diff --git a/.babelrc b/.babelrc index bdd05c1..55c4629 100644 --- 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 index d994740..f9bfde4 100644 --- a/.gitignore +++ b/.gitignore @@ -5,4 +5,6 @@ build/ dist/ node_modules/ -*.log \ No newline at end of file +*.log +.yalc/ +yalc.lock \ No newline at end of file diff --git a/package.json b/package.json index 7e74b03..ddf1132 100644 --- 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__/", + "/dist/" + ] + } } diff --git a/public/index.html b/public/index.html index b8f8c6f..a936c6b 100644 --- a/public/index.html +++ b/public/index.html @@ -3,7 +3,7 @@ - UniProt - ProtVista + protvista-uniprot @@ -46,7 +46,6 @@ - diff --git a/test/filterConfig.spec.js b/src/__spec__/filter-config.spec.ts similarity index 88% rename from test/filterConfig.spec.js rename to src/__spec__/filter-config.spec.ts index 2e9c8ab..bb74332 100644 --- a/test/filterConfig.spec.js +++ b/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 new file mode 100644 index 0000000..24873e6 --- /dev/null +++ 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; diff --git a/src/adapters/__tests__/__snapshots__/structure-adapter.spec.ts.snap b/src/adapters/__tests__/__snapshots__/structure-adapter.spec.ts.snap new file mode 100644 index 0000000..cee7de7 --- /dev/null +++ b/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", + }, +] +`; diff --git a/src/adapters/__tests__/structure-adapter.spec.ts b/src/adapters/__tests__/structure-adapter.spec.ts new file mode 100644 index 0000000..17d3699 --- /dev/null +++ b/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(); + }); +}); diff --git a/src/protvista-alphafold-confidence.ts b/src/adapters/alphafold-confidence-adapter.ts similarity index 84% rename from src/protvista-alphafold-confidence.ts rename to src/adapters/alphafold-confidence-adapter.ts index 7ceb33d..ed90ab4 100644 --- a/src/protvista-alphafold-confidence.ts +++ b/src/adapters/alphafold-confidence-adapter.ts @@ -1,4 +1,4 @@ -import { AlphafoldPayload } from './commonTypes'; +import { AlphafoldPayload } from './types/alphafold'; type AlphafoldConfidencePayload = { residueNumber: Array; @@ -6,7 +6,7 @@ type AlphafoldConfidencePayload = { confidenceCategory: Array; }; -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; diff --git a/src/protvista-alphamissense-heatmap.ts b/src/adapters/alphamissense-heatmap-adapter.ts similarity index 80% rename from src/protvista-alphamissense-heatmap.ts rename to src/adapters/alphamissense-heatmap-adapter.ts index 09ee460..073c4a3 100644 --- a/src/protvista-alphamissense-heatmap.ts +++ b/src/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> => { const data = []; @@ -24,7 +24,9 @@ const parseCSV = (rawText: string): Array> => { }; // Load and parse -const loadAndParseAnnotations = async (url: string): Promise>> => { +const loadAndParseAnnotations = async ( + url: string +): Promise>> => { 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; diff --git a/src/protvista-alphamissense-pathogenicity.ts b/src/adapters/alphamissense-pathogenicity-adapter.ts similarity index 95% rename from src/protvista-alphamissense-pathogenicity.ts rename to src/adapters/alphamissense-pathogenicity-adapter.ts index 0165114..7c9e006 100644 --- a/src/protvista-alphamissense-pathogenicity.ts +++ b/src/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; diff --git a/src/adapters/config/evidence.ts b/src/adapters/config/evidence.ts new file mode 100644 index 0000000..6de078e --- /dev/null +++ b/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; diff --git a/src/adapters/feature-adapter.ts b/src/adapters/feature-adapter.ts new file mode 100644 index 0000000..a775f68 --- /dev/null +++ b/src/adapters/feature-adapter.ts @@ -0,0 +1,19 @@ +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; diff --git a/src/adapters/interpro-adapter.ts b/src/adapters/interpro-adapter.ts new file mode 100644 index 0000000..cd750ee --- /dev/null +++ b/src/adapters/interpro-adapter.ts @@ -0,0 +1,71 @@ +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) => { + try { + return data?.results?.map(({ metadata, proteins }) => ({ + ...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( + ...proteins[0].entry_protein_locations?.map((location) => + Math.max(...location.fragments.map((fragment) => fragment.end)) + ) + ) + : '', + color: colorHash.hex( + metadata.accession.toLowerCase().split('').reverse().join('') + ), + tooltipContent: ` +
Accession
+

