protvista-uniprot 3.0.1 → 3.0.7

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "3.0.1",
+  "version": "3.0.7",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "build:es": "tsc",
-    "build": "webpack --mode=production && yarn build:es",
+    "build:es": "tsc --emitDeclarationOnly",
+    "build": "webpack --mode=production --config webpack.config.js && yarn build:es",
     "watch": "webpack --mode=development -w",
     "start": "webpack serve --mode=development",
     "test:lint": "eslint src --ext .ts ",
@@ -18,7 +18,15 @@
     "clear-cdn-cache": "./scripts/clearCDNcaches.sh"
   },
   "main": "dist/protvista-uniprot.js",
-  "module": "dist/es/protvista-uniprot.js",
+  "module": "dist/protvista-uniprot.mjs",
+  "types": "dist/types/index.d.ts",
+  "exports": {
+    ".": {
+      "import": "./dist/protvista-uniprot.mjs",
+      "require": "./dist/protvista-uniprot.js"
+    }
+  },
+  "sideEffects": false,
   "keywords": [],
   "author": "Xavier Watkins <xwatkins@ebi.ac.uk>",
   "license": "MIT",
@@ -52,10 +60,10 @@
     "@types/url-join": "^4.0.0",
     "@typescript-eslint/eslint-plugin": "4.26.1",
     "@typescript-eslint/parser": "4.26.1",
-    "babel-jest": "^27.0.1",
-    "babel-loader": "^8.2.2",
+    "babel-jest": "^29.7.0",
+    "babel-loader": "^9.2.1",
     "concurrently": "^4.1.0",
-    "copy-webpack-plugin": "^9.0.1",
+    "copy-webpack-plugin": "^12.0.2",
     "css-loader": "^5.2.6",
     "eslint": "^7.27.0",
     "eslint-config-prettier": "^8.3.0",
@@ -63,10 +71,10 @@
     "npm-run-all": "^4.1.5",
     "style-loader": "^2.0.0",
     "svg-inline-loader": "^0.8.0",
-    "typescript": "^4.3.2",
+    "typescript": "^5.6.3",
     "webpack": "^5.91.0",
-    "webpack-cli": "^4.7.0",
-    "webpack-dev-server": "^3.11.2"
+    "webpack-cli": "^5.1.4",
+    "webpack-dev-server": "^5.1.0"
   },
   "jest": {
     "testRegex": "(/__tests__/.*|(\\.|/))spec\\.ts$",

package/dist/es/__spec__/filter-config.spec.js

@@ -1,123 +0,0 @@
-import { colorConfig, getFilteredVariants, } 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, (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 === null || transformedVariantPositions === void 0 ? void 0 : 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');
-    });
-});
-//# sourceMappingURL=filter-config.spec.js.map

package/dist/es/__spec__/filter-config.spec.js.map

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package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js

@@ -1,75 +0,0 @@
-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;
-//# sourceMappingURL=uniprotkb-entry-data.js.map

package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js.map

@@ -1 +0,0 @@
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package/dist/es/adapters/__tests__/structure-adapter.spec.js

@@ -1,14 +0,0 @@
-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();
-    });
-});
-//# sourceMappingURL=structure-adapter.spec.js.map

package/dist/es/adapters/__tests__/structure-adapter.spec.js.map

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package/dist/es/adapters/alphafold-confidence-adapter.js

@@ -1,26 +0,0 @@
-const getConfidenceURLFromPayload = (data) => {
-    var _a;
-    const cifURL = (_a = data === null || data === void 0 ? void 0 : data[0]) === null || _a === void 0 ? void 0 : _a.cifUrl;
-    return (cifURL === null || cifURL === void 0 ? void 0 : cifURL.length)
-        ? cifURL.replace('-model', '-confidence').replace('.cif', '.json')
-        : null;
-};
-const loadConfidence = async (url) => {
-    try {
-        const payload = await fetch(url);
-        return payload.json();
-    }
-    catch (e) {
-        console.error('Could not load AlphaFold confidence', e);
-    }
-};
-const transformData = async (data, protein) => {
-    const confidenceUrl = getConfidenceURLFromPayload(data);
-    const { uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
-    if (confidenceUrl && uniprotSequence === protein.sequence.sequence) {
-        const confidenceData = await loadConfidence(confidenceUrl);
-        return confidenceData === null || confidenceData === void 0 ? void 0 : confidenceData.confidenceCategory.join('');
-    }
-};
-export default transformData;
-//# sourceMappingURL=alphafold-confidence-adapter.js.map

