From 215ba49ffa7a6c6b9d3f9f3fb241f925a23581b0 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Wed, 21 Oct 2020 22:59:37 -0400 Subject: [PATCH 1/5] Workaround for "only default export available soon" error in newest webpack version --- esm/index.js | 2 +- esm/layouts/index.js | 2 +- esm/version.js | 1 + package.json | 3 ++- 4 files changed, 5 insertions(+), 3 deletions(-) create mode 100644 esm/version.js diff --git a/esm/index.js b/esm/index.js index afbef386..e03a1fd7 100644 --- a/esm/index.js +++ b/esm/index.js @@ -2,7 +2,7 @@ * Compatibility layer: expose symbols via UMD module to match the old LocusZoom API * A library using this file will need to load `locuszoom.css` separately. */ -import {version} from '../package.json'; +import version from './version'; import {default as DataSources} from './data'; import { populate } from './helpers/display'; diff --git a/esm/layouts/index.js b/esm/layouts/index.js index 7023b07b..41b7e64a 100644 --- a/esm/layouts/index.js +++ b/esm/layouts/index.js @@ -4,7 +4,7 @@ * @private */ -import { version } from '../../package.json'; +import version from '../version'; import {deepCopy, merge} from '../helpers/layouts'; const LZ_SIG_THRESHOLD_LOGP = 7.301; // -log10(.05/1e6) diff --git a/esm/version.js b/esm/version.js new file mode 100644 index 00000000..c0b40952 --- /dev/null +++ b/esm/version.js @@ -0,0 +1 @@ +export default '0.13.0-beta.1'; diff --git a/package.json b/package.json index a5ab54e6..6d050c3f 100644 --- a/package.json +++ b/package.json @@ -30,11 +30,12 @@ "url": "https://github.com/statgen/locuszoom.git" }, "scripts": { + "echo_version": "echo \"export default '${npm_package_version}';\" > esm/version.js", "test": "eslint esm/ test/ && mocha --recursive test", "test:coverage": "nyc --reporter=text mocha --recursive test/**/*.js", "css": "sass --style compressed ./css/locuszoom.scss ./dist/locuszoom.css", "dev": "npm run css && webpack --watch --config webpack.dev.cjs", - "build": "npm run test && npm run css && webpack --config webpack.prod.cjs", + "build": "npm run echo_version && npm run test && npm run css && webpack --config webpack.prod.cjs", "docs": "jsdoc --recurse --readme ./README.md --destination jsdoc esm/ && pandoc -s --toc --css css/pandoc.css assets/docs/layout_tutorial.md -o docs/layout_tutorial.html" }, "dependencies": { From 196bf42bf7e214f09261aeb4bba767845b26050e Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Tue, 27 Oct 2020 10:12:28 -0400 Subject: [PATCH 2/5] Update offline mode demo with new gene_type field in API --- index.html | 2 +- staticdata/genes_10_114550452-115067678.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/index.html b/index.html index 23a04667..92af0635 100644 --- a/index.html +++ b/index.html @@ -211,7 +211,7 @@
Multiple Phenotypes (Layered)
apiBase = window.location.origin + window.location.pathname.substr(0, window.location.pathname.lastIndexOf("/") + 1) + "staticdata/"; data_sources = new LocusZoom.DataSources() .add("assoc", ["AssociationLZ", {url: apiBase + "assoc_10_114550452-115067678.json?", params: { source: 45, id_field: "variant" }}]) - .add("ld", ["LDLZ", { url: apiBase + "ld_10_114550452-115067678.json?" }]) + .add("ld", ["LDServer", { url: apiBase + "ld_10_114550452-115067678.json?" }]) .add("gene", ["GeneLZ", { url: apiBase + "genes_10_114550452-115067678.json?", params: { build: 'GRCh37' } }]) .add("recomb", ["RecombLZ", { url: apiBase + "recomb_10_114550452-115067678.json?", params: { build: 'GRCh37' } }]) .add("constraint", ["GeneConstraintLZ", { url: apiBase + "constraint_10_114550452-115067678.json?", params: { build: 'GRCh37' } }]); diff --git a/staticdata/genes_10_114550452-115067678.json b/staticdata/genes_10_114550452-115067678.json index 163b63e4..c895c784 100644 --- a/staticdata/genes_10_114550452-115067678.json +++ b/staticdata/genes_10_114550452-115067678.json @@ -1 +1 @@ -{"data":[{"gene_id":"ENSG00000148737.11","gene_name":"TCF7L2","chrom":"10","start":114710009,"end":114927437,"strand":"+","transcripts":[{"transcript_id":"ENST00000277945.7","transcript_name":"TCF7L2-010","transcript_chrom":"10","start":114905831,"end":114925391,"strand":"+","exons":[{"exon_id":"ENSE00002258101.1","chrom":"10","start":114710009,"end":114710704,"strand":"+"},{"exon_id":"ENSE00003644651.1","chrom":"10","start":114710966,"end":114711032,"strand":"+"},{"exon_id":"ENSE00003496147.1","chrom":"10","start":114711242,"end":114711366,"strand":"+"},{"exon_id":"ENSE00000987139.1","chrom":"10","start":114724315,"end":114724383,"strand":"+"},{"exon_id":"ENSE00003683398.1","chrom":"10","start":114799784,"end":114799885,"strand":"+"},{"exon_id":"ENSE00003618124.1","chrom":"10","start":114900943,"end":114901075,"strand":"+"},{"exon_id":"ENSE00003644692.1","chrom":"10","start":114903682,"end":114903784,"strand":"+"},{"exon_id":"ENSE00003527108.1","chrom":"10","start":114905770,"end":114905856,"strand":"+"},{"exon_id":"ENSE00001699148.1","chrom":"10","start":114910757,"end":114910882,"strand":"+"},{"exon_id":"ENSE00003517323.1","chrom":"10","start":114911484,"end":114911643,"strand":"+"},{"exon_id":"ENSE00003524030.1","chrom":"10","start":114912092,"end":114912199,"strand":"+"},{"exon_id":"ENSE00003620069.1","chrom":"10","start":114917780,"end":114917828,"strand":"+"},{"exon_id":"ENSE00003590241.1","chrom":"10","start":114918426,"end":114918476,"strand":"+"},{"exon_id":"ENSE00003601851.1","chrom":"10","start":114919679,"end":114919751,"strand":"+"},{"exon_id":"ENSE00003656283.1","chrom":"10","start":114925314,"end":114927437,"strand":"+"},{"exon_id":"ENSE00002258101.1","chrom":"10","start":114710009,"end":114710704,"strand":"+"},{"exon_id":"ENSE00003644651.1","chrom":"10","start":114710966,"end":114711032,"strand":"+"},{"exon_id":"ENSE00003496147.1","chrom":"10","start":114711242,"end":114711366,"strand":"+"},{"exon_id":"ENSE00000987139.1","chrom":"10","start":114724315,"end":114724383,"strand":"+"},{"exon_id":"ENSE00003683398.1","chrom":"10","start":114799784,"end":114799885,"strand":"+"},{"exon_id":"ENSE00003618124.1","chrom":"10","start":114900943,"end":114901075,"strand":"+"},{"exon_id":"ENSE00003644692.1","chrom":"10","start":114903682,"end":114903784,"strand":"+"},{"exon_id":"ENSE00003527108.1","chrom":"10","start":114905770,"end":114905856,"strand":"+"},{"exon_id":"ENSE00001699148.1","chrom":"10","start":114910757,"end":114910882,"strand":"+"},{"exon_id":"ENSE00003517323.1","chrom":"10","start":114911484,"end":114911643,"strand":"+"},{"exon_id":"ENSE00003524030.1","chrom":"10","start":114912092,"end":114912199,"strand":"+"},{"exon_id":"ENSE00003620069.1","chrom":"10","start":114917780,"end":114917828,"strand":"+"},{"exon_id":"ENSE00003590241.1","chrom":"10","start":114918426,"end":114918476,"strand":"+"},{"exon_id":"ENSE00003487390.1","chrom":"10","start":114920378,"end":114920450,"strand":"+"},{"exon_id":"ENSE00003656283.1","chrom":"10","start":114925314,"end":114927437,"strand":"+"},{"exon_id":"ENSE00002258101.1","chrom":"10","start":114710009,"end":114710704,"strand":"+"},{"exon_id":"ENSE00003644651.1","chrom":"10","start":114710966,"end":114711032,"strand":"+"},{"exon_id":"ENSE00003496147.1","chrom":"10","start":114711242,"end":114711366,"strand":"+"},{"exon_id":"ENSE00000987139.1","chrom":"10","start":114724315,"end":114724383,"strand":"+"},{"exon_id":"ENSE00003683398.1","chrom":"10","start":114799784,"end":114799885,"strand":"+"},{"exon_id":"ENSE00003618124.1","chrom":"10","start":114900943,"end":114901075,"strand":"+"},{"exon_id":"ENSE00003644692.1","chrom":"10","start":114903682,"end":114903784,"strand":"+"},{"exon_id":"ENSE00003527108.1","chrom":"10","start":114905770,"end":114905856,"strand":"+"},{"exon_id":"ENSE00001699148.1","chrom":"10","start":114910757,"end":114910882,"strand":"+"},{"exon_id":"ENSE00003517323.1","chrom":"10","start":114911484,"end":114911643,"strand":"+"},{"exon_id":"ENSE00003524030.1","chrom":"10","start":114912092,"end":114912199,"strand":"+"},{"exon_id":"ENSE00003620069.1","chrom":"10","start":114917780,"end":114917828,"strand":"+"},{"exon_id":"ENSE00003487390.1","chrom":"10","start":114920378,"end":114920450,"strand":"+"},{"exon_id":"ENSE00003656283.1","chrom":"10","start":114925314,"end":114927437,"strand":"+"},{"exon_id":"ENSE00002258101.1","chrom":"10","start":114710009,"end":114710704,"strand":"+"},{"exon_id":"ENSE00003644651.1","chrom":"10","start":114710966,"end":114711032,"strand":"+"},{"exon_id":"ENSE00003496147.1","chrom":"10","start":114711242,"end":114711366,"strand":"+"},{"exon_id":"ENSE00000987139.1","chrom":"10","start":114724315,"end":114724383,"strand":"+"},{"exon_id":"ENSE00003683398.1","chrom":"10","start":114799784,"end":114799885,"strand":"+"},{"exon_id":"ENSE00003618124.1","chrom":"10","start":114900943,"end":114901075,"strand":"+"},{"exon_id":"ENSE00003644692.1","chrom":"10","start":114903682,"end":114903784,"strand":"+"},{"exon_id":"ENSE000035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From 990c3523f9f5eb0b04b1c489c34e4be87756ee83 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Tue, 27 Oct 2020 11:36:13 -0400 Subject: [PATCH 3/5] Ensure that "LD refvar" is tagged and shown correctly, even when variant spec omits ref/alt Also fix "make ld reference" buggy behavior for incomplete datasets --- esm/data/adapters.js | 11 +++++++++-- test/unit/data/test_adapters.js | 15 +++++++++++++++ 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/esm/data/adapters.js b/esm/data/adapters.js index e01decce..0bfe9248 100644 --- a/esm/data/adapters.js +++ b/esm/data/adapters.js @@ -548,8 +548,15 @@ class LDServer extends BaseApiAdapter { if (!match) { throw new Error('Could not request LD for a missing or incomplete marker format'); } - refVar = [match[1], ':', match[2], '_', match[3], '/', match[4]].join(''); - chain.header.ldrefvar = refVar; + const [original, chrom, pos, ref, alt] = match; + // Currently, the LD server only accepts full variant specs; it won't return LD w/o ref+alt. Allowing + // a partial match at most leaves room for potential future features. + refVar = `${chrom}:${pos}`; + if (ref && alt) { + refVar += `_${ref}/${alt}`; + } + // Preserve the user-provided variant spec for use when matching to assoc data + chain.header.ldrefvar = original; return [ this.url, 'genome_builds/', build, '/references/', source, '/populations/', population, '/variants', diff --git a/test/unit/data/test_adapters.js b/test/unit/data/test_adapters.js index 6cbd13ef..2d0251be 100644 --- a/test/unit/data/test_adapters.js +++ b/test/unit/data/test_adapters.js @@ -502,6 +502,21 @@ describe('Data adapters', function () { assert.ok(request_url.includes(encodeURIComponent(ldserver_format))); }); + it('coerces variant formats, omitting ref-alt if not provided', function () { + const source = new LDServer({ url: 'www.fake.test', params: { build: 'GRCh37' } }); + const norefvar_topmed = '8-117974679'; + const ldserver_format = '8:117974679'; + const request_url = source.getURL({ ldrefvar: norefvar_topmed }, { + header: {}, + body: [], + }, ['isrefvar', 'state']); + assert.equal( + request_url, + source.getURL({ ldrefvar: ldserver_format }, { header: {}, body: [] }, ['isrefvar', 'state']) + ); + assert.ok(request_url.includes(encodeURIComponent(ldserver_format))); + }); + it('chooses best 1000G panel for the given build', function () { const source37 = new LDServer({ url: 'www.fake.test', params: { source: '1000G', build: 'GRCh37' } }); let request_url = source37.getURL({ ldrefvar: '1:2_A/B' }, { From 87efec2d3b780d41bba57fd0a963988c7a730703 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Tue, 27 Oct 2020 11:37:00 -0400 Subject: [PATCH 4/5] Linting: allow discarding "dummy" vars in destructuring assignment (_, __, etc) --- .eslintrc.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.eslintrc.js b/.eslintrc.js index 1860c70c..2bc22599 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -22,7 +22,7 @@ module.exports = { 'no-trailing-spaces': 'error', 'no-unused-vars': [ 'error', - { 'args': 'none' }, + { 'args': 'none', 'varsIgnorePattern': '^_+$' }, ], 'prefer-template': 'error', 'quotes': [ From 7648892ef267de0e43ca3002b6a12acd9096b114 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Tue, 27 Oct 2020 14:34:29 -0400 Subject: [PATCH 5/5] Bump version 0.13.0-beta.2 --- dist/ext/lz-aggregation-tests.min.js | 4 ++-- dist/ext/lz-aggregation-tests.min.js.map | 2 +- dist/ext/lz-credible-sets.min.js | 4 ++-- dist/ext/lz-credible-sets.min.js.map | 2 +- dist/ext/lz-dynamic-urls.min.js | 4 ++-- dist/ext/lz-dynamic-urls.min.js.map | 2 +- dist/ext/lz-intervals-track.min.js | 4 ++-- dist/ext/lz-intervals-track.min.js.map | 2 +- dist/ext/lz-tabix-source.min.js | 4 ++-- dist/ext/lz-tabix-source.min.js.map | 2 +- dist/ext/lz-widget-addons.min.js | 4 ++-- dist/ext/lz-widget-addons.min.js.map | 2 +- dist/locuszoom.app.min.js | 4 ++-- dist/locuszoom.app.min.js.map | 2 +- esm/version.js | 2 +- index.html | 4 ++-- package-lock.json | 2 +- package.json | 2 +- 18 files changed, 26 insertions(+), 26 deletions(-) diff --git a/dist/ext/lz-aggregation-tests.min.js b/dist/ext/lz-aggregation-tests.min.js index 1e76206d..7c0f1983 100644 --- a/dist/ext/lz-aggregation-tests.min.js +++ b/dist/ext/lz-aggregation-tests.min.js @@ -1,3 +1,3 @@ -/*! 