+ + ${metadata.accession} + +

+
Name
+

${metadata.name}

+ ${ + metadata.integrated + ? `
Integrated into
+

+ + ${metadata.integrated} + +

` + : '' + } + `, + length: proteins[0].protein_length, + })); + } catch (error) { + throw new Error('Failed transforming the data'); + } +}; + +export default transformData; diff --git a/src/adapters/proteomics-adapter.ts b/src/adapters/proteomics-adapter.ts new file mode 100644 index 0000000..cd29dab --- /dev/null +++ b/src/adapters/proteomics-adapter.ts @@ -0,0 +1,76 @@ +import { renameProperties } from '../utils'; +import formatTooltip from '../tooltips/featureTooltip'; + +const proteomicsTrackProperties = (feature) => { + return { + category: 'PROTEOMICS', + type: feature.unique ? 'unique' : 'non_unique', + tooltipContent: formatTooltip(feature), + }; +}; + +const transformData = (data) => { + let adaptedData = []; + + if (data && data.length !== 0) { + /* Important: The PTM map is a temporary patch until multiple modifications are shown in the peptide. At this point, only 'phospho' sites are of interest. + Once they are available in the data, there is no need for the below merging */ + + // To merge PTM data present in same residue in a same length peptide, have a map [key: start-end-phospho site 1-... phosphosite n, value: corresponding feature elements] + const ptmMap: Record = {}; + data.features.forEach((feature) => { + let ft = `${feature.begin}-${feature.end}`; + if (feature.ptms) { + feature.ptms.forEach((ptm) => { + ft += `-${ptm.position}`; + }); + ptmMap[ft] = ft in ptmMap ? [...ptmMap[ft], feature] : [feature]; + } + }); + + // The else part alone is enough if the PTM information need not be merged. + if (Object.keys(ptmMap).length) { + adaptedData = Object.values(ptmMap).map((features) => { + // Only the dbReferences have to be merged as the rest is all the same + const mergedDbReferences = []; + features.forEach((feature) => { + feature.ptms.forEach((ptm) => { + ptm.dbReferences.forEach((dbReference) => { + mergedDbReferences.push(dbReference); + }); + }); + }); + + const mergedFeatures = { + type: features[0].type, + begin: features[0].begin, + end: features[0].end, + xrefs: features[0].xrefs, + evidences: features[0].evidences, + peptide: features[0].peptide, + unique: features[0].unique, + ptms: features[0].ptms.map((ptm) => ({ + name: ptm.name, + position: ptm.position, + sources: ptm.sources, + dbReferences: mergedDbReferences, + })), + }; + + return Object.assign( + mergedFeatures, + proteomicsTrackProperties(mergedFeatures) + ); + }, []); + } else { + adaptedData = data.features.map((feature) => { + return Object.assign(feature, proteomicsTrackProperties(feature)); + }); + } + + adaptedData = renameProperties(adaptedData); + } + return adaptedData; +}; + +export default transformData; diff --git a/src/protvista-ptm-exchange.ts b/src/adapters/ptm-exchange-adapter.ts similarity index 98% rename from src/protvista-ptm-exchange.ts rename to src/adapters/ptm-exchange-adapter.ts index 5d513b4..8f0ae10 100644 --- a/src/protvista-ptm-exchange.ts +++ b/src/adapters/ptm-exchange-adapter.ts @@ -135,7 +135,7 @@ const convertPtmExchangePtms = ( }; }; -export const transformData = (data: ProteomicsPtm) => { +const transformData = (data: ProteomicsPtm) => { if (data) { const { features } = data; @@ -178,3 +178,5 @@ export const transformData = (data: ProteomicsPtm) => { } return []; }; + +export default transformData; diff --git a/src/adapters/structure-adapter.ts b/src/adapters/structure-adapter.ts new file mode 100644 index 0000000..1d52ed8 --- /dev/null +++ b/src/adapters/structure-adapter.ts @@ -0,0 +1,105 @@ +import formatTooltip from '../tooltips/structureTooltip'; + +const featureType = 'PDBE_COVER'; +const featureCategory = 'STRUCTURE_COVERAGE'; + +const capitalizeFirstLetter = (word) => { + return word.charAt(0).toUpperCase() + word.slice(1); +}; + +const getDescription = (properties) => { + return Object.keys(properties).reduce( + (accumulator, propertyKey) => + `${accumulator}${capitalizeFirstLetter(propertyKey)}: ${ + properties[propertyKey] + }. `, + '' + ); +}; + +const parseChainString = (value) => { + const posEqual = value.indexOf('='); + const posDash = value.indexOf('-'); + if (posEqual === -1 || posDash === -1) { + return { start: 0, end: 0 }; + } + return { + start: +value.slice(posEqual + 1, posDash), + end: +value.slice(posDash + 1), + }; +}; + +// Iterate over references and extract chain start and end +export const getAllFeatureStructures = (data) => { + return data.dbReferences + .filter((reference) => { + return reference.type === 'PDB'; + }) + .map((structureReference) => { + const parsedChain = structureReference.properties.chains + ? parseChainString(structureReference.properties.chains) + : { start: 0, end: 0 }; + return { + type: featureType, + category: featureCategory, + structures: [ + { + description: getDescription(structureReference.properties), + start: parsedChain.start, + end: parsedChain.end, + source: { + id: structureReference.id, + url: `http://www.ebi.ac.uk/pdbe-srv/view/entry/${structureReference.id}`, + }, + }, + ], + start: parsedChain.start, + end: parsedChain.end, + }; + }); +}; + +export const mergeOverlappingIntervals = (structures) => { + if (!structures || structures.length <= 0) { + return []; + } + // Sort by start position + const sortedStructures = structures.sort((a, b) => a.start - b.start); + const mergedIntervals = []; + sortedStructures.forEach((structure) => { + const lastItem = mergedIntervals[mergedIntervals.length - 1]; + if ( + !lastItem || + // If item doesn't overlap, push it + lastItem.end < structure.start + ) { + mergedIntervals.push(structure); + } + // If the end is bigger update the last one + else if (lastItem.end < structure.end) { + lastItem.end = structure.end; + lastItem.structures.push(structure.structures[0]); + } + // Otherwise just add to last item + else { + lastItem.structures.push(structure.structures[0]); + } + }); + return mergedIntervals; +}; + +const transformData = (data) => { + let transformedData = []; + if (data && data.length !== 0) { + const allFeatureStructures = getAllFeatureStructures(data); + transformedData = mergeOverlappingIntervals(allFeatureStructures); + + transformedData.forEach((feature) => { + /* eslint-disable no-param-reassign */ + feature.tooltipContent = formatTooltip(feature); + }); + } + return transformedData; +}; + +export default transformData; diff --git a/src/commonTypes.ts b/src/adapters/types/alphafold.ts similarity index 100% rename from src/commonTypes.ts rename to src/adapters/types/alphafold.ts diff --git a/src/adapters/variation-adapter.ts b/src/adapters/variation-adapter.ts new file mode 100644 index 0000000..b9e53f2 --- /dev/null +++ b/src/adapters/variation-adapter.ts @@ -0,0 +1,44 @@ +import { + ProteinsAPIVariation, + AminoAcid, + SourceType, + Variant, + Xref, + VariationDatum, +} from '@nightingale-elements/nightingale-variation'; + +import formatTooltip from '../tooltips/variationTooltip'; + +export type TransformedVariant = VariationDatum & Variant; + +const getSourceType = (xrefs: Xref[], sourceType: SourceType) => { + const xrefNames = xrefs ? xrefs.map((ref) => ref.name) : []; + if (sourceType === 'uniprot' || sourceType === 'mixed') { + xrefNames.push('uniprot'); + } + return xrefNames; +}; + +const transformData = ( + data: ProteinsAPIVariation +): { + sequence: string; + variants: TransformedVariant[]; +} => { + const { sequence, features } = data; + const variants = features.map((variant) => ({ + ...variant, + accession: variant.genomicLocation?.join(', '), + variant: variant.alternativeSequence + ? variant.alternativeSequence + : AminoAcid.Empty, + start: +variant.begin, + xrefNames: getSourceType(variant.xrefs, variant.sourceType), + hasPredictions: variant.predictions && variant.predictions.length > 0, + tooltipContent: formatTooltip(variant), + })); + if (!variants) return null; + return { sequence, variants }; +}; + +export default transformData; diff --git a/src/protvista-variation-graph-adapter.ts b/src/adapters/variation-graph-adapter.ts similarity index 55% rename from src/protvista-variation-graph-adapter.ts rename to src/adapters/variation-graph-adapter.ts index 72cabdf..39ca99f 100644 --- a/src/protvista-variation-graph-adapter.ts +++ b/src/adapters/variation-graph-adapter.ts @@ -1,10 +1,10 @@ -export const transformData = (data) => { +const transformData = (data) => { if (data.sequence && data.features.length) { const variants = data.features.map((variant) => ({ - ...variant, - accession: variant.genomicLocation?.join(", "), - start: variant.begin, - })); + ...variant, + accession: variant.genomicLocation?.join(', '), + start: variant.begin, + })); const total = new Uint8ClampedArray(data.sequence.length); const diseaseTotal = new Uint8ClampedArray(data.sequence.length); @@ -28,20 +28,27 @@ export const transformData = (data) => { } const graphData = [ - { - name: 'variant', - range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))], - color: 'darkgrey', - values: [...total].map((value, index) => ({ position: index, value: value })), - }, - { - name: 'disease causing variant', - range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))], - color: 'red', - values: [...diseaseTotal].map((value, index) => ({ position: index, value: value })), - }, - ]; + { + name: 'variant', + range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))], + color: 'darkgrey', + values: [...total].map((value, index) => ({ + position: index, + value: value, + })), + }, + { + name: 'disease causing variant', + range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))], + color: 'red', + values: [...diseaseTotal].map((value, index) => ({ + position: index, + value: value, + })), + }, + ]; return graphData; } }; +export default transformData; diff --git a/src/config.json b/src/config.json index 515926c..6e56bc3 100644 --- a/src/config.json +++ b/src/config.json @@ -12,7 +12,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -25,7 +25,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -38,7 +38,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -51,7 +51,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -65,7 +65,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -78,7 +78,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -98,7 +98,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -111,7 +111,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -124,7 +124,7 @@ "label": "Non-adjacent residues", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -137,7 +137,7 @@ "label": "Non-terminal residue", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -150,7 +150,7 @@ "label": "Sequence uncertainty", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -163,7 +163,7 @@ "label": "Non-standard residue", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -183,7 +183,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -196,7 +196,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -209,7 +209,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -229,7 +229,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -241,7 +241,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-interpro-adapter", + "adapter": "interpro-adapter", "url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/{accession}?type=domain&page_size=100" } ], @@ -254,7 +254,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -267,7 +267,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -280,7 +280,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -293,7 +293,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -313,7 +313,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -326,7 +326,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -339,7 +339,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -352,7 +352,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -365,7 +365,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -378,7 +378,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -391,7 +391,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -411,7 +411,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -424,7 +424,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-proteomics-ptm-adapter", + "adapter": "proteomics-ptm-adapter", "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}" } ], @@ -437,7 +437,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -450,7 +450,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -463,7 +463,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -476,7 +476,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -495,7 +495,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/epitope/{accession}" } ], @@ -514,7 +514,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/antigen/{accession}" } ], @@ -534,7 +534,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -546,7 +546,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/mutagenesis/{accession}" } ], @@ -565,7 +565,7 @@ "trackType": "nightingale-linegraph-track", "data": [ { - "adapter": "protvista-variation-graph-adapter", + "adapter": "variation-graph-adapter", "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}" } ], @@ -573,11 +573,11 @@ }, { "name": "variation", - "filterComponent": "protvista-filter", + "filterComponent": "nightingale-filter", "trackType": "nightingale-variation", "data": [ { - "adapter": "protvista-variation-adapter", + "adapter": "variation-adapter", "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}" } ], @@ -589,7 +589,7 @@ "name": "PROTEOMICS", "label": "Proteomics", "trackType": "nightingale-track", - "adapter": "protvista-proteomics-adapter", + "adapter": "proteomics-adapter", "urls": [ "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}", "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}" @@ -602,7 +602,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-proteomics-adapter", + "adapter": "proteomics-adapter", "url": "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}" } ], @@ -615,7 +615,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-proteomics-adapter", + "adapter": "proteomics-adapter", "url": "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}" } ], @@ -627,7 +627,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-proteomics-adapter", + "adapter": "proteomics-adapter", "url": "https://www.ebi.ac.uk/proteins/api/hpp/{accession}" } ], @@ -639,7 +639,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-proteomics-adapter", + "adapter": "proteomics-adapter", "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}" } ], @@ -659,7 +659,7 @@ "tooltip": "PDBe 3D structure coverage", "data": [ { - "adapter": "protvista-structure-adapter", + "adapter": "structure-adapter", "url": "https://www.ebi.ac.uk/proteins/api/proteins/{accession}" } ] @@ -680,7 +680,7 @@ "trackType": "nightingale-colored-sequence", "data": [ { - "adapter": "protvista-alphafold-confidence-adapter", + "adapter": "alphafold-confidence-adapter", "url": [ "https://alphafold.ebi.ac.uk/api/prediction/{accession}", "https://www.ebi.ac.uk/proteins/api/proteins/{accession}" @@ -704,7 +704,7 @@ "trackType": "nightingale-colored-sequence", "data": [ { - "adapter": "protvista-alphamissense-pathogenicity-adapter", + "adapter": "alphamissense-pathogenicity-adapter", "url": [ "https://alphafold.ebi.ac.uk/api/prediction/{accession}", "https://www.ebi.ac.uk/proteins/api/proteins/{accession}" @@ -720,7 +720,7 @@ "trackType": "nightingale-sequence-heatmap", "data": [ { - "adapter": "protvista-alphamissense-heatmap-adapter", + "adapter": "alphamissense-heatmap-adapter", "url": [ "https://alphafold.ebi.ac.uk/api/prediction/{accession}", "https://www.ebi.ac.uk/proteins/api/proteins/{accession}" @@ -743,7 +743,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -756,7 +756,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -769,7 +769,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], @@ -782,7 +782,7 @@ "trackType": "nightingale-track", "data": [ { - "adapter": "protvista-feature-adapter", + "adapter": "feature-adapter", "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}" } ], diff --git a/src/filterConfig.ts b/src/filter-config.ts similarity index 86% rename from src/filterConfig.ts rename to src/filter-config.ts index 984195d..77b9dae 100644 --- a/src/filterConfig.ts +++ b/src/filter-config.ts @@ -1,4 +1,5 @@ -import { ClinicalSignificance } from 'protvista-variation-adapter/dist/es/variants'; +import { VariationDatum } from '@nightingale-elements/nightingale-variation'; +import { ClinicalSignificance } from '@nightingale-elements/nightingale-variation'; const scaleColors = { UPDiseaseColor: '#990000', @@ -19,9 +20,13 @@ const significanceMatches = ( return values.some((rx) => rx.test(type)); }); +export type VariantsForFilter = { + variants: VariationDatum[]; +}[]; + export const getFilteredVariants = ( - variants: ProtvistaVariationData, - callbackFilter: (variantPos: ProtvistaVariant) => void + variants: VariantsForFilter, + callbackFilter: (variantPos: VariationDatum) => void ) => variants.map((variant) => { const matchingVariants = variant.variants.filter((variantPos) => @@ -74,7 +79,7 @@ const filterConfig = [ color: scaleColors.UPDiseaseColor, }, filterPredicate: filterPredicates['disease'], - filterData: (variants: ProtvistaVariationData) => + filterData: (variants: VariantsForFilter) => getFilteredVariants(variants, filterPredicates['disease']), }, { @@ -88,7 +93,7 @@ const filterConfig = [ color: scaleColors.predictedColor, }, filterPredicate: filterPredicates['predicted'], - filterData: (variants: ProtvistaVariationData) => + filterData: (variants: VariantsForFilter) => getFilteredVariants(variants, filterPredicates['predicted']), }, { @@ -102,7 +107,7 @@ const filterConfig = [ color: scaleColors.UPNonDiseaseColor, }, filterPredicate: filterPredicates['nonDisease'], - filterData: (variants: ProtvistaVariationData) => + filterData: (variants: VariantsForFilter) => getFilteredVariants(variants, filterPredicates['nonDisease']), }, { @@ -116,7 +121,7 @@ const filterConfig = [ color: scaleColors.othersColor, }, filterPredicate: filterPredicates['uncertain'], - filterData: (variants: ProtvistaVariationData) => + filterData: (variants: VariantsForFilter) => getFilteredVariants(variants, filterPredicates['uncertain']), }, { @@ -130,7 +135,7 @@ const filterConfig = [ color: '#9f9f9f', }, filterPredicate: filterPredicates['UniProt'], - filterData: (variants: ProtvistaVariationData) => + filterData: (variants: VariantsForFilter) => getFilteredVariants(variants, filterPredicates['UniProt']), }, { @@ -144,7 +149,7 @@ const filterConfig = [ color: '#9f9f9f', }, filterPredicate: filterPredicates['ClinVar'], - filterData: (variants: ProtvistaVariationData) => + filterData: (variants: VariantsForFilter) => getFilteredVariants(variants, filterPredicates['ClinVar']), }, { @@ -158,16 +163,16 @@ const filterConfig = [ color: '#9f9f9f', }, filterPredicate: filterPredicates['LSS'], - filterData: (variants: ProtvistaVariationData) => + filterData: (variants: VariantsForFilter) => getFilteredVariants(variants, filterPredicates['LSS']), }, ]; const countVariantsForFilter = ( filterName: 'disease' | 'nonDisease' | 'uncertain' | 'predicted', - variant: ProtvistaVariant + variant: VariationDatum ) => { - const variantWrapper = [{ variants: [variant] }]; + const variantWrapper: VariantsForFilter = [{ variants: [variant] }]; const filter = filterConfig.find((filter) => filter.name === filterName); if (filter) { return filter.filterData(variantWrapper)[0].variants.length > 0; diff --git a/src/index.ts b/src/index.ts index 1bf7cc3..5faee2e 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,22 +1,18 @@ -import { loadComponent } from './loadComponents'; - import ProtvistaUniprot from './protvista-uniprot'; -import _ProtvistaUniprotStructure from './protvista-uniprot-structure'; - -import { transformDataFeatureAdapter as _transformDataFeatureAdapter } from './protvista-uniprot'; -import { transformDataProteomicsAdapter as _transformDataProteomicsAdapter } from './protvista-uniprot'; -import { transformDataStructureAdapter as _transformDataStructureAdapter } from './protvista-uniprot'; -import { transformDataVariationAdapter as _transformDataVariationAdapter } from './protvista-uniprot'; -import { transformDataInterproAdapter as _transformDataInterproAdapter } from './protvista-uniprot'; +import ProtvistaUniprotStructure from './protvista-uniprot-structure'; -export const transformDataFeatureAdapter = _transformDataFeatureAdapter; -export const transformDataProteomicsAdapter = _transformDataProteomicsAdapter; -export const transformDataStructureAdapter = _transformDataStructureAdapter; -export const transformDataVariationAdapter = _transformDataVariationAdapter; -export const transformDataInterproAdapter = _transformDataInterproAdapter; -export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure; +import filterConfig, { colorConfig } from './filter-config'; -loadComponent('protvista-uniprot', ProtvistaUniprot); -loadComponent('protvista-uniprot-structure', _ProtvistaUniprotStructure); +import getFeatureTooltip from './tooltips/featureTooltip'; +import getStructureTooltip from './tooltips/structureTooltip'; +import getVariationTooltip from './tooltips/variationTooltip'; -export default ProtvistaUniprot; +export { + ProtvistaUniprot as default, + ProtvistaUniprotStructure, + filterConfig, + colorConfig, + getFeatureTooltip, + getStructureTooltip, + getVariationTooltip, +}; diff --git a/src/loadComponents.ts b/src/loadComponents.ts deleted file mode 100644 index c33025a..0000000 --- a/src/loadComponents.ts +++ /dev/null @@ -1,10 +0,0 @@ -const loadComponent = function ( - name: string, - elementConstructor: CustomElementConstructor -) { - if (!customElements.get(name)) { - customElements.define(name, elementConstructor); - } -}; - -export { loadComponent }; diff --git a/src/protvista-uniprot-structure.ts b/src/protvista-uniprot-structure.ts index f68109d..102692f 100644 --- a/src/protvista-uniprot-structure.ts +++ b/src/protvista-uniprot-structure.ts @@ -1,12 +1,13 @@ import { LitElement, html, svg, TemplateResult, css } from 'lit'; +// eslint-disable-next-line @typescript-eslint/no-unused-vars +import { customElement } from 'lit/decorators.js'; import { unsafeHTML } from 'lit/directives/unsafe-html.js'; -import { load } from 'data-loader'; import NightingaleStructure, { PredictionData, StructureData, } from '@nightingale-elements/nightingale-structure'; import ProtvistaDatatable from 'protvista-datatable'; -import { loadComponent } from './loadComponents'; +import { fetchAll, loadComponent } from './utils'; import loaderIcon from './icons/spinner.svg'; import downloadIcon from './icons/download.svg'; @@ -140,6 +141,8 @@ const foldseekURL = (accession, sourceDB) => { }; const styleId = 'protvista-styles'; + +@customElement('protvista-uniprot-structure') class ProtvistaUniprotStructure extends LitElement { accession?: string; data?: ProcessedStructureData[]; @@ -175,18 +178,7 @@ class ProtvistaUniprotStructure extends LitElement { const pdbUrl = `https://www.ebi.ac.uk/proteins/api/proteins/${this.accession}`; const alphaFoldURl = `https://alphafold.ebi.ac.uk/api/prediction/${this.accession}`; - const rawData: { [key: string]: any } = []; - - await Promise.all( - [pdbUrl, alphaFoldURl].map((url: string) => - load(url).then( - (data) => (rawData[url] = data.payload), - // TODO handle this better based on error code - // Fail silently for now - (error) => console.warn(error) - ) - ) - ); + const rawData = await fetchAll([pdbUrl, alphaFoldURl]); this.loading = false; // TODO: return if no data at all diff --git a/src/protvista-uniprot.ts b/src/protvista-uniprot.ts index fc01e16..ff1afef 100644 --- a/src/protvista-uniprot.ts +++ b/src/protvista-uniprot.ts @@ -1,4 +1,6 @@ import { LitElement, html, svg } from 'lit'; +// eslint-disable-next-line @typescript-eslint/no-unused-vars +import { customElement } from 'lit/decorators.js'; import { unsafeHTML } from 'lit/directives/unsafe-html.js'; import { frame } from 'timing-functions'; @@ -14,68 +16,42 @@ import NightingaleLinegraphTrack from '@nightingale-elements/nightingale-linegra import NightingaleSequenceHeatmap from '@nightingale-elements/nightingale-sequence-heatmap'; import NightingaleFilter from '@nightingale-elements/nightingale-filter'; -import { load } from 'data-loader'; // adapters -import { transformData as _transformDataFeatureAdapter } from 'protvista-feature-adapter'; -import { transformData as _transformDataProteomicsAdapter } from 'protvista-proteomics-adapter'; -import { transformData as _transformDataStructureAdapter } from 'protvista-structure-adapter'; -import { - transformData as _transformDataVariationAdapter, +import featureAdapter from './adapters/feature-adapter'; +import proteomicsAdapter from './adapters/proteomics-adapter'; +import structureAdapter from './adapters/structure-adapter'; +import variationAdapter, { TransformedVariant, -} from 'protvista-variation-adapter'; -import { transformData as _transformDataVariationGraphAdapter } from './protvista-variation-graph-adapter'; -import { transformData as _transformDataInterproAdapter } from 'protvista-interpro-adapter'; -import { transformData as _transformDataProteomicsPTMApdapter } from './protvista-ptm-exchange'; -import { transformData as _transformDataAlphaFoldConfidenceAdapter } from './protvista-alphafold-confidence'; -import { transformData as _transformDataAlphaMissensePathogenicityAdapter } from './protvista-alphamissense-pathogenicity'; -import { transformData as _transformDataAlphaMissenseHeatmapAdapter } from './protvista-alphamissense-heatmap'; +} from './adapters/variation-adapter'; +import interproAdapter from './adapters/interpro-adapter'; +import variationGraphAdapter from './adapters/variation-graph-adapter'; +import proteomicsPTMApdapter from './adapters/ptm-exchange-adapter'; +import alphaFoldConfidenceAdapter from './adapters/alphafold-confidence-adapter'; +import alphaMissensePathogenicityAdapter from './adapters/alphamissense-pathogenicity-adapter'; +import alphaMissenseHeatmapAdapter from './adapters/alphamissense-heatmap-adapter'; +import ProtvistaUniprotStructure from './protvista-uniprot-structure'; + +import { fetchAll, loadComponent } from './utils'; + +import filterConfig, { colorConfig } from './filter-config'; import defaultConfig from './config.json'; -import _ProtvistaUniprotStructure from './protvista-uniprot-structure'; -import { loadComponent } from './loadComponents'; -import _filterConfig, { colorConfig as _colorConfig } from './filterConfig'; -import { NightingaleEvent } from './types/nightingale-components'; import loaderIcon from './icons/spinner.svg'; import protvistaStyles from './styles/protvista-styles'; import loaderStyles from './styles/loader-styles'; -export const transformDataFeatureAdapter = _transformDataFeatureAdapter; -export const transformDataProteomicsAdapter = _transformDataProteomicsAdapter; -export const transformDataStructureAdapter = _transformDataStructureAdapter; -export const transformDataVariationAdapter = _transformDataVariationAdapter; -export const transformDataVariationGraphAdapter = - _transformDataVariationGraphAdapter; -export const transformDataInterproAdapter = _transformDataInterproAdapter; -export const transformDataProteomicsPTMApdapter = - _transformDataProteomicsPTMApdapter; -export const transformDataAlphaFoldConfidenceAdapter = - _transformDataAlphaFoldConfidenceAdapter; - -export const transformDataAlphaMissensePathogenicityAdapter = - _transformDataAlphaMissensePathogenicityAdapter; - -export const transformDataAlphaMissenseHeatmapAdapter = - _transformDataAlphaMissenseHeatmapAdapter; - -export const filterConfig = _filterConfig; -export const colorConfig = _colorConfig; -export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure; - const adapters = { - 'protvista-feature-adapter': transformDataFeatureAdapter, - 'protvista-interpro-adapter': transformDataInterproAdapter, - 'protvista-proteomics-adapter': transformDataProteomicsAdapter, - 'protvista-structure-adapter': transformDataStructureAdapter, - 'protvista-variation-adapter': transformDataVariationAdapter, - 'protvista-variation-graph-adapter': transformDataVariationGraphAdapter, - 'protvista-proteomics-ptm-adapter': transformDataProteomicsPTMApdapter, - 'protvista-alphafold-confidence-adapter': - transformDataAlphaFoldConfidenceAdapter, - 'protvista-alphamissense-pathogenicity-adapter': - transformDataAlphaMissensePathogenicityAdapter, - 'protvista-alphamissense-heatmap-adapter': - transformDataAlphaMissenseHeatmapAdapter, + 'feature-adapter': featureAdapter, + 'interpro-adapter': interproAdapter, + 'proteomics-adapter': proteomicsAdapter, + 'structure-adapter': structureAdapter, + 'variation-adapter': variationAdapter, + 'variation-graph-adapter': variationGraphAdapter, + 'proteomics-ptm-adapter': proteomicsPTMApdapter, + 'alphafold-confidence-adapter': alphaFoldConfidenceAdapter, + 'alphamissense-pathogenicity-adapter': alphaMissensePathogenicityAdapter, + 'alphamissense-heatmap-adapter': alphaMissenseHeatmapAdapter, }; type TrackType = @@ -95,15 +71,15 @@ type ProtvistaTrackConfig = { data: { url: string | string[]; adapter?: - | 'protvista-feature-adapter' - | 'protvista-structure-adapter' - | 'protvista-proteomics-adapter' - | 'protvista-variation-adapter' - | 'protvista-variation-graph-adapter' - | 'protvista-interpro-adapter' - | 'protvista-alphafold-confidence-adapter' - | 'protvista-alphamissense-pathogenicity-adapter' - | 'protvista-alphamissense-heatmap-adapter'; + | 'feature-adapter' + | 'structure-adapter' + | 'proteomics-adapter' + | 'variation-adapter' + | 'variation-graph-adapter' + | 'interpro-adapter' + | 'alphafold-confidence-adapter' + | 'alphamissense-pathogenicity-adapter' + | 'alphamissense-heatmap-adapter'; }[]; tooltip: string; color?: string; @@ -124,16 +100,21 @@ type ProtvistaCategory = { 'color-range'?: string; }; -export type DownloadConfig = { - type: string; - url: string; -}[]; - type ProtvistaConfig = { categories: ProtvistaCategory[]; - download: DownloadConfig; }; +type NightingaleEvent = Event & { + detail?: { + displaystart?: number; + displayend?: number; + eventType?: 'click' | 'mouseover' | 'mouseout' | 'reset'; + feature?: any; + coords?: [number, number]; + }; +}; + +@customElement('protvista-uniprot') class ProtvistaUniprot extends LitElement { private openCategories: string[]; private nostructure: boolean; @@ -196,7 +177,7 @@ class ProtvistaUniprot extends LitElement { loadComponent('nightingale-linegraph-track', NightingaleLinegraphTrack); loadComponent('nightingale-filter', NightingaleFilter); loadComponent('nightingale-manager', NightingaleManager); - loadComponent('protvista-uniprot-structure', _ProtvistaUniprotStructure); + loadComponent('protvista-uniprot-structure', ProtvistaUniprotStructure); loadComponent('nightingale-sequence-heatmap', NightingaleSequenceHeatmap); } @@ -207,28 +188,17 @@ class ProtvistaUniprot extends LitElement { const urls = this.config.categories.flatMap(({ tracks }) => tracks.flatMap(({ data }) => data[0].url) ); - const uniqueUrls = [...new Set(urls)]; + // Get the data for all urls and store it - await Promise.all( - uniqueUrls.map((url: string) => - load(url.replace('{accession}', accession)) - .then( - (data) => { - this.rawData[url] = data.payload; - // Some endpoints return empty arrays, while most fail 🙄 - if (!this.hasData && data.payload?.features?.length) - this.hasData = true; - }, - // TODO handle this better based on error code - // Fail silently for now - (error) => console.warn(error) - ) - .catch((e) => { - console.log(e); - }) - ) + this.rawData = await fetchAll([...new Set(urls)], (url) => + url.replace('{accession}', accession) ); + // Some endpoints return empty arrays, while most fail 🙄 + this.hasData = + this.hasData || + Object.values(this.rawData).some((d) => !!d?.features?.length); + // Now iterate over tracks and categories, transforming the data // and assigning it as adequate for (const { name: categoryName, tracks, trackType } of this.config @@ -242,18 +212,17 @@ class ProtvistaUniprot extends LitElement { if ( !trackData || - (adapter === 'protvista-variation-adapter' && - trackData[0].length === 0) + (adapter === 'variation-adapter' && trackData[0].length === 0) ) { return; } // 1. Convert data let transformedData = adapter - ? await adapters[adapter](...trackData) + ? await adapters[adapter].apply(null, trackData) : trackData; - if (adapter === 'protvista-interpro-adapter') { + if (adapter === 'interpro-adapter') { const representativeDomains = []; transformedData?.forEach((feature) => { feature.locations?.forEach((location) => { @@ -322,7 +291,7 @@ class ProtvistaUniprot extends LitElement { currentCategory.tracks && data && // Check there's data and special case for variants - // NOTE: should refactor protvista-variation-adapter + // NOTE: should refactor variation-adapter // to return a list of variants and set the sequence // on protvista-variation separately (data.length > 0 || data.variants?.length) @@ -350,9 +319,10 @@ class ProtvistaUniprot extends LitElement { ) { for (const track of currentCategory.tracks) { if (track.trackType === 'nightingale-sequence-heatmap') { - const heatmapComponent = this.querySelector< - typeof NightingaleSequenceHeatmap - >('nightingale-sequence-heatmap'); + const heatmapComponent = + this.querySelector( + 'nightingale-sequence-heatmap' + ); if (heatmapComponent) { const heatmapData = this.data[`${id}-${track.name}`]; const xDomain = Array.from( @@ -361,7 +331,7 @@ class ProtvistaUniprot extends LitElement { ); const yDomain = [ ...new Set(heatmapData.map((hotMapItem) => hotMapItem.yValue)), - ]; + ] as string[]; heatmapComponent.setHeatmapData(xDomain, yDomain, heatmapData); } } diff --git a/src/tooltips/featureTooltip.ts b/src/tooltips/featureTooltip.ts new file mode 100644 index 0000000..3c6a17c --- /dev/null +++ b/src/tooltips/featureTooltip.ts @@ -0,0 +1,223 @@ +import ecoMap from '../adapters/config/evidence'; + +const formatSource = (source) => { + if (source.name?.toLowerCase() === 'PubMed'.toLowerCase()) { + return `${source.id} (${source.name} EuropePMC)`; + } + const sourceLink = ` ${source.id}`; + if (source.name) { + // Temporary until we get the expected value as 'PeptideAtlas' instead of 'HppPeptideAtlas' + if (source.name.startsWith('Hpp')) { + return `${sourceLink} (${source.name.slice(3)})`; + } + return `${sourceLink} (${source.name})`; + } + return sourceLink; +}; + +export const getEvidenceFromCodes = (evidenceList) => { + if (!evidenceList) return ``; + return ` +
    ${evidenceList + .map((ev) => { + const ecoMatch = ecoMap.find((eco) => eco.name === ev.code); + if (!ecoMatch) return ``; + return `
  • ${ecoMatch.shortDescription}: ${ + ev.source ? formatSource(ev.source) : '' + }
    • `; + }) + .join('')}
+ `; +}; + +export const formatXrefs = (xrefs) => { + return `
    ${xrefs + .map( + (xref) => + `
  • ${xref.name} ${ + xref.url + ? `${xref.id}` + : `${xref.name} ${xref.id}` + }
    • ` + ) + .join('')}
`; +}; + +const getPTMEvidence = (ptms) => { + if (!ptms) return ``; + const ids = ptms.flatMap(({ dbReferences }) => + dbReferences.map((ref) => ref.id) + ); + const uniqueIds = [...new Set(ids.flat())]; + // Urls in the payload are not relevant. For 'Glue project' dataset, Dataset ID and publication reference is hardcoded. Need to be checked in 2024 if it still exists in the payload + const proteomexchange = + 'https://proteomecentral.proteomexchange.org/dataset/'; + return ` +
    ${uniqueIds + .map((id) => { + const datasetID = id === 'Glue project' ? 'PXD012174' : id; + return `
  • ${datasetID} (ProteomeXchange${ + id === 'Glue project' + ? `)
  • Publication: 31819260 (PubMed)
    • ` + : ` PeptideAtlas)` + }`; + }) + .join('')}
+ `; +}; + +const formatPTMPeptidoform = (peptide, ptms) => { + if (!ptms) return ``; + const modificationValues = ptms.map((ptm) => ({ + name: ptm.name, + position: ptm.position, + })); + let peptidoform = ''; + let lastModPosition = 0; + modificationValues.forEach((p) => { + peptidoform = `${peptidoform}${peptide.slice( + lastModPosition, + p.position + )}[${p.name}]`; + lastModPosition = p.position; + }); + // Add last remaining part of the peptide if any + peptidoform = `${peptidoform}${peptide.slice(lastModPosition)}`; + return `

