fix(pencil): fix lint and add pre-commit restr

Author: ladeirarodolfo

.eslintrc.js

@@ -0,0 +1,36 @@
+module.exports = {
+  env: {
+    node: true,
+    commonjs: true,
+    es2021: true,
+    "jest/globals": true
+  },
+  extends: [
+    'airbnb-base',
+    "prettier",
+    "plugin:node/recommended"
+  ],
+  plugins: [
+    "eslint-plugin-prettier",
+    "jest"
+  ],
+  parserOptions: {
+    "ecmaVersion": 2020
+  },
+  rules: {
+    "no-param-reassign": "warn",
+    'prettier/prettier': 'warn',
+    "no-console": 0,
+    eqeqeq: 0,
+    "max-len": [2, {"code": 168, "ignoreUrls": true}],
+    "no-await-in-loop": 0,
+    "no-mixed-operators": 0,
+    "no-plusplus": ["error", { "allowForLoopAfterthoughts": true }],
+    "no-continue": 0,
+    "radix": 0,
+    "no-underscore-dangle": 0,
+    "no-restricted-syntax": "warn",
+    "consistent-return": "warn",
+    "prefer-destructuring": 0,
+  },
+};

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "test_data"]
-	path = test_data
+[submodule "testdata"]
+	path = testdata
 	url = https://github.com/OHIF/viewer-testdata

.husky/pre-commit

@@ -2,3 +2,4 @@
 . "$(dirname "$0")/_/husky.sh"
 
 yarn run lint:fix
+git add $(git diff --name-only --cached)

package.json

@@ -7,13 +7,20 @@
     "yarn": ">=1.22.4"
   },
   "devDependencies": {
+    "eslint": "^8.9.0",
+    "eslint-config-airbnb-base": "^15.0.0",
+    "eslint-config-prettier": "^8.3.0",
+    "eslint-plugin-import": "^2.25.4",
+    "eslint-plugin-jest": "^26.1.0",
+    "eslint-plugin-node": "^11.1.0",
+    "eslint-plugin-prettier": "^4.0.0",
     "jest": "^27.5.1",
     "lerna": "^4.0.0",
     "must": "^0.13.4",
-    "prettier": "^2.5.1"
+    "prettier": "^2.5.1",
+    "prettier-eslint": "^13.0.0"
   },
   "dependencies": {
-    "commander": "^9.0.0",
     "husky": "^7.0.4"
   },
   "workspaces": [
@@ -23,7 +30,8 @@
     "test": "lerna run test --parallel --stream",
     "build": "lerna run build --stream",
     "link:exec": "lerna run link:exec --stream",
-    "lint": "lerna run lint --parallel --stream -- ./lib/**/*.js ./tests/**/*.js",
-    "lint:fix": "lerna run lint:fix --parallel --stream -- ./lib/**/*.js ./tests/**/*.js"
+    "lint": "lerna run lint --parallel --stream -- --color ./lib/**/*.js ./tests/**/*.js",
+    "lint:fix": "lerna run lint:fix --parallel --stream -- --color ./lib/**/*.js ./tests/**/*.js",
+    "postinstall": "git config core.hooksPath '.husky' && echo 'Pre-commit configured'"
   }
 }

packages/static-wado-creator/.eslintrc.js

@@ -0,0 +1,10 @@
+module.exports = {
+ 
+  extends: [
+    '../../.eslintrc.js'
+  ],
+  globals: {
+    "TEST_DATA_PATH": true,
+    "OUTPUT_TEMP_PATH": true
+  },
+};

packages/static-wado-creator/lib/index.js

@@ -1,22 +1,19 @@
-"use strict";
 const dicomCodec = require("@cornerstonejs/dicom-codec");
 const { program, Stats } = require("@ohif/static-wado-util");
 const dicomParser = require("dicom-parser");
+const fs = require("fs");
+const path = require("path");
+const homedir = require("os").homedir();
 const asyncIterableToBuffer = require("./operation/adapter/asyncIterableToBuffer");
 const getDataSet = require("./operation/getDataSet");
-const JSONWriter = require("./writer/JSONWriter");
 const InstanceDeduplicate = require("./operation/InstanceDeduplicate");
 const DeduplicateWriter = require("./writer/DeduplicateWriter");
 const ImageFrameWriter = require("./writer/ImageFrameWriter");
 const CompleteStudyWriter = require("./writer/CompleteStudyWriter");
 const IdCreator = require("./util/IdCreator");
-const fs = require("fs");
 const dirScanner = require("./reader/dirScanner");
 const ScanStudy = require("./operation/ScanStudy");
 const HashDataWriter = require("./writer/HashDataWriter");
-const JSONReader = require("./reader/JSONReader");
-const path = require("path");
-const homedir = require("os").homedir();
 const VideoWriter = require("./writer/VideoWriter");
 const {
   transcodeImageFrame,
@@ -150,8 +147,11 @@ class StaticWado {
     let bulkDataIndex = 0;
     let imageFrameIndex = 0;
     const generator = {
-      bulkdata: async (bulkData) =>
-        this.callback.bulkdata(targetId, bulkDataIndex++, bulkData),
+      bulkdata: async (bulkData) => {
+        const _bulkDataIndex = bulkDataIndex;
+        bulkDataIndex += 1;
+        this.callback.bulkdata(targetId, _bulkDataIndex, bulkData);
+      },
       imageFrame: async (originalImageFrame) => {
         const { imageFrame, id: transcodedId } = await transcodeImageFrame(
           id,
@@ -161,9 +161,12 @@ class StaticWado {
           this.options
         );
 