package/dist/es/adapters/alphafold-confidence-adapter.js.map

@@ -1 +0,0 @@
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package/dist/es/adapters/alphamissense-heatmap-adapter.js

@@ -1,36 +0,0 @@
-import { cellSplitter, rowSplitter, } from './alphamissense-pathogenicity-adapter';
-const parseCSV = (rawText) => {
-    const data = [];
-    for (const [i, row] of rawText.split(rowSplitter).entries()) {
-        if (i === 0 || !row) {
-            continue;
-        }
-        const [, , positionString, mutated, pathogenicityScore] = row.match(cellSplitter);
-        data.push({
-            xValue: +positionString,
-            yValue: mutated,
-            score: +pathogenicityScore,
-        });
-    }
-    return data;
-};
-// Load and parse
-const loadAndParseAnnotations = async (url) => {
-    try {
-        const payload = await fetch(url);
-        const rawCSV = await payload.text();
-        return parseCSV(rawCSV);
-    }
-    catch (e) {
-        console.error('Could not load AlphaMissense pathogenicity', e);
-    }
-};
-const transformData = async (data, protein) => {
-    const { amAnnotationsUrl, uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
-    if (amAnnotationsUrl && uniprotSequence === protein.sequence.sequence) {
-        const heatmapData = await loadAndParseAnnotations(amAnnotationsUrl);
-        return heatmapData;
-    }
-};
-export default transformData;
-//# sourceMappingURL=alphamissense-heatmap-adapter.js.map

package/dist/es/adapters/alphamissense-heatmap-adapter.js.map

@@ -1 +0,0 @@
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package/dist/es/adapters/alphamissense-pathogenicity-adapter.js

@@ -1,68 +0,0 @@
-// from example data
-// benign: [0.0448,0.3397]: x < 0.34
-// ambiguous: [0.34,0.564]: 0.34 <= x <= 0.564
-// pathogenic: [0.5646,0.9999]: 0.564 < x
-const benign = 0.34;
-const pathogenic = 0.564;
-export const rowSplitter = /\s*\n\s*/;
-export const cellSplitter = /^(.)(\d+)(.),(.+),(\w+)$/;
-const parseCSV = (rawText) => {
-    const positions = [];
-    for (const [i, row] of rawText.split(rowSplitter).entries()) {
-        if (i === 0 || !row) {
-            continue;
-        }
-        const [, wildType, positionString, mutated, pathogenicityScore, pathogenicityLabel,] = row.match(cellSplitter);
-        const position = +positionString;
-        const index = position - 1;
-        if (!positions[index]) {
-            positions[index] = [];
-        }
-        positions[index].push({
-            wildType,
-            position,
-            mutated,
-            pathogenicityScore: +pathogenicityScore,
-            pathogenicityLabel,
-        });
-    }
-    const out = [];
-    for (const position of positions) {
-        let letter = 'A';
-        // maximum
-        // const value = Math.max(
-        //   ...position.map((variation) => variation.pathogenicityScore)
-        // );
-        // average
-        const value = position.reduce((acc, variation) => acc + +variation.pathogenicityScore, 0) / position.length;
-        if (value > pathogenic) {
-            letter = 'P';
-        }
-        else if (value < benign) {
-            letter = 'B';
-        }
-        out.push(letter);
-    }
-    return out.join('');
-};
-// Load and parse
-const loadAndParseAnnotations = async (url) => {
-    try {
-        const payload = await fetch(url);
-        const rawCSV = await payload.text();
-        return parseCSV(rawCSV);
-    }
-    catch (e) {
-        console.error('Could not load AlphaMissense pathogenicity', e);
-    }
-};
-const transformData = async (data, protein) => {
-    const { amAnnotationsUrl, uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
-    if (amAnnotationsUrl && uniprotSequence === protein.sequence.sequence) {
-        const variationData = await loadAndParseAnnotations(amAnnotationsUrl);
-        // return confidenceData?.confidenceCategory.join('');
-        return variationData;
-    }
-};
-export default transformData;
-//# sourceMappingURL=alphamissense-pathogenicity-adapter.js.map