${peptidoform}

`; +}; + +// At the moment, there is only phospho data. In future we may have more, the below AA sites have to be updated to accomodate more. +const AAPhosphoSites = { + A: 'alanine', + S: 'serine', + T: 'threonine', + Y: 'tyrosine', +}; + +const findModifiedResidueName = (feature, ptm) => { + const { peptide, begin: peptideStart } = feature; + const proteinLocation = Number(peptideStart) + ptm.position - 1; + const modifiedResidue = peptide.charAt(ptm.position - 1); // CharAt index starts from 0 + return `${proteinLocation} phospho${AAPhosphoSites[modifiedResidue]}`; +}; + +const formatTooltip = (feature) => { + const evidenceHTML = + feature.type === 'PROTEOMICS_PTM' + ? getPTMEvidence(feature.ptms) + : getEvidenceFromCodes(feature.evidences); + const ptms = + feature.type === 'PROTEOMICS_PTM' && + feature.ptms.map((ptm) => findModifiedResidueName(feature, ptm)); + + const dataset = + feature.type === 'PROTEOMICS_PTM' && + feature.ptms.flatMap(({ dbReferences }) => + dbReferences.map((ref) => ref.id) + ); + + let { description } = feature; + + if (feature.type === 'BINDING' || feature.type === 'Binding site') { + let bindingDescription = ''; + if (feature.ligandPart) { + bindingDescription += `${feature.ligandPart.name} of `; + } + if (feature.ligand) { + bindingDescription += feature.ligand.name; + } + if (feature.description) { + bindingDescription += `; ${feature.description}`; + } + description = bindingDescription; + } + + try { + return ` + ${description ? `
Description

${description}

` : ``} + ${ + feature.matchScore + ? `
Match score

${feature.matchScore}%

` + : `` + } + ${feature.ftId ? `
Feature ID

${feature.ftId}

` : ``} + ${ + feature.alternativeSequence + ? `
Alternative sequence

${feature.alternativeSequence}

` + : `` + } + ${ + ptms + ? `
PTMs
    ${ptms + .map((item) => `
  • ${item}
    • `) + .join('')}
+ ` + : '' + } + ${ + feature.peptide && feature.type === 'PROTEOMICS_PTM' + ? `
Peptidoform

${formatPTMPeptidoform( + feature.peptide, + feature.ptms + )}

` + : `` + } + ${ + feature.peptide && feature.type !== 'PROTEOMICS_PTM' + ? `
Peptide

${feature.peptide}

` + : `` + } + ${ + feature.xrefs + ? `
Cross-references
${formatXrefs(feature.xrefs)}` + : `` + } + ${evidenceHTML ? `
Evidence
${evidenceHTML}` : ``} + ${ + feature.ptms && dataset && !dataset.includes('Glue project') + ? `
PTM statistical attributes
    ${feature.ptms + .map((ptm) => + ptm.dbReferences + .map( + (ref) => + `
  • ${ref.id}
    • +
  • ${findModifiedResidueName( + feature, + ptm + )}
    • +
  • PubMed ID: + ${ref.properties['Pubmed ID']} +
    • +
  • Confidence score: ${ + ref.properties['Confidence score'] + }
    • +
  • Universal Spectrum Id: + View on ProteomeXchange +
    • +
  • PSM Count (0.05 gFLR): ${ + ref.properties['PSM Count (0.05 gFLR)'] + }
    • +
  • Final site probability: ${ + ref.properties['Final site probability'] + }
    • + ` + ) + .join('') + ) + .join('')}
` + : '' + } + `; + } catch (error) { + console.error(error); + return ''; + } +}; + +export default formatTooltip; diff --git a/src/tooltips/structureTooltip.ts b/src/tooltips/structureTooltip.ts new file mode 100644 index 0000000..bde3660 --- /dev/null +++ b/src/tooltips/structureTooltip.ts @@ -0,0 +1,20 @@ +const getStructuresHTML = (structureList) => { + return ``; +}; + +const formatTooltip = (feature) => { + const structuresHTML = getStructuresHTML(feature.structures); + return `${structuresHTML ? `
Structures
${structuresHTML}` : ``}`; +}; + +export default formatTooltip; diff --git a/src/tooltips/variationTooltip.ts b/src/tooltips/variationTooltip.ts new file mode 100644 index 0000000..51ae7e2 --- /dev/null +++ b/src/tooltips/variationTooltip.ts @@ -0,0 +1,139 @@ +import { + Association, + Description, + PopulationFrequency, + Variant, + Prediction, +} from '@nightingale-elements/nightingale-variation'; +import groupBy from 'lodash-es/groupBy'; + +import { formatXrefs, getEvidenceFromCodes } from './featureTooltip'; + +const getDiseaseAssociations = (associations: Association[]): string => + associations + ?.map( + (association) => ` +

Disease association

${association.name}

+ ${ + association.description + ? `<>${association.description}

` + : '' + } + ${ + association.dbReferences + ? `
Cross-references
${formatXrefs( + association.dbReferences + )}` + : '' + } + ${getEvidenceFromCodes(association.evidences)} + ` + ) + .join(''); + +const getDescriptions = (descriptions: Description[]): string => + `
Description
${descriptions + .map((description) => `

${description.value}

`) + .join('')} + `; + +const getPopulationFrequencies = ( + popFrequencies: PopulationFrequency[] +): string => + `
Population frequencies
${popFrequencies + .map( + (freq) => + `

${freq.frequency} - ${freq.populationName} (${freq.source})

` + ) + .join('')}`; + +const getEnsemblCovidLinks = (variant: Variant): string => { + const shouldGenerateLink = variant.locations.some( + (location) => location.source === 'EnsemblViruses' + ); + if (shouldGenerateLink) { + const xref = variant.xrefs.find((xref) => xref.name === 'ENA'); + return xref.id + ? `
Ensembl COVID-19
+

+ ${xref.id} +

` + : ''; + } + return ''; +}; + +const getPredictions = (predictions: Prediction[]): string => { + const groupedPredictions = groupBy(predictions, 'predAlgorithmNameType'); + const counts = Object.keys(groupedPredictions).map((key) => { + const valueGroups = groupBy(groupedPredictions[key], 'predictionValType'); + return { + algorithm: key, + values: Object.keys(valueGroups).map((valKey) => ({ + name: valKey, + count: valueGroups[valKey].length, + })), + }; + }); + return counts + .map( + (countItem) => + `
${countItem.algorithm}
    ${countItem.values + .map((countValue) => `
  • ${countValue.name}
    • `) + .join('')}
` + ) + .join(''); +}; + +const formatTooltip = (variant: Variant): string => + ` +
Variant

${variant.wildType} > ${ + variant.alternativeSequence || '' + }

+ ${ + variant.populationFrequencies + ? getPopulationFrequencies(variant.populationFrequencies) + : '' + } + ${ + variant.consequenceType + ? `
Consequence