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JSON.parse(resp) : resp;\n if (json.error) {\n // RAREMETAL-server quirk: The API sometimes returns a 200 status code for failed requests,\n // with a human-readable error description as a key\n // For now, this should be treated strictly as an error\n throw new Error(json.error);\n }\n return json;\n });\n }\n\n annotateData(records, chain) {\n // Operate on the calculated results. The result of this method will be added to chain.discrete\n\n // In a page using live API data, the UI would only request the masks it needs from the API.\n // But in our demos, sometimes boilerplate JSON has more masks than the UI asked for. Limit what calcs we run (by\n // type, and to the set of groups requested by the user)\n\n // The Raremetal-server API has a quirk: it returns a different payload structure if no groups are defined\n // for the request region. Detect when that happens and end the calculation immediately in that case\n if (!records.groups) {\n return { groups: [], variants: [] };\n }\n\n records.groups = records.groups.filter(function (item) {\n return item.groupType === 'GENE';\n });\n\n const parsed = helpers.parsePortalJSON(records);\n let groups = parsed[0];\n const variants = parsed[1];\n // Some APIs may return more data than we want (eg simple sites that are just serving up premade scorecov json files).\n // Filter the response to just what the user has chosen to analyze.\n groups = groups.byMask(chain.header.aggregation_mask_ids);\n\n // Determine what calculations to run\n const calcs = chain.header.aggregation_calcs;\n if (!calcs || Object.keys(calcs).length === 0) {\n // If no calcs have been requested, then return a dummy placeholder immediately\n return { variants: [], groups: [], results: [] };\n }\n const runner = new helpers.PortalTestRunner(groups, variants, calcs);\n\n return runner.toJSON()\n .then(function (res) {\n // Internally, raremetal helpers track how the calculation is done, but not any display-friendly values\n // We will annotate each mask name (id) with a human-friendly description for later use\n const mask_id_to_desc = chain.header.aggregation_masks.reduce(function (acc, val) {\n acc[val.name] = val.description;\n return acc;\n }, {});\n res.data.groups.forEach(function (group) {\n group.mask_name = mask_id_to_desc[group.mask];\n });\n return res.data;\n })\n .catch(function (e) {\n console.error(e);\n throw new Error('Failed to calculate aggregation test results');\n });\n }\n\n normalizeResponse(data) {\n return data;\n }\n\n combineChainBody(records, chain) {\n // aggregation tests are a bit unique, in that the data is rarely used directly- instead it is used to annotate many\n // other layers in different ways. The calculated result has been added to `chain.discrete`, but will not be returned\n // as part of the response body built up by the chain\n return chain.body;\n }\n\n }\n\n class AssocFromAggregationLZ extends BaseAdapter {\n constructor(config) {\n if (!config || !config.from) {\n throw 'Must specify the name of the source that contains association data';\n }\n super(...arguments);\n }\n parseInit(config) {\n super.parseInit(config);\n this._from = config.from;\n }\n\n getRequest(state, chain, fields) {\n // Does not actually make a request. Just pick off the specific bundle of data from a known payload structure.\n if (chain.discrete && !chain.discrete[this._from]) {\n throw `${this.constructor.SOURCE_NAME} cannot be used before loading required data for: ${this._from}`;\n }\n // Copy the data so that mutations (like sorting) don't affect the original\n return Promise.resolve(JSON.parse(JSON.stringify(chain.discrete[this._from]['variants'])));\n }\n\n normalizeResponse(data) {\n // The payload structure of the association source is slightly different than the one required by association\n // plots. For example, we need to parse variant names and convert to log_pvalue\n const REGEX_EPACTS = new RegExp('(?:chr)?(.+):(\\\\d+)_?(\\\\w+)?/?([^_]+)?_?(.*)?'); // match API variant strings\n return data.map((one_variant) => {\n const match = one_variant.variant.match(REGEX_EPACTS);\n return {\n variant: one_variant.variant,\n chromosome: match[1],\n position: +match[2],\n ref_allele: match[3],\n ref_allele_freq: 1 - one_variant.altFreq,\n log_pvalue: -Math.log10(one_variant.pvalue),\n };\n }).sort((a, b) => {\n a = a.variant;\n b = b.variant;\n if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n } else {\n // names must be equal\n return 0;\n }\n });\n }\n }\n\n /**\n * A sample connector that aligns calculated aggregation test data with corresponding gene information. Returns a body\n * suitable for use with the genes datalayer.\n *\n * To use this source, one must specify a fields array that calls first the genes source, then a dummy field from\n * this source. The output will be to transparently add several new fields to the genes data.\n * @public\n */\n class GeneAggregationConnectorLZ extends ConnectorSource {\n _getRequiredSources() {\n return ['gene_ns', 'aggregation_ns'];\n }\n\n combineChainBody(data, chain) {\n // The genes layer receives all results, and displays only the best pvalue for each gene\n\n // Tie the calculated group-test results to genes with a matching name\n const aggregation_source_id = this._source_name_mapping['aggregation_ns'];\n const gene_source_id = this._source_name_mapping['gene_ns'];\n // This connector assumes that genes are the main body of records from the chain, and that aggregation tests are\n // a standalone source that has not acted on genes data yet\n const aggregationData = chain.discrete[aggregation_source_id];\n const genesData = chain.discrete[gene_source_id];\n\n const groupedAggregation = {}; // Group together all tests done on that gene- any mask, any test\n\n aggregationData.groups.forEach(function (result) {\n if (!Object.prototype.hasOwnProperty.call(groupedAggregation, result.group)) {\n groupedAggregation[result.group] = [];\n }\n groupedAggregation[result.group].push(result.pvalue);\n });\n\n // Annotate any genes that have test results\n genesData.forEach(function (gene) {\n const gene_id = gene.gene_name;\n const tests = groupedAggregation[gene_id];\n if (tests) {\n gene.aggregation_best_pvalue = Math.min.apply(null, tests);\n }\n });\n return genesData;\n }\n }\n\n\n LocusZoom.Adapters.add('AggregationTestSourceLZ', AggregationTestSource);\n LocusZoom.Adapters.add('AssocFromAggregationLZ', AssocFromAggregationLZ);\n LocusZoom.Adapters.add('GeneAggregationConnectorLZ', GeneAggregationConnectorLZ);\n}\n\n\nif (typeof LocusZoom !== 'undefined') {\n // Auto-register the plugin when included as a script tag. ES6 module users must register via LocusZoom.use()\n // eslint-disable-next-line no-undef\n LocusZoom.use(install);\n}\n\n\nexport default install;\n","/**\n * Define standard data adapters used to retrieve data (usually from REST APIs)\n * @module\n */\n\nfunction validateBuildSource(class_name, build, source) {\n // Build OR Source, not both\n if ((build && source) || !(build || source)) {\n throw new Error(`${class_name} must provide a parameter specifying either \"build\" or \"source\". It should not specify both.`);\n }\n // If the build isn't recognized, our APIs can't transparently select a source to match\n if (build && !['GRCh37', 'GRCh38'].includes(build)) {\n throw new Error(`${class_name} must specify a valid genome build number`);\n }\n}\n\n\n/**\n * Base class for LocusZoom data sources (any). See also: BaseApiAdapter\n * @public\n */\nclass BaseAdapter {\n constructor(config) {\n /**\n * Whether this source should enable caching\n * @member {Boolean}\n */\n this._enableCache = true;\n this._cachedKey = null;\n\n /**\n * Whether this data source type is dependent on previous requests- for example, the LD source cannot annotate\n * association data if no data was found for that region.\n * @member {boolean}\n */\n this.__dependentSource = false;\n\n // Parse configuration options\n this.parseInit(config);\n }\n\n /**\n * Parse configuration used to create the data source. Many custom sources will override this method to suit their\n * needs (eg specific config options, or for sources that do not retrieve data from a URL)\n * @protected\n * @param {String|Object} config Basic configuration- either a url, or a config object\n * @param {String} [config.url] The datasource URL\n * @param {String} [config.params] Initial config params for the datasource\n */\n parseInit(config) {\n /** @member {Object} */\n this.params = config.params || {};\n }\n\n /**\n * A unique identifier that indicates whether cached data is valid for this request. For most sources using GET\n * requests to a REST API, this is usually the URL.\n * @protected\n * @param {Object} state Information available in plot.state (chr, start, end). Sometimes used to inject globally\n * available information that influences the request being made.\n * @param {Object} chain The data chain from previous requests made in a sequence.\n * @param fields\n * @returns {String|undefined}\n */\n getCacheKey(state, chain, fields) {\n return this.getURL(state, chain, fields);\n }\n\n /**\n * Stub: build the URL for any requests made by this source.\n * @protected\n */\n getURL(state, chain, fields) {\n return this.url;\n }\n\n /**\n * Perform a network request to fetch data for this source. This is usually the method that is used to override\n * when defining how to retrieve data.\n * @protected\n * @param {Object} state The state of the parent plot\n * @param chain\n * @param fields\n * @returns {Promise}\n */\n fetchRequest(state, chain, fields) {\n const url = this.getURL(state, chain, fields);\n return fetch(url).then((response) => {\n if (!response.ok) {\n throw new Error(response.statusText);\n }\n return response.text();\n });\n }\n\n /**\n * Gets the data for just this source, typically via a network request (but using cache where possible)\n *\n * For most use cases, it is better to override `fetchRequest` instead, to avoid bypassing the cache mechanism\n * by accident.\n * @protected\n */\n getRequest(state, chain, fields) {\n let req;\n const cacheKey = this.getCacheKey(state, chain, fields);\n if (this._enableCache && typeof(cacheKey) !== 'undefined' && cacheKey === this._cachedKey) {\n req = Promise.resolve(this._cachedResponse); // Resolve to the value of the current promise\n } else {\n req = this.fetchRequest(state, chain, fields);\n if (this._enableCache) {\n this._cachedKey = cacheKey;\n this._cachedResponse = req;\n }\n }\n return req;\n }\n\n /**\n * Ensure the server response is in a canonical form, an array of one object per record. [ {field: oneval} ].\n * If the server response contains columns, reformats the response from {column1: [], column2: []} to the above.\n *\n * Does not apply namespacing, transformations, or field extraction.\n *\n * May be overridden by data sources that inherently return more complex payloads, or that exist to annotate other\n * sources (eg, if the payload provides extra data rather than a series of records).\n * @protected\n * @param {Object[]|Object} data The original parsed server response\n */\n normalizeResponse(data) {\n if (Array.isArray(data)) {\n // Already in the desired form\n return data;\n }\n // Otherwise, assume the server response is an object representing columns of data.\n // Each array should have the same length (verify), and a given array index corresponds to a single row.\n const keys = Object.keys(data);\n const N = data[keys[0]].length;\n const sameLength = keys.every(function (key) {\n const item = data[key];\n return item.length === N;\n });\n if (!sameLength) {\n throw new Error(`${this.constructor.name} expects a response in which all arrays of data are the same length`);\n }\n\n // Go down the rows, and create an object for each record\n const records = [];\n const fields = Object.keys(data);\n for (let i = 0; i < N; i++) {\n const record = {};\n for (let j = 0; j < fields.length; j++) {\n record[fields[j]] = data[fields[j]][i];\n }\n records.push(record);\n }\n return records;\n }\n\n /**\n * Hook to post-process the data returned by this source with new, additional behavior.\n * (eg cleaning up API values or performing complex calculations on the returned data)\n *\n * @protected\n * @param {Object[]} records The parsed data from the source (eg standardized api response)\n * @param {Object} chain The data chain object. For example, chain.headers may provide useful annotation metadata\n * @returns {Object[]|Promise} The modified set of records\n */\n annotateData(records, chain) {\n // Default behavior: no transformations\n return records;\n }\n\n /**\n * Clean up the server records for use by datalayers: extract only certain fields, with the specified names.\n * Apply per-field transformations as appropriate.\n *\n * This hook can be overridden, eg to create a source that always returns all records and ignores the \"fields\" array.