+        const currentImageFrameIndex = imageFrameIndex;
+        imageFrameIndex += 1;
+
         return this.callback.imageFrame(
           transcodedId,
-          imageFrameIndex++,
+          currentImageFrameIndex,
           imageFrame
         );
       },

packages/static-wado-creator/lib/model/TagLists.js

@@ -1,6 +1,7 @@
 const hashFactory = require("node-object-hash");
+const Tags = require("../dictionary/Tags");
+
 const hasher = hashFactory();
-const Tags = require("../../lib/dictionary/Tags");
 
 const { PatientID, PatientName, IssuerOfPatientID } = Tags;
 const {

packages/static-wado-creator/lib/operation/InstanceDeduplicate.js

@@ -1,6 +1,8 @@
-const JSONWriter = require("../../lib/writer/JSONWriter");
-const TagLists = require("../../lib/model/TagLists");
-const Tags = require("../../lib/dictionary/Tags");
+// TODO review returning type of some methods
+const JSONWriter = require("../writer/JSONWriter");
+const TagLists = require("../model/TagLists");
+const Tags = require("../dictionary/Tags");
+
 const extractors = {
   patient: TagLists.PatientQuery,
   study: TagLists.StudyQuery,
@@ -15,18 +17,18 @@ const extractors = {
  * Whenever the study UID changes, a new event is fired to indicate the deduplicated data is ready.
  */
 async function deduplicateSingleInstance(id, imageFrame) {
-  if (!imageFrame) return;
+  if (!imageFrame) return {};
   const studyData = await this.completeStudy.getCurrentStudyData(this, id);
   const seriesUID = imageFrame[Tags.SeriesInstanceUID];
   const sopUID = imageFrame[Tags.SOPInstanceUID];
   if (!sopUID) {
     console.warn("No sop instance UID in", imageFrame);
-    return;
+    return {};
   }
   if (studyData.sopExists(sopUID)) {
     // console.log('SOP Instance UID', sopUID.Value[0], 'already exists, skipping');
     // TODO - allow replace as an option
-    return;
+    return {};
   }
   const deduplicated = { ...imageFrame };
 
@@ -59,6 +61,7 @@ const canonicalize = (json) => {
   Object.keys(json).forEach((tag) => {
     if (!tag || tag === "undefined") {
       // console.error('Got an undefined tag:', tag, typeof(tag));
+      // TODO check returning value
       return;
     }
     const val = json[tag];
@@ -71,23 +74,28 @@ const canonicalize = (json) => {
 };
 
 const InstanceDeduplicate = (options) =>
-  async function InstanceDeduplicate(id, imageFrame) {
+  async function run(id, sourceImageFrame) {
     // Notify the existing listeners, if any
-    imageFrame = canonicalize(imageFrame);
+    const imageFrame = canonicalize(sourceImageFrame);
     if (options.isInstanceMetadata) {
       await JSONWriter(id.sopInstanceRootPath, "metadata", imageFrame);
     }
     if (!options.isDeduplicate && !options.isGroup) {
       return;
     }
-    if (!this.deduplicateSingleInstance)
+
+    if (!this.deduplicateSingleInstance) {
       this.deduplicateSingleInstance = deduplicateSingleInstance;
+    }
+
     const deduppedInstance = await this.deduplicateSingleInstance(
       id,
       imageFrame
     );
-    if (!deduppedInstance) return;
-    await this.deduplicated(id, deduppedInstance);
+    if (deduppedInstance) {
+      // this refers to callee
+      await this.deduplicated(id, deduppedInstance);
+    }
   };
 
 module.exports = InstanceDeduplicate;

packages/static-wado-creator/lib/operation/ScanStudy.js

@@ -1,11 +1,10 @@
 const path = require("path");
-const StudyData = require("./StudyData");
 
 function ScanStudy(options) {
   const { directoryName, deduplicatedRoot, deduplicatedInstancesRoot } =
     options;
 
