ebi-webcomponents · dlrice · Nov 8, 2024 · Nov 5, 2024 · Nov 5, 2024 · Nov 5, 2024
diff --git a/.babelrc b/.babelrc
@@ -1,16 +1,21 @@
 {
   "presets": [
     [
-      "@babel/preset-env", {
+      "@babel/preset-env",
+      {
         "useBuiltIns": "usage",
-        "corejs":  "3"
+        "corejs": "3"
       }
     ],
     "@babel/preset-typescript"
   ],
   "plugins": [
-      ["@babel/plugin-transform-runtime", {
+    [
+      "@babel/plugin-transform-runtime",
+      {
         "corejs": "3"
-      }]
+      }
+    ],
+    ["@babel/plugin-proposal-decorators", { "version": "2023-11" }]
   ]
 }
diff --git a/.gitignore b/.gitignore
@@ -5,4 +5,6 @@
 build/
 dist/
 node_modules/
-*.log
+*.log
+.yalc/
+yalc.lock
diff --git a/package.json b/package.json
@@ -10,8 +10,6 @@
     "build:es": "tsc",
     "build": "webpack --mode=production && yarn build:es",
     "watch": "webpack --mode=development -w",
-    "link-all": "yarn link protvista-interpro-adapter protvista-feature-adapter protvista-interpro-track nightingale-filter nightingale-manager nightingale-navigation protvista-proteomics-adapter nightingale-sequence protvista-structure-adapter nightingale-track nightingale-variation protvista-variation-adapter nightingale-linegraph-track protvista-datatable nightingale-structure data-loader",
-    "add-all": "yarn add protvista-feature-adapter nightingale-filter nightingale-manager nightingale-navigation protvista-proteomics-adapter nightingale-sequence protvista-structure-adapter nightingale-track nightingale-variation protvista-variation-adapter nightingale-linegraph-track protvista-datatable nightingale-structure data-loader",
     "start": "webpack serve --mode=development",
     "test:lint": "eslint src --ext .ts ",
     "test:types": "tsc",
@@ -36,26 +34,21 @@
     "@nightingale-elements/nightingale-structure": "5.2.0",
     "@nightingale-elements/nightingale-track": "5.2.0",
     "@nightingale-elements/nightingale-variation": "5.2.0",
-    "core-js": "^3.13.0",
-    "data-loader": "^2.9.1",
-    "file-saver": "^2.0.2",
+    "color-hash": "2.0.2",
+    "core-js": "3.13.0",
     "lit": "3.1.3",
     "protvista-datatable": "3.8.22",
-    "protvista-feature-adapter": "3.8.22",
-    "protvista-interpro-adapter": "3.8.22",
-    "protvista-proteomics-adapter": "3.8.22",
-    "protvista-structure-adapter": "3.8.22",
-    "protvista-variation-adapter": "3.8.22",
-    "timing-functions": "^2.0.1",
-    "url-join": "^4.0.1"
+    "timing-functions": "2.0.1",
+    "url-join": "4.0.1"
   },
   "devDependencies": {
     "@babel/core": "^7.14.3",
+    "@babel/plugin-proposal-decorators": "^7.25.9",
     "@babel/plugin-transform-runtime": "^7.14.3",
     "@babel/preset-env": "^7.14.2",
     "@babel/preset-typescript": "^7.13.0",
     "@babel/runtime-corejs3": "^7.14.0",
-    "@types/file-saver": "^2.0.2",
+    "@types/jest": "^29.5.14",
     "@types/url-join": "^4.0.0",
     "@typescript-eslint/eslint-plugin": "4.26.1",
     "@typescript-eslint/parser": "4.26.1",
@@ -64,7 +57,6 @@
     "concurrently": "^4.1.0",
     "copy-webpack-plugin": "^9.0.1",
     "css-loader": "^5.2.6",
-    "d3": "5.X",
     "eslint": "^7.27.0",
     "eslint-config-prettier": "^8.3.0",
     "jest": "^26.4.2",
@@ -76,8 +68,11 @@
     "webpack-cli": "^4.7.0",
     "webpack-dev-server": "^3.11.2"
   },
-  "peerDependencies": {
-    "d3": "5.X"
-  },
-  "gitHead": "5a756316482fa31d085602d46438861fb45e5178"
+  "jest": {
+    "testRegex": "(/__tests__/.*|(\\.|/))spec\\.ts$",
+    "testPathIgnorePatterns": [
+      "/__mocks__/",
+      "<rootDir>/dist/"
+    ]
+  }
 }
diff --git a/public/index.html b/public/index.html
@@ -3,7 +3,7 @@
   <head>
     <meta charset="utf-8" />
     <meta http-equiv="x-ua-compatible" content="ie=edge" />
-    <title>UniProt - ProtVista</title>
+    <title>protvista-uniprot</title>
     <meta name="description" content="" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -46,7 +46,6 @@
       <!-- <protvista-uniprot accession="P27958"></protvista-uniprot> -->
     </div>
 
