protvista-uniprot 2.13.2 → 3.0.0

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "2.13.2",
+  "version": "3.0.0",
   "files": [
     "dist",
     "src"
@@ -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",
@@ -25,37 +23,32 @@
   "author": "Xavier Watkins <xwatkins@ebi.ac.uk>",
   "license": "MIT",
   "dependencies": {
-    "@nightingale-elements/nightingale-colored-sequence": "5.2.0",
-    "@nightingale-elements/nightingale-filter": "5.2.0",
-    "@nightingale-elements/nightingale-interpro-track": "5.2.0",
-    "@nightingale-elements/nightingale-linegraph-track": "5.2.0",
-    "@nightingale-elements/nightingale-manager": "5.2.0",
-    "@nightingale-elements/nightingale-navigation": "5.2.0",
-    "@nightingale-elements/nightingale-sequence": "5.2.0",
-    "@nightingale-elements/nightingale-sequence-heatmap": "5.1.0",
-    "@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",
+    "@nightingale-elements/nightingale-colored-sequence": "5.3.0",
+    "@nightingale-elements/nightingale-filter": "5.3.0",
+    "@nightingale-elements/nightingale-interpro-track": "5.3.0",
+    "@nightingale-elements/nightingale-linegraph-track": "5.3.0",
+    "@nightingale-elements/nightingale-manager": "5.3.0",
+    "@nightingale-elements/nightingale-navigation": "5.3.0",
+    "@nightingale-elements/nightingale-sequence": "5.3.0",
+    "@nightingale-elements/nightingale-sequence-heatmap": "5.3.0",
+    "@nightingale-elements/nightingale-structure": "5.3.0",
+    "@nightingale-elements/nightingale-track": "5.3.0",
+    "@nightingale-elements/nightingale-variation": "5.3.0",
+    "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/"
+    ]
+  }
 }

package/src/__spec__/filter-config.spec.ts

@@ -0,0 +1,143 @@
+import {
+  colorConfig,
+  getFilteredVariants,
+  VariantsForFilter,
+} from '../filter-config';
+
+const transformedVariantPositions = [
+  {
+    variants: [
+      {
+        accession: 'A',
+        begin: 1,
+        end: 1,
+        start: 1,
+        tooltipContent: '',
+        sourceType: 'source',
+        variant: 'V',
+        protvistaFeatureId: 'id1',
+        xrefNames: [],
+        type: 'VARIANT',
+        wildType: 'A',
+        alternativeSequence: 'V',
+        consequenceType: 'disease',
+        clinicalSignificances: [
+          {
+            type: 'Variant of uncertain significance',
+            sources: ['Ensembl'],
+          },
+        ],
+        xrefs: [],
+        hasPredictions: false,
+      },
+      {
+        accession: 'B',
+        begin: 1,
+        end: 1,
+        start: 1,
+        tooltipContent: '',
+        sourceType: 'source',
+        variant: 'D',
+        protvistaFeatureId: 'id2',
+        xrefNames: [],
+        type: 'VARIANT',
+        wildType: 'A',
+        alternativeSequence: 'D',
+        consequenceType: 'disease',
+        xrefs: [],
+        hasPredictions: false,
+      },
+    ],
+  },
+  {
+    variants: [
+      {
+        accession: 'C',
+        begin: 2,
+        end: 2,
+        start: 2,
+        tooltipContent: '',
+        sourceType: 'source',
+        variant: 'V',
+        protvistaFeatureId: 'id1',
+        xrefNames: [],
+        type: 'VARIANT',
+        wildType: 'A',
+        alternativeSequence: 'V',
+        consequenceType: 'disease',
+        xrefs: [],
+        hasPredictions: false,
+      },
+    ],
+  },
+  {
+    variants: [
+      {
+        accession: 'D',
+        begin: 3,
+        end: 3,
+        start: 3,
+        tooltipContent: '',
+        sourceType: 'source',
+        variant: 'V',
+        protvistaFeatureId: 'id1',
+        xrefNames: [],
+        type: 'VARIANT',
+        wildType: 'A',
+        alternativeSequence: 'V',
+        consequenceType: 'disease',
+        siftScore: 0.5,
+        xrefs: [],
+        hasPredictions: false,
+      },
+    ],
+  },
+];
+
+describe('Variation filter config', () => {
+  test('it should filter according to the callback function', () => {
+    const filteredVariants = getFilteredVariants(
+      transformedVariantPositions as VariantsForFilter,
+      (variant) => variant.accession === 'A'
+    );
+    expect(filteredVariants).toEqual([
+      {
+        variants: [transformedVariantPositions[0].variants[0]],
+      },
+      {
+        variants: [],
+      },
+      {
+        variants: [],
+      },
+    ]);
+  });
+
+  test('it should get the right colour for disease', () => {
+    const firstVariant = colorConfig(
+      transformedVariantPositions[0].variants[0]
+    );
+    expect(firstVariant).toEqual('#009e73');
+  });
+
+  test('it should get the right colour for non disease', () => {
+    const secondVariant = colorConfig(
+      transformedVariantPositions[0].variants[1]
+    );
+    expect(secondVariant).toEqual('#009e73');
+  });
+
+  test('it should get the right colour for other', () => {
+    const thirdVariant = colorConfig(
+      transformedVariantPositions?.[1].variants[0]
+    );
+    expect(thirdVariant).toEqual('#009e73');
+  });
+
+  test('it should get the right colour for predicted', () => {
+    const thirdVariant = colorConfig(
+      transformedVariantPositions[2].variants[0]
+    );
+    expect(thirdVariant).toEqual('#009e73');
+  });
+});

