From 9d160ff784b6679441b55cf55d1de1dc59a3f07b Mon Sep 17 00:00:00 2001 From: nkumar2 Date: Thu, 9 Feb 2023 14:22:34 +0000 Subject: [PATCH] rearrange project and fix fetch issue --- jest.config.js | 4 + jest.config.json | 4 - jest.setup.js | 19 + package-lock.json | 1804 +- package.json | 7 +- src/__tests_data/GenotypesFilterData.js | 2557 -- src/__tests_data/GenotypesTableData.js | 20081 ---------------- src/mocks/handlers.js | 16 + src/mocks/server.js | 5 + src/{__tests__ => test}/DemoApp.test.js | 0 src/{__tests__ => test}/GenotypeView.test.js | 0 .../GenotypesFilter.test.js | 2 +- .../GenotypesTable.test.js | 6 +- src/{__tests__ => test}/Pagination.test.js | 0 src/test/test_data/GenotypesFilterData.js | 378 + src/test/test_data/GenotypesTableData.js | 833 + src/test/test_data/GenotypesViewData.js | 282 + 17 files changed, 3203 insertions(+), 22795 deletions(-) create mode 100644 jest.config.js delete mode 100644 jest.config.json create mode 100644 jest.setup.js delete mode 100644 src/__tests_data/GenotypesFilterData.js delete mode 100644 src/__tests_data/GenotypesTableData.js create mode 100644 src/mocks/handlers.js create mode 100644 src/mocks/server.js rename src/{__tests__ => test}/DemoApp.test.js (100%) rename src/{__tests__ => test}/GenotypeView.test.js (100%) rename src/{__tests__ => test}/GenotypesFilter.test.js (97%) rename src/{__tests__ => test}/GenotypesTable.test.js (90%) rename src/{__tests__ => test}/Pagination.test.js (100%) create mode 100644 src/test/test_data/GenotypesFilterData.js create mode 100644 src/test/test_data/GenotypesTableData.js create mode 100644 src/test/test_data/GenotypesViewData.js diff --git a/jest.config.js b/jest.config.js new file mode 100644 index 0000000..a76308c --- /dev/null +++ b/jest.config.js @@ -0,0 +1,4 @@ +module.exports = { + testEnvironment: 'jsdom', + setupFilesAfterEnv: ['./jest.setup.js'], +} \ No newline at end of file diff --git a/jest.config.json b/jest.config.json deleted file mode 100644 index 492564c..0000000 --- a/jest.config.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "testRegex": "(/__tests__/.*|(\\.|/)(test|spec))\\.jsx?$", - "testEnvironment": "jsdom" -} \ No newline at end of file diff --git a/jest.setup.js b/jest.setup.js new file mode 100644 index 0000000..5823659 --- /dev/null +++ b/jest.setup.js @@ -0,0 +1,19 @@ +// Polyfill "window.fetch" used in the React component. +import 'whatwg-fetch' + +// Extend Jest "expect" functionality with Testing Library assertions. +import '@testing-library/jest-dom' + +import { server } from './src/mocks/server' + +beforeAll(() => { + server.listen() +}) + +afterEach(() => { + server.resetHandlers() +}) + +afterAll(() => { + server.close() +}) diff --git a/package-lock.json b/package-lock.json index 56b59f3..e88394a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -25,11 +25,12 @@ "css-loader": "^6.7.3", "jest": "^29.4.1", "jest-environment-jsdom": "^29.4.1", - "node-fetch": "^3.3.0", + "msw": "^1.0.0", "style-loader": "^0.23.0", "webpack": "^5.75.0", "webpack-cli": "^5.0.1", - "webpack-dev-server": "^4.11.1" + "webpack-dev-server": "^4.11.1", + "whatwg-fetch": "^3.6.2" } }, "node_modules/@adobe/css-tools": { @@ -2377,6 +2378,70 @@ "integrity": "sha512-Hcv+nVC0kZnQ3tD9GVu5xSMR4VVYOteQIr/hwFPVEvPdlXqgGEuRjiheChHgdM+JyqdgNcmzZOX/tnl0JOiI7A==", "dev": true }, + "node_modules/@mswjs/cookies": { + "version": "0.2.2", + "resolved": "https://registry.npmjs.org/@mswjs/cookies/-/cookies-0.2.2.tgz", + "integrity": "sha512-mlN83YSrcFgk7Dm1Mys40DLssI1KdJji2CMKN8eOlBqsTADYzj2+jWzsANsUTFbxDMWPD5e9bfA1RGqBpS3O1g==", + "dev": true, + "dependencies": { + "@types/set-cookie-parser": "^2.4.0", + "set-cookie-parser": "^2.4.6" + }, + "engines": { + "node": ">=14" + } + }, + "node_modules/@mswjs/interceptors": { + "version": "0.17.7", + "resolved": "https://registry.npmjs.org/@mswjs/interceptors/-/interceptors-0.17.7.tgz", + "integrity": "sha512-dPInyLEF6ybLxfKGY99euI+mbT6ls4PVO9qPgGIsRk3+2VZVfT7fo9Sq6Q8eKT9W38QtUyhG74hN7xMtKWioGw==", + "dev": true, + "dependencies": { + "@open-draft/until": "^1.0.3", + "@types/debug": "^4.1.7", + "@xmldom/xmldom": "^0.8.3", + "debug": "^4.3.3", + "headers-polyfill": "^3.1.0", + "outvariant": "^1.2.1", + "strict-event-emitter": "^0.2.4", + "web-encoding": "^1.1.5" + }, + "engines": { + "node": ">=14" + } + }, + "node_modules/@mswjs/interceptors/node_modules/debug": { + "version": "4.3.4", + "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz", + "integrity": "sha512-PRWFHuSU3eDtQJPvnNY7Jcket1j0t5OuOsFzPPzsekD52Zl8qUfFIPEiswXqIvHWGVHOgX+7G/vCNNhehwxfkQ==", + "dev": true, + "dependencies": { + "ms": "2.1.2" + }, + "engines": { + "node": ">=6.0" + }, + "peerDependenciesMeta": { + "supports-color": { + "optional": true + } + } + }, + "node_modules/@mswjs/interceptors/node_modules/ms": { + "version": "2.1.2", + "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz", + 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"punycode": "^2.1.1" } }, + "tslib": { + "version": "2.5.0", + "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.5.0.tgz", + "integrity": "sha512-336iVw3rtn2BUK7ORdIAHTyxHGRIHVReokCR3XjbckJMK7ms8FysBfhLR8IXnAgy7T0PTPNBWKiH514FOW/WSg==", + "dev": true + }, "type-check": { "version": "0.3.2", "resolved": "https://registry.npmjs.org/type-check/-/type-check-0.3.2.tgz", @@ -19851,6 +21327,19 @@ "requires-port": "^1.0.0" } }, + "util": { + "version": "0.12.5", + "resolved": "https://registry.npmjs.org/util/-/util-0.12.5.tgz", + "integrity": "sha512-kZf/K6hEIrWHI6XqOFUiiMa+79wE/D8Q+NCNAWclkyg3b4d2k7s0QGepNjiABc+aR3N1PAyHL7p6UcLY6LmrnA==", + "dev": true, + "requires": { + "inherits": "^2.0.3", + "is-arguments": "^1.0.4", + "is-generator-function": "^1.0.7", + "is-typed-array": "^1.1.3", + "which-typed-array": "^1.1.2" + } + }, "util-deprecate": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz", @@ -19936,11 +21425,24 @@ "minimalistic-assert": "^1.0.0" } }, - "web-streams-polyfill": { - "version": "3.2.1", - "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.2.1.tgz", - "integrity": "sha512-e0MO3wdXWKrLbL0DgGnUV7WHVuw9OUvL4hjgnPkIeEvESk74gAITi5G606JtZPp39cd8HA9VQzCIvA49LpPN5Q==", - "dev": true + "wcwidth": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/wcwidth/-/wcwidth-1.0.1.tgz", + "integrity": "sha512-XHPEwS0q6TaxcvG85+8EYkbiCux2XtWG2mkc47Ng2A77BQu9+DqIOJldST4HgPkuea7dvKSj5VgX3P1d4rW8Tg==", + "dev": true, + "requires": { + "defaults": "^1.0.3" + } + }, + "web-encoding": { + "version": "1.1.5", + "resolved": "https://registry.npmjs.org/web-encoding/-/web-encoding-1.1.5.tgz", + "integrity": "sha512-HYLeVCdJ0+lBYV2FvNZmv3HJ2Nt0QYXqZojk3d9FJOLkwnuhzM9tmamh8d7HPM8QqjKH8DeHkFTx+CFlWpZZDA==", + "dev": true, + "requires": { + "@zxing/text-encoding": "0.9.0", + "util": "^0.12.3" + } }, "webidl-conversions": { "version": "7.0.0", @@ -20207,6 +21709,12 @@ } } }, + "whatwg-fetch": { + "version": "3.6.2", + "resolved": "https://registry.npmjs.org/whatwg-fetch/-/whatwg-fetch-3.6.2.tgz", + "integrity": "sha512-bJlen0FcuU/0EMLrdbJ7zOnW6ITZLrZMIarMUVmdKtsGvZna8vxKYaexICWPfZ8qwf9fzNq+UEIZrnSaApt6RA==", + "dev": true + }, "whatwg-mimetype": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-3.0.0.tgz", diff --git a/package.json b/package.json index 11f1ec2..f3ad296 100644 --- a/package.json +++ b/package.json @@ -6,7 +6,7 @@ "scripts": { "start": "webpack-dev-server --mode development --hot", "build": "webpack --mode development", - "test": "jest --config ./jest.config.json" + "test": "jest" }, "repository": { "type": "git", @@ -24,11 +24,12 @@ "css-loader": "^6.7.3", "jest": "^29.4.1", "jest-environment-jsdom": "^29.4.1", - "node-fetch": "^3.3.0", + "msw": "^1.0.0", "style-loader": "^0.23.0", "webpack": "^5.75.0", "webpack-cli": "^5.0.1", - "webpack-dev-server": "^4.11.1" + "webpack-dev-server": "^4.11.1", + "whatwg-fetch": "^3.6.2" }, "dependencies": { "lodash": "^4.17.21", diff --git a/src/__tests_data/GenotypesFilterData.js b/src/__tests_data/GenotypesFilterData.js deleted file mode 100644 index 547b836..0000000 --- a/src/__tests_data/GenotypesFilterData.js +++ /dev/null @@ -1,2557 +0,0 @@ -export const genotypes_filter_test_data = { - "speciesList": [ - { - "taxonomyCode": "dmelanogaster", - "taxonomyCommonName": "Fruit fly", - "taxonomyScientificName": "Drosophila melanogaster" - }, - { - "taxonomyCode": "hsapiens", - "taxonomyCommonName": "Human", - "taxonomyScientificName": "Homo sapiens" - }, - { - "taxonomyCode": "mmusculus", - "taxonomyCommonName": "House mouse", - "taxonomyScientificName": "Mus musculus" - }, - { - "taxonomyCode": "athaliana", - "taxonomyCommonName": "thale cress", - "taxonomyScientificName": "Arabidopsis thaliana" - }, - { - "taxonomyCode": "rnorvegicus", - "taxonomyCommonName": "rat", - "taxonomyScientificName": "Rattus norvegicus" - }, - { - "taxonomyCode": "drerio", - "taxonomyCommonName": "Zebrafish", - "taxonomyScientificName": "Danio rerio" - }, - { - "taxonomyCode": "cfamiliaris", - "taxonomyCommonName": "Dog", - "taxonomyScientificName": "Canis lupus familiaris" - }, - { - "taxonomyCode": "ecaballus", - "taxonomyCommonName": "Horse", - "taxonomyScientificName": "Equus caballus" - }, - { - "taxonomyCode": "ggallus", - "taxonomyCommonName": "Chicken", - "taxonomyScientificName": "Gallus gallus" - }, - { - "taxonomyCode": "tcastaneum", - "taxonomyCommonName": "red flour beetle", - "taxonomyScientificName": "Tribolium castaneum" - }, - { - "taxonomyCode": "afumigatus", - "taxonomyCommonName": "Ascomycetes", - "taxonomyScientificName": "Aspergillus fumigatus Af293" - }, - { - "taxonomyCode": "pfalciparum", - "taxonomyCommonName": "Plasmodium falciparum", - "taxonomyScientificName": "Plasmodium falciparum" - }, - { - "taxonomyCode": "sscrofa", - "taxonomyCommonName": "Pig", - "taxonomyScientificName": "Sus scrofa" - }, - { - "taxonomyCode": "btaurus", - "taxonomyCommonName": "Cattle", - "taxonomyScientificName": "Bos taurus" - }, - { - "taxonomyCode": "bindicus", - "taxonomyCommonName": "Zebu cattle", - "taxonomyScientificName": "Bos indicus" - }, - { - "taxonomyCode": "bbison", - "taxonomyCommonName": "Bison", - "taxonomyScientificName": "Bison bison" - }, - { - "taxonomyCode": "bgrunniens", - "taxonomyCommonName": "domestic yak", - "taxonomyScientificName": "Bos grunniens" - }, - { - "taxonomyCode": "bbonasus", - "taxonomyCommonName": "European bison", - "taxonomyScientificName": "Bison bonasus" - }, - { - "taxonomyCode": "sbicolor", - "taxonomyCommonName": "Sorghum", - "taxonomyScientificName": "Sorghum bicolor" - }, - { - "taxonomyCode": "vvinifera", - "taxonomyCommonName": "wine grape", - "taxonomyScientificName": "Vitis vinifera" - }, - { - "taxonomyCode": "aaegypti", - "taxonomyCommonName": "yellow fever mosquito", - "taxonomyScientificName": "Aedes aegypti" - }, - { - "taxonomyCode": "csativus", - "taxonomyCommonName": "Cucumber", - "taxonomyScientificName": "Cucumis sativus var. sativus" - }, - { - "taxonomyCode": "gmax", - "taxonomyCommonName": "soybean", - "taxonomyScientificName": "Glycine max" - }, - { - "taxonomyCode": "smacromomyceticus", - "taxonomyCommonName": "Streptomyces macromomyceticus", - "taxonomyScientificName": "Streptomyces macromomyceticus" - }, - { - "taxonomyCode": "cjacchus", - "taxonomyCommonName": "Marmoset", - "taxonomyScientificName": "Callithrix jacchus" - }, - { - "taxonomyCode": "ddiscoideum", - "taxonomyCommonName": "Amoeba", - "taxonomyScientificName": "Dictyostelium discoideum" - }, - { - "taxonomyCode": "zmays", - "taxonomyCommonName": "Maize", - "taxonomyScientificName": "Zea mays" - }, - { - "taxonomyCode": "agambiae", - "taxonomyCommonName": "African malaria mosquito", - "taxonomyScientificName": "Anopheles gambiae" - }, - { - "taxonomyCode": "banthracis", - "taxonomyCommonName": "Firmicutes", - "taxonomyScientificName": "Bacillus anthracis str. Ames" - }, - { - "taxonomyCode": "msubspparatuberculosis", - "taxonomyCommonName": "high GC Gram+", - "taxonomyScientificName": "Mycobacterium avium subsp. paratuberculosis" - }, - { - "taxonomyCode": "scerevisiae", - "taxonomyCommonName": "Saccharomyces cerevisiae S288C\n", - "taxonomyScientificName": "Saccharomyces cerevisiae S288C\n" - }, - { - "taxonomyCode": "mgallopavo", - "taxonomyCommonName": "turkey", - "taxonomyScientificName": "Meleagris gallopavo" - }, - { - "taxonomyCode": "cporcellus", - "taxonomyCommonName": "Guinea pig", - "taxonomyScientificName": "Cavia porcellus" - }, - { - "taxonomyCode": "tguttata", - "taxonomyCommonName": "zebra finch", - "taxonomyScientificName": "Taeniopygia guttata" - }, - { - "taxonomyCode": "vpacos", - "taxonomyCommonName": "Alpaca", - "taxonomyScientificName": "Vicugna pacos" - }, - { - "taxonomyCode": "lcatta", - "taxonomyCommonName": "Ring-tailed lemur", - "taxonomyScientificName": "Lemur catta" - }, - { - "taxonomyCode": "fcatus", - "taxonomyCommonName": "Cat", - "taxonomyScientificName": "Felis catus" - }, - { - "taxonomyCode": "slycopersicum", - "taxonomyCommonName": "Tomato", - "taxonomyScientificName": "Solanum lycopersicum" - }, - { - "taxonomyCode": "hchromini", - "taxonomyCommonName": "Cichlid", - "taxonomyScientificName": "Haplochromini" - }, - { - "taxonomyCode": "lmonocytogenesegde", - "taxonomyCommonName": "Listeria monocytogenes", - "taxonomyScientificName": "Listeria