\n * This is particularly common for sources at the end of a chain- many \"dependent\" sources do not allow\n * cherry-picking individual fields, in which case by **convention** the fields array specifies \"last_source_name:all\"\n *\n * @protected\n * @param {Object[]} data One record object per element\n * @param {String[]} fields The names of fields to extract (as named in the source data). Eg \"afield\"\n * @param {String[]} outnames How to represent the source fields in the output. Eg \"namespace:afield|atransform\"\n * @param {function[]} trans An array of transformation functions (if any). One function per data element, or null.\n * @protected\n */\n extractFields (data, fields, outnames, trans) {\n //intended for an array of objects\n // [ {\"id\":1, \"val\":5}, {\"id\":2, \"val\":10}]\n // Since a number of sources exist that do not obey this format, we will provide a convenient pass-through\n if (!Array.isArray(data)) {\n return data;\n }\n\n if (!data.length) {\n // Sometimes there are regions that just don't have data- this should not trigger a missing field error message!\n return data;\n }\n\n const fieldFound = [];\n for (let k = 0; k < fields.length; k++) {\n fieldFound[k] = 0;\n }\n\n const records = data.map(function (item) {\n const output_record = {};\n for (let j = 0; j < fields.length; j++) {\n let val = item[fields[j]];\n if (typeof val != 'undefined') {\n fieldFound[j] = 1;\n }\n if (trans && trans[j]) {\n val = trans[j](val);\n }\n output_record[outnames[j]] = val;\n }\n return output_record;\n });\n fieldFound.forEach(function(v, i) {\n if (!v) {\n throw new Error(`field ${fields[i]} not found in response for ${outnames[i]}`);\n }\n });\n return records;\n }\n\n /**\n * Combine records from this source with others in the chain to yield final chain body.\n * Handles merging this data with other sources (if applicable).\n *\n * @protected\n * @param {Object[]} data The data That would be returned from this source alone\n * @param {Object} chain The data chain built up during previous requests\n * @param {String[]} fields\n * @param {String[]} outnames\n * @param {String[]} trans\n * @return {Promise|Object[]} The new chain body\n */\n combineChainBody(data, chain, fields, outnames, trans) {\n return data;\n }\n\n /**\n * Coordinates the work of parsing a response and returning records. This is broken into 4 steps, which may be\n * overridden separately for fine-grained control. Each step can return either raw data or a promise.\n *\n * @protected\n *\n * @param {String|Object} resp The raw data associated with the response\n * @param {Object} chain The combined parsed response data from this and all other requests made in the chain\n * @param {String[]} fields Array of requested field names (as they would appear in the response payload)\n * @param {String[]} outnames Array of field names as they will be represented in the data returned by this source,\n * including the namespace. This must be an array with the same length as `fields`\n * @param {Function[]} trans The collection of transformation functions to be run on selected fields.\n * This must be an array with the same length as `fields`\n * @returns {Promise} A promise that resolves to an object containing\n * request metadata (`headers: {}`), the consolidated data for plotting (`body: []`), and the individual responses that would be\n * returned by each source in the chain in isolation (`discrete: {}`)\n */\n parseResponse (resp, chain, fields, outnames, trans) {\n const source_id = this.source_id || this.constructor.name;\n if (!chain.discrete) {\n chain.discrete = {};\n }\n\n const json = typeof resp == 'string' ? JSON.parse(resp) : resp;\n\n // Perform the 4 steps of parsing the payload and return a combined chain object\n return Promise.resolve(this.normalizeResponse(json.data || json))\n .then((standardized) => {\n // Perform calculations on the data from just this source\n return Promise.resolve(this.annotateData(standardized, chain));\n }).then((data) => {\n return Promise.resolve(this.extractFields(data, fields, outnames, trans));\n }).then((one_source_body) => {\n // Store a copy of the data that would be returned by parsing this source in isolation (and taking the\n // fields array into account). This is useful when we want to re-use the source output in many ways.\n chain.discrete[source_id] = one_source_body;\n return Promise.resolve(this.combineChainBody(one_source_body, chain, fields, outnames, trans));\n }).then((new_body) => {\n return { header: chain.header || {}, discrete: chain.discrete, body: new_body };\n });\n }\n\n /**\n * Fetch the data from the specified data source, and apply transformations requested by an external consumer.\n * This is the public-facing datasource method that will most be called by the plot, but custom data sources will\n * almost never want to override this method directly- more specific hooks are provided to control individual pieces\n * of the request lifecycle.\n *\n * @private\n * @param {Object} state The current \"state\" of the plot, such as chromosome and start/end positions\n * @param {String[]} fields Array of field names that the plot has requested from this data source. (without the \"namespace\" prefix)\n * @param {String[]} outnames Array describing how the output data should refer to this field. This represents the\n * originally requested field name, including the namespace. This must be an array with the same length as `fields`\n * @param {Function[]} trans The collection of transformation functions to be run on selected fields.\n * This must be an array with the same length as `fields`\n * @returns {function} A callable operation that can be used as part of the data chain\n */\n getData(state, fields, outnames, trans) {\n if (this.preGetData) { // TODO try to remove this method if at all possible\n const pre = this.preGetData(state, fields, outnames, trans);\n if (this.pre) {\n state = pre.state || state;\n fields = pre.fields || fields;\n outnames = pre.outnames || outnames;\n trans = pre.trans || trans;\n }\n }\n\n return (chain) => {\n if (this.__dependentSource && chain && chain.body && !chain.body.length) {\n // A \"dependent\" source should not attempt to fire a request if there is no data for it to act on.\n // Therefore, it should simply return the previous data chain.\n return Promise.resolve(chain);\n }\n\n return this.getRequest(state, chain, fields).then((resp) => {\n return this.parseResponse(resp, chain, fields, outnames, trans);\n });\n };\n }\n}\n\n/**\n * Base source for LocusZoom data sources that receive their data over the web. Adds default config parameters\n * (and potentially other behavior) that are relevant to URL-based requests.\n */\nclass BaseApiAdapter extends BaseAdapter {\n parseInit(config) {\n super.parseInit(config);\n\n /** @member {String} */\n this.url = config.url;\n if (!this.url) {\n throw new Error('Source not initialized with required URL');\n }\n }\n}\n\n/**\n * Data Source for Association Data from the LocusZoom/ Portaldev API (or compatible). Defines how to make a requesr\n * @public\n */\nclass AssociationLZ extends BaseApiAdapter {\n preGetData (state, fields, outnames, trans) {\n // TODO: Modify internals to see if we can go without this method\n const id_field = this.params.id_field || 'id';\n [id_field, 'position'].forEach(function(x) {\n if (!fields.includes(x)) {\n fields.unshift(x);\n outnames.unshift(x);\n trans.unshift(null);\n }\n });\n return {fields: fields, outnames:outnames, trans:trans};\n }\n\n getURL (state, chain, fields) {\n const analysis = chain.header.analysis || this.params.source || this.params.analysis; // Old usages called this param \"analysis\"\n if (typeof analysis == 'undefined') {\n throw new Error('Association source must specify an analysis ID to plot');\n }\n return `${this.url}results/?filter=analysis in ${analysis} and chromosome in '${state.chr}' and position ge ${state.start} and position le ${state.end}`;\n }\n\n normalizeResponse (data) {\n // Some association sources do not sort their data in a predictable order, which makes it hard to reliably\n // align with other sources (such as LD). For performance reasons, sorting is an opt-in argument.\n // TODO: Consider more fine grained sorting control in the future. This was added as a very specific\n // workaround for the original T2D portal.\n data = super.normalizeResponse(data);\n if (this.params && this.params.sort && data.length && data[0]['position']) {\n data.sort(function (a, b) {\n return a['position'] - b['position'];\n });\n }\n return data;\n }\n}\n\n/**\n * Fetch linkage disequilibrium information from a UMich LDServer-compatible API\n *\n * This source is designed to connect its results to association data, and therefore depends on association data having\n * been loaded by a previous request in the data chain.\n *\n * In older versions of LocusZoom, this was known as \"LDServer\". A prior source (targeted at older APIs) has been removed.\n */\nclass LDServer extends BaseApiAdapter {\n constructor(config) {\n super(config);\n this.__dependentSource = true;\n }\n\n preGetData(state, fields) {\n if (fields.length > 1) {\n if (fields.length !== 2 || !fields.includes('isrefvar')) {\n throw new Error(`LD does not know how to get all fields: ${fields.join(', ')}`);\n }\n }\n }\n\n findMergeFields(chain) {\n // Find the fields (as provided by a previous step in the chain, like an association source) that will be needed to\n // combine LD data with existing information\n\n // Since LD information may be shared across multiple assoc sources with different namespaces,\n // we use regex to find columns to join on, rather than requiring exact matches\n const exactMatch = function (arr) {\n return function () {\n const regexes = arguments;\n for (let i = 0; i < regexes.length; i++) {\n const regex = regexes[i];\n const m = arr.filter(function (x) {\n return x.match(regex);\n });\n if (m.length) {\n return m[0];\n }\n }\n return null;\n };\n };\n let dataFields = {\n id: this.params.id_field,\n position: this.params.position_field,\n pvalue: this.params.pvalue_field,\n _names_:null,\n };\n if (chain && chain.body && chain.body.length > 0) {\n const names = Object.keys(chain.body[0]);\n const nameMatch = exactMatch(names);\n // Internally, fields are generally prefixed with the name of the source they come from.\n // If the user provides an id_field (like `variant`), it should work across data sources( `assoc1:variant`,\n // assoc2:variant), but not match fragments of other field names (assoc1:variant_thing)\n // Note: these lookups hard-code a couple of common fields that will work based on known APIs in the wild\n const id_match = dataFields.id && nameMatch(new RegExp(`${dataFields.id}\\\\b`));\n dataFields.id = id_match || nameMatch(/\\bvariant\\b/) || nameMatch(/\\bid\\b/);\n dataFields.position = dataFields.position || nameMatch(/\\bposition\\b/i, /\\bpos\\b/i);\n dataFields.pvalue = dataFields.pvalue || nameMatch(/\\bpvalue\\b/i, /\\blog_pvalue\\b/i);\n dataFields._names_ = names;\n }\n return dataFields;\n }\n\n findRequestedFields (fields, outnames) {\n // Assumption: all usages of this source will only ever ask for \"isrefvar\" or \"state\". This maps to output names.\n let obj = {};\n for (let i = 0; i < fields.length; i++) {\n if (fields[i] === 'isrefvar') {\n obj.isrefvarin = fields[i];\n obj.isrefvarout = outnames && outnames[i];\n } else {\n obj.ldin = fields[i];\n obj.ldout = outnames && outnames[i];\n }\n }\n return obj;\n }\n\n normalizeResponse (data) {\n // The LD API payload does not obey standard format conventions; do not try to transform it.\n return data;\n }\n\n /**\n * Get the LD reference variant, which by default will be the most significant hit in the assoc results\n * This will be used in making the original query to the LD server for pairwise LD information\n * @returns {*|string} The marker id (expected to be in `chr:pos_ref/alt` format) of the reference variant\n */\n getRefvar(state, chain, fields) {\n let findExtremeValue = function(records, pval_field) {\n // Finds the most significant hit (smallest pvalue, or largest -log10p). Will try to auto-detect the appropriate comparison.\n pval_field = pval_field || 'log_pvalue'; // The official LZ API returns log_pvalue\n const is_log = /log/.test(pval_field);\n let cmp;\n if (is_log) {\n cmp = function(a, b) {\n return a > b;\n };\n } else {\n cmp = function(a, b) {\n return a < b;\n };\n }\n let extremeVal = records[0][pval_field], extremeIdx = 0;\n for (let i = 1; i < records.length; i++) {\n if (cmp(records[i][pval_field], extremeVal)) {\n extremeVal = records[i][pval_field];\n extremeIdx = i;\n }\n }\n return extremeIdx;\n };\n\n let reqFields = this.findRequestedFields(fields);\n let refVar = reqFields.ldin;\n if (refVar === 'state') {\n refVar = state.ldrefvar || chain.header.ldrefvar || 'best';\n }\n if (refVar === 'best') {\n if (!chain.body) {\n throw new Error('No association data found to find best pvalue');\n }\n let keys = this.findMergeFields(chain);\n if (!keys.pvalue || !keys.id) {\n let columns = '';\n if (!keys.id) {\n columns += `${columns.length ? ', ' : ''}id`;\n }\n if (!keys.pvalue) {\n columns += `${columns.length ? ', ' : ''}pvalue`;\n }\n throw new Error(`Unable to find necessary column(s) for merge: ${columns} (available: ${keys._names_})`);\n }\n refVar = chain.body[findExtremeValue(chain.body, keys.pvalue)][keys.id];\n }\n return refVar;\n }\n\n getURL(state, chain, fields) {\n // Accept the following params in this.params:\n // - method (r, rsquare, cov)\n // - source (aka panel)\n // - population (ALL, AFR, EUR, etc)\n // - build\n // The LD source/pop can be overridden from plot.state for dynamic layouts\n const build = state.genome_build || this.params.build || 'GRCh37';\n let source = state.ld_source || this.params.source || '1000G';\n const population = state.ld_pop || this.params.population || 'ALL'; // LDServer panels will always have an ALL\n const method = this.params.method || 'rsquare';\n\n if (source === '1000G' && build === 'GRCh38') {\n // For build 38 (only), there is a newer/improved 1000G LD panel available that uses WGS data. Auto upgrade by default.