${variant.consequenceType}

` + : `` + } + ${ + variant.somaticStatus + ? `
Somatic

${ + variant.somaticStatus === 0 ? 'No' : 'Yes' + }

` + : `` + } + ${ + variant.genomicLocation?.length + ? `
Location

${variant.genomicLocation.join( + ', ' + )}

` + : `` + } + ${ + variant.ftId + ? `
Feature ID

${variant.ftId}

` + : `` + } + ${ + variant.descriptions + ? getDescriptions(variant.descriptions) + : '' + } + ${ + variant.association + ? getDiseaseAssociations(variant.association) + : '' + } + ${ + variant.predictions ? getPredictions(variant.predictions) : '' + } + ${getEnsemblCovidLinks(variant)} + + `; + +export default formatTooltip; diff --git a/src/types/nightingale-components.d.ts b/src/types/nightingale-components.d.ts deleted file mode 100644 index bd76d99..0000000 --- a/src/types/nightingale-components.d.ts +++ /dev/null @@ -1,13 +0,0 @@ -export type NightingaleEvent = Event & { - detail?: { - displaystart?: number; - displayend?: number; - eventType?: "click" | "mouseover" | "mouseout" | "reset"; - feature?: any; - coords?: [number, number]; - }; -}; - -type NightingaleDataAdapter = { - transformData; -}; diff --git a/src/types/nightingale-sequence-heatmap.d.ts b/src/types/nightingale-sequence-heatmap.d.ts deleted file mode 100644 index c6a5b72..0000000 --- a/src/types/nightingale-sequence-heatmap.d.ts +++ /dev/null @@ -1 +0,0 @@ -declare module '@nightingale-elements/nightingale-sequence-heatmap'; \ No newline at end of file diff --git a/src/types/protvista-feature-adapter.d.ts b/src/types/protvista-feature-adapter.d.ts deleted file mode 100644 index 40627c6..0000000 --- a/src/types/protvista-feature-adapter.d.ts +++ /dev/null @@ -1 +0,0 @@ -declare module 'protvista-feature-adapter'; diff --git a/src/types/protvista-interpro-adapter.d.ts b/src/types/protvista-interpro-adapter.d.ts deleted file mode 100644 index 7709ef3..0000000 --- a/src/types/protvista-interpro-adapter.d.ts +++ /dev/null @@ -1 +0,0 @@ -declare module 'protvista-interpro-adapter'; diff --git a/src/types/protvista-proteomics-adapter.d.ts b/src/types/protvista-proteomics-adapter.d.ts deleted file mode 100644 index 60b3bf6..0000000 --- a/src/types/protvista-proteomics-adapter.d.ts +++ /dev/null @@ -1 +0,0 @@ -declare module 'protvista-proteomics-adapter'; diff --git a/src/types/protvista-structure-adapter.d.ts b/src/types/protvista-structure-adapter.d.ts deleted file mode 100644 index dccff2b..0000000 --- a/src/types/protvista-structure-adapter.d.ts +++ /dev/null @@ -1 +0,0 @@ -declare module 'protvista-structure-adapter'; diff --git a/src/types/protvista-structure.d.ts b/src/types/protvista-structure.d.ts deleted file mode 100644 index 2568ec7..0000000 --- a/src/types/protvista-structure.d.ts +++ /dev/null @@ -1 +0,0 @@ -declare module 'protvista-structure'; diff --git a/src/types/protvista-variation.d.ts b/src/types/protvista-variation.d.ts deleted file mode 100644 index 49f4255..0000000 --- a/src/types/protvista-variation.d.ts +++ /dev/null @@ -1,15 +0,0 @@ -declare module 'protvista-variation'; - -type ProtvistaVariant = - import('protvista-variation-adapter/dist/es/variants').Variant & { - hasPredictions?: boolean; - xrefNames?: string[]; - }; - -type ProtvistaVariationData = { - variants: ProtvistaVariant[]; -}[]; - -declare class ProtvistaVariation extends HTMLElement { - colorConfig: (variant: any) => string; -} diff --git a/src/utils.ts b/src/utils.ts new file mode 100644 index 0000000..80a4d09 --- /dev/null +++ b/src/utils.ts @@ -0,0 +1,37 @@ +export const renameProperties = (features) => + features.map((ft) => ({ + ...ft, + start: ft.begin || undefined, + })); + +export const loadComponent = ( + name: string, + elementConstructor: CustomElementConstructor +) => { + if (!customElements.get(name)) { + customElements.define(name, elementConstructor); + } +}; + +// Returns an object of the form url => payload json +// getUrl optional function modifies url string +export const fetchAll = async (urls: string[], getUrl = null) => + Object.fromEntries( + await Promise.all( + urls.map(async (url) => { + try { + const response = await fetch(getUrl ? getUrl(url) : url); + if (!response.ok) { + // TODO handle this better based on error code + // Fail silently for now + console.warn(`HTTP error status: ${response.status} at ${url}`); + return [url, null]; + } + return [url, await response.json()]; + } catch (error) { + console.warn(`Failed to fetch or parse JSON from ${url}:`, error); + return [url, null]; // or handle error data as needed + } + }) + ) + ); diff --git a/tsconfig.json b/tsconfig.json index 3c23c2f..3fa4f54 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -7,7 +7,7 @@ "target": "es2019", /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', 'ES2021', or 'ESNEXT'. */ // "module": "commonjs", /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */ // "lib": [], /* Specify library files to be included in the compilation. */ - // "allowJs": true, /* Allow javascript files to be compiled. */ + "allowJs": true, /* Allow javascript files to be compiled. */ // "checkJs": true, /* Report errors in .js files. */ // "jsx": "preserve", /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */ "declaration": true, /* Generates corresponding '.d.ts' file. */ @@ -62,7 +62,7 @@ // "inlineSources": true, /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */ /* Experimental Options */ - // "experimentalDecorators": true, /* Enables experimental support for ES7 decorators. */ + "experimentalDecorators": true, /* Enables experimental support for ES7 decorators. */ // "emitDecoratorMetadata": true, /* Enables experimental support for emitting type metadata for decorators. */ /* Advanced Options */ diff --git a/yarn.lock b/yarn.lock index e154e3d..7f78c3a 100644 --- a/yarn.lock +++ b/yarn.lock @@ -17,95 +17,97 @@ dependencies: "@babel/highlight" "^7.10.4" -"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.25.7": - version "7.25.7" - resolved 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-1275,6 +1273,18 @@ "@types/yargs" "^16.0.0" chalk "^4.0.0" +"@jest/types@^29.6.3": + version "29.6.3" + resolved "https://registry.yarnpkg.com/@jest/types/-/types-29.6.3.tgz#1131f8cf634e7e84c5e77bab12f052af585fba59" + integrity sha512-u3UPsIilWKOM3F9CXtrG8LEJmNxwoCQC/XVj4IKYXvvpx7QIi/Kg1LI5uDmDpKlac62NUtX7eLjRh+jVZcLOzw== + dependencies: + "@jest/schemas" "^29.6.3" + "@types/istanbul-lib-coverage" "^2.0.0" + "@types/istanbul-reports" "^3.0.0" + "@types/node" "*" + "@types/yargs" "^17.0.8" + chalk "^4.0.0" + "@jridgewell/gen-mapping@^0.3.5": version "0.3.5" resolved "https://registry.yarnpkg.com/@jridgewell/gen-mapping/-/gen-mapping-0.3.5.tgz#dcce6aff74bdf6dad1a95802b69b04a2fcb1fb36" @@ -1498,6 +1508,16 @@ mkdirp "^1.0.4" rimraf "^3.0.2" +"@scarf/scarf@=1.4.0": + version "1.4.0" + resolved "https://registry.yarnpkg.com/@scarf/scarf/-/scarf-1.4.0.tgz#3bbb984085dbd6d982494538b523be1ce6562972" + integrity 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+ "@types/estree" "*" + "@types/json-schema" "*" + "@types/estree-jsx@^1.0.0": version "1.0.5" resolved "https://registry.yarnpkg.com/@types/estree-jsx/-/estree-jsx-1.0.5.tgz#858a88ea20f34fe65111f005a689fa1ebf70dc18" @@ -1601,7 +1637,7 @@ dependencies: "@types/estree" "*" -"@types/estree@*", "@types/estree@^1.0.0", "@types/estree@^1.0.5": +"@types/estree@*", "@types/estree@^1.0.0", "@types/estree@^1.0.6": version "1.0.6" resolved "https://registry.yarnpkg.com/@types/estree/-/estree-1.0.6.tgz#628effeeae2064a1b4e79f78e81d87b7e5fc7b50" integrity sha512-AYnb1nQyY49te+VRAVgmzfcgjYS91mY5P0TKUDCLEM+gNnA+3T6rWITXRLYCpahpqSQbN5cE+gHpnPyXjHWxcw== @@ -1617,9 +1653,9 @@ "@types/send" "*" "@types/express-serve-static-core@^5.0.0": - version "5.0.0" - resolved "https://registry.yarnpkg.com/@types/express-serve-static-core/-/express-serve-static-core-5.0.0.tgz#91f06cda1049e8f17eeab364798ed79c97488a1c" - integrity 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-"@types/json-schema@^7.0.5", "@types/json-schema@^7.0.7", "@types/json-schema@^7.0.8": +"@types/jest@^29.5.14": + version "29.5.14" + resolved "https://registry.yarnpkg.com/@types/jest/-/jest-29.5.14.tgz#2b910912fa1d6856cadcd0c1f95af7df1d6049e5" + integrity sha512-ZN+4sdnLUbo8EVvVc2ao0GFW6oVrQRPn4K2lglySj7APvSrgzxHiNNK99us4WDMi57xxA2yggblIAMNhXOotLQ== + dependencies: + expect "^29.0.0" + pretty-format "^29.0.0" + +"@types/json-schema@*", "@types/json-schema@^7.0.5", "@types/json-schema@^7.0.7", "@types/json-schema@^7.0.8": version "7.0.15" resolved "https://registry.yarnpkg.com/@types/json-schema/-/json-schema-7.0.15.tgz#596a1747233694d50f6ad8a7869fcb6f56cf5841" integrity sha512-5+fP8P8MFNC+AyZCDxrB2pkZFPGzqQWUzpSeuuVLvm8VMcorNYavBqoFcxK8bQz4Qsbn4oUEEem4wDLfcysGHA== -"@types/lodash-es@4.17.3": - version "4.17.3" - resolved "https://registry.yarnpkg.com/@types/lodash-es/-/lodash-es-4.17.3.tgz#87eb0b3673b076b8ee655f1890260a136af09a2d" - integrity 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"https://registry.yarnpkg.com/@typescript-eslint/eslint-plugin/-/eslint-plugin-4.26.1.tgz#b9c7313321cb837e2bf8bebe7acc2220659e67d3" @@ -1917,125 +1951,125 @@ resolved "https://registry.yarnpkg.com/@ungap/structured-clone/-/structured-clone-1.2.0.tgz#756641adb587851b5ccb3e095daf27ae581c8406" integrity sha512-zuVdFrMJiuCDQUMCzQaD6KL28MjnqqN8XnAqiEq9PNm/hCPTSGfrXCOfwj1ow4LFb/tNymJPwsNbVePc1xFqrQ== -"@webassemblyjs/ast@1.12.1", "@webassemblyjs/ast@^1.12.1": - version "1.12.1" - resolved "https://registry.yarnpkg.com/@webassemblyjs/ast/-/ast-1.12.1.tgz#bb16a0e8b1914f979f45864c23819cc3e3f0d4bb" - integrity