monocytogenes EGD-e" - }, - { - "taxonomyCode": "apalmata", - "taxonomyCommonName": "stoney corals", - "taxonomyScientificName": "Acropora palmata" - }, - { - "taxonomyCode": "ssalar", - "taxonomyCommonName": "Salmon", - "taxonomyScientificName": "Salmo salar" - }, - { - "taxonomyCode": "smansoni", - "taxonomyCommonName": "Blood fluke", - "taxonomyScientificName": "Schistosoma mansoni" - }, - { - "taxonomyCode": "falbicollis", - "taxonomyCommonName": "collared flycatcher", - "taxonomyScientificName": "Ficedula albicollis" - }, - { - "taxonomyCode": "foxysporum", - "taxonomyCommonName": "Ascomycete fungus", - "taxonomyScientificName": "Fusarium oxysporum f. cubense" - }, - { - "taxonomyCode": "sitalica", - "taxonomyCommonName": "foxtail millet", - "taxonomyScientificName": "Setaria italica" - }, - { - "taxonomyCode": "bmutus", - "taxonomyCommonName": "wild yak", - "taxonomyScientificName": "Bos mutus" - }, - { - "taxonomyCode": "oaries", - "taxonomyCommonName": "Sheep", - "taxonomyScientificName": "Ovis aries" - }, - { - "taxonomyCode": "oorientalis", - "taxonomyCommonName": "Asiatic mouflon", - "taxonomyScientificName": "Ovis orientalis" - }, - { - "taxonomyCode": "oddalli", - "taxonomyCommonName": "Dall sheep", - "taxonomyScientificName": "Ovis dalli dalli" - }, - { - "taxonomyCode": "chircus", - "taxonomyCommonName": "Goat", - "taxonomyScientificName": "Capra hircus" - }, - { - "taxonomyCode": "ccajan", - "taxonomyCommonName": "Pigeonpea ", - "taxonomyScientificName": "Cajanus cajan" - }, - { - "taxonomyCode": "aminimus", - "taxonomyCommonName": "Mosquito", - "taxonomyScientificName": "Anopheles minimus" - 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"speciesAssemblyCode": "dexilis_foniocm05836" - } - ], - "oanatinus": [ - { - "assemblyAccession": "GCF_000002275.2", - "assemblyChain": "GCF_000002275", - "assemblyVersion": "2", - "assemblyName": "Ornithorhynchus_anatinus-5.0.1", - "assemblyCode": "501", - "taxonomyId": 9258, - "taxonomyCommonName": "platypus", - "taxonomyScientificName": "Ornithorhynchus anatinus", - "taxonomyCode": "oanatinus", - "taxonomyEvaName": "platypus", - "speciesAssemblyCode": "oanatinus_501" - } - ] - }, - "assemblyList": [ - { - "assemblyAccession": "GCA_000002305.1", - "assemblyChain": "GCA_000002305", - "assemblyVersion": "1", - "assemblyName": "EquCab2.0", - "assemblyCode": "20", - "taxonomyId": 9796, - "taxonomyCommonName": "Horse", - "taxonomyScientificName": "Equus caballus", - "taxonomyCode": "ecaballus", - "taxonomyEvaName": "horse", - "speciesAssemblyCode": "ecaballus_20" - }, - { - "assemblyAccession": "GCA_002863925.1", - "assemblyChain": "GCA_002863925", - "assemblyVersion": "1", - "assemblyName": "EquCab3.0", - "assemblyCode": "30", - "taxonomyId": 9796, - "taxonomyCommonName": "Horse", - "taxonomyScientificName": "Equus caballus", - "taxonomyCode": "ecaballus", - "taxonomyEvaName": "horse", - "speciesAssemblyCode": "ecaballus_30" - } - ], - "selectedSpecies": "ecaballus", - "selectedAssembly": "ecaballus_20", - "location": "1:3000000-3100000", - "studies": [ - "BROAD_EQUCAB2.0:2008.08.08", - "PRJEB22866", - "PRJEB23301", - "PRJEB23441", - "PRJEB24624", - "PRJEB24630", - "PRJEB25439", - "PRJEB26741", - "PRJEB27771", - "PRJEB30116", - "PRJEB32686", - "PRJEB38010", - "PRJEB9799" - ], - "selectedStudies": [ - "BROAD_EQUCAB2.0:2008.08.08", - "PRJEB22866", - "PRJEB23301", - "PRJEB23441", - "PRJEB24624", - "PRJEB24630", - "PRJEB25439", - "PRJEB26741", - "PRJEB27771", - "PRJEB30116", - "PRJEB32686", - "PRJEB38010", - "PRJEB9799" - ], - "resultsPerPage": 50 -} \ No newline at end of file diff --git a/src/__tests_data/GenotypesTableData.js b/src/__tests_data/GenotypesTableData.js deleted file mode 100644 index 7549558..0000000 --- a/src/__tests_data/GenotypesTableData.js +++ /dev/null @@ -1,20081 +0,0 @@ -export const genotypes_table_test_data = { - "studies": [ - "BROAD_EQUCAB2.0:2008.08.08", - "PRJEB22866", - "PRJEB23301", - "PRJEB23441", - "PRJEB24624", - "PRJEB24630", - "PRJEB25439", - "PRJEB26741", - "PRJEB27771", - "PRJEB30116", - "PRJEB32686", - "PRJEB38010", - "PRJEB9799" -], - "variants": [ - { - "chromosome": "1", - "start": 3000829, - "end": 3000829, - "reference": "C", - "alternate": "T", - "hgvs": { - "genomic": [ - "1:g.3000829C>T" - ] - }, - "sourceEntries": { - "PRJEB9799_ERZ780739": { - "fileId": "ERZ780739", - "studyId": "PRJEB9799", - "format": "GT:AD:DP:GQ:PL", - "cohortStats": { - "ALL": { - "refAllele": "C", - "altAllele": "T", - "variantType": "SNV", - "refAlleleCount": 0, - "altAlleleCount": 0, - "missingAlleles": 0, - "missingGenotypes": 0, - "refAlleleFreq": 0, - "altAlleleFreq": 0, - "maf": 0.083333336, - "mgf": 0, - "mafAllele": "T", - "mgfGenotype": "1/1", - "numSamples": 0, - "transition": true, - "transversion": false - } - }, - "attributes": { - "AC": "1", - "MQRankSum": "-2.298", - "FILTER": "PASS", - "set": "variant", - "MQ": "12784", - "AF": "0.083", - "src": "chr1\t3000829\t.\tC\tT\t177.17\tPASS\tAC=1;AF=0.083;AN=12;BaseQRankSum=-1.778;ClippingRankSum=0.480;DP=62;FS=0.000;MLEAC=1;MLEAF=0.083;MQ=55.49;MQ0=0;MQRankSum=-2.298;QD=12.66;ReadPosRankSum=0.619;VQSLOD=0.573;culprit=FS;set=variant", - "MLEAC": "1", - "QUAL": "177.17", - "BaseQRankSum": "-1.778", - "MLEAF": "0.083", - "DP": "62", - "ReadPosRankSum": "0.619", - "AN": "12", - "FS": "0.000", - "MQ0": "0", - "culprit": "FS", - "QD": "12.66", - "VQSLOD": "0.573", - "ClippingRankSum": "0.480" - }, - "samplesData": { - "CH": { - "GT": "0/0" - }, - "MM": { - "GT": "0/1" - }, - "AMH": { - "GT": "0/0" - }, - "PER": { - "GT": "0/0" - }, - "ARB": { - "GT": "0/0" - }, - "TWH": { - "GT": "0/0" - } - } - } - }, - "annotation": { - "chromosome": "1", - "start": 3000829, - "end": 3000829, - "vepVersion": "89", - "vepCacheVersion": "89", - "consequenceTypes": [ - { - "soTerms": [ - { - "soName": "intergenic_variant", - "soAccession": "SO:0001628" - } - ] - } - ] - }, - "length": 1, - "type": "SNV", - "alleleFreqs": { - "PRJEB9799": 0.083333336 - }, - "color": "#636363", - "consequenceName": "intergenic_variant" - }, - { - "chromosome": "1", - "start": 3001637, - "end": 3001637, - "reference": "C", - "alternate": "T", - "hgvs": { - "genomic": [ - "1:g.3001637C>T" - ] - }, - "sourceEntries": { - "PRJEB23301_ERZ481891": { - "fileId": "ERZ481891", - "studyId": "PRJEB23301", - "format": "GT:DS", - "cohortStats": { - "ALL": { - "refAllele": "C", - "altAllele": "T", - "variantType": "SNV", - "refAlleleCount": 0, - "altAlleleCount": 0, - "missingAlleles": 0, - "missingGenotypes": 0, - "refAlleleFreq": 0, - "altAlleleFreq": 0, - "maf": 0.09630607, - "mgf": 0, - "mafAllele": "T", - "mgfGenotype": "0/0", - 