package/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;

package/src/adapters/__tests__/__snapshots__/structure-adapter.spec.ts.snap

@@ -0,0 +1,157 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`structure data should merge Overlapping Intervals 1`] = `
+Array [
+  Object {
+    "category": "STRUCTURE_COVERAGE",
+    "end": 0,
+    "start": 0,
+    "structures": Array [
+      Object {
+        "description": "Method: X-ray. Resolution: 1.50 A. ",
+        "end": 0,
+        "source": Object {
+          "id": "1AAP",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AAP",
+        },
+        "start": 0,
+      },
+    ],
+    "type": "PDBE_COVER",
+  },
+  Object {
+    "category": "STRUCTURE_COVERAGE",
+    "end": 711,
+    "start": 672,
+    "structures": Array [
+      Object {
+        "description": "Method: NMR. Chains: A=672-699. ",
+        "end": 699,
+        "source": Object {
+          "id": "1AMB",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMB",
+        },
+        "start": 672,
+      },
+      Object {
+        "description": "Method: NMR. Chains: A=672-699. ",
+        "end": 699,
+        "source": Object {
+          "id": "1AMC",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMC",
+        },
+        "start": 672,
+      },
+      Object {
+        "description": "Method: NMR. Chains: A=672-711. ",
+        "end": 711,
+        "source": Object {
+          "id": "1AML",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AML",
+        },
+        "start": 672,
+      },
+      Object {
+        "description": "Method: NMR. Chains: A=672-711. ",
+        "end": 711,
+        "source": Object {
+          "id": "1BA4",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1BA4",
+        },
+        "start": 672,
+      },
+    ],
+    "type": "PDBE_COVER",
+  },
+]
+`;
+
+exports[`structure data should turn structures into features 1`] = `
+Array [
+  Object {
+    "category": "STRUCTURE_COVERAGE",
+    "end": 0,
+    "start": 0,
+    "structures": Array [
+      Object {
+        "description": "Method: X-ray. Resolution: 1.50 A. ",
+        "end": 0,
+        "source": Object {
+          "id": "1AAP",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AAP",
+        },
+        "start": 0,
+      },
+    ],
+    "type": "PDBE_COVER",
+  },
+  Object {
+    "category": "STRUCTURE_COVERAGE",
+    "end": 699,
+    "start": 672,
+    "structures": Array [
+      Object {
+        "description": "Method: NMR. Chains: A=672-699. ",
+        "end": 699,
+        "source": Object {
+          "id": "1AMB",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMB",
+        },
+        "start": 672,
+      },
+    ],
+    "type": "PDBE_COVER",
+  },
+  Object {
+    "category": "STRUCTURE_COVERAGE",
+    "end": 699,
+    "start": 672,
+    "structures": Array [
+      Object {
+        "description": "Method: NMR. Chains: A=672-699. ",
+        "end": 699,
+        "source": Object {
+          "id": "1AMC",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMC",
+        },
+        "start": 672,
+      },
+    ],
+    "type": "PDBE_COVER",
+  },
+  Object {
+    "category": "STRUCTURE_COVERAGE",
+    "end": 711,
+    "start": 672,
+    "structures": Array [
+      Object {
+        "description": "Method: NMR. Chains: A=672-711. ",
+        "end": 711,
+        "source": Object {
+          "id": "1AML",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AML",
+        },
+        "start": 672,
+      },
+    ],
+    "type": "PDBE_COVER",
+  },
+  Object {
+    "category": "STRUCTURE_COVERAGE",
+    "end": 711,
+    "start": 672,
+    "structures": Array [
+      Object {
+        "description": "Method: NMR. Chains: A=672-711. ",
+        "end": 711,
+        "source": Object {
+          "id": "1BA4",
+          "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1BA4",
+        },
+        "start": 672,
+      },
+    ],
+    "type": "PDBE_COVER",
+  },
+]
+`;