\n source = '1000G-FRZ09';\n }\n\n validateBuildSource(this.constructor.name, build, null); // LD doesn't need to validate `source` option\n\n let refVar = this.getRefvar(state, chain, fields);\n // Some datasets, notably the Portal, use a different marker format.\n // Coerce it into one that will work with the LDServer API. (CHROM:POS_REF/ALT)\n const REGEX_MARKER = /^(?:chr)?([a-zA-Z0-9]+?)[_:-](\\d+)[_:|-]?(\\w+)?[/_:|-]?([^_]+)?_?(.*)?/;\n const match = refVar && refVar.match(REGEX_MARKER);\n\n if (!match) {\n throw new Error('Could not request LD for a missing or incomplete marker format');\n }\n refVar = [match[1], ':', match[2], '_', match[3], '/', match[4]].join('');\n chain.header.ldrefvar = refVar;\n\n return [\n this.url, 'genome_builds/', build, '/references/', source, '/populations/', population, '/variants',\n '?correlation=', method,\n '&variant=', encodeURIComponent(refVar),\n '&chrom=', encodeURIComponent(state.chr),\n '&start=', encodeURIComponent(state.start),\n '&stop=', encodeURIComponent(state.end),\n ].join('');\n }\n\n combineChainBody(data, chain, fields, outnames, trans) {\n let keys = this.findMergeFields(chain);\n let reqFields = this.findRequestedFields(fields, outnames);\n if (!keys.position) {\n throw new Error(`Unable to find position field for merge: ${keys._names_}`);\n }\n const leftJoin = function (left, right, lfield, rfield) {\n let i = 0, j = 0;\n while (i < left.length && j < right.position2.length) {\n if (left[i][keys.position] === right.position2[j]) {\n left[i][lfield] = right[rfield][j];\n i++;\n j++;\n } else if (left[i][keys.position] < right.position2[j]) {\n i++;\n } else {\n j++;\n }\n }\n };\n const tagRefVariant = function (data, refvar, idfield, outrefname, outldname) {\n for (let i = 0; i < data.length; i++) {\n if (data[i][idfield] && data[i][idfield] === refvar) {\n data[i][outrefname] = 1;\n data[i][outldname] = 1; // For label/filter purposes, implicitly mark the ref var as LD=1 to itself\n } else {\n data[i][outrefname] = 0;\n }\n }\n };\n\n // LD servers vary slightly. Some report corr as \"rsquare\", others as \"correlation\"\n let corrField = data.rsquare ? 'rsquare' : 'correlation';\n leftJoin(chain.body, data, reqFields.ldout, corrField);\n if (reqFields.isrefvarin && chain.header.ldrefvar) {\n tagRefVariant(chain.body, chain.header.ldrefvar, keys.id, reqFields.isrefvarout, reqFields.ldout);\n }\n return chain.body;\n }\n\n fetchRequest(state, chain, fields) {\n // The API is paginated, but we need all of the data to render a plot. Depaginate and combine where appropriate.\n let url = this.getURL(state, chain, fields);\n let combined = { data: {} };\n let chainRequests = function (url) {\n return fetch(url).then().then((response) => {\n if (!response.ok) {\n throw new Error(response.statusText);\n }\n return response.text();\n }).then(function(payload) {\n payload = JSON.parse(payload);\n Object.keys(payload.data).forEach(function (key) {\n combined.data[key] = (combined.data[key] || []).concat(payload.data[key]);\n });\n if (payload.next) {\n return chainRequests(payload.next);\n }\n return combined;\n });\n };\n return chainRequests(url);\n }\n}\n\n/**\n * Data source for GWAS catalogs of known variants\n * @public\n * @class\n * @param {Object|String} init Configuration (URL or object)\n * @param {Object} [init.params] Optional configuration parameters\n * @param {Number} [init.params.source=2] The ID of the chosen catalog. Defaults to EBI GWAS catalog, GRCh37\n * @param {('strict'|'loose')} [init.params.match_type='strict'] Whether to match on exact variant, or just position.\n */\nclass GwasCatalogLZ extends BaseApiAdapter {\n constructor(config) {\n super(config);\n this.__dependentSource = true;\n }\n\n getURL(state, chain, fields) {\n // This is intended to be aligned with another source- we will assume they are always ordered by position, asc\n // (regardless of the actual match field)\n const build_option = state.genome_build || this.params.build;\n validateBuildSource(this.constructor.name, build_option, null); // Source can override build- not mutually exclusive\n\n // Most of our annotations will respect genome build before any other option.\n // But there can be more than one GWAS catalog version available in the same API, for the same build- an\n // explicit config option will always take\n // precedence.\n // See: http://portaldev.sph.umich.edu/api/v1/annotation/gwascatalog/?format=objects\n const default_source = (build_option === 'GRCh38') ? 5 : 6; // EBI GWAS catalog\n const source = this.params.source || default_source;\n return `${this.url }?format=objects&sort=pos&filter=id eq ${source} and chrom eq '${state.chr}' and pos ge ${state.start} and pos le ${state.end}`;\n }\n\n findMergeFields(records) {\n // Data from previous sources is already namespaced. Find the alignment field by matching.\n const knownFields = Object.keys(records);\n // Note: All API endoints involved only give results for 1 chromosome at a time; match is implied\n const posMatch = knownFields.find(function (item) {\n return item.match(/\\b(position|pos)\\b/i);\n });\n\n if (!posMatch) {\n throw new Error('Could not find data to align with GWAS catalog results');\n }\n return { 'pos': posMatch };\n }\n\n extractFields (data, fields, outnames, trans) {\n // Skip the \"individual field extraction\" step; extraction will be handled when building chain body instead\n return data;\n }\n\n combineChainBody(data, chain, fields, outnames, trans) {\n if (!data.length) {\n return chain.body;\n }\n\n // TODO: Better reuse options in the future. This source is very specifically tied to the PortalDev API, where\n // the field name is always \"log_pvalue\". Relatively few sites will write their own gwas-catalog endpoint.\n const decider = 'log_pvalue';\n const decider_out = outnames[fields.indexOf(decider)];\n\n function leftJoin(left, right, fields, outnames, trans) { // Add `fields` from `right` to `left`\n // Add a synthetic, un-namespaced field to all matching records\n const n_matches = left['n_catalog_matches'] || 0;\n left['n_catalog_matches'] = n_matches + 1;\n if (decider && left[decider_out] && left[decider_out] > right[decider]) {\n // There may be more than one GWAS catalog entry for the same SNP. This source is intended for a 1:1\n // annotation scenario, so for now it only joins the catalog entry that has the best -log10 pvalue\n return;\n }\n\n for (let j = 0; j < fields.length; j++) {\n const fn = fields[j];\n const outn = outnames[j];\n\n let val = right[fn];\n if (trans && trans[j]) {\n val = trans[j](val);\n }\n left[outn] = val;\n }\n }\n\n const chainNames = this.findMergeFields(chain.body[0]);\n const catNames = this.findMergeFields(data[0]);\n\n var i = 0, j = 0;\n while (i < chain.body.length && j < data.length) {\n var left = chain.body[i];\n var right = data[j];\n\n if (left[chainNames.pos] === right[catNames.pos]) {\n // There may be multiple catalog entries for each matching SNP; evaluate match one at a time\n leftJoin(left, right, fields, outnames, trans);\n j += 1;\n } else if (left[chainNames.pos] < right[catNames.pos]) {\n i += 1;\n } else {\n j += 1;\n }\n }\n return chain.body;\n }\n}\n\n/**\n * Data Source for Gene Data, as fetched from the LocusZoom/Portaldev API server (or compatible format)\n * @public\n */\nclass GeneLZ extends BaseApiAdapter {\n getURL(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n let source = this.params.source;\n validateBuildSource(this.constructor.name, build, source);\n\n if (build) {\n // If build specified, we auto-select the best current portaldev API dataset for that build\n // If build is not specified, we use the exact source ID provided by the user.\n // See: https://portaldev.sph.umich.edu/api/v1/annotation/genes/sources/?format=objects\n source = (build === 'GRCh38') ? 4 : 5;\n }\n return `${this.url}?filter=source in ${source} and chrom eq '${state.chr}' and start le ${state.end} and end ge ${state.start}`;\n }\n\n normalizeResponse(data) {\n // Genes have a very complex internal data format. Bypass any record parsing, and provide the data layer with\n // the exact information returned by the API. (ignoring the fields array in the layout)\n return data;\n }\n\n extractFields(data, fields, outnames, trans) {\n return data;\n }\n}\n\n/**\n * Data Source for Gene Constraint Data, as fetched from the gnomAD server (or compatible)\n *\n * This is intended to be the second request in a chain, with special logic that connects it to Genes data\n * already fetched.\n *\n * @public\n*/\nclass GeneConstraintLZ extends BaseApiAdapter {\n constructor(config) {\n super(config);\n this.__dependentSource = true;\n }\n getURL() {\n // GraphQL API: request details are encoded in the body, not the URL\n return this.url;\n }\n getCacheKey(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n // GraphQL API: request not defined solely by the URL\n // Gather the state params that govern constraint query for a given region.\n return `${this.url} ${state.chr} ${state.start} ${state.end} ${build}`;\n }\n\n normalizeResponse(data) {\n return data;\n }\n\n fetchRequest(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n if (!build) {\n throw new Error(`Data source ${this.constructor.name} must specify a 'genome_build' option`);\n }\n\n const unique_gene_names = chain.body.reduce(\n // In rare cases, the same gene symbol may appear at multiple positions. (issue #179) We de-duplicate the\n // gene names to avoid issuing a malformed GraphQL query.\n function (acc, gene) {\n acc[gene.gene_name] = null;\n return acc;\n },\n {}\n );\n let query = Object.keys(unique_gene_names).map(function (gene_name) {\n // GraphQL alias names must match a specific set of allowed characters: https://stackoverflow.com/a/45757065/1422268\n const alias = `_${gene_name.replace(/[^A-Za-z0-9_]/g, '_')}`;\n // Each gene symbol is a separate graphQL query, grouped into one request using aliases\n return `${alias}: gene(gene_symbol: \"${gene_name}\", reference_genome: ${build}) { gnomad_constraint { exp_syn obs_syn syn_z oe_syn oe_syn_lower oe_syn_upper exp_mis obs_mis mis_z oe_mis oe_mis_lower oe_mis_upper exp_lof obs_lof pLI oe_lof oe_lof_lower oe_lof_upper } } `;\n });\n\n if (!query.length) {\n // If there are no genes, skip the network request\n return Promise.resolve({ data: null });\n }\n\n query = `{${query.join(' ')} }`; // GraphQL isn't quite JSON; items are separated by spaces but not commas\n const url = this.getURL(state, chain, fields);\n // See: https://graphql.org/learn/serving-over-http/\n const body = JSON.stringify({ query: query });\n const headers = { 'Content-Type': 'application/json' };\n\n // FIXME: The gnomAD API sometimes has temporary CORS changes that temporarily break the genes track\n // If request blocked, return a fake \"no data\" signal so the genes track can still render w/o constraint info\n return fetch(url, { method: 'POST', body, headers }).then((response) => {\n if (!response.ok) {\n return [];\n }\n return response.text();\n }).catch((err) => []);\n }\n\n combineChainBody(data, chain, fields, outnames, trans) {\n if (!data) {\n return chain;\n }\n\n chain.body.forEach(function(gene) {\n // Find payload keys that match gene names in this response\n const alias = `_${gene.gene_name.replace(/[^A-Za-z0-9_]/g, '_')}`; // aliases are modified gene names\n const constraint = data[alias] && data[alias]['gnomad_constraint']; // gnomad API has two ways of specifying missing data for a requested gene\n if (constraint) {\n // Add all fields from constraint data- do not override fields present in the gene source\n Object.keys(constraint).forEach(function (key) {\n let val = constraint[key];\n if (typeof gene[key] === 'undefined') {\n if (typeof val == 'number' && val.toString().includes('.')) {\n val = parseFloat(val.toFixed(2));\n }\n gene[key] = val; // These two sources are both designed to bypass namespacing\n }\n });\n }\n });\n return chain.body;\n }\n}\n\n/**\n * Data Source for Recombination Rate Data, as fetched from the LocusZoom API server (or compatible)\n * @public\n */\nclass RecombLZ extends BaseApiAdapter {\n getURL(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n let source = this.params.source;\n validateBuildSource(this.constructor.SOURCE_NAME, build, source);\n\n if (build) { // If build specified, choose a known Portal API dataset IDs (build 37/38)\n source = (build === 'GRCh38') ? 