sha512-EKfMUOPRRUTy5UII4qJDGPpqfwjOmZ5jeGFwid9mnoqIFK+e0vqoi1qH56JpmZSzEL53jKnNzScdmftJyG5xWg== +"@webassemblyjs/ast@1.14.1", "@webassemblyjs/ast@^1.12.1": + version "1.14.1" + resolved "https://registry.yarnpkg.com/@webassemblyjs/ast/-/ast-1.14.1.tgz#a9f6a07f2b03c95c8d38c4536a1fdfb521ff55b6" + integrity 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ansi-styles@^4.0.0, ansi-styles@^4.1.0: dependencies: color-convert "^2.0.1" +ansi-styles@^5.0.0: + version "5.2.0" + resolved "https://registry.yarnpkg.com/ansi-styles/-/ansi-styles-5.2.0.tgz#07449690ad45777d1924ac2abb2fc8895dba836b" + integrity sha512-Cxwpt2SfTzTtXcfOlzGEee8O+c+MmUgGrNiBcXnuWxuFJHe6a5Hz7qwhwe5OgaSYI0IJvkLqWX1ASG+cJOkEiA== + anymatch@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/anymatch/-/anymatch-2.0.0.tgz#bcb24b4f37934d9aa7ac17b4adaf89e7c76ef2eb" @@ -2666,15 +2700,15 @@ browser-process-hrtime@^1.0.0: resolved "https://registry.yarnpkg.com/browser-process-hrtime/-/browser-process-hrtime-1.0.0.tgz#3c9b4b7d782c8121e56f10106d84c0d0ffc94626" integrity sha512-9o5UecI3GhkpM6DrXr69PblIuWxPKk9Y0jHBRhdocZ2y7YECBFCsHm79Pr3OyR2AvjhDkabFJaDJMYRazHgsow== -browserslist@^4.21.10, browserslist@^4.23.3, browserslist@^4.24.0: - version "4.24.0" - resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.24.0.tgz#a1325fe4bc80b64fda169629fc01b3d6cecd38d4" - 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-3018,16 +3047,16 @@ comma-separated-tokens@^2.0.0: resolved "https://registry.yarnpkg.com/comma-separated-tokens/-/comma-separated-tokens-2.0.3.tgz#4e89c9458acb61bc8fef19f4529973b2392839ee" integrity sha512-Fu4hJdvzeylCfQPp9SGWidpzrMs7tTrlu6Vb8XGaRGck8QSNZJJp538Wrb60Lax4fPwR64ViY468OIUTbRlGZg== -commander@2, commander@^2.20.0: - version "2.20.3" - resolved "https://registry.yarnpkg.com/commander/-/commander-2.20.3.tgz#fd485e84c03eb4881c20722ba48035e8531aeb33" - integrity sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ== - commander@7, commander@^7.0.0: version "7.2.0" resolved "https://registry.yarnpkg.com/commander/-/commander-7.2.0.tgz#a36cb57d0b501ce108e4d20559a150a391d97ab7" integrity sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw== +commander@^2.20.0: + version "2.20.3" + resolved "https://registry.yarnpkg.com/commander/-/commander-2.20.3.tgz#fd485e84c03eb4881c20722ba48035e8531aeb33" + 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3", d3-array@3, d3-array@^3.2.0: version "3.2.4" resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-3.2.4.tgz#15fec33b237f97ac5d7c986dc77da273a8ed0bb5" @@ -3244,27 +3261,11 @@ d3-array@2, d3-array@^2.3.0: dependencies: internmap "1 - 2" -d3-axis@1: - version "1.0.12" - resolved "https://registry.yarnpkg.com/d3-axis/-/d3-axis-1.0.12.tgz#cdf20ba210cfbb43795af33756886fb3638daac9" - integrity sha512-ejINPfPSNdGFKEOAtnBtdkpr24c4d4jsei6Lg98mxf424ivoDP2956/5HDpIAtmHo85lqT4pruy+zEgvRUBqaQ== - d3-axis@3: version "3.0.0" resolved "https://registry.yarnpkg.com/d3-axis/-/d3-axis-3.0.0.tgz#c42a4a13e8131d637b745fc2973824cfeaf93322" integrity sha512-IH5tgjV4jE/GhHkRV0HiVYPDtvfjHQlQfJHs0usq7M30XcSBvOotpmH1IgkcXsO/5gEQZD43B//fc7SRT5S+xw== -d3-brush@1: - version "1.1.6" - resolved "https://registry.yarnpkg.com/d3-brush/-/d3-brush-1.1.6.tgz#b0a22c7372cabec128bdddf9bddc058592f89e9b" - integrity sha512-7RW+w7HfMCPyZLifTz/UnJmI5kdkXtpCbombUSs8xniAyo0vIbrDzDwUJB6eJOgl9u5DQOt2TQlYumxzD1SvYA== - dependencies: - d3-dispatch "1" - d3-drag "1" - d3-interpolate "1" - d3-selection "1" - d3-transition "1" - d3-brush@3: version "3.0.0" resolved "https://registry.yarnpkg.com/d3-brush/-/d3-brush-3.0.0.tgz#6f767c4ed8dcb79de7ede3e1c0f89e63ef64d31c" @@ -3276,14 +3277,6 @@ d3-brush@3: d3-selection "3" d3-transition "3" -d3-chord@1: - version "1.0.6" - resolved "https://registry.yarnpkg.com/d3-chord/-/d3-chord-1.0.6.tgz#309157e3f2db2c752f0280fedd35f2067ccbb15f" - integrity sha512-JXA2Dro1Fxw9rJe33Uv+Ckr5IrAa74TlfDEhE/jfLOaXegMQFQTAgAw9WnZL8+HxVBRXaRGCkrNU7pJeylRIuA== - dependencies: - d3-array "1" - d3-path "1" - d3-chord@3: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-chord/-/d3-chord-3.0.1.tgz#d156d61f485fce8327e6abf339cb41d8cbba6966" @@ -3291,33 +3284,11 @@ d3-chord@3: dependencies: d3-path "1 - 3" -d3-collection@1: - version "1.0.7" - resolved "https://registry.yarnpkg.com/d3-collection/-/d3-collection-1.0.7.tgz#349bd2aa9977db071091c13144d5e4f16b5b310e" - integrity 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"https://registry.yarnpkg.com/d3-dsv/-/d3-dsv-3.0.1.tgz#c63af978f4d6a0d084a52a673922be2160789b73" @@ -3376,23 +3325,11 @@ d3-dsv@1: iconv-lite "0.6" rw "1" -d3-ease@1: - version "1.0.7" - resolved "https://registry.yarnpkg.com/d3-ease/-/d3-ease-1.0.7.tgz#9a834890ef8b8ae8c558b2fe55bd57f5993b85e2" - integrity sha512-lx14ZPYkhNx0s/2HX5sLFUI3mbasHjSSpwO/KaaNACweVwxUruKyWVcb293wMv1RqTPZyZ8kSZ2NogUZNcLOFQ== - "d3-ease@1 - 3", d3-ease@3: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-ease/-/d3-ease-3.0.1.tgz#9658ac38a2140d59d346160f1f6c30fda0bd12f4" integrity sha512-wR/XK3D3XcLIZwpbvQwQ5fK+8Ykds1ip7A2Txe0yxncXSdq1L9skcG7blcedkOX+ZcgxGAmLX1FrRGbADwzi0w== -d3-fetch@1: - version "1.2.0" - resolved "https://registry.yarnpkg.com/d3-fetch/-/d3-fetch-1.2.0.tgz#15ce2ecfc41b092b1db50abd2c552c2316cf7fc7" - integrity sha512-yC78NBVcd2zFAyR/HnUiBS7Lf6inSCoWcSxFfw8FYL7ydiqe80SazNwoffcqOfs95XaLo7yebsmQqDKSsXUtvA== - dependencies: - d3-dsv "1" - d3-fetch@3: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-fetch/-/d3-fetch-3.0.1.tgz#83141bff9856a0edb5e38de89cdcfe63d0a60a22" @@ -3400,16 +3337,6 @@ d3-fetch@3: dependencies: d3-dsv "1 - 3" -d3-force@1: - version "1.2.1" - resolved "https://registry.yarnpkg.com/d3-force/-/d3-force-1.2.1.tgz#fd29a5d1ff181c9e7f0669e4bd72bdb0e914ec0b" - integrity sha512-HHvehyaiUlVo5CxBJ0yF/xny4xoaxFxDnBXNvNcfW9adORGZfyNF1dj6DGLKyk4Yh3brP/1h3rnDzdIAwL08zg== - dependencies: - d3-collection "1" - d3-dispatch "1" - d3-quadtree "1" - d3-timer "1" - d3-force@3: version "3.0.0" resolved "https://registry.yarnpkg.com/d3-force/-/d3-force-3.0.0.tgz#3e2ba1a61e70888fe3d9194e30d6d14eece155c4" @@ -3419,28 +3346,11 @@ d3-force@3: d3-quadtree "1 - 3" d3-timer "1 - 3" -d3-format@1: - version "1.4.5" - resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-1.4.5.tgz#374f2ba1320e3717eb74a9356c67daee17a7edb4" - integrity sha512-J0piedu6Z8iB6TbIGfZgDzfXxUFN3qQRMofy2oPdXzQibYGqPB/9iMcxr/TGalU+2RsyDO+U4f33id8tbnSRMQ== - -"d3-format@1 - 2": - version "2.0.0" - resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-2.0.0.tgz#a10bcc0f986c372b729ba447382413aabf5b0767" - integrity sha512-Ab3S6XuE/Q+flY96HXT0jOXcM4EAClYFnRGY5zsjRGNy6qCYrQsMffs7cV5Q9xejb35zxW5hf/guKw34kvIKsA== - "d3-format@1 - 3", d3-format@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-3.1.0.tgz#9260e23a28ea5cb109e93b21a06e24e2ebd55641" integrity sha512-YyUI6AEuY/Wpt8KWLgZHsIU86atmikuoOmCfommt0LYHiQSPjvX2AcFc38PX0CBpr2RCyZhjex+NS/LPOv6YqA== -d3-geo@1: - version "1.12.1" - resolved "https://registry.yarnpkg.com/d3-geo/-/d3-geo-1.12.1.tgz#7fc2ab7414b72e59fbcbd603e80d9adc029b035f" - integrity sha512-XG4d1c/UJSEX9NfU02KwBL6BYPj8YKHxgBEw5om2ZnTRSbIcego6dhHwcxuSR3clxh0EpE38os1DVPOmnYtTPg== - dependencies: - d3-array "1" - d3-geo@3: version "3.1.1" resolved "https://registry.yarnpkg.com/d3-geo/-/d3-geo-3.1.1.tgz#6027cf51246f9b2ebd64f99e01dc7c3364033a4d" @@ -3448,23 +3358,11 @@ d3-geo@3: dependencies: d3-array "2.5.0 - 3" -d3-hierarchy@1: - version "1.1.9" - resolved "https://registry.yarnpkg.com/d3-hierarchy/-/d3-hierarchy-1.1.9.tgz#2f6bee24caaea43f8dc37545fa01628559647a83" - integrity sha512-j8tPxlqh1srJHAtxfvOUwKNYJkQuBFdM1+JAUfq6xqH5eAqf93L7oG1NVqDa4CpFZNvnNKtCYEUC8KY9yEn9lQ== - d3-hierarchy@3: version "3.1.2" resolved "https://registry.yarnpkg.com/d3-hierarchy/-/d3-hierarchy-3.1.2.tgz#b01cd42c1eed3d46db77a5966cf726f8c09160c6" integrity sha512-FX/9frcub54beBdugHjDCdikxThEqjnR93Qt7PvQTOHxyiNCAlvMrHhclk3cD5VeAaq9fxmfRp+CnWw9rEMBuA== -d3-interpolate@1: - version "1.4.0" - resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-1.4.0.tgz#526e79e2d80daa383f9e0c1c1c7dcc0f0583e987" - integrity sha512-V9znK0zc3jOPV4VD2zZn0sDhZU3WAE2bmlxdIwwQPPzPjvyLkd8B3JUVdS1IDUFDkWZ72c9qnv1GK2ZagTZ8EA== - dependencies: - d3-color "1" - "d3-interpolate@1 - 3", "d3-interpolate@1.2.0 - 3", d3-interpolate@3: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-3.0.1.tgz#3c47aa5b32c5b3dfb56ef3fd4342078a632b400d" @@ -3472,61 +3370,26 @@ d3-interpolate@1: dependencies: d3-color "1 - 3" -"d3-interpolate@1.2.0 - 2": - version "2.0.1" - resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-2.0.1.tgz#98be499cfb8a3b94d4ff616900501a64abc91163" - integrity sha512-c5UhwwTs/yybcmTpAVqwSFl6vrQ8JZJoT5F7xNFK9pymv5C0Ymcc9/LIJHtYIggg/yS9YHw8i8O8tgb9pupjeQ== - dependencies: - d3-color "1 - 2" - -d3-path@1: - version "1.0.9" - resolved "https://registry.yarnpkg.com/d3-path/-/d3-path-1.0.9.tgz#48c050bb1fe8c262493a8caf5524e3e9591701cf" - integrity sha512-VLaYcn81dtHVTjEHd8B+pbe9yHWpXKZUC87PzoFmsFrJqgFwDe/qxfp5MlfsfM1V5E/iVt0MmEbWQ7FVIXh/bg== - "d3-path@1 - 3", d3-path@3, d3-path@^3.1.0: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-path/-/d3-path-3.1.0.tgz#22df939032fb5a71ae8b1800d61ddb7851c42526" integrity 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- dependencies: - d3-color "1" - d3-interpolate "1" - d3-scale-chromatic@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-scale-chromatic/-/d3-scale-chromatic-3.1.0.tgz#34c39da298b23c20e02f1a4b239bd0f22e7f1314" @@ -3535,18 +3398,6 @@ d3-scale-chromatic@3: d3-color "1 - 3" d3-interpolate "1 - 3" -d3-scale@2: - version "2.2.2" - resolved "https://registry.yarnpkg.com/d3-scale/-/d3-scale-2.2.2.tgz#4e880e0b2745acaaddd3ede26a9e908a9e17b81f" - integrity sha512-LbeEvGgIb8UMcAa0EATLNX0lelKWGYDQiPdHj+gLblGVhGLyNbaCn3EvrJf0A3Y/uOOU5aD6MTh5ZFCdEwGiCw== - dependencies: - d3-array "^1.2.0" - d3-collection "1" - d3-format "1" - d3-interpolate "1" - d3-time "1" - d3-time-format "2" - d3-scale@4: version "4.0.2" resolved "https://registry.yarnpkg.com/d3-scale/-/d3-scale-4.0.2.tgz#82b38e8e8ff7080764f8dcec77bd4be393689396" @@ -3558,34 +3409,11 @@ d3-scale@4: d3-time "2.1.1 - 3" d3-time-format "2 - 4" -d3-scale@^3.2.3: - version "3.3.0" - resolved 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"https://registry.yarnpkg.com/d3-shape/-/d3-shape-1.3.7.tgz#df63801be07bc986bc54f63789b4fe502992b5d7" - integrity sha512-EUkvKjqPFUAZyOlhY5gzCxCeI0Aep04LwIRpsZ/mLFelJiUfnK56jo5JMDSE7yyP2kLSb6LtF+S5chMk7uqPqw== - dependencies: - d3-path "1" - d3-shape@3: version "3.2.0" resolved "https://registry.yarnpkg.com/d3-shape/-/d3-shape-3.2.0.tgz#a1a839cbd9ba45f28674c69d7f855bcf91dfc6a5" @@ -3593,20 +3421,6 @@ d3-shape@3: dependencies: d3-path "^3.1.0" -d3-time-format@2: - version "2.3.0" - resolved "https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-2.3.0.tgz#107bdc028667788a8924ba040faf1fbccd5a7850" - integrity sha512-guv6b2H37s2Uq/GefleCDtbe0XZAuy7Wa49VGkPVPMfLL9qObgBST3lEHJBMUp8S7NdLQAGIvr2KXk8Hc98iKQ== - dependencies: - d3-time "1" - -"d3-time-format@2 - 3": - version "3.0.0" - resolved "https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-3.0.0.tgz#df8056c83659e01f20ac5da5fdeae7c08d5f1bb6" - integrity sha512-UXJh6EKsHBTjopVqZBhFysQcoXSv/5yLONZvkQ5Kk3qbwiUYkdX17Xa1PT6U1ZWXGGfB1ey5L8dKMlFq2DO0Ag== - dependencies: - d3-time "1 - 2" - "d3-time-format@2 - 4", d3-time-format@4: version "4.1.0" resolved "https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-4.1.0.tgz#7ab5257a5041d11ecb4fe70a5c7d16a195bb408a" @@ -3614,18 +3428,6 @@ d3-time-format@2: dependencies: d3-time "1 - 3" -d3-time@1: - version "1.1.0" - resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-1.1.0.tgz#b1e19d307dae9c900b7e5b25ffc5dcc249a8a0f1" - integrity sha512-Xh0isrZ5rPYYdqhAVk8VLnMEidhz5aP7htAADH6MfzgmmicPkTo8LhkLxci61/lCB7n7UmE3bN0leRt+qvkLxA== - -"d3-time@1 - 2", d3-time@^2.1.1: - version "2.1.1" - resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-2.1.1.tgz#e9d8a8a88691f4548e68ca085e5ff956724a6682" - integrity sha512-/eIQe/eR4kCQwq7yxi7z4c6qEXf2IYGcjoWB5OOQy4Tq9Uv39/947qlDcN2TLkiTzQWzvnsuYPB9TrWaNfipKQ== - dependencies: - d3-array "2" - "d3-time@1 - 3", "d3-time@2.1.1 - 3", d3-time@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-3.1.0.tgz#9310db56e992e3c0175e1ef385e545e48a9bb5c7" @@ -3633,28 +3435,11 @@ d3-time@1: dependencies: d3-array "2 - 3" -d3-timer@1: - version "1.0.10" - resolved "https://registry.yarnpkg.com/d3-timer/-/d3-timer-1.0.10.tgz#dfe76b8a91748831b13b6d9c793ffbd508dd9de5" - integrity sha512-B1JDm0XDaQC+uvo4DT79H0XmBskgS3l6Ve+1SBCfxgmtIb1AVrPIoqd+nPSv+loMX8szQ0sVUhGngL7D5QPiXw== - "d3-timer@1 - 3", d3-timer@3: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-timer/-/d3-timer-3.0.1.tgz#6284d2a2708285b1abb7e201eda4380af35e63b0" integrity sha512-ndfJ/JxxMd3nw31uyKoY2naivF+r29V+Lc0svZxe1JvvIRmi8hUsrMvdOwgS1o6uBHmiz91geQ0ylPP0aj1VUA== -d3-transition@1: - version "1.3.2" - resolved "https://registry.yarnpkg.com/d3-transition/-/d3-transition-1.3.2.tgz#a98ef2151be8d8600543434c1ca80140ae23b398" - integrity sha512-sc0gRU4PFqZ47lPVHloMn9tlPcv8jxgOQg+0zjhfZXMQuvppjG6YuwdMBE0TuqCZjeJkLecku/l9R0JPcRhaDA== - dependencies: - d3-color "1" - d3-dispatch "1" - d3-ease "1" - d3-interpolate "1" - d3-selection "^1.1.0" - d3-timer "1" - "d3-transition@2 - 3", d3-transition@3: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-transition/-/d3-transition-3.0.1.tgz#6869fdde1448868077fdd5989200cb61b2a1645f" @@ -3666,22 +3451,6 @@ d3-transition@1: d3-interpolate "1 - 3" d3-timer "1 - 3" -d3-voronoi@1: - version "1.1.4" - resolved "https://registry.yarnpkg.com/d3-voronoi/-/d3-voronoi-1.1.4.tgz#dd3c78d7653d2bb359284ae478645d95944c8297" - integrity sha512-dArJ32hchFsrQ8uMiTBLq256MpnZjeuBtdHpaDlYuQyjU0CVzCJl/BVW+SkszaAeH95D/8gxqAhgx0ouAWAfRg== - -d3-zoom@1: - version "1.8.3" - resolved "https://registry.yarnpkg.com/d3-zoom/-/d3-zoom-1.8.3.tgz#b6a3dbe738c7763121cd05b8a7795ffe17f4fc0a" - integrity sha512-VoLXTK4wvy1a0JpH2Il+F2CiOhVu7VRXWF5M/LroMIh3/zBAC3WAt7QoIvPibOavVo20hN6/37vwAsdBejLyKQ== - dependencies: - d3-dispatch "1" - d3-drag "1" - d3-interpolate "1" - d3-selection "1" - d3-transition "1" - d3-zoom@3: version "3.0.0" resolved "https://registry.yarnpkg.com/d3-zoom/-/d3-zoom-3.0.0.tgz#d13f4165c73217ffeaa54295cd6969b3e7aee8f3" @@ -3693,43 +3462,6 @@ d3-zoom@3: d3-selection "2 - 3" d3-transition "2 - 3" -d3@5.X: - version "5.16.0" - resolved "https://registry.yarnpkg.com/d3/-/d3-5.16.0.tgz#9c5e8d3b56403c79d4ed42fbd62f6113f199c877" - integrity sha512-4PL5hHaHwX4m7Zr1UapXW23apo6pexCgdetdJ5kTmADpG/7T9Gkxw0M0tf/pjoB63ezCCm0u5UaFYy2aMt0Mcw== - dependencies: - d3-array "1" - d3-axis "1" - d3-brush "1" - d3-chord "1" - d3-collection "1" - d3-color "1" - d3-contour "1" - d3-dispatch "1" - d3-drag "1" - d3-dsv "1" - d3-ease "1" - d3-fetch "1" - d3-force "1" - d3-format "1" - d3-geo "1" - d3-hierarchy "1" - d3-interpolate "1" - d3-path "1" - d3-polygon "1" - d3-quadtree "1" - d3-random "1" - d3-scale "2" - d3-scale-chromatic "1" - d3-selection "1" - d3-shape "1" - d3-time "1" - d3-time-format "2" - d3-timer "1" - d3-transition "1" - d3-voronoi "1" - d3-zoom "1" - d3@7.8.5: version "7.8.5" resolved "https://registry.yarnpkg.com/d3/-/d3-7.8.5.tgz#fde4b760d4486cdb6f0cc8e2cbff318af844635c" @@ -3802,22 +3534,6 @@ d3@7.9.0, d3@^7.9.0: d3-transition "3" d3-zoom "3" -data-loader@^2.9.1: - version "2.12.0" - resolved "https://registry.yarnpkg.com/data-loader/-/data-loader-2.12.0.tgz#e14158ed1c6ffa5314590871a7b8758da9617add" - integrity sha512-HhFGutLwfMIfz96ctq4FZ03WMQ9W8zdMBHkEKJGaaTaChKhczVIoRtldWd4MkERHNIFWJJkTgi+pjNAZjzwfeA== - dependencies: - "@types/lodash-es" "4.17.3" - lodash-es "^4.17.11" - -data-loader@^3.8.22: - version "3.8.22" - resolved "https://registry.yarnpkg.com/data-loader/-/data-loader-3.8.22.tgz#2b73a9ddf7d12b267d5775a7a29f08899191026d" - integrity sha512-x62gXAb7kW1wLo+laGrLRJ4yVLsIr+WQ23Jebe89EnzuvpUFf0ckmxtK2lvllBJ9U1ZEwCeSfX9xGc3kwI3Otg== - dependencies: - "@types/lodash-es" "4.17.3" - lodash-es "^4.17.11" - data-urls@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/data-urls/-/data-urls-2.0.0.tgz#156485a72963a970f5d5821aaf642bef2bf2db9b" @@ -4068,6 +3784,11 @@ diff-sequences@^26.6.2: resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-26.6.2.tgz#48ba99157de1923412eed41db6b6d4aa9ca7c0b1" integrity sha512-Mv/TDa3nZ9sbc5soK+OoA74BsS3mL37yixCvUAQkiuA4Wz6YtwP/K47n2rv2ovzHZvoiQeA5FTQOschKkEwB0Q== +diff-sequences@^29.6.3: + version "29.6.3" + resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-29.6.3.tgz#4deaf894d11407c51efc8418012f9e70b84ea921" + integrity sha512-EjePK1srD3P08o2j4f0ExnylqRs5B9tJjcp9t1krH2qRi8CCdsYfwe9JgSLurFBWwq4uOlipzfk5fHNvwFKr8Q== + dir-glob@^3.0.1: version "3.0.1" resolved "https://registry.yarnpkg.com/dir-glob/-/dir-glob-3.0.1.tgz#56dbf73d992a4a93ba1584f4534063fd2e41717f" @@ -4114,10 +3835,10 @@ ee-first@1.1.1: resolved "https://registry.yarnpkg.com/ee-first/-/ee-first-1.1.1.tgz#590c61156b0ae2f4f0255732a158b266bc56b21d" integrity sha512-WMwm9LhRUo+WUaRN+vRuETqG89IgZphVSNkdFgeb6sS/E4OrDIN7t48CAewSHXc6C8lefD8KKfr5vY61brQlow== -electron-to-chromium@^1.5.28: - version "1.5.34" - 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jest-matcher-utils "^29.7.0" + jest-message-util "^29.7.0" + jest-util "^29.7.0" + exponential-backoff@^3.1.1: version "3.1.1" resolved "https://registry.yarnpkg.com/exponential-backoff/-/exponential-backoff-3.1.1.tgz#64ac7526fe341ab18a39016cd22c787d01e00bf6" @@ -4665,9 +4397,9 @@ fast-levenshtein@^2.0.6: integrity sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw== fast-uri@^3.0.1: - version "3.0.2" - resolved "https://registry.yarnpkg.com/fast-uri/-/fast-uri-3.0.2.tgz#d78b298cf70fd3b752fd951175a3da6a7b48f024" - integrity sha512-GR6f0hD7XXyNJa25Tb9BuIdN0tdr+0BMi6/CJPH3wJO1JjNG3n/VsSw38AwRdKZABm8lGbPfakLRkYzx2V9row== + version "3.0.3" + resolved "https://registry.yarnpkg.com/fast-uri/-/fast-uri-3.0.3.tgz#892a1c91802d5d7860de728f18608a0573142241" + integrity sha512-aLrHthzCjH5He4Z2H9YZ+v6Ujb9ocRuW6ZzkJQOrTxleEijANq4v1TsaPaVG1PZcuurEzrLcWRyYBYXD5cEiaw== fastest-levenshtein@^1.0.12: version "1.0.16" @@ -4702,11 +4434,6 @@ file-entry-cache@^6.0.1: dependencies: flat-cache "^3.0.4" -file-saver@^2.0.2: - version "2.0.5" - resolved "https://registry.yarnpkg.com/file-saver/-/file-saver-2.0.5.tgz#d61cfe2ce059f414d899e9dd6d4107ee25670c38" - integrity sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA== - file-uri-to-path@1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz#553a7b8446ff6f684359c445f1e37a05dacc33dd" @@ -4803,18 +4530,18 @@ for-in@^1.0.2: integrity sha512-7EwmXrOjyL+ChxMhmG5lnW9MPt1aIeZEwKhQzoBUdTV0N3zuwWDZYVJatDvZ2OyzPUvdIAZDsCetk3coyMfcnQ== form-data@^3.0.0: - version "3.0.1" - resolved "https://registry.yarnpkg.com/form-data/-/form-data-3.0.1.tgz#ebd53791b78356a99af9a300d4282c4d5eb9755f" - integrity sha512-RHkBKtLWUVwd7SqRIvCZMEvAMoGUp0XU+seQiZejj0COz3RI3hWP4sCv3gZWWLjJTd7rGwcsF5eKZGii0r/hbg== + version "3.0.2" + resolved 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"https://registry.yarnpkg.com/hast-util-to-jsx-runtime/-/hast-util-to-jsx-runtime-2.3.0.tgz#3ed27caf8dc175080117706bf7269404a0aa4f7c" - integrity