package/src/adapters/__tests__/structure-adapter.spec.ts

@@ -0,0 +1,19 @@
+import {
+  getAllFeatureStructures,
+  mergeOverlappingIntervals,
+} from '../structure-adapter';
+
+import entryData from './__mocks__/uniprotkb-entry-data';
+
+describe('structure data', () => {
+  it('should turn structures into features', () => {
+    const features = getAllFeatureStructures(entryData);
+    expect(features).toMatchSnapshot();
+  });
+
+  it('should merge Overlapping Intervals', () => {
+    const features = getAllFeatureStructures(entryData);
+    const overlapping = mergeOverlappingIntervals(features);
+    expect(overlapping).toMatchSnapshot();
+  });
+});

package/src/{protvista-alphafold-confidence.ts → adapters/alphafold-confidence-adapter.ts}

@@ -1,4 +1,4 @@
-import { AlphafoldPayload } from './commonTypes';
+import { AlphafoldPayload } from './types/alphafold';
 
 type AlphafoldConfidencePayload = {
   residueNumber: Array<number>;
@@ -6,7 +6,7 @@ type AlphafoldConfidencePayload = {
   confidenceCategory: Array<string>;
 };
 
-export const getConfidenceURLFromPayload = (data: AlphafoldPayload) => {
+const getConfidenceURLFromPayload = (data: AlphafoldPayload) => {
   const cifURL = data?.[0]?.cifUrl;
   return cifURL?.length
     ? cifURL.replace('-model', '-confidence').replace('.cif', '.json')
@@ -30,7 +30,7 @@ type PartialProtein = {
   };
 };
 
-export const transformData = async (
+const transformData = async (
   data: AlphafoldPayload,
   protein: PartialProtein
 ) => {
@@ -41,3 +41,5 @@ export const transformData = async (
     return confidenceData?.confidenceCategory.join('');
   }
 };
+
+export default transformData;

package/src/{protvista-alphamissense-heatmap.ts → adapters/alphamissense-heatmap-adapter.ts}

@@ -1,8 +1,8 @@
 import {
   cellSplitter,
   rowSplitter,
-} from './protvista-alphamissense-pathogenicity';
-import { AlphafoldPayload } from './commonTypes';
+} from './alphamissense-pathogenicity-adapter';
+import { AlphafoldPayload } from './types/alphafold';
 
 const parseCSV = (rawText: string): Array<Record<string, string>> => {
   const data = [];
@@ -24,7 +24,9 @@ const parseCSV = (rawText: string): Array<Record<string, string>> => {
 };
 