-    <script src="https://d3js.org/d3.v4.min.js" charset="utf-8" defer></script>
     <script src="./protvista-uniprot.js" charset="utf-8" defer></script>
   </body>
 </html>
diff --git a/test/filterConfig.spec.js → src/__spec__/filter-config.spec.ts b/test/filterConfig.spec.js → src/__spec__/filter-config.spec.ts
@@ -1,4 +1,8 @@
-import { colorConfig, getFilteredVariants } from '../src/filterConfig';
+import {
+  colorConfig,
+  getFilteredVariants,
+  VariantsForFilter,
+} from '../filter-config';
 
 const transformedVariantPositions = [
   {
@@ -7,7 +11,7 @@ const transformedVariantPositions = [
         accession: 'A',
         begin: 1,
         end: 1,
-        start: '1',
+        start: 1,
         tooltipContent: '',
         sourceType: 'source',
         variant: 'V',
@@ -24,12 +28,13 @@ const transformedVariantPositions = [
           },
         ],
         xrefs: [],
+        hasPredictions: false,
       },
       {
         accession: 'B',
         begin: 1,
         end: 1,
-        start: '1',
+        start: 1,
         tooltipContent: '',
         sourceType: 'source',
         variant: 'D',
@@ -40,6 +45,7 @@ const transformedVariantPositions = [
         alternativeSequence: 'D',
         consequenceType: 'disease',
         xrefs: [],
+        hasPredictions: false,
       },
     ],
   },
@@ -49,7 +55,7 @@ const transformedVariantPositions = [
         accession: 'C',
         begin: 2,
         end: 2,
-        start: '2',
+        start: 2,
         tooltipContent: '',
         sourceType: 'source',
         variant: 'V',
@@ -60,6 +66,7 @@ const transformedVariantPositions = [
         alternativeSequence: 'V',
         consequenceType: 'disease',
         xrefs: [],
+        hasPredictions: false,
       },
     ],
   },
@@ -69,7 +76,7 @@ const transformedVariantPositions = [
         accession: 'D',
         begin: 3,
         end: 3,
-        start: '3',
+        start: 3,
         tooltipContent: '',
         sourceType: 'source',
         variant: 'V',
@@ -81,6 +88,7 @@ const transformedVariantPositions = [
         consequenceType: 'disease',
         siftScore: 0.5,
         xrefs: [],
+        hasPredictions: false,
       },
     ],
   },
@@ -89,7 +97,7 @@ const transformedVariantPositions = [
 describe('Variation filter config', () => {
   test('it should filter according to the callback function', () => {
     const filteredVariants = getFilteredVariants(
-      transformedVariantPositions,
+      transformedVariantPositions as VariantsForFilter,
       (variant) => variant.accession === 'A'
     );
     expect(filteredVariants).toEqual([
@@ -121,7 +129,7 @@ describe('Variation filter config', () => {
 
   test('it should get the right colour for other', () => {
     const thirdVariant = colorConfig(
-      transformedVariantPositions[1].variants[0]
+      transformedVariantPositions?.[1].variants[0]
     );
     expect(thirdVariant).toEqual('#009e73');
   });

diff --git a/src/adapters/__tests__/__mocks__/uniprotkb-entry-data.ts b/src/adapters/__tests__/__mocks__/uniprotkb-entry-data.ts
@@ -0,0 +1,76 @@
+const data = {
+  accession: 'P01234',
+  id: 'A4_HUMAN_mocked',
+  dbReferences: [
+    {
+      type: 'UniGene',
+      id: 'Hs.434980',
+    },
+    {
+      type: 'PDB',
+      id: '1AAP',
+      properties: {
+        method: 'X-ray',
+        resolution: '1.50 A',
+      },
+    },
+    {
+      type: 'PDB',
+      id: '1AMB',
+      properties: {
+        method: 'NMR',
+        chains: 'A=672-699',
+      },
+    },
+    {
+      type: 'PDB',
+      id: '1AMC',
+      properties: {
+        method: 'NMR',
+        chains: 'A=672-699',
+      },
+    },
+    {
+      type: 'PDB',
+      id: '1AML',
+      properties: {
+        method: 'NMR',
+        chains: 'A=672-711',
+      },
+    },
+    {
+      type: 'PDB',
+      id: '1BA4',
+      properties: {
+        method: 'NMR',
+        chains: 'A=672-711',
+      },
+    },
+    {
+      type: 'PROSITE',
+      id: 'PS00280',
+      properties: {
+        'match status': '1',
+        'entry name': 'BPTI_KUNITZ_1',
+      },
+    },
+    {
+      type: 'PROSITE',
+      id: 'PS50279',
+      properties: {
+        'match status': '1',
+        'entry name': 'BPTI_KUNITZ_2',
+      },
+    },
+  ],
+  sequence: {
+    version: 3,
+    length: 770,
+    mass: 86943,
+    modified: '1991-11-01',
+    sequence:
+      'MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEAEEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSAMSQSLLKTTQEPLARDPVKLPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN',
+  },
+};
+
+export default data;
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,4 +5,6 @@ @@
     build/
     dist/
     node_modules/
-    *.log
+    *.log
+    .yalc/
+    yalc.lock