sha512-H/y0+IWPdsLLS738P8tDnrQ8Z+dj12zQQ6WC11TIM21C8WFVoIxcqWXf2H3hiTVZjF1AWqoimGwrTWecWrnmRQ== + version "2.3.2" + resolved "https://registry.yarnpkg.com/hast-util-to-jsx-runtime/-/hast-util-to-jsx-runtime-2.3.2.tgz#6d11b027473e69adeaa00ca4cfb5bb68e3d282fa" + integrity sha512-1ngXYb+V9UT5h+PxNRa1O1FYguZK/XL+gkeqvp7EdHlB9oHUG0eYRo/vY5inBdcqo3RkPMC58/H94HvkbfGdyg== dependencies: "@types/estree" "^1.0.0" "@types/hast" "^3.0.0" @@ -5381,7 +5108,7 @@ humanize-ms@^1.2.1: dependencies: ms "^2.0.0" -iconv-lite@0.4, iconv-lite@0.4.24: +iconv-lite@0.4.24: version "0.4.24" resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.4.24.tgz#2022b4b25fbddc21d2f524974a474aafe733908b" integrity sha512-v3MXnZAcvnywkTUEZomIActle7RXXeedOR31wwl7VlyoXO4Qi9arvSenNQWne1TcRwhCL1HwLI21bEqdpj8/rA== @@ -5514,11 +5241,6 @@ internal-slot@^1.0.7: resolved "https://registry.yarnpkg.com/internmap/-/internmap-2.0.3.tgz#6685f23755e43c524e251d29cbc97248e3061009" integrity sha512-5Hh7Y1wQbvY5ooGgPbDaL5iYLAPzMTUrjMulskHLH6wnv/A+1q5rgEaiuqEjB+oxGXIVZs1FF+R/KPN3ZSQYYg== -internmap@^1.0.0: - version "1.0.1" - resolved "https://registry.yarnpkg.com/internmap/-/internmap-1.0.1.tgz#0017cc8a3b99605f0302f2b198d272e015e5df95" - integrity sha512-lDB5YccMydFBtasVtxnZ3MRBHuaoE8GKsppq+EchKL2U4nK/DmEpPHNH8MZe5HkMtpSiTSOZwfN0tzYjO/lJEw== - interpret@^2.2.0: version "2.2.0" resolved "https://registry.yarnpkg.com/interpret/-/interpret-2.2.0.tgz#1a78a0b5965c40a5416d007ad6f50ad27c417df9" @@ -6040,6 +5762,16 @@ jest-diff@^26.6.2: jest-get-type "^26.3.0" pretty-format "^26.6.2" +jest-diff@^29.7.0: + version "29.7.0" + resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-29.7.0.tgz#017934a66ebb7ecf6f205e84699be10afd70458a" + integrity sha512-LMIgiIrhigmPrs03JHpxUh2yISK3vLFPkAodPeo0+BuF7wA2FoQbkEg1u8gBYBThncu7e1oEDUfIXVuTqLRUjw== + dependencies: + chalk "^4.0.0" + diff-sequences "^29.6.3" + jest-get-type "^29.6.3" + pretty-format "^29.7.0" + jest-docblock@^26.0.0: version "26.0.0" resolved "https://registry.yarnpkg.com/jest-docblock/-/jest-docblock-26.0.0.tgz#3e2fa20899fc928cb13bd0ff68bd3711a36889b5" @@ -6088,6 +5820,11 @@ jest-get-type@^26.3.0: resolved "https://registry.yarnpkg.com/jest-get-type/-/jest-get-type-26.3.0.tgz#e97dc3c3f53c2b406ca7afaed4493b1d099199e0" integrity sha512-TpfaviN1R2pQWkIihlfEanwOXK0zcxrKEE4MlU6Tn7keoXdN6/3gK/xl0yEh8DOunn5pOVGKf8hB4R9gVh04ig== +jest-get-type@^29.6.3: + version "29.6.3" + resolved "https://registry.yarnpkg.com/jest-get-type/-/jest-get-type-29.6.3.tgz#36f499fdcea197c1045a127319c0481723908fd1" + integrity sha512-zrteXnqYxfQh7l5FHyL38jL39di8H8rHoecLH3JNxH3BwOrBsNeabdap5e0I23lD4HHI8W5VFBZqG4Eaq5LNcw== + jest-haste-map@^26.6.2: version "26.6.2" resolved "https://registry.yarnpkg.com/jest-haste-map/-/jest-haste-map-26.6.2.tgz#dd7e60fe7dc0e9f911a23d79c5ff7fb5c2cafeaa" @@ -6171,6 +5908,16 @@ jest-matcher-utils@^26.6.2: jest-get-type "^26.3.0" pretty-format "^26.6.2" +jest-matcher-utils@^29.7.0: + version "29.7.0" + resolved "https://registry.yarnpkg.com/jest-matcher-utils/-/jest-matcher-utils-29.7.0.tgz#ae8fec79ff249fd592ce80e3ee474e83a6c44f12" + integrity sha512-sBkD+Xi9DtcChsI3L3u0+N0opgPYnCRPtGcQYrgXmR+hmt/fYfWAL0xRXYU8eWOdfuLgBe0YCW3AFtnRLagq/g== + dependencies: + chalk "^4.0.0" + jest-diff "^29.7.0" + jest-get-type "^29.6.3" + pretty-format "^29.7.0" + jest-message-util@^26.6.2: version "26.6.2" resolved "https://registry.yarnpkg.com/jest-message-util/-/jest-message-util-26.6.2.tgz#58173744ad6fc0506b5d21150b9be56ef001ca07" @@ -6186,6 +5933,21 @@ jest-message-util@^26.6.2: slash "^3.0.0" stack-utils "^2.0.2" +jest-message-util@^29.7.0: + version "29.7.0" + resolved "https://registry.yarnpkg.com/jest-message-util/-/jest-message-util-29.7.0.tgz#8bc392e204e95dfe7564abbe72a404e28e51f7f3" + integrity sha512-GBEV4GRADeP+qtB2+6u61stea8mGcOT4mCtrYISZwfu9/ISHFJ/5zOMXYbpBE9RsS5+Gb63DW4FgmnKJ79Kf6w== + dependencies: + "@babel/code-frame" "^7.12.13" + "@jest/types" "^29.6.3" + "@types/stack-utils" "^2.0.0" + chalk "^4.0.0" + graceful-fs "^4.2.9" + micromatch "^4.0.4" + pretty-format "^29.7.0" + slash "^3.0.0" + stack-utils "^2.0.3" + jest-mock@^26.6.2: version "26.6.2" resolved "https://registry.yarnpkg.com/jest-mock/-/jest-mock-26.6.2.tgz#d6cb712b041ed47fe0d9b6fc3474bc6543feb302" @@ -6353,6 +6115,18 @@ jest-util@^27.5.1: graceful-fs "^4.2.9" picomatch "^2.2.3" +jest-util@^29.7.0: + version "29.7.0" + resolved "https://registry.yarnpkg.com/jest-util/-/jest-util-29.7.0.tgz#23c2b62bfb22be82b44de98055802ff3710fc0bc" + integrity sha512-z6EbKajIpqGKU56y5KBUgy1dt1ihhQJgWzUlZHArA/+X2ad7Cb5iF+AK1EWVL/Bo7Rz9uurpqw6SiBCefUbCGA== + dependencies: + "@jest/types" "^29.6.3" + "@types/node" "*" + chalk "^4.0.0" + ci-info "^3.2.0" + graceful-fs "^4.2.9" + picomatch "^2.2.3" + jest-validate@^26.6.2: version "26.6.2" resolved "https://registry.yarnpkg.com/jest-validate/-/jest-validate-26.6.2.tgz#23d380971587150467342911c3d7b4ac57ab20ec" @@ -6789,9 +6563,9 @@ map-visit@^1.0.0: object-visit "^1.0.0" mdast-util-from-markdown@^2.0.0: - version "2.0.1" - resolved "https://registry.yarnpkg.com/mdast-util-from-markdown/-/mdast-util-from-markdown-2.0.1.tgz#32a6e8f512b416e1f51eb817fc64bd867ebcd9cc" - integrity sha512-aJEUyzZ6TzlsX2s5B4Of7lN7EQtAxvtradMMglCQDyaTFgse6CmtmdJ15ElnVRlCg1vpNyVtbem0PWzlNieZsA== + version "2.0.2" + resolved "https://registry.yarnpkg.com/mdast-util-from-markdown/-/mdast-util-from-markdown-2.0.2.tgz#4850390ca7cf17413a9b9a0fbefcd1bc0eb4160a" + integrity sha512-uZhTV/8NBuw0WHkPTrCqDOl0zVe1BIng5ZtHoDk49ME1qqcjYmmLmOf0gELgcRMxN4w2iuIeVso5/6QymSrgmA== dependencies: "@types/mdast" "^4.0.0" "@types/unist" "^3.0.0" @@ -6872,15 +6646,16 @@ mdast-util-to-hast@^13.0.0: vfile "^6.0.0" mdast-util-to-markdown@^2.0.0: - version "2.1.0" - resolved 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"https://registry.yarnpkg.com/safe-regex-test/-/safe-regex-test-1.0.3.tgz#a5b4c0f06e0ab50ea2c395c14d8371232924c377" @@ -9115,7 +8838,7 @@ ssri@^9.0.0: dependencies: minipass "^3.1.1" -stack-utils@^2.0.2: +stack-utils@^2.0.2, stack-utils@^2.0.3: version "2.0.6" resolved "https://registry.yarnpkg.com/stack-utils/-/stack-utils-2.0.6.tgz#aaf0748169c02fc33c8232abccf933f54a1cc34f" integrity sha512-XlkWvfIm6RmsWtNJx+uqtKLS8eqFbxUg0ZzLXqY0caEy9l7hruX8IpiDnjsLavoBgqCCR71TqWO8MaXYheJ3RQ== @@ -9379,9 +9102,11 @@ svg-inline-loader@^0.8.0: simple-html-tokenizer "^0.1.1" swagger-ui-dist@^5.10.5: - version "5.17.14" - resolved "https://registry.yarnpkg.com/swagger-ui-dist/-/swagger-ui-dist-5.17.14.tgz#e2c222e5bf9e15ccf80ec4bc08b4aaac09792fd6" - integrity sha512-CVbSfaLpstV65OnSjbXfVd6Sta3q3F7Cj/yYuvHMp1P90LztOLs6PfUnKEVAeiIVQt9u2SaPwv0LiH/OyMjHRw== + version "5.18.2" + resolved "https://registry.yarnpkg.com/swagger-ui-dist/-/swagger-ui-dist-5.18.2.tgz#62013074374d272c04ed3030704b88db5aa8c0b7" + 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"https://registry.yarnpkg.com/to-object-path/-/to-object-path-0.3.0.tgz#297588b7b0e7e0ac08e04e672f85c1f4999e17af" @@ -9593,9 +9313,9 @@ tslib@^1.8.1, tslib@^1.9.0: integrity sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg== tslib@^2.1.0, tslib@^2.6.2: - version "2.7.0" - resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.7.0.tgz#d9b40c5c40ab59e8738f297df3087bf1a2690c01" - integrity sha512-gLXCKdN1/j47AiHiOkJN69hJmcbGTHI0ImLmbYLHykhgeN0jVGola9yVjFgzCUklsZQMW55o+dW7IXv3RCXDzA== + version "2.8.1" + resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.8.1.tgz#612efe4ed235d567e8aba5f2a5fab70280ade83f" + integrity sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w== tsutils@^3.21.0: version "3.21.0" @@ -9727,7 +9447,7 @@ unbox-primitive@^1.0.2: has-symbols "^1.0.3" which-boxed-primitive "^1.0.2" -undici-types@~6.19.2: +undici-types@~6.19.8: version "6.19.8" resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-6.19.8.tgz#35111c9d1437ab83a7cdc0abae2f26d88eda0a02" integrity sha512-ve2KP6f/JnbPBFyobGHuerC9g1FYGn/F8n1LWTwNxCEzd6IfqTwUQcNXgEtmmQ6DlRrC1hrSrBnCZPokRrDHjw== @@ -9853,7 +9573,7 @@ upath@^1.1.1: resolved "https://registry.yarnpkg.com/upath/-/upath-1.2.0.tgz#8f66dbcd55a883acdae4408af8b035a5044c1894" integrity sha512-aZwGpamFO61g3OlfT7OQCHqhGnW43ieH9WZeP7QxN/G/jS4jfqUkZxoryvJgVPEcrl5NL/ggHsSmLMHuH64Lhg== -update-browserslist-db@^1.1.0: +update-browserslist-db@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/update-browserslist-db/-/update-browserslist-db-1.1.1.tgz#80846fba1d79e82547fb661f8d141e0945755fe5" integrity sha512-R8UzCaa9Az+38REPiJ1tXlImTJXlVfgHZsglwBD/k6nj76ctsH1E3q4doGrukiLQd3sGQYu56r5+lo5r94l29A== @@ -9873,7 +9593,7 @@ urix@^0.1.0: resolved "https://registry.yarnpkg.com/urix/-/urix-0.1.0.tgz#da937f7a62e21fec1fd18d49b35c2935067a6c72" integrity sha512-Am1ousAhSLBeB9cG/7k7r2R0zj50uDRlZHPGbazid5s9rlF1F/QKYObEKSIunSjIOkJZqwRRLpvewjEkM7pSqg== -url-join@^4.0.1: +url-join@4.0.1: version "4.0.1" resolved "https://registry.yarnpkg.com/url-join/-/url-join-4.0.1.tgz#b642e21a2646808ffa178c4c5fda39844e12cde7" integrity sha512-jk1+QP6ZJqyOiuEI9AEWQfju/nB2Pw466kbA0LEZljHwKeMgd9WrAEgEGxjPDD2+TNbbb37rTyhEfrCXfuKXnA== @@ -10117,17 +9837,17 @@ webpack-sources@^3.2.3: integrity sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w== webpack@^5.91.0: - version "5.95.0" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.95.0.tgz#8fd8c454fa60dad186fbe36c400a55848307b4c0" - integrity sha512-2t3XstrKULz41MNMBF+cJ97TyHdyQ8HCt//pqErqDvNjU9YQBnZxIHa11VXsi7F3mb5/aO2tuDxdeTPdU7xu9Q== + version "5.96.1" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.96.1.tgz#3676d1626d8312b6b10d0c18cc049fba7ac01f0c" + integrity 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