 // Load and parse
-const loadAndParseAnnotations = async (url: string): Promise<Array<Record<string, string>>> => {
+const loadAndParseAnnotations = async (
+  url: string
+): Promise<Array<Record<string, string>>> => {
   try {
     const payload = await fetch(url);
     const rawCSV = await payload.text();
@@ -40,7 +42,7 @@ type PartialProtein = {
   };
 };
 
-export const transformData = async (
+const transformData = async (
   data: AlphafoldPayload,
   protein: PartialProtein
 ) => {
@@ -50,3 +52,5 @@ export const transformData = async (
     return heatmapData;
   }
 };
+
+export default transformData;

package/src/{protvista-alphamissense-pathogenicity.ts → adapters/alphamissense-pathogenicity-adapter.ts}

@@ -1,4 +1,4 @@
-import { AlphafoldPayload } from './commonTypes';
+import { AlphafoldPayload } from './types/alphafold';
 
 // from example data
 // benign: [0.0448,0.3397]: x < 0.34
@@ -87,7 +87,7 @@ type PartialProtein = {
   };
 };
 
-export const transformData = async (
+const transformData = async (
   data: AlphafoldPayload,
   protein: PartialProtein
 ) => {
@@ -98,3 +98,5 @@ export const transformData = async (
     return variationData;
   }
 };
+
+export default transformData;

package/src/adapters/config/evidence.ts

@@ -0,0 +1,105 @@
+const ecoMap = [
+  {
+    name: 'ECO:0000269',
+    description: 'Manual assertion based on experiment',
+    shortDescription: 'Publication',
+    acronym: 'EXP',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0000303',
+    description: 'Manual assertion based on opinion',
+    shortDescription: 'Publication',
+    acronym: 'NAS',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0000305',
+    description: 'Manual assertion inferred by curator',
+    shortDescription: 'Curated',
+    acronym: 'IC',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0000250',
+    description: 'Manual assertion inferred from sequence similarity',
+    shortDescription: 'By similarity',
+    acronym: 'ISS',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0000255',
+    description: 'Manual assertion according to rules',
+    shortDescription: 'Sequence Analysis',
+    acronym: 'ISM',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0007744',
+    description:
+      'Manual assertion inferred from combination of experimental and computational evidence',
+    shortDescription: 'Combined sources',
+    acronym: 'MIXM',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0000312',
+    description: 'Manual assertion inferred from database entries',
+    shortDescription: 'Imported',
+    acronym: 'MI',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0000256',
+    description: 'Automatic assertion according to rules',
+    shortDescription: 'Automatic annotation',
+    acronym: 'AA',
+  },
+  {
+    name: 'ECO:0000259',
+    description: 'Automatic assertion inferred from signature match',
+    shortDescription: 'Automatic annotation',
+    acronym: 'AA',
+  },
+  {
+    name: 'ECO:0007829',
+    description:
+      'Automatic assertion inferred from combination of experimental and computational evidence',
+    shortDescription: 'Combined sources',
+    acronym: 'MIXA',
+  },
+  /* ECO:0007829 replaced ECO:0000213 from release 2022_02. 
+    Some evidences still have the obsolete code. eg: https://www.ebi.ac.uk/proteins/api/antigen/P49841
+    It is better to show the evidence rather than being it empty */
+  {
+    name: 'ECO:0000213',
+    description:
+      'Automatic assertion inferred from combination of experimental and computational evidence',
+    shortDescription: 'Combined sources',
+    acronym: 'MIXA',
+  },
+  // ECO:0007744 replaced ECO:0000244 from release 2022_02. Same as above
+  {
+    name: 'ECO:0000244',
+    description:
+      'Manual assertion inferred from combination of experimental and computational evidence',
+    shortDescription: 'Combined sources',
+    acronym: 'MIXM',
+    isManual: true,
+  },
+  {
+    name: 'ECO:0000313',
+    description: 'Automatic assertion inferred from database entries',
+    shortDescription: 'Imported',
+    acronym: 'AI',
+  },
+  {
+    name: 'ECO:0000260',
+    description: 'Manual assertion inferred from signature match',
+    shortDescription: 'InterPro annotation',
+    acronym: 'SGNM',
+    isManual: true,
+  },
+];
+
+export default ecoMap;