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"intergenic_variant", - "soAccession": "SO:0001628" - } - ] - } - ] - }, - "length": 1, - "type": "SNV", - "alleleFreqs": { - "PRJEB9799": 0.33333334 - }, - "color": "#636363", - "consequenceName": "intergenic_variant" - } -], - "isLoaded": true, - "currentPage": 1, - "numPages": 10 -} \ No newline at end of file diff --git a/src/mocks/handlers.js b/src/mocks/handlers.js new file mode 100644 index 0000000..fe51343 --- /dev/null +++ b/src/mocks/handlers.js @@ -0,0 +1,16 @@ +import { rest } from 'msw' + +export const handlers = [ + rest.post('/login', (req, res, ctx) => { + const { username } = req.body + + return res( + ctx.json({ + id: 'f79e82e8-c34a-4dc7-a49e-9fadc0979fda', + username, + firstName: 'John', + lastName: 'Maverick', + }), + ) + }), +] diff --git a/src/mocks/server.js b/src/mocks/server.js new file mode 100644 index 0000000..8c5b183 --- /dev/null +++ b/src/mocks/server.js @@ -0,0 +1,5 @@ +import { setupServer } from 'msw/node' +import { handlers } from './handlers' + +// Setup requests interception using the given handlers. +export const server = setupServer(...handlers) diff --git a/src/__tests__/DemoApp.test.js b/src/test/DemoApp.test.js similarity index 100% rename from src/__tests__/DemoApp.test.js rename to src/test/DemoApp.test.js diff --git a/src/__tests__/GenotypeView.test.js b/src/test/GenotypeView.test.js similarity index 100% rename from src/__tests__/GenotypeView.test.js rename to src/test/GenotypeView.test.js diff --git a/src/__tests__/GenotypesFilter.test.js b/src/test/GenotypesFilter.test.js similarity index 97% rename from src/__tests__/GenotypesFilter.test.js rename to src/test/GenotypesFilter.test.js index 3322dd6..30078e0 100644 --- a/src/__tests__/GenotypesFilter.test.js +++ b/src/test/GenotypesFilter.test.js @@ -2,7 +2,7 @@ import React from 'react' import {render, screen} from '@testing-library/react' import '@testing-library/jest-dom/extend-expect' import GenotypesFilter from "../components/GenotypesFilter" -import {genotypes_filter_test_data} from "../__tests_data/GenotypesFilterData" +import {genotypes_filter_test_data} from "./test_data/GenotypesFilterData" test('check genotype filter view component is loading everything correctly', () => { diff --git a/src/__tests__/GenotypesTable.test.js b/src/test/GenotypesTable.test.js similarity index 90% rename from src/__tests__/GenotypesTable.test.js rename to src/test/GenotypesTable.test.js index d93404c..aa31147 100644 --- a/src/__tests__/GenotypesTable.test.js +++ b/src/test/GenotypesTable.test.js @@ -2,7 +2,7 @@ import React from 'react' import {render, screen} from '@testing-library/react' import '@testing-library/jest-dom/extend-expect' -import {genotypes_table_test_data} from "../__tests_data/GenotypesTableData" +import {genotypes_table_test_data} from "./test_data/GenotypesTableData" import GenotypesTable from "../components/GenotypesTable" test('check genotype table view component is loading everything correctly', () => { @@ -58,5 +58,9 @@ function rgbToHex(rgb) { let r = rgb_val[0] let g = rgb_val[1] let b = rgb_val[2] + /* + see stackoverflow(https://stackoverflow.com/questions/5623838/rgb-to-hex-and-hex-to-rgb/5624139#5624139) + Author : Tim Down (https://stackoverflow.com/users/96100/tim-down) + */ return "#" + (1 << 24 | r << 16 | g << 8 | b).toString(16).slice(1) } \ No newline at end of file diff --git a/src/__tests__/Pagination.test.js b/src/test/Pagination.test.js similarity index 100% rename from src/__tests__/Pagination.test.js rename to src/test/Pagination.test.js diff --git a/src/test/test_data/GenotypesFilterData.js b/src/test/test_data/GenotypesFilterData.js new file mode 100644 index 0000000..eb88a40 --- /dev/null +++ b/src/test/test_data/GenotypesFilterData.js @@ -0,0 +1,378 @@ +export const genotypes_filter_test_data = { + "speciesList": [ + { + "taxonomyCode": "dmelanogaster", + "taxonomyCommonName": "Fruit fly", + "taxonomyScientificName": "Drosophila melanogaster" + }, + { + "taxonomyCode": "hsapiens", + "taxonomyCommonName": "Human", + "taxonomyScientificName": "Homo sapiens" + }, + { + "taxonomyCode": "mmusculus", + "taxonomyCommonName": "House mouse", + "taxonomyScientificName": "Mus musculus" + }, + { + "taxonomyCode": "athaliana", + "taxonomyCommonName": "thale cress", + "taxonomyScientificName": "Arabidopsis thaliana" + }, + { + "taxonomyCode": "rnorvegicus", + "taxonomyCommonName": "rat", + "taxonomyScientificName": "Rattus norvegicus" + }, + { + "taxonomyCode": "drerio", + "taxonomyCommonName": "Zebrafish", + "taxonomyScientificName": "Danio rerio" + }, + { + "taxonomyCode": "cfamiliaris", + "taxonomyCommonName": "Dog", + "taxonomyScientificName": "Canis lupus familiaris" + }, + { + "taxonomyCode": "ecaballus", + "taxonomyCommonName": "Horse", + "taxonomyScientificName": "Equus caballus" + }, + { + "taxonomyCode": "ggallus", + "taxonomyCommonName": "Chicken", + "taxonomyScientificName": "Gallus gallus" + } + ], + "speciesAssemblyMap": { + "dmelanogaster": [ + { + "assemblyAccession": "GCA_000001215.4", + "assemblyChain": "GCA_000001215", + "assemblyVersion": "4", + "assemblyName": "Release 6 plus ISO1 MT", + "assemblyCode": "6", + "taxonomyId": 7227, + "taxonomyCommonName": "Fruit fly", + "taxonomyScientificName": "Drosophila melanogaster", + "taxonomyCode": "dmelanogaster", + "taxonomyEvaName": "fruit fly", + "speciesAssemblyCode": "dmelanogaster_6" + } + ], + "hsapiens": [ + { + "assemblyAccession": "GCA_000001405.1", + "assemblyChain": "GCA_000001405", + "assemblyVersion": "1", + "assemblyName": "GRCh37", + "assemblyCode": "grch37", + "taxonomyId": 9606, + "taxonomyCommonName": "Human", + "taxonomyScientificName": "Homo sapiens", + "taxonomyCode": "hsapiens", + "taxonomyEvaName": "human", + "speciesAssemblyCode": "hsapiens_grch37" + }, + { + "assemblyAccession": "GCA_000001405.15", + "assemblyChain": "GCA_000001405", + "assemblyVersion": "15", + "assemblyName": "GRCh38", + "assemblyCode": "grch38", + "taxonomyId": 9606, + "taxonomyCommonName": "Human", + "taxonomyScientificName": "Homo sapiens", + "taxonomyCode": "hsapiens", + "taxonomyEvaName": "human", + "speciesAssemblyCode": "hsapiens_grch38" + }, + { + "assemblyAccession": "GCA_000001405.25", + "assemblyChain": "GCA_000001405", + "assemblyVersion": "25", + "assemblyName": "GRCh38.p10", + "assemblyCode": "grch38p10", + "taxonomyId": 9606, + "taxonomyCommonName": "Human", + "taxonomyScientificName": "Homo sapiens", + "taxonomyCode": "hsapiens", + "taxonomyEvaName": "human", + "speciesAssemblyCode": "hsapiens_grch38p10" + }, + { + "assemblyAccession": "GCA_002402265.1", + "assemblyChain": "GCA_002402265", + "assemblyVersion": "1", + "assemblyName": "ASM240226v1", + "assemblyCode": "asm240226v1", + "taxonomyId": 9606, + "taxonomyCommonName": "Human", + "taxonomyScientificName": "Homo sapiens", + "taxonomyCode": "hsapiens", + "taxonomyEvaName": "human", + "speciesAssemblyCode": "hsapiens_asm240226v1" + } + ], + "mmusculus": [ + { + "assemblyAccession": "GCA_000001635.1", + "assemblyChain": "GCA_000001635", + "assemblyVersion": "1", + "assemblyName": "MGSCv37", + "assemblyCode": "mgscv37", + "taxonomyId": 10090, + "taxonomyCommonName": "House mouse", + "taxonomyScientificName": "Mus musculus", + "taxonomyCode": "mmusculus", + "taxonomyEvaName": "mouse", + "speciesAssemblyCode": "mmusculus_mgscv37" + }, + { + "assemblyAccession": "GCA_000001635.2", + "assemblyChain": "GCA_000001635", + "assemblyVersion": "2", + "assemblyName": "GRCm38", + "assemblyCode": "grcm38", + "taxonomyId": 10090, + "taxonomyCommonName": "House mouse", + "taxonomyScientificName": "Mus musculus", + "taxonomyCode": "mmusculus", + "taxonomyEvaName": "mouse", + "speciesAssemblyCode": "mmusculus_grcm38" + }, + { + "assemblyAccession": "GCA_000001635.9", + "assemblyChain": "GCA_000001635", + "assemblyVersion": "9", + "assemblyName": "GRCm39", + "assemblyCode": "grcm39", + "taxonomyId": 10090, + "taxonomyCommonName": "House mouse", + "taxonomyScientificName": "Mus musculus", + "taxonomyCode": "mmusculus", + "taxonomyEvaName": "mouse", + "speciesAssemblyCode": "mmusculus_grcm39" + } + ], + "athaliana": [ + { + "assemblyAccession": "GCA_000001735.1", + "assemblyChain": "GCA_000001735", + "assemblyVersion": "1", + "assemblyName": "TAIR10", + "assemblyCode": "tair10", + "taxonomyId": 3702, + "taxonomyCommonName": "thale cress", + "taxonomyScientificName": "Arabidopsis thaliana", + "taxonomyCode": "athaliana", + "taxonomyEvaName": "thale cress", + "speciesAssemblyCode": "athaliana_tair10" + } + ], + "rnorvegicus": [ + { + "assemblyAccession": "GCA_000001895.4", + "assemblyChain": "GCA_000001895", + "assemblyVersion": "4", + "assemblyName": "Rnor_6.0", + "assemblyCode": "60", + "taxonomyId": 10116, + "taxonomyCommonName": "rat", + "taxonomyScientificName": "Rattus norvegicus", + "taxonomyCode": "rnorvegicus", + "taxonomyEvaName": " rat", + "speciesAssemblyCode": "rnorvegicus_60" + } + ], + "drerio": [ + { + "assemblyAccession": "GCA_000002035.3", + "assemblyChain": "GCA_000002035", + "assemblyVersion": "3", + "assemblyName": "GRCz10", + "assemblyCode": "grcz10", + "taxonomyId": 7955, + "taxonomyCommonName": "Zebrafish", + "taxonomyScientificName": "Danio rerio", + "taxonomyCode": "drerio", + "taxonomyEvaName": "zebrafish", + "speciesAssemblyCode": "drerio_grcz10" + }, + { + "assemblyAccession": "GCA_000002035.4", + "assemblyChain": "GCA_000002035", + "assemblyVersion": "4", + "assemblyName": "GRCz11", + "assemblyCode": "grcz11", + "taxonomyId": 7955, + "taxonomyCommonName": "Zebrafish", + "taxonomyScientificName": "Danio rerio", + "taxonomyCode": "drerio", + "taxonomyEvaName": "zebrafish", + "speciesAssemblyCode": "drerio_grcz11" + } + ], + "cfamiliaris": [ + { + "assemblyAccession": "GCA_000002285.2", + "assemblyChain": "GCA_000002285", + "assemblyVersion": "2", + "assemblyName": "CanFam3.1", + "assemblyCode": "31", + "taxonomyId": 9615, + "taxonomyCommonName": "Dog", + "taxonomyScientificName": "Canis lupus familiaris", + "taxonomyCode": "cfamiliaris", + "taxonomyEvaName": "dog", + "speciesAssemblyCode": "cfamiliaris_31" + }, + { + "assemblyAccession": "GCA_000002285.4", + "assemblyChain": "GCA_000002285", + "assemblyVersion": "4", + "assemblyName": "Dog10K_Boxer_Tasha", + "assemblyCode": "dog10kboxertasha", + "taxonomyId": 9615, + "taxonomyCommonName": "Dog", + "taxonomyScientificName": "Canis lupus familiaris", + "taxonomyCode": "cfamiliaris", + "taxonomyEvaName": "dog", + "speciesAssemblyCode": "cfamiliaris_dog10kboxertasha" + }, + { + "assemblyAccession": "GCA_014441545.1", + "assemblyChain": "GCA_014441545", + "assemblyVersion": "1", + "assemblyName": "ROS_Cfam_1.0", + "assemblyCode": "roscfam10", + "taxonomyId": 9615, + "taxonomyCommonName": "Dog", + "taxonomyScientificName": "Canis lupus familiaris", + "taxonomyCode": "cfamiliaris", + "taxonomyEvaName": "dog", + "speciesAssemblyCode": "cfamiliaris_roscfam10" + } + ], + "ecaballus": [ + { + "assemblyAccession": "GCA_000002305.1", + "assemblyChain": "GCA_000002305", + "assemblyVersion": "1", + "assemblyName": "EquCab2.0", + "assemblyCode": "20", + "taxonomyId": 9796, + "taxonomyCommonName": "Horse", + "taxonomyScientificName": "Equus caballus", + "taxonomyCode": "ecaballus", + "taxonomyEvaName": "horse", + "speciesAssemblyCode": "ecaballus_20" + }, + { + "assemblyAccession": "GCA_002863925.1", + "assemblyChain": "GCA_002863925", + "assemblyVersion": "1", + "assemblyName": "EquCab3.0", + "assemblyCode": "30", + "taxonomyId": 9796, + "taxonomyCommonName": "Horse", + "taxonomyScientificName": "Equus caballus", + "taxonomyCode": "ecaballus", + "taxonomyEvaName": "horse", + "speciesAssemblyCode": "ecaballus_30" + } + ], + "ggallus": [ + { + "assemblyAccession": "GCA_000002315.3", + "assemblyChain": "GCA_000002315", + "assemblyVersion": "3", + "assemblyName": "Gallus_gallus-5.0", + "assemblyCode": "galgal5", + "taxonomyId": 9031, + "taxonomyCommonName": "Chicken", + "taxonomyScientificName": "Gallus gallus", + "taxonomyCode": "ggallus", + "taxonomyEvaName": "chicken", + "speciesAssemblyCode": "ggallus_galgal5" + }, + { + "assemblyAccession": "GCA_000002315.5", + "assemblyChain": "GCA_000002315", + "assemblyVersion": "5", + "assemblyName": "GRCg6a", + "assemblyCode": "grcg6a", + "taxonomyId": 9031, + "taxonomyCommonName": "Chicken", + "taxonomyScientificName": "Gallus gallus", + "taxonomyCode": "ggallus", + "taxonomyEvaName": "chicken", + "speciesAssemblyCode": "ggallus_grcg6a" + } + ] + }, + "assemblyList": [ + { + "assemblyAccession": "GCA_000002305.1", + "assemblyChain": "GCA_000002305", + "assemblyVersion": "1", + "assemblyName": "EquCab2.0", + "assemblyCode": "20", + "taxonomyId": 9796, + "taxonomyCommonName": "Horse", + "taxonomyScientificName": "Equus caballus", + "taxonomyCode": "ecaballus", + "taxonomyEvaName": "horse", + "speciesAssemblyCode": "ecaballus_20" + }, + { + "assemblyAccession": "GCA_002863925.1", + "assemblyChain": "GCA_002863925", + "assemblyVersion": "1", + "assemblyName": "EquCab3.0", + "assemblyCode": "30", + "taxonomyId": 9796, + "taxonomyCommonName": "Horse", + "taxonomyScientificName": "Equus caballus", + "taxonomyCode": "ecaballus", + "taxonomyEvaName": "horse", + "speciesAssemblyCode": "ecaballus_30" + } + ], + "selectedSpecies": "ecaballus", + "selectedAssembly": "ecaballus_20", + "location": "1:3000000-3100000", + "studies": [ + "BROAD_EQUCAB2.0:2008.08.08", + "PRJEB22866", + "PRJEB23301", + "PRJEB23441", + "PRJEB24624", + "PRJEB24630", + "PRJEB25439", + "PRJEB26741", + "PRJEB27771", + "PRJEB30116", + "PRJEB32686", + "PRJEB38010", + "PRJEB9799" + ], + "selectedStudies": [ + "BROAD_EQUCAB2.0:2008.08.08", + "PRJEB22866", + "PRJEB23301", + "PRJEB23441", + "PRJEB24624", + "PRJEB24630", + "PRJEB25439", + "PRJEB26741", + "PRJEB27771", + "PRJEB30116", + "PRJEB32686", + "PRJEB38010", + "PRJEB9799" + ], + "resultsPerPage": 50 +} \ No newline at end of file diff --git a/src/test/test_data/GenotypesTableData.js b/src/test/test_data/GenotypesTableData.js new file mode 100644 index 0000000..6f43932 --- /dev/null +++ b/src/test/test_data/GenotypesTableData.js @@ -0,0 +1,833 @@ +export const genotypes_table_test_data = { + "studies": [ + "BROAD_EQUCAB2.0:2008.08.08", + "PRJEB22866", + "PRJEB23301", + "PRJEB23441", + "PRJEB24624", + "PRJEB24630", + "PRJEB25439", + "PRJEB26741", + "PRJEB27771", + "PRJEB30116", + "PRJEB32686", + "PRJEB38010", + "PRJEB9799" +], + "variants": [ + { + "chromosome": "1", + "start": 3000829, + "end": 3000829, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3001637, + "end": 3001637, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.09630607, + "PRJEB9799": 0.5 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3001683, + "end": 3001683, + "reference": "A", + "alternate": "C", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.49604222, + "PRJEB9799": 0.25 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3002480, + "end": 3002480, + "reference": "T", + "alternate": "C", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.25 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3002750, + "end": 3002750, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.079155676 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3002807, + "end": 3002807, + "reference": "A", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3003058, + "end": 3003058, + "reference": "A", + "alternate": "C", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3003059, + "end": 3003059, + "reference": "A", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3003105, + "end": 3003105, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3004246, + "end": 3004246, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.41666666 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3004381, + "end": 3004381, + "reference": "T", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.41666666 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3004453, + "end": 3004453, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.41666666 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3004546, + "end": 3004546, + "reference": "T", + "alternate": "C", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.25 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3004613, + "end": 3004613, + "reference": "C", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3004930, + "end": 3004930, + "reference": "G", + "alternate": "", + "length": 1, + "type": "DEL", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3005121, + "end": 3005121, + "reference": "C", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3005228, + "end": 3005228, + "reference": "A", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.33333334 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3005538, + "end": 3005538, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.072559364 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3005949, + "end": 3005949, + "reference": "C", + "alternate": "", + "length": 1, + "type": "DEL", + "alleleFreqs": { + "PRJEB9799": 0 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3006066, + "end": 3006066, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.013192612 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3006316, + "end": 3006322, + "reference": "", + "alternate": "GCAACCC", + "length": 7, + "type": "INS", + "alleleFreqs": { + "PRJEB9799": 0.5 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3006319, + "end": 3006321, + "reference": "", + "alternate": "CTG", + "length": 3, + "type": "INS", + "alleleFreqs": { + "PRJEB9799": 0.5 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3006659, + "end": 3006659, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.027704485 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3006845, + "end": 3006845, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3006897, + "end": 3006897, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.006596306 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3007440, + "end": 3007440, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3007473, + "end": 3007473, + "reference": "A", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.41666666 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3007587, + "end": 3007587, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3007644, + "end": 3007644, + "reference": "T", + "alternate": "C", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3007955, + "end": 3007955, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3008125, + "end": 3008125, + "reference": "G", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3008755, + "end": 3008755, + "reference": "T", + "alternate": "C", + "mainId": "rs68485566", + "ids": [ + "ss105144628", + "rs68485566" + ], + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3008759, + "end": 3008759, + "reference": "G", + "alternate": "T", + "mainId": "rs68485567", + "ids": [ + "rs68485567", + "ss105144629" + ], + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.41666666 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3010141, + "end": 3010141, + "reference": "A", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.25 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3010317, + "end": 3010317, + "reference": "G", + "alternate": "", + "length": 1, + "type": "DEL", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3011552, + "end": 3011552, + "reference": "G", + "alternate": "A", + "mainId": "rs68485568", + "ids": [ + "ss105144630", + "rs68485568" + ], + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3011897, + "end": 3011897, + "reference": "A", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.13324538 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3012333, + "end": 3012333, + "reference": "G", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3012497, + "end": 3012497, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.33333334 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3012533, + "end": 3012533, + "reference": "C", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.083333336 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3012542, + "end": 3012542, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.33333334 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3012602, + "end": 3012602, + "reference": "C", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.39709762, + "PRJEB9799": 0.25 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3012845, + "end": 3012845, + "reference": "A", + "alternate": "C", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.25 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3012924, + "end": 3012924, + "reference": "C", + "alternate": "T", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.33333334 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3013130, + "end": 3013130, + "reference": "A", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.035620052 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3013263, + "end": 3013263, + "reference": "T", + "alternate": "C", + "hgvs": { + "genomic": [ + "1:g.3013263T>C" + ] + }, + "sourceEntries": { + "PRJEB9799_ERZ780739": { + "fileId": "ERZ780739", + "studyId": "PRJEB9799", + "format": "GT:AD:DP:GQ:PL", + "cohortStats": { + "ALL": { + "refAllele": "T", + "altAllele": "C", + "variantType": "SNV", + "refAlleleCount": 0, + "altAlleleCount": 0, + "missingAlleles": 0, + "missingGenotypes": 0, + "refAlleleFreq": 0, + "altAlleleFreq": 0, + "maf": 0.16666667, + "mgf": 0, + "mafAllele": "T", + "mgfGenotype": "0/0", + "numSamples": 0, + "transition": true, + "transversion": false + } + }, + "attributes": { + "AC": "10", + "MQRankSum": "2.893", + "FILTER": "PASS", + "set": "variant", + "MQ": "8080", + "AF": "0.833", + "src": "chr1\t3013263\t.\tT\tC\t837.14\tPASS\tAC=10;AF=0.833;AN=12;BaseQRankSum=3.214;ClippingRankSum=-4.466;DP=60;FS=0.000;MLEAC=10;MLEAF=0.833;MQ=55.49;MQ0=0;MQRankSum=2.893;QD=13.95;ReadPosRankSum=-1.199;VQSLOD=1.73;culprit=FS;set=variant", + "MLEAC": "10", + "QUAL": "837.14", + "BaseQRankSum": "3.214", + "MLEAF": "0.833", + "DP": "59", + "ReadPosRankSum": "-1.199", + "AN": "12", + "FS": "0.000", + "MQ0": "0", + "culprit": "FS", + "QD": "13.95", + "VQSLOD": "1.73", + "ClippingRankSum": "-4.466" + }, + "samplesData": { + "CH": { + "GT": "1/1" + }, + "MM": { + "GT": "0/1" + }, + "AMH": { + "GT": "1/1" + }, + "PER": { + "GT": "1/1" + }, + "ARB": { + "GT": "1/1" + }, + "TWH": { + "GT": "0/1" + } + } + } + }, + "annotation": { + "chromosome": "1", + "start": 3013263, + "end": 3013263, + "vepVersion": "89", + "vepCacheVersion": "89", + "consequenceTypes": [ + { + "soTerms": [ + { + "soName": "intergenic_variant", + "soAccession": "SO:0001628" + } + ] + } + ] + }, + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3013351, + "end": 3013351, + "reference": "A", + "alternate": "G", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.42348284, + "PRJEB9799": 0.16666667 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3013423, + "end": 3013423, + "reference": "G", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.09894459, + "PRJEB9799": 0.41666666 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3013475, + "end": 3013475, + "reference": "T", + "alternate": "C", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB23301": 0.07387863 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + }, + { + "chromosome": "1", + "start": 3014040, + "end": 3014040, + "reference": "C", + "alternate": "A", + "length": 1, + "type": "SNV", + "alleleFreqs": { + "PRJEB9799": 0.33333334 + }, + "color": "#636363", + "consequenceName": "intergenic_variant" + } +], + "isLoaded": true, + "currentPage": 1, + "numPages": 10 +} \ No newline at end of file diff --git a/src/test/test_data/GenotypesViewData.js b/src/test/test_data/GenotypesViewData.js new file mode 100644 index 0000000..8d347b6 --- /dev/null +++ b/src/test/test_data/GenotypesViewData.js @@ -0,0 +1,282 @@ +export const genotypes_view_test_consequences_data = [ + { + "label": "start retained variant", + "description": "A sequence variant where at least one base in the start codon is changed, but the start remains", + "SO_term": "start_retained_variant", + "SO_accession": "SO:0002019", + "consequence_ranking": "15" + }, + { + "label": "non coding transcript exon variant", + "description": "A sequence variant that changes non-coding exon sequence in a non-coding transcript", + "SO_term": "non_coding_transcript_exon_variant", + "SO_accession": "SO:0001792", + "consequence_ranking": "20" + }, + { + "SO_term": "non_coding_transcript_variant", + "description": "A transcript variant of a non coding RNA gene", + "label": "non coding transcript variant", + "consequence_ranking": "23", + "SO_accession": "SO:0001619" + }, + { + "description": "A sequence variant located within a transcription factor binding site", + "SO_term": "TF_binding_site_variant", + "label": "TF binding site", + "consequence_ranking": "30", + "SO_accession": "SO:0001782" + }, + { + "SO_accession": "SO:0002012", + "consequence_ranking": "7", + "label": "start lost", + "SO_term": "start_lost", + "description": "A codon variant that changes at least one base of the canonical start codon" + }, + { + "SO_accession": "SO:0001587", + "consequence_ranking": "4", + "label": "stop gained", + "SO_term": "stop_gained", + "description": "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript" + }, + { + "SO_accession": "SO:0001889", + "consequence_ranking": "8", + "label": "transcript amplification", + "SO_term": "transcript_amplification", + "description": "A feature amplification of a region containing a transcript" + }, + { + "consequence_ranking": "3", + "SO_accession": "SO:0001574", + "description": "A splice variant that changes the 2 base region at the 3' end of an intron", + "SO_term": "splice_acceptor_variant", + "label": "splice acceptor variant" + }, + { + "SO_accession": "SO:0001822", + "consequence_ranking": "11", + "label": "inframe deletion", + "description": "An inframe non synonymous variant that deletes bases from the coding sequence", + "SO_term": "inframe_deletion" + }, + { + "SO_accession": "SO:0001891", + "consequence_ranking": "33", + "label": "regulatory region amplification", + "description": "A feature amplification of a region containing a regulatory region", + "SO_term": "regulatory_region_amplification" + }, + { + "label": "regulatory region ablation", + "SO_term": "regulatory_region_ablation", + "description": "A feature ablation whereby the deleted region