-  return async function (dir, studyInstanceUid) {
+  return async function run(dir, studyInstanceUid) {
     const studyPath = path.join(directoryName, "studies", studyInstanceUid);
     const deduplicatedPath = path.join(deduplicatedRoot, studyInstanceUid);
     const deduplicatedInstancesPath = path.join(

packages/static-wado-creator/lib/operation/StudyData.js

@@ -1,10 +1,11 @@
-const Tags = require("../../lib/dictionary/Tags");
-const TagLists = require("../../lib/model/TagLists");
 const path = require("path");
 const fs = require("fs");
-const JSONReader = require("../../lib/reader/JSONReader");
-const JSONWriter = require("../../lib/writer/JSONWriter");
 const hashFactory = require("node-object-hash");
+const Tags = require("../dictionary/Tags");
+const TagLists = require("../model/TagLists");
+const JSONReader = require("../reader/JSONReader");
+const JSONWriter = require("../writer/JSONWriter");
+
 const hasher = hashFactory();
 
 const getSeriesInstanceUid = (seriesInstance) =>
@@ -23,19 +24,6 @@ const getSeriesInstanceUid = (seriesInstance) =>
  * level data multiple times when it already exists.
  */
 class StudyData {
-  deduplicated = [];
-  extractData = {};
-  // The list of already existing files read in to create this object
-  existingFiles = [];
-  // The read hashes is the hashes of the files that are read, both as groups and internally
-  readHashes = {};
-  // The deduplicated hashes are just the hashes for individual items
-  deduplicatedHashes = {};
-  sopInstances = {};
-
-  // Used to track if new instances have been added.
-  newInstancesAdded = 0;
-
   constructor(
     {
       studyInstanceUid,
@@ -45,6 +33,18 @@ class StudyData {
     },
     { isGroup }
   ) {
+    this.deduplicated = [];
+    this.extractData = {};
+    // The list of already existing files read in to create this object
+    this.existingFiles = [];
+    // The read hashes is the hashes of the files that are read, both as groups and internally
+    this.readHashes = {};
+    // The deduplicated hashes are just the hashes for individual items
+    this.deduplicatedHashes = {};
+    this.sopInstances = {};
+
+    // Used to track if new instances have been added.
+    this.newInstancesAdded = 0;
     this.studyInstanceUid = studyInstanceUid;
     this.studyPath = studyPath;
     this.isGroup = isGroup;
@@ -138,7 +138,7 @@ class StudyData {
       console.log("No refs for", deduplicated);
       return deduplicated;
     }
-    const ret = Object.assign({}, deduplicated);
+    const ret = { ...deduplicated };
     for (const hashKey of refs.Value) {
       const item = await this.getOrLoadExtract(hashKey);
       Object.assign(ret, item);
@@ -161,23 +161,23 @@ class StudyData {
     if (!this.isGroup) return;
     // TODO - check the hash code on the added data, if it has already been seen then ignore this item.
     if (this.internalAddDeduplicated(data)) {
-      this.newInstancesAdded++;
+      this.newInstancesAdded += 1;
     }
   }
 
   /** Add the instance if not already present */
   internalAddDeduplicated(data, fileName = "internal") {
     const hashValue = TagLists.addHash(data, Tags.InstanceType);
-    if (this.deduplicatedHashes[hashValue]) {
+    if (!hashValue || this.deduplicatedHashes[hashValue]) {
       // console.log('Not adding', hashValue, 'because the hash exists');
-      return;
+      return false;
     }
     const sopUID = data[Tags.SOPInstanceUID];
     const sopValue = (sopUID && sopUID.Value && sopUID.Value[0]) || sopUID;
     const sopIndex = this.sopInstances[sopValue];
     if (!sopValue) {
       console.warn("No sop value in ", data);
-      return;
+      return false;
     }
     this.deduplicatedHashes[hashValue] = data;
     this.readHashes[hashValue] = fileName;
@@ -188,7 +188,8 @@ class StudyData {
       this.sopInstances[sopValue] = this.deduplicated.length;
       this.deduplicated.push(data);
     }
-    return hashValue;
+
+    return !!hashValue;
   }
 
   async listJsonFiles(dir) {
@@ -259,7 +260,7 @@ class StudyData {
           const refs = item[Tags.DeduppedRef];
           if (refs && refs.Value) {
             refs.Value.forEach((hashValue) => {
-              this.readHashes[hashValue] = hashValue + ".gz";
+              this.readHashes[hashValue] = `${hashValue}.gz`;
             });
           }
         } else {
@@ -327,7 +328,7 @@ class StudyData {
         Value: [instances.length],
       };
       numberOfInstances += instances.length;
-      numberOfSeries++;
+      numberOfSeries += 1;
       seriesList.push(seriesQuery);
       const modality = seriesQuery[Tags.Modality].Value[0];
       if (modalitiesInStudy.indexOf(modality) == -1)
@@ -391,6 +392,7 @@ class StudyData {
     return data;
   }
 
+  /* eslint-disable-next-line class-methods-use-this */
   removeGz(name) {
     const gzIndex = name.indexOf(".gz");
     return (gzIndex > 0 && name.substring(0, gzIndex)) || name;
@@ -410,7 +412,7 @@ class StudyData {
     data[Tags.DeduppedRef] = {
       vr: "CS",
       Value: Object.keys(this.readHashes).filter(
-        (hash) => this.deduplicatedHashes[hashValue] == undefined
+        () => this.deduplicatedHashes[hashValue] == undefined
       ),
     };
     await JSONWriter(