16 : 15;\n }\n return `${this.url}?filter=id in ${source} and chromosome eq '${state.chr}' and position le ${state.end} and position ge ${state.start}`;\n }\n}\n\n/**\n * Data Source for static blobs of data as raw JS objects. 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11);\n","/** @module */\n/*\n * LocusZoom extensions used to calculate and render aggregation test results. Because these calculations depend on an\n * external library, the special data sources are defined here, rather than in LocusZoom core code.\n *\n * The page must incorporate and load all libraries before this file can be used, including:\n * - Vendor assets\n * - LocusZoom\n * - raremetal.js (available via NPM or a related CDN)\n */\n// This is defined as a UMD module, to work with multiple different module systems / bundlers\n// Arcane build note: everything defined here gets registered globally. This is not a \"pure\" module, and some build\n// systems may require being told that this file has side effects.\n\nimport {helpers} from 'raremetal.js';\nimport {BaseApiAdapter} from '../data/adapters';\n\n\nfunction install (LocusZoom) {\n /**\n * Data Source that calculates gene or region-based tests based on provided data\n * It will rarely be used by itself, but rather using a connector that attaches the results to data from\n * another source (like genes). 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For example, we need to parse variant names and convert to log_pvalue\n const REGEX_EPACTS = new RegExp('(?:chr)?(.+):(\\\\d+)_?(\\\\w+)?/?([^_]+)?_?(.*)?'); // match API variant strings\n return data.map((one_variant) => {\n const match = one_variant.variant.match(REGEX_EPACTS);\n return {\n variant: one_variant.variant,\n chromosome: match[1],\n position: +match[2],\n ref_allele: match[3],\n ref_allele_freq: 1 - one_variant.altFreq,\n log_pvalue: -Math.log10(one_variant.pvalue),\n };\n }).sort((a, b) => {\n a = a.variant;\n b = b.variant;\n if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n } else {\n // names must be equal\n return 0;\n }\n });\n }\n }\n\n /**\n * A sample connector that aligns calculated aggregation test data with corresponding gene information. Returns a body\n * suitable for use with the genes datalayer.\n *\n * To use this source, one must specify a fields array that calls first the genes source, then a dummy field from\n * this source. The output will be to transparently add several new fields to the genes data.\n * @public\n */\n class GeneAggregationConnectorLZ extends ConnectorSource {\n _getRequiredSources() {\n return ['gene_ns', 'aggregation_ns'];\n }\n\n combineChainBody(data, chain) {\n // The genes layer receives all results, and displays only the best pvalue for each gene\n\n // Tie the calculated group-test results to genes with a matching name\n const aggregation_source_id = this._source_name_mapping['aggregation_ns'];\n const gene_source_id = this._source_name_mapping['gene_ns'];\n // This connector assumes that genes are the main body of records from the chain, and that aggregation tests are\n // a standalone source that has not acted on genes data yet\n const aggregationData = chain.discrete[aggregation_source_id];\n const genesData = chain.discrete[gene_source_id];\n\n const groupedAggregation = {}; // Group together all tests done on that gene- any mask, any test\n\n aggregationData.groups.forEach(function (result) {\n if (!Object.prototype.hasOwnProperty.call(groupedAggregation, result.group)) {\n groupedAggregation[result.group] = [];\n }\n groupedAggregation[result.group].push(result.pvalue);\n });\n\n // Annotate any genes that have test results\n genesData.forEach(function (gene) {\n const gene_id = gene.gene_name;\n const tests = groupedAggregation[gene_id];\n if (tests) {\n gene.aggregation_best_pvalue = Math.min.apply(null, tests);\n }\n });\n return genesData;\n }\n }\n\n\n LocusZoom.Adapters.add('AggregationTestSourceLZ', AggregationTestSource);\n LocusZoom.Adapters.add('AssocFromAggregationLZ', AssocFromAggregationLZ);\n LocusZoom.Adapters.add('GeneAggregationConnectorLZ', GeneAggregationConnectorLZ);\n}\n\n\nif (typeof LocusZoom !== 'undefined') {\n // Auto-register the plugin when included as a script tag. ES6 module users must register via LocusZoom.use()\n // eslint-disable-next-line no-undef\n LocusZoom.use(install);\n}\n\n\nexport default install;\n","/**\n * Define standard data adapters used to retrieve data (usually from REST APIs)\n * @module\n */\n\nfunction validateBuildSource(class_name, build, source) {\n // Build OR Source, not both\n if ((build && source) || !(build || source)) {\n throw new Error(`${class_name} must provide a parameter specifying either \"build\" or \"source\". It should not specify both.`);\n }\n // If the build isn't recognized, our APIs can't transparently select a source to match\n if (build && !['GRCh37', 'GRCh38'].includes(build)) {\n throw new Error(`${class_name} must specify a valid genome build number`);\n }\n}\n\n\n/**\n * Base class for LocusZoom data sources (any). See also: BaseApiAdapter\n * @public\n */\nclass BaseAdapter {\n constructor(config) {\n /**\n * Whether this source should enable caching\n * @member {Boolean}\n */\n this._enableCache = true;\n this._cachedKey = null;\n\n /**\n * Whether this data source type is dependent on previous requests- for example, the LD source cannot annotate\n * association data if no data was found for that region.\n * @member {boolean}\n */\n this.__dependentSource = false;\n\n // Parse configuration options\n this.parseInit(config);\n }\n\n /**\n * Parse configuration used to create the data source. Many custom sources will override this method to suit their\n * needs (eg specific config options, or for sources that do not retrieve data from a URL)\n * @protected\n * @param {String|Object} config Basic configuration- either a url, or a config object\n * @param {String} [config.url] The datasource URL\n * @param {String} [config.params] Initial config params for the datasource\n */\n parseInit(config) {\n /** @member {Object} */\n this.params = config.params || {};\n }\n\n /**\n * A unique identifier that indicates whether cached data is valid for this request. For most sources using GET\n * requests to a REST API, this is usually the URL.\n * @protected\n * @param {Object} state Information available in plot.state (chr, start, end). Sometimes used to inject globally\n * available information that influences the request being made.\n * @param {Object} chain The data chain from previous requests made in a sequence.\n * @param fields\n * @returns {String|undefined}\n */\n getCacheKey(state, chain, fields) {\n return this.getURL(state, chain, fields);\n }\n\n /**\n * Stub: build the URL for any requests made by this source.\n * @protected\n */\n getURL(state, chain, fields) {\n return this.url;\n }\n\n /**\n * Perform a network request to fetch data for this source. This is usually the method that is used to override\n * when defining how to retrieve data.\n * @protected\n * @param {Object} state The state of the parent plot\n * @param chain\n * @param fields\n * @returns {Promise}\n */\n fetchRequest(state, chain, fields) {\n const url = this.getURL(state, chain, fields);\n return fetch(url).then((response) => {\n if (!response.ok) {\n throw new Error(response.statusText);\n }\n return response.text();\n });\n }\n\n /**\n * Gets the data for just this source, typically via a network request (but using cache where possible)\n *\n * For most use cases, it is better to override `fetchRequest` instead, to avoid bypassing the cache mechanism\n * by accident.\n * @protected\n */\n getRequest(state, chain, fields) {\n let req;\n const cacheKey = this.getCacheKey(state, chain, fields);\n if (this._enableCache && typeof(cacheKey) !== 'undefined' && cacheKey === this._cachedKey) {\n req = Promise.resolve(this._cachedResponse); // Resolve to the value of the current promise\n } else {\n req = this.fetchRequest(state, chain, fields);\n if (this._enableCache) {\n this._cachedKey = cacheKey;\n this._cachedResponse = req;\n }\n }\n return req;\n }\n\n /**\n * Ensure the server response is in a canonical form, an array of one object per record. [ {field: oneval} ].\n * If the server response contains columns, reformats the response from {column1: [], column2: []} to the above.\n *\n * Does not apply namespacing, transformations, or field extraction.\n *\n * May be overridden by data sources that inherently return more complex payloads, or that exist to annotate other\n * sources (eg, if the payload provides extra data rather than a series of records).\n * @protected\n * @param {Object[]|Object} data The original parsed server response\n */\n normalizeResponse(data) {\n if (Array.isArray(data)) {\n // Already in the desired form\n return data;\n }\n // Otherwise, assume the server response is an object representing columns of data.\n // Each array should have the same length (verify), and a given array index corresponds to a single row.\n const keys = Object.keys(data);\n const N = data[keys[0]].length;\n const sameLength = keys.every(function (key) {\n const item = data[key];\n return item.length === N;\n });\n if (!sameLength) {\n throw new Error(`${this.constructor.name} expects a response in which all arrays of data are the same length`);\n }\n\n // Go down the rows, and create an object for each record\n const records = [];\n const fields = Object.keys(data);\n for (let i = 0; i < N; i++) {\n const record = {};\n for (let j = 0; j < fields.length; j++) {\n record[fields[j]] = data[fields[j]][i];\n }\n records.push(record);\n }\n return records;\n }\n\n /**\n * Hook to post-process the data returned by this source with new, additional behavior.\n * (eg cleaning up API values or performing complex calculations on the returned data)\n *\n * @protected\n * @param {Object[]} records The parsed data from the source (eg standardized api response)\n * @param {Object} chain The data chain object. For example, chain.headers may provide useful annotation metadata\n * @returns {Object[]|Promise} The modified set of records\n */\n annotateData(records, chain) {\n // Default behavior: no transformations\n return records;\n }\n\n /**\n * Clean up the server records for use by datalayers: extract only certain fields, with the specified names.\n * Apply per-field transformations as appropriate.\n *\n * This hook can be overridden, eg to create a source that always returns all records and ignores the \"fields\" array.\n * This is particularly common for sources at the end of a chain- many \"dependent\" sources do not allow\n * cherry-picking individual fields, in which case by **convention** the fields array specifies \"last_source_name:all\"\n *\n * @protected\n * @param {Object[]} data One record object per element\n * @param {String[]} fields The names of fields to extract (as named in the source data). Eg \"afield\"\n * @param {String[]} outnames How to represent the source fields in the output. Eg \"namespace:afield|atransform\"\n * @param {function[]} trans An array of transformation functions (if any). One function per data element, or null.\n * @protected\n */\n extractFields (data, fields, outnames, trans) {\n //intended for an array of objects\n // [ {\"id\":1, \"val\":5}, {\"id\":2, \"val\":10}]\n // Since a number of sources exist that do not obey this format, we will provide a convenient pass-through\n if (!Array.isArray(data)) {\n return data;\n }\n\n if (!data.length) {\n // Sometimes there are regions that just don't have data- this should not trigger a missing field error message!\n return data;\n }\n\n const fieldFound = [];\n for (let k = 0; k < fields.length; k++) {\n fieldFound[k] = 0;\n }\n\n const records = data.map(function (item) {\n const output_record = {};\n for (let j = 0; j < fields.length; j++) {\n let val = item[fields[j]];\n if (typeof val != 'undefined') {\n fieldFound[j] = 1;\n }\n if (trans && trans[j]) {\n val = trans[j](val);\n }\n output_record[outnames[j]] = val;\n }\n return output_record;\n });\n fieldFound.forEach(function(v, i) {\n if (!v) {\n throw new Error(`field ${fields[i]} not found in response for ${outnames[i]}`);\n }\n });\n return records;\n }\n\n /**\n * Combine records from this source with others in the chain to yield final chain body.\n * Handles merging this data with other sources (if applicable).\n *\n * @protected\n * @param {Object[]} data The data That would be returned from this source alone\n * @param {Object} chain The data chain built up during previous requests\n * @param {String[]} fields\n * @param {String[]} outnames\n * @param {String[]} trans\n * @return {Promise|Object[]} The new chain body\n */\n combineChainBody(data, chain, fields, outnames, trans) {\n return data;\n }\n\n /**\n * Coordinates the work of parsing a response and returning records. This is broken into 4 steps, which may be\n * overridden separately for fine-grained control. Each step can return either raw data or a promise.