includes a regulatory region", + "SO_accession": "SO:0001894", + "consequence_ranking": "31" + }, + { + "SO_accession": "SO:0001907", + "consequence_ranking": "36", + "label": "feature elongation", + "description": "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence", + "SO_term": "feature_elongation" + }, + { + "consequence_ranking": "14", + "SO_accession": "SO:0002170", + "description": "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron).", + "SO_term": "splice_donor_region_variant", + "label": "splice donor region variant" + }, + { + "SO_accession": "SO:0001620", + "consequence_ranking": "17", + "label": "mature miRNA variant", + "description": "A transcript variant located with the sequence of the mature miRNA", + "SO_term": "mature_miRNA_variant" + }, + { + "SO_accession": "SO:0001575", + "consequence_ranking": "3", + "label": "splice donor variant", + "SO_term": "splice_donor_variant", + "description": "A splice variant that changes the 2 base region at the 5' end of an intron" + }, + { + "label": "3 prime UTR variant", + "description": "A UTR variant of the 3' UTR", + "SO_term": "3_prime_UTR_variant", + "SO_accession": "SO:0001624", + "consequence_ranking": "19" + }, + { + "label": "coding sequence variant", + "SO_term": "coding_sequence_variant", + "description": "A sequence variant that changes the coding sequence", + "SO_accession": "SO:0001580", + "consequence_ranking": "16" + }, + { + "label": "inframe insertion", + "SO_term": "inframe_insertion", + "description": "An inframe non synonymous variant that inserts bases into in the coding sequence", + "SO_accession": "SO:0001821", + "consequence_ranking": "10" + }, + { + "consequence_ranking": "21", + "SO_accession": "SO:0001627", + "SO_term": "intron_variant", + "description": "A transcript variant occurring within an intron", + "label": "intron variant" + }, + { + "description": "A variant in a transcript that is the target of NMD", + "SO_term": "NMD_transcript_variant", + "label": "NMD transcript variant", + "consequence_ranking": "22", + "SO_accession": "SO:0001621" + }, + { + "consequence_ranking": "25", + "SO_accession": "SO:0001632", + "SO_term": "downstream_gene_variant", + "description": "A sequence variant located 3' of a gene", + "label": "downstream gene variant" + }, + { + "consequence_ranking": "12", + "SO_accession": "SO:0001583", + "SO_term": "missense_variant", + "description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved", + "label": "missense variant" + }, + { + "label": "splice polypyrimidine tract variant", + "description": "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17)", + "SO_term": "splice_polypyrimidine_tract_variant", + "SO_accession": "SO:0002169", + "consequence_ranking": "13" + }, + { + "consequence_ranking": "15", + "SO_accession": "SO:0001819", + "SO_term": "synonymous_variant", + "description": "A sequence variant where there is no resulting change to the encoded amino acid", + "label": "synonymous variant" + }, + { + "consequence_ranking": "38", + "SO_accession": "SO:0001628", + "SO_term": "intergenic_variant", + "description": "A sequence variant located in the intergenic region, between genes", + "label": "intergenic variant" + }, + { + "label": "splice donor 5th base variant", + "SO_term": "splice_donor_5th_base_variant", + "description": "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript", + "SO_accession": "SO:0001787", + "consequence_ranking": "4" + }, + { + "consequence_ranking": "37", + "SO_accession": "SO:0001906", + "description": "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence", + "SO_term": "feature_truncation", + "label": "feature truncation" + }, + { + "consequence_ranking": "14", + "SO_accession": "SO:0001626", + "SO_term": "incomplete_terminal_codon_variant", + "description": "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed", + "label": "incomplete terminal codon variant" + }, + { + "consequence_ranking": "5", + "SO_accession": "SO:0001589", + "description": "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three", + "SO_term": "frameshift_variant", + "label": "frameshift variant" + }, + { + "description": "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript", + "SO_term": "stop_lost", + "label": "stop lost", + "consequence_ranking": "6", + "SO_accession": "SO:0001578" + }, + { + "SO_accession": "SO:0001623", + "consequence_ranking": "18", + "label": "5 prime UTR variant", + "SO_term": "5_prime_UTR_variant", + "description": "A UTR variant of the 5' UTR" + }, + { + "consequence_ranking": "13", + "SO_accession": "SO:0001630", + "SO_term": "splice_region_variant", + "description": "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron", + "label": "splice region variant" + }, + { + "label": "regulatory region variant", + "description": "A sequence variant located within a regulatory region", + "SO_term": "regulatory_region_variant", + "SO_accession": "SO:0001566", + "consequence_ranking": "36" + }, + { + "SO_accession": "SO:0001895", + "consequence_ranking": "26", + "label": "TFBS ablation", + "description": "A feature ablation whereby the deleted region includes a transcription factor binding site", + "SO_term": "TFBS_ablation" + }, + { + "consequence_ranking": "24", + "SO_accession": "SO:0001631", + "SO_term": "upstream_gene_variant", + "description": "A sequence variant located 5' of a gene", + "label": "upstream gene variant" + }, + { + "consequence_ranking": "28", + "SO_accession": "SO:0001892", + "SO_term": "TFBS_amplification", + "description": "A feature amplification of a region containing a transcription factor binding site", + "label": "TFBS amplification" + }, + { + "label": "transcript ablation", + "SO_term": "transcript_ablation", + "description": "A feature ablation whereby the deleted region includes a transcript feature", + "SO_accession": "SO:0001893", + "consequence_ranking": "1" + }, + { + "description": "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains", + "SO_term": "stop_retained_variant", + "label": "stop retained variant", + "consequence_ranking": "15", + "SO_accession": "SO:0001567" + }, + { + "SO_term": "sequence_variant", + "description": "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration", + "label": "sequence variant", + "consequence_ranking": "39", + "SO_accession": "SO:0001060" + }, + { + "description": "A sequence_variant which is predicted to change the protein encoded in the coding sequence", + "SO_term": "protein_altering_variant", + "label": "protein altering variant", + "consequence_ranking": "12", + "SO_accession": "SO:0001818" + } +] \ No newline at end of file