package/dist/es/adapters/alphamissense-pathogenicity-adapter.js.map

@@ -1 +0,0 @@
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package/dist/es/adapters/config/evidence.js

@@ -1,101 +0,0 @@
-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;
-//# sourceMappingURL=evidence.js.map

package/dist/es/adapters/config/evidence.js.map

@@ -1 +0,0 @@
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package/dist/es/adapters/feature-adapter.js

@@ -1,18 +0,0 @@
-import { renameProperties } from '../utils';
-import formatTooltip from '../tooltips/featureTooltip';
-const transformData = (data) => {
-    let transformedData = [];
-    const { features } = data;
-    if (features && features.length > 0) {
-        transformedData = features.map((feature) => {
-            return {
-                ...feature,
-                tooltipContent: formatTooltip(feature),
-            };
-        });
-        transformedData = renameProperties(transformedData);
-    }
-    return transformedData;
-};
-export default transformData;
-//# sourceMappingURL=feature-adapter.js.map

package/dist/es/adapters/feature-adapter.js.map

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package/dist/es/adapters/interpro-adapter.js

@@ -1,60 +0,0 @@
-import ColorHash from 'color-hash';
-// Copied from InterPro to replicate the same colours for the representative domains
-/* eslint-disable no-magic-numbers */
-const colorHash = new ColorHash({
-    hash: 'bkdr',
-    saturation: [0.65, 0.35, 0.5],
-    lightness: [0.65, 0.35, 0.5],
-});
-/* eslint-enable no-magic-numbers */
-const transformData = (data) => {
-    var _a;
-    try {
-        return (_a = data === null || data === void 0 ? void 0 : data.results) === null || _a === void 0 ? void 0 : _a.map(({ metadata, proteins }) => {
-            var _a;
-            return ({
-                ...metadata,
-                locations: proteins[0].entry_protein_locations,
-                start: proteins[0].entry_protein_locations
-                    ? Math.min(...proteins[0].entry_protein_locations.map((location) => Math.min(...location.fragments.map((fragment) => fragment.start))))
-                    : '',
-                end: proteins[0].entry_protein_locations
-                    ? Math.max(...(_a = proteins[0].entry_protein_locations) === null || _a === void 0 ? void 0 : _a.map((location) => Math.max(...location.fragments.map((fragment) => fragment.end))))
-                    : '',
-                color: colorHash.hex(metadata.accession.toLowerCase().split('').reverse().join('')),
-                tooltipContent: `
-        <h5>Accession</h5>
-        <p>
-        <a
-          target="_blank"
-          rel="noopener"
-          href="https://www.ebi.ac.uk/interpro/entry/${metadata.source_database}/${metadata.accession}/"
-        >
-        ${metadata.accession}
-        </a>
-        </p>
-        <h5>Name</h5>
-        <p>${metadata.name}</p>
-        ${metadata.integrated
-                    ? `<h5>Integrated into </h5>
-        <p>
-        <a
-          target="_blank"
-          rel="noopener"
-          href="https://www.ebi.ac.uk/interpro/entry/InterPro/${metadata.integrated}/"
-        >
-          ${metadata.integrated}
-        </a>
-        </p>`
-                    : ''}
-      `,
-                length: proteins[0].protein_length,
-            });
-        });
-    }
-    catch (error) {
-        throw new Error('Failed transforming the data');
-    }
-};
-export default transformData;
-//# sourceMappingURL=interpro-adapter.js.map

package/dist/es/adapters/interpro-adapter.js.map

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