\n *\n * @protected\n *\n * @param {String|Object} resp The raw data associated with the response\n * @param {Object} chain The combined parsed response data from this and all other requests made in the chain\n * @param {String[]} fields Array of requested field names (as they would appear in the response payload)\n * @param {String[]} outnames Array of field names as they will be represented in the data returned by this source,\n * including the namespace. This must be an array with the same length as `fields`\n * @param {Function[]} trans The collection of transformation functions to be run on selected fields.\n * This must be an array with the same length as `fields`\n * @returns {Promise} A promise that resolves to an object containing\n * request metadata (`headers: {}`), the consolidated data for plotting (`body: []`), and the individual responses that would be\n * returned by each source in the chain in isolation (`discrete: {}`)\n */\n parseResponse (resp, chain, fields, outnames, trans) {\n const source_id = this.source_id || this.constructor.name;\n if (!chain.discrete) {\n chain.discrete = {};\n }\n\n const json = typeof resp == 'string' ? JSON.parse(resp) : resp;\n\n // Perform the 4 steps of parsing the payload and return a combined chain object\n return Promise.resolve(this.normalizeResponse(json.data || json))\n .then((standardized) => {\n // Perform calculations on the data from just this source\n return Promise.resolve(this.annotateData(standardized, chain));\n }).then((data) => {\n return Promise.resolve(this.extractFields(data, fields, outnames, trans));\n }).then((one_source_body) => {\n // Store a copy of the data that would be returned by parsing this source in isolation (and taking the\n // fields array into account). This is useful when we want to re-use the source output in many ways.\n chain.discrete[source_id] = one_source_body;\n return Promise.resolve(this.combineChainBody(one_source_body, chain, fields, outnames, trans));\n }).then((new_body) => {\n return { header: chain.header || {}, discrete: chain.discrete, body: new_body };\n });\n }\n\n /**\n * Fetch the data from the specified data source, and apply transformations requested by an external consumer.\n * This is the public-facing datasource method that will most be called by the plot, but custom data sources will\n * almost never want to override this method directly- more specific hooks are provided to control individual pieces\n * of the request lifecycle.\n *\n * @private\n * @param {Object} state The current \"state\" of the plot, such as chromosome and start/end positions\n * @param {String[]} fields Array of field names that the plot has requested from this data source. (without the \"namespace\" prefix)\n * @param {String[]} outnames Array describing how the output data should refer to this field. This represents the\n * originally requested field name, including the namespace. This must be an array with the same length as `fields`\n * @param {Function[]} trans The collection of transformation functions to be run on selected fields.\n * This must be an array with the same length as `fields`\n * @returns {function} A callable operation that can be used as part of the data chain\n */\n getData(state, fields, outnames, trans) {\n if (this.preGetData) { // TODO try to remove this method if at all possible\n const pre = this.preGetData(state, fields, outnames, trans);\n if (this.pre) {\n state = pre.state || state;\n fields = pre.fields || fields;\n outnames = pre.outnames || outnames;\n trans = pre.trans || trans;\n }\n }\n\n return (chain) => {\n if (this.__dependentSource && chain && chain.body && !chain.body.length) {\n // A \"dependent\" source should not attempt to fire a request if there is no data for it to act on.\n // Therefore, it should simply return the previous data chain.\n return Promise.resolve(chain);\n }\n\n return this.getRequest(state, chain, fields).then((resp) => {\n return this.parseResponse(resp, chain, fields, outnames, trans);\n });\n };\n }\n}\n\n/**\n * Base source for LocusZoom data sources that receive their data over the web. Adds default config parameters\n * (and potentially other behavior) that are relevant to URL-based requests.\n */\nclass BaseApiAdapter extends BaseAdapter {\n parseInit(config) {\n super.parseInit(config);\n\n /** @member {String} */\n this.url = config.url;\n if (!this.url) {\n throw new Error('Source not initialized with required URL');\n }\n }\n}\n\n/**\n * Data Source for Association Data from the LocusZoom/ Portaldev API (or compatible). Defines how to make a requesr\n * @public\n */\nclass AssociationLZ extends BaseApiAdapter {\n preGetData (state, fields, outnames, trans) {\n // TODO: Modify internals to see if we can go without this method\n const id_field = this.params.id_field || 'id';\n [id_field, 'position'].forEach(function(x) {\n if (!fields.includes(x)) {\n fields.unshift(x);\n outnames.unshift(x);\n trans.unshift(null);\n }\n });\n return {fields: fields, outnames:outnames, trans:trans};\n }\n\n getURL (state, chain, fields) {\n const analysis = chain.header.analysis || this.params.source || this.params.analysis; // Old usages called this param \"analysis\"\n if (typeof analysis == 'undefined') {\n throw new Error('Association source must specify an analysis ID to plot');\n }\n return `${this.url}results/?filter=analysis in ${analysis} and chromosome in '${state.chr}' and position ge ${state.start} and position le ${state.end}`;\n }\n\n normalizeResponse (data) {\n // Some association sources do not sort their data in a predictable order, which makes it hard to reliably\n // align with other sources (such as LD). For performance reasons, sorting is an opt-in argument.\n // TODO: Consider more fine grained sorting control in the future. This was added as a very specific\n // workaround for the original T2D portal.\n data = super.normalizeResponse(data);\n if (this.params && this.params.sort && data.length && data[0]['position']) {\n data.sort(function (a, b) {\n return a['position'] - b['position'];\n });\n }\n return data;\n }\n}\n\n/**\n * Fetch linkage disequilibrium information from a UMich LDServer-compatible API\n *\n * This source is designed to connect its results to association data, and therefore depends on association data having\n * been loaded by a previous request in the data chain.\n *\n * In older versions of LocusZoom, this was known as \"LDServer\". A prior source (targeted at older APIs) has been removed.\n */\nclass LDServer extends BaseApiAdapter {\n constructor(config) {\n super(config);\n this.__dependentSource = true;\n }\n\n preGetData(state, fields) {\n if (fields.length > 1) {\n if (fields.length !== 2 || !fields.includes('isrefvar')) {\n throw new Error(`LD does not know how to get all fields: ${fields.join(', ')}`);\n }\n }\n }\n\n findMergeFields(chain) {\n // Find the fields (as provided by a previous step in the chain, like an association source) that will be needed to\n // combine LD data with existing information\n\n // Since LD information may be shared across multiple assoc sources with different namespaces,\n // we use regex to find columns to join on, rather than requiring exact matches\n const exactMatch = function (arr) {\n return function () {\n const regexes = arguments;\n for (let i = 0; i < regexes.length; i++) {\n const regex = regexes[i];\n const m = arr.filter(function (x) {\n return x.match(regex);\n });\n if (m.length) {\n return m[0];\n }\n }\n return null;\n };\n };\n let dataFields = {\n id: this.params.id_field,\n position: this.params.position_field,\n pvalue: this.params.pvalue_field,\n _names_:null,\n };\n if (chain && chain.body && chain.body.length > 0) {\n const names = Object.keys(chain.body[0]);\n const nameMatch = exactMatch(names);\n // Internally, fields are generally prefixed with the name of the source they come from.\n // If the user provides an id_field (like `variant`), it should work across data sources( `assoc1:variant`,\n // assoc2:variant), but not match fragments of other field names (assoc1:variant_thing)\n // Note: these lookups hard-code a couple of common fields that will work based on known APIs in the wild\n const id_match = dataFields.id && nameMatch(new RegExp(`${dataFields.id}\\\\b`));\n dataFields.id = id_match || nameMatch(/\\bvariant\\b/) || nameMatch(/\\bid\\b/);\n dataFields.position = dataFields.position || nameMatch(/\\bposition\\b/i, /\\bpos\\b/i);\n dataFields.pvalue = dataFields.pvalue || nameMatch(/\\bpvalue\\b/i, /\\blog_pvalue\\b/i);\n dataFields._names_ = names;\n }\n return dataFields;\n }\n\n findRequestedFields (fields, outnames) {\n // Assumption: all usages of this source will only ever ask for \"isrefvar\" or \"state\". This maps to output names.\n let obj = {};\n for (let i = 0; i < fields.length; i++) {\n if (fields[i] === 'isrefvar') {\n obj.isrefvarin = fields[i];\n obj.isrefvarout = outnames && outnames[i];\n } else {\n obj.ldin = fields[i];\n obj.ldout = outnames && outnames[i];\n }\n }\n return obj;\n }\n\n normalizeResponse (data) {\n // The LD API payload does not obey standard format conventions; do not try to transform it.\n return data;\n }\n\n /**\n * Get the LD reference variant, which by default will be the most significant hit in the assoc results\n * This will be used in making the original query to the LD server for pairwise LD information\n * @returns {*|string} The marker id (expected to be in `chr:pos_ref/alt` format) of the reference variant\n */\n getRefvar(state, chain, fields) {\n let findExtremeValue = function(records, pval_field) {\n // Finds the most significant hit (smallest pvalue, or largest -log10p). Will try to auto-detect the appropriate comparison.\n pval_field = pval_field || 'log_pvalue'; // The official LZ API returns log_pvalue\n const is_log = /log/.test(pval_field);\n let cmp;\n if (is_log) {\n cmp = function(a, b) {\n return a > b;\n };\n } else {\n cmp = function(a, b) {\n return a < b;\n };\n }\n let extremeVal = records[0][pval_field], extremeIdx = 0;\n for (let i = 1; i < records.length; i++) {\n if (cmp(records[i][pval_field], extremeVal)) {\n extremeVal = records[i][pval_field];\n extremeIdx = i;\n }\n }\n return extremeIdx;\n };\n\n let reqFields = this.findRequestedFields(fields);\n let refVar = reqFields.ldin;\n if (refVar === 'state') {\n refVar = state.ldrefvar || chain.header.ldrefvar || 'best';\n }\n if (refVar === 'best') {\n if (!chain.body) {\n throw new Error('No association data found to find best pvalue');\n }\n let keys = this.findMergeFields(chain);\n if (!keys.pvalue || !keys.id) {\n let columns = '';\n if (!keys.id) {\n columns += `${columns.length ? ', ' : ''}id`;\n }\n if (!keys.pvalue) {\n columns += `${columns.length ? ', ' : ''}pvalue`;\n }\n throw new Error(`Unable to find necessary column(s) for merge: ${columns} (available: ${keys._names_})`);\n }\n refVar = chain.body[findExtremeValue(chain.body, keys.pvalue)][keys.id];\n }\n return refVar;\n }\n\n getURL(state, chain, fields) {\n // Accept the following params in this.params:\n // - method (r, rsquare, cov)\n // - source (aka panel)\n // - population (ALL, AFR, EUR, etc)\n // - build\n // The LD source/pop can be overridden from plot.state for dynamic layouts\n const build = state.genome_build || this.params.build || 'GRCh37';\n let source = state.ld_source || this.params.source || '1000G';\n const population = state.ld_pop || this.params.population || 'ALL'; // LDServer panels will always have an ALL\n const method = this.params.method || 'rsquare';\n\n if (source === '1000G' && build === 'GRCh38') {\n // For build 38 (only), there is a newer/improved 1000G LD panel available that uses WGS data. Auto upgrade by default.\n source = '1000G-FRZ09';\n }\n\n validateBuildSource(this.constructor.name, build, null); // LD doesn't need to validate `source` option\n\n let refVar = this.getRefvar(state, chain, fields);\n // Some datasets, notably the Portal, use a different marker format.\n // Coerce it into one that will work with the LDServer API. (CHROM:POS_REF/ALT)\n const REGEX_MARKER = /^(?:chr)?([a-zA-Z0-9]+?)[_:-](\\d+)[_:|-]?(\\w+)?[/_:|-]?([^_]+)?_?(.*)?/;\n const match = refVar && refVar.match(REGEX_MARKER);\n\n if (!match) {\n throw new Error('Could not request LD for a missing or incomplete marker format');\n }\n const [original, chrom, pos, ref, alt] = match;\n // Currently, the LD server only accepts full variant specs; it won't return LD w/o ref+alt. Allowing\n // a partial match at most leaves room for potential future features.