos_trb_vj_gene_usage',
-    'mixcr\\.dominance_vs_alpha_beta_t-cells_scatter',
-    'scpPlot',
-    'msi.scatter',
-    'pathwayAnalysis.legend',
-    'copyNumber(.*)',
-  ].map((patt) => {
-    return `(${patt})`;
-  }).join('|')}$`,
   REPORT_CREATE_BASE_URI: '/reports/create',
   REPORT_UPDATE_BASE_URI: '/reports/update',
   GERMLINE_CREATE_BASE_URI: '/germline/create',
@@ -57,4 +37,6 @@ module.exports = {
   MASTER_REPORT_ACCESS: ['admin', 'manager'],
   ALL_PROJECTS_ACCESS: ['admin', 'all projects access'],
   UPDATE_METHODS: ['POST', 'PUT', 'DELETE'],
+  IMAGE_UPLOAD_LIMIT: 3000000,
+  IMAGE_SIZE_LIMIT: 20000, // in bytes
 };

app/libs/createReport.js

@@ -4,7 +4,7 @@ const path = require('path');
 const db = require('../models');
 const {uploadReportImage} = require('../routes/report/images');
 const logger = require('../log');
-const {GENE_LINKED_VARIANT_MODELS, KB_PIVOT_MAPPING} = require('../constants');
+const {GENE_LINKED_VARIANT_MODELS, KB_PIVOT_MAPPING, IMAGE_UPLOAD_LIMIT} = require('../constants');
 const {sanitizeHtml} = require('./helperFunctions');
 
 const EXCLUDE_SECTIONS = new Set([
@@ -418,6 +418,26 @@ const createReport = async (data) => {
   // Create report sections
   try {
     await createReportSections(report, data, transaction);
+
+    const result = await db.query(
+      `SELECT
+            SUM(pg_column_size("reports_image_data")) AS avg_size_bytes
+          FROM
+            "reports_image_data"
+          WHERE
+            "report_id" = :reportId`,
+      {
+        replacements: {reportId: report.id},
+        type: 'select',
+        transaction,
+      },
+    );
+
+    const totalImageSize = result[0].avg_size_bytes;
+    if (totalImageSize > IMAGE_UPLOAD_LIMIT) {
+      throw new Error(`Total image size exceeds ${IMAGE_UPLOAD_LIMIT / 1000000} megabytes`);
+    }
+
     await transaction.commit();
     return report;
   } catch (error) {

app/libs/image.js

@@ -1,5 +1,34 @@
 const sharp = require('sharp');
 const db = require('../models');
+const {IMAGE_SIZE_LIMIT} = require('../constants');
+
+/**
+ * Delete image from images table
+ *
+ * @param {string} ident - Ident of image to delete
+ * @param {boolean} force - Whether it is a hard delete or not
+ * @param {object} transaction - Transaction to run delete under
+ * @returns {Promise<object>} - Returns the newly updated image data
+ */
+const autoDownsize = async (image, size, format = 'png') => {
+  // Base case: If the image size is less than or equal to size, return the image
+  if (image.info.size <= size) {
+    return image;
+  }
+
+  // Process the image (resize and format) and update the size
+  const resizedImage = await sharp(image.data)
+    .resize(
+      Math.floor(image.info.width / 1.5),
+      Math.floor(image.info.height / 1.5),
+      {fit: 'inside', withoutEnlargement: true},
+    )
+    .toFormat(format.toLowerCase())
+    .toBuffer({resolveWithObject: true});
+
+  // Recursive call with the resized image
+  return autoDownsize(resizedImage, size, format);
+};
 
 /**
  * Resize, reformat and return base64 representation of image.
@@ -12,13 +41,14 @@ const db = require('../models');
  * @returns {Promise<string>} - Returns base64 representation of image
  * @throws {Promise<Error>} - File doesn't exist, incorrect permissions, etc.
  */
-const processImage = async (image, width, height, format = 'png') => {
-  const imageData = await sharp(image)
-    .resize(width, height, {fit: 'inside', withoutEnlargement: true})
+const processImage = async (image, size = IMAGE_SIZE_LIMIT, format = 'png') => {
+  let imageData = await sharp(image)
     .toFormat(format.toLowerCase())
-    .toBuffer();
+    .toBuffer({resolveWithObject: true});
+
+  imageData = await autoDownsize(imageData, size, format);
 
-  return imageData.toString('base64');
+  return imageData.data.toString('base64');
 };
 
 /**
@@ -37,11 +67,11 @@ const processImage = async (image, width, height, format = 'png') => {
  */
 const uploadImage = async (image, options = {}) => {
   const {
-    data, width, height, filename, format, type,
+    data, filename, format, type,
   } = image;
 
   // Resize image
-  const imageData = await processImage(data, width, height, format.replace('image/', ''));
+  const imageData = await processImage(data, IMAGE_SIZE_LIMIT, format.replace('image/', ''));
 
   // Upload image data
   return db.models.image.create({

app/routes/report/image/index.js

@@ -5,7 +5,6 @@ const {Op} = require('sequelize');
 const db = require('../../../models');
 const logger = require('../../../log');
 const {uploadReportImage} = require('../images');
-const {VALID_IMAGE_KEY_PATTERN} = require('../../../constants');
 
 const router = express.Router({mergeParams: true});
 
@@ -62,19 +61,11 @@ router.route('/')
       return res.status(HTTP_STATUS.BAD_REQUEST).json({error: {message: 'No attached images to upload'}});
     }
 
-    // Check for valid and duplicate keys
     const keys = [];
-    const pattern = new RegExp(VALID_IMAGE_KEY_PATTERN);
 
     for (let [key, value] of Object.entries(req.files)) {
       key = key.trim();
 
-      // Check if key is valid
-      if (!pattern.test(key)) {
-        logger.error(`Invalid key: ${key}`);
-        return res.status(HTTP_STATUS.BAD_REQUEST).json({error: {message: `Invalid key: ${key}`}});
-      }
-
       // Check if key is a duplicate
       if (keys.includes(key) || Array.isArray(value)) {
         logger.error(`Duplicate keys are not allowed. Duplicate key: ${key}`);