\n refVar = `${chrom}:${pos}`;\n if (ref && alt) {\n refVar += `_${ref}/${alt}`;\n }\n // Preserve the user-provided variant spec for use when matching to assoc data\n chain.header.ldrefvar = original;\n\n return [\n this.url, 'genome_builds/', build, '/references/', source, '/populations/', population, '/variants',\n '?correlation=', method,\n '&variant=', encodeURIComponent(refVar),\n '&chrom=', encodeURIComponent(state.chr),\n '&start=', encodeURIComponent(state.start),\n '&stop=', encodeURIComponent(state.end),\n ].join('');\n }\n\n combineChainBody(data, chain, fields, outnames, trans) {\n let keys = this.findMergeFields(chain);\n let reqFields = this.findRequestedFields(fields, outnames);\n if (!keys.position) {\n throw new Error(`Unable to find position field for merge: ${keys._names_}`);\n }\n const leftJoin = function (left, right, lfield, rfield) {\n let i = 0, j = 0;\n while (i < left.length && j < right.position2.length) {\n if (left[i][keys.position] === right.position2[j]) {\n left[i][lfield] = right[rfield][j];\n i++;\n j++;\n } else if (left[i][keys.position] < right.position2[j]) {\n i++;\n } else {\n j++;\n }\n }\n };\n const tagRefVariant = function (data, refvar, idfield, outrefname, outldname) {\n for (let i = 0; i < data.length; i++) {\n if (data[i][idfield] && data[i][idfield] === refvar) {\n data[i][outrefname] = 1;\n data[i][outldname] = 1; // For label/filter purposes, implicitly mark the ref var as LD=1 to itself\n } else {\n data[i][outrefname] = 0;\n }\n }\n };\n\n // LD servers vary slightly. Some report corr as \"rsquare\", others as \"correlation\"\n let corrField = data.rsquare ? 'rsquare' : 'correlation';\n leftJoin(chain.body, data, reqFields.ldout, corrField);\n if (reqFields.isrefvarin && chain.header.ldrefvar) {\n tagRefVariant(chain.body, chain.header.ldrefvar, keys.id, reqFields.isrefvarout, reqFields.ldout);\n }\n return chain.body;\n }\n\n fetchRequest(state, chain, fields) {\n // The API is paginated, but we need all of the data to render a plot. Depaginate and combine where appropriate.\n let url = this.getURL(state, chain, fields);\n let combined = { data: {} };\n let chainRequests = function (url) {\n return fetch(url).then().then((response) => {\n if (!response.ok) {\n throw new Error(response.statusText);\n }\n return response.text();\n }).then(function(payload) {\n payload = JSON.parse(payload);\n Object.keys(payload.data).forEach(function (key) {\n combined.data[key] = (combined.data[key] || []).concat(payload.data[key]);\n });\n if (payload.next) {\n return chainRequests(payload.next);\n }\n return combined;\n });\n };\n return chainRequests(url);\n }\n}\n\n/**\n * Data source for GWAS catalogs of known variants\n * @public\n * @class\n * @param {Object|String} init Configuration (URL or object)\n * @param {Object} [init.params] Optional configuration parameters\n * @param {Number} [init.params.source=2] The ID of the chosen catalog. Defaults to EBI GWAS catalog, GRCh37\n * @param {('strict'|'loose')} [init.params.match_type='strict'] Whether to match on exact variant, or just position.\n */\nclass GwasCatalogLZ extends BaseApiAdapter {\n constructor(config) {\n super(config);\n this.__dependentSource = true;\n }\n\n getURL(state, chain, fields) {\n // This is intended to be aligned with another source- we will assume they are always ordered by position, asc\n // (regardless of the actual match field)\n const build_option = state.genome_build || this.params.build;\n validateBuildSource(this.constructor.name, build_option, null); // Source can override build- not mutually exclusive\n\n // Most of our annotations will respect genome build before any other option.\n // But there can be more than one GWAS catalog version available in the same API, for the same build- an\n // explicit config option will always take\n // precedence.\n // See: http://portaldev.sph.umich.edu/api/v1/annotation/gwascatalog/?format=objects\n const default_source = (build_option === 'GRCh38') ? 5 : 6; // EBI GWAS catalog\n const source = this.params.source || default_source;\n return `${this.url }?format=objects&sort=pos&filter=id eq ${source} and chrom eq '${state.chr}' and pos ge ${state.start} and pos le ${state.end}`;\n }\n\n findMergeFields(records) {\n // Data from previous sources is already namespaced. Find the alignment field by matching.\n const knownFields = Object.keys(records);\n // Note: All API endoints involved only give results for 1 chromosome at a time; match is implied\n const posMatch = knownFields.find(function (item) {\n return item.match(/\\b(position|pos)\\b/i);\n });\n\n if (!posMatch) {\n throw new Error('Could not find data to align with GWAS catalog results');\n }\n return { 'pos': posMatch };\n }\n\n extractFields (data, fields, outnames, trans) {\n // Skip the \"individual field extraction\" step; extraction will be handled when building chain body instead\n return data;\n }\n\n combineChainBody(data, chain, fields, outnames, trans) {\n if (!data.length) {\n return chain.body;\n }\n\n // TODO: Better reuse options in the future. This source is very specifically tied to the PortalDev API, where\n // the field name is always \"log_pvalue\". Relatively few sites will write their own gwas-catalog endpoint.\n const decider = 'log_pvalue';\n const decider_out = outnames[fields.indexOf(decider)];\n\n function leftJoin(left, right, fields, outnames, trans) { // Add `fields` from `right` to `left`\n // Add a synthetic, un-namespaced field to all matching records\n const n_matches = left['n_catalog_matches'] || 0;\n left['n_catalog_matches'] = n_matches + 1;\n if (decider && left[decider_out] && left[decider_out] > right[decider]) {\n // There may be more than one GWAS catalog entry for the same SNP. This source is intended for a 1:1\n // annotation scenario, so for now it only joins the catalog entry that has the best -log10 pvalue\n return;\n }\n\n for (let j = 0; j < fields.length; j++) {\n const fn = fields[j];\n const outn = outnames[j];\n\n let val = right[fn];\n if (trans && trans[j]) {\n val = trans[j](val);\n }\n left[outn] = val;\n }\n }\n\n const chainNames = this.findMergeFields(chain.body[0]);\n const catNames = this.findMergeFields(data[0]);\n\n var i = 0, j = 0;\n while (i < chain.body.length && j < data.length) {\n var left = chain.body[i];\n var right = data[j];\n\n if (left[chainNames.pos] === right[catNames.pos]) {\n // There may be multiple catalog entries for each matching SNP; evaluate match one at a time\n leftJoin(left, right, fields, outnames, trans);\n j += 1;\n } else if (left[chainNames.pos] < right[catNames.pos]) {\n i += 1;\n } else {\n j += 1;\n }\n }\n return chain.body;\n }\n}\n\n/**\n * Data Source for Gene Data, as fetched from the LocusZoom/Portaldev API server (or compatible format)\n * @public\n */\nclass GeneLZ extends BaseApiAdapter {\n getURL(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n let source = this.params.source;\n validateBuildSource(this.constructor.name, build, source);\n\n if (build) {\n // If build specified, we auto-select the best current portaldev API dataset for that build\n // If build is not specified, we use the exact source ID provided by the user.\n // See: https://portaldev.sph.umich.edu/api/v1/annotation/genes/sources/?format=objects\n source = (build === 'GRCh38') ? 4 : 5;\n }\n return `${this.url}?filter=source in ${source} and chrom eq '${state.chr}' and start le ${state.end} and end ge ${state.start}`;\n }\n\n normalizeResponse(data) {\n // Genes have a very complex internal data format. Bypass any record parsing, and provide the data layer with\n // the exact information returned by the API. (ignoring the fields array in the layout)\n return data;\n }\n\n extractFields(data, fields, outnames, trans) {\n return data;\n }\n}\n\n/**\n * Data Source for Gene Constraint Data, as fetched from the gnomAD server (or compatible)\n *\n * This is intended to be the second request in a chain, with special logic that connects it to Genes data\n * already fetched.\n *\n * @public\n*/\nclass GeneConstraintLZ extends BaseApiAdapter {\n constructor(config) {\n super(config);\n this.__dependentSource = true;\n }\n getURL() {\n // GraphQL API: request details are encoded in the body, not the URL\n return this.url;\n }\n getCacheKey(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n // GraphQL API: request not defined solely by the URL\n // Gather the state params that govern constraint query for a given region.\n return `${this.url} ${state.chr} ${state.start} ${state.end} ${build}`;\n }\n\n normalizeResponse(data) {\n return data;\n }\n\n fetchRequest(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n if (!build) {\n throw new Error(`Data source ${this.constructor.name} must specify a 'genome_build' option`);\n }\n\n const unique_gene_names = chain.body.reduce(\n // In rare cases, the same gene symbol may appear at multiple positions. (issue #179) We de-duplicate the\n // gene names to avoid issuing a malformed GraphQL query.\n function (acc, gene) {\n acc[gene.gene_name] = null;\n return acc;\n },\n {}\n );\n let query = Object.keys(unique_gene_names).map(function (gene_name) {\n // GraphQL alias names must match a specific set of allowed characters: https://stackoverflow.com/a/45757065/1422268\n const alias = `_${gene_name.replace(/[^A-Za-z0-9_]/g, '_')}`;\n // Each gene symbol is a separate graphQL query, grouped into one request using aliases\n return `${alias}: gene(gene_symbol: \"${gene_name}\", reference_genome: ${build}) { gnomad_constraint { exp_syn obs_syn syn_z oe_syn oe_syn_lower oe_syn_upper exp_mis obs_mis mis_z oe_mis oe_mis_lower oe_mis_upper exp_lof obs_lof pLI oe_lof oe_lof_lower oe_lof_upper } } `;\n });\n\n if (!query.length) {\n // If there are no genes, skip the network request\n return Promise.resolve({ data: null });\n }\n\n query = `{${query.join(' ')} }`; // GraphQL isn't quite JSON; items are separated by spaces but not commas\n const url = this.getURL(state, chain, fields);\n // See: https://graphql.org/learn/serving-over-http/\n const body = JSON.stringify({ query: query });\n const headers = { 'Content-Type': 'application/json' };\n\n // FIXME: The gnomAD API sometimes has temporary CORS changes that temporarily break the genes track\n // If request blocked, return a fake \"no data\" signal so the genes track can still render w/o constraint info\n return fetch(url, { method: 'POST', body, headers }).then((response) => {\n if (!response.ok) {\n return [];\n }\n return response.text();\n }).catch((err) => []);\n }\n\n combineChainBody(data, chain, fields, outnames, trans) {\n if (!data) {\n return chain;\n }\n\n chain.body.forEach(function(gene) {\n // Find payload keys that match gene names in this response\n const alias = `_${gene.gene_name.replace(/[^A-Za-z0-9_]/g, '_')}`; // aliases are modified gene names\n const constraint = data[alias] && data[alias]['gnomad_constraint']; // gnomad API has two ways of specifying missing data for a requested gene\n if (constraint) {\n // Add all fields from constraint data- do not override fields present in the gene source\n Object.keys(constraint).forEach(function (key) {\n let val = constraint[key];\n if (typeof gene[key] === 'undefined') {\n if (typeof val == 'number' && val.toString().includes('.')) {\n val = parseFloat(val.toFixed(2));\n }\n gene[key] = val; // These two sources are both designed to bypass namespacing\n }\n });\n }\n });\n return chain.body;\n }\n}\n\n/**\n * Data Source for Recombination Rate Data, as fetched from the LocusZoom API server (or compatible)\n * @public\n */\nclass RecombLZ extends BaseApiAdapter {\n getURL(state, chain, fields) {\n const build = state.genome_build || this.params.build;\n let source = this.params.source;\n validateBuildSource(this.constructor.SOURCE_NAME, build, source);\n\n if (build) { // If build specified, choose a known Portal API dataset IDs (build 37/38)\n source = (build === 'GRCh38') ? 16 : 15;\n }\n return `${this.url}?filter=id in ${source} and chromosome eq '${state.chr}' and position le ${state.end} and position ge ${state.start}`;\n }\n}\n\n/**\n * Data Source for static blobs of data as raw JS objects. This does not perform additional parsing, and it bypasses\n * namespaces. Therefore it is the responsibility of the user to pass information in a format that can be read and\n * understood by the chosen plot- a StaticJSON source is rarely a drop-in replacement.\n *\n * This source is largely here for legacy reasons. More often, a convenient way to serve static data is as separate\n * JSON files to an existing source (with the JSON url in place of an API).\n * @public\n */\nclass StaticSource extends BaseAdapter {\n parseInit(data) {\n // Does not receive any config; the only argument is the raw data, embedded when source is created\n this._data = data;\n }\n getRequest(state, chain, fields) {\n return Promise.resolve(this._data);\n }\n}\n\n\n/**\n * Data source for PheWAS data retrieved from a LocusZoom/PortalDev compatible API\n * @public\n * @param {String[]} init.params.build This datasource expects to be provided the name of the genome build that will\n * be used to provide pheWAS results for this position. Note positions may not translate between builds.\n */\nclass PheWASLZ extends BaseApiAdapter {\n getURL(state, chain, fields) {\n const build = (state.genome_build ? [state.genome_build] : null) || this.params.build;\n if (!build || !Array.isArray(build) || !build.length) {\n throw new Error(['Data source', this.constructor.SOURCE_NAME, 'requires that you specify array of one or more desired genome build names'].join(' '));\n }\n const url = [\n this.url,\n \"?filter=variant eq '\", encodeURIComponent(state.variant), \"'&format=objects&\",\n build.map(function (item) {\n return `build=${encodeURIComponent(item)}`;\n }).join('&'),\n ];\n return url.join('');\n }\n}\n\n\n/**\n * Base class for \"connectors\"- this is meant to be subclassed, rather than used directly.\n *\n * A connector is a source that makes no server requests and caches no data of its own. Instead, it decides how to\n * combine data from other sources in the chain. Connectors are useful when we want to request (or calculate) some\n * useful piece of information once, but apply it to many different kinds of record types.\n *\n * Typically, a subclass will implement the field merging logic in `combineChainBody`.\n *\n * @public\n * @param {Object} init Configuration for this source\n * @param {Object} init.sources Specify how the hard-coded logic should find the data it relies on in the chain,\n * as {internal_name: chain_source_id} pairs. This allows writing a reusable connector that does not need to make\n * assumptions about what namespaces a source is using.\n * @type {*|Function}\n */\nclass ConnectorSource extends BaseAdapter {\n constructor(config) {\n super(config);\n\n if (!config || !config.sources) {\n throw new Error('Connectors must specify the data they require as init.sources = {internal_name: chain_source_id}} pairs');\n }\n\n /**\n * Tells the connector how to find the data it relies on\n *\n * For example, a connector that applies burden test information to the genes layer might specify:\n * {gene_ns: \"gene\", aggregation_ns: \"aggregation\"}\n *\n * @member {Object}\n */\n this._source_name_mapping = config.sources;\n\n // Validate that this source has been told how to find the required information\n const specified_ids = Object.keys(config.sources);\n /** @property {String[]} Specifies the sources that must be provided in the original config object */\n\n this._getRequiredSources().forEach((k) => {\n if (!specified_ids.includes(k)) {\n // TODO: Fix constructor.name usage in minified bundles\n throw new Error(`Configuration for ${this.constructor.name} must specify a source ID corresponding to ${k}`);\n }\n });\n }\n\n // Stub- connectors don't have their own url or data, so the defaults don't make sense\n parseInit() {}\n\n getRequest(state, chain, fields) {\n // Connectors do not request their own data by definition, but they *do* depend on other sources having been loaded\n // first. This method performs basic validation, and preserves the accumulated body from the chain so far.\n Object.keys(this._source_name_mapping).forEach((ns) => {\n const chain_source_id = this._source_name_mapping[ns];\n if (chain.discrete && !chain.discrete[chain_source_id]) {\n throw new Error(`${this.constructor.name} cannot be used before loading required data for: ${chain_source_id}`);\n }\n });\n return Promise.resolve(chain.body || []);\n }\n\n parseResponse(data, chain, fields, outnames, trans) {\n // A connector source does not update chain.discrete, but it may use it. It bypasses data formatting\n // and field selection (both are assumed to have been done already, by the previous sources this draws from)\n\n // Because of how the chain works, connectors are not very good at applying new transformations or namespacing.\n // Typically connectors are called with `connector_name:all` in the fields array.\n return Promise.resolve(this.combineChainBody(data, chain, fields, outnames, trans))\n .then(function(new_body) {\n return {header: chain.header || {}, discrete: chain.discrete || {}, body: new_body};\n });\n }\n\n combineChainBody(records, chain) {\n // Stub method: specifies how to combine the data\n throw new Error('This method must be implemented in a subclass');\n }\n\n /**\n * Helper method since ES6 doesn't support class fields\n * @private\n */\n _getRequiredSources() {\n throw new Error('Must specify an array that identifes the kind of data required by this source');\n }\n}\n\nexport { BaseAdapter, BaseApiAdapter };\n\nexport {\n AssociationLZ,\n ConnectorSource,\n GeneConstraintLZ,\n GeneLZ,\n GwasCatalogLZ,\n LDServer,\n PheWASLZ,\n RecombLZ,\n StaticSource,\n};\n","module.exports = raremetal;"],"sourceRoot":""} \ No newline at end of file diff --git a/dist/ext/lz-credible-sets.min.js b/dist/ext/lz-credible-sets.min.js index e42a2b6d..f73f4c72 100644 --- a/dist/ext/lz-credible-sets.min.js +++ b/dist/ext/lz-credible-sets.min.js @@ -1,3 +1,3 @@ -/*! Locuszoom 0.13.0-beta.1 */ -var LzCredibleSets=function(e){var t={};function a(o){if(t[o])return t[o].exports;var r=t[o]={i:o,l:!1,exports:{}};return e[o].call(r.exports,r,r.exports,a),r.l=!0,r.exports}return a.m=e,a.c=t,a.d=function(e,t,o){a.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:o})},a.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},a.t=function(e,t){if(1&t&&(e=a(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var o=Object.create(null);if(a.r(o),Object.defineProperty(o,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var r in e)a.d(o,r,function(t){return e[t]}.bind(null,r));return o},a.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return a.d(t,"a",t),t},a.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},a.p="",a(a.s=10)}({10:function(e,t,a){"use strict";a.r(t);var o=a(3);function r(e){return(r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e})(e)}function n(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function s(e,t){for(var a=0;a=a.params.significance_threshold})))return Promise.resolve([]);var s=[];try{for(var i=o.scoring.bayesFactors(n),c=o.scoring.normalizeProbabilities(i),l=o.marking.findCredibleSet(c,r),u=o.marking.rescaleCredibleSet(l),p=o.marking.markBoolean(l),d=0;dPosterior probability: {{{{namespace[credset]}}posterior_prob|scinotation|htmlescape}}{{/if}}",t)),e.Layouts.add("tooltip","annotation_credible_set",{namespace:{assoc:"assoc",credset:"credset"},closable:!0,show:{or:["highlighted","selected"]},hide:{and:["unhighlighted","unselected"]},html:"{{{{namespace[assoc]}}variant|htmlescape}}
P Value: {{{{namespace[assoc]}}log_pvalue|logtoscinotation|htmlescape}}

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Locuszoom 0.13.0-beta.2 */ +var LzCredibleSets=function(e){var t={};function a(o){if(t[o])return t[o].exports;var r=t[o]={i:o,l:!1,exports:{}};return e[o].call(r.exports,r,r.exports,a),r.l=!0,r.exports}return a.m=e,a.c=t,a.d=function(e,t,o){a.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:o})},a.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},a.t=function(e,t){if(1&t&&(e=a(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var o=Object.create(null);if(a.r(o),Object.defineProperty(o,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var r in e)a.d(o,r,function(t){return e[t]}.bind(null,r));return o},a.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return a.d(t,"a",t),t},a.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},a.p="",a(a.s=9)}({3:function(e,t){e.exports=gwasCredibleSets},9:function(e,t,a){"use strict";a.r(t);var o=a(3);function r(e){return(r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e})(e)}function n(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function s(e,t){for(var a=0;a=a.params.significance_threshold})))return Promise.resolve([]);var s=[];try{for(var i=o.scoring.bayesFactors(n),c=o.scoring.normalizeProbabilities(i),l=o.marking.findCredibleSet(c,r),u=o.marking.rescaleCredibleSet(l),p=o.marking.markBoolean(l),d=0;dPosterior probability: {{{{namespace[credset]}}posterior_prob|scinotation|htmlescape}}{{/if}}",t)),e.Layouts.add("tooltip","annotation_credible_set",{namespace:{assoc:"assoc",credset:"credset"},closable:!0,show:{or:["highlighted","selected"]},hide:{and:["unhighlighted","unselected"]},html:"{{{{namespace[assoc]}}variant|htmlescape}}
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This is not part of the core LocusZoom library,\n but can be included as a standalone file.\n\n The page must incorporate and load all libraries before this file can be used, including:\n - Vendor assets\n - LocusZoom\n - gwas-credible-sets (available via NPM or a related CDN)\n @module\n*/\n\nimport {marking, scoring} from 'gwas-credible-sets';\n\nfunction install (LocusZoom) {\n const BaseAdapter = LocusZoom.Adapters.get('BaseAdapter');\n /**\n * Custom data source that calculates the 95% credible set based on provided data.\n * This source must be requested as the second step in a chain, after a previous step that returns fields required\n * for the calculation.\n *\n * @param {Object} init.params\n * @param {Object} init.params.fields\n * @param {String} init.params.fields.log_pvalue The name of the field containing -log10 pvalue information\n * @param {Number} [init.params.threshold=0.95] The credible set threshold (eg 95%). Will continue selecting SNPs\n * until the posterior probabilities add up to at least this fraction of the total.\n * @param {Number} [init.params.significance_threshold=7.301] Do not perform a credible set calculation for this\n * region unless AT LEAST ONE SNP (as -log10p) exceeds the line of GWAS signficance. Otherwise we are declaring a\n * credible set when there is no evidence of anything being significant at all. If one snp is significant, it will\n * create a credible set for the entire region; the resulting set may include things below the line of significance.\n */\n class CredibleSetLZ extends BaseAdapter {\n constructor(config) {\n super(...arguments);\n this.dependentSource = true; // Don't do calcs for a region with no assoc data\n }\n\n parseInit(config) {\n super.parseInit(...arguments);\n if (!(this.params.fields && this.params.fields.log_pvalue)) {\n throw new Error(`Source config for ${this.constructor.SOURCE_NAME} must specify how to find 'fields.log_pvalue'`);\n }\n\n // Set defaults. Default sig threshold is the line of GWAS significance. (as -log10p)\n this.params = Object.assign(\n { threshold: 0.95, significance_threshold: 7.301 },\n this.params\n );\n }\n\n getCacheKey (state, chain, fields) {\n const threshold = state.credible_set_threshold || this.params.threshold;\n return [threshold, state.chr, state.start, state.end].join('_');\n }\n\n fetchRequest(state, chain) {\n if (!chain.body.length) {\n // No credible set can be calculated because there is no association data for this region\n return Promise.resolve([]);\n }\n\n const self = this;\n // The threshold can be overridden dynamically via `plot.state`, or set when the source is created\n const threshold = state.credible_set_threshold || this.params.threshold;\n // Calculate raw bayes factors and posterior probabilities based on information returned from the API\n if (typeof chain.body[0][self.params.fields.log_pvalue] === 'undefined') {\n throw new Error('Credible set source could not locate the required fields from a previous request.');\n }\n const nlogpvals = chain.body.map((item) => item[self.params.fields.log_pvalue]);\n\n if (!nlogpvals.some((val) => val >= self.params.significance_threshold)) {\n // If NO points have evidence of significance, define the credible set to be empty\n // (rather than make a credible set that we don't think is meaningful)\n return Promise.resolve([]);\n }\n\n const credset_data = [];\n try {\n const scores = scoring.bayesFactors(nlogpvals);\n const posteriorProbabilities = scoring.normalizeProbabilities(scores);\n\n // Use scores to mark the credible set in various ways (depending on your visualization preferences,\n // some of these may not be needed)\n const credibleSet = marking.findCredibleSet(posteriorProbabilities, threshold);\n const credSetScaled = marking.rescaleCredibleSet(credibleSet);\n const credSetBool = marking.markBoolean(credibleSet);\n\n // Annotate each response record based on credible set membership\n for (let i = 0; i < chain.body.length; i++) {\n credset_data.push({\n posterior_prob: posteriorProbabilities[i],\n contrib_fraction: credSetScaled[i],\n is_member: credSetBool[i],\n });\n }\n } catch (e) {\n // If the calculation cannot be completed, return the data without annotation fields\n console.error(e);\n }\n return Promise.resolve(credset_data);\n }\n\n combineChainBody(data, chain, fields, outnames, trans) {\n // At this point namespacing has been applied; add the calculated fields for this source to the chain\n if (chain.body.length && data.length) {\n for (let i = 0; i < data.length; i++) {\n const src = data[i];\n const dest = chain.body[i];\n Object.keys(src).forEach(function (attr) {\n dest[attr] = src[attr];\n });\n }\n }\n return chain.body;\n }\n }\n\n\n LocusZoom.Adapters.add('CredibleSetLZ', CredibleSetLZ);\n\n // Add related layouts to the central global registry\n LocusZoom.Layouts.add('tooltip', 'association_credible_set', function () {\n // Extend a known tooltip with an extra row of info showing posterior probabilities\n const l = LocusZoom.Layouts.get('tooltip', 'standard_association', { unnamespaced: true });\n l.html += '{{#if {{namespace[credset]}}posterior_prob}}
Posterior probability: {{{{namespace[credset]}}posterior_prob|scinotation|htmlescape}}{{/if}}';\n return l;\n }());\n\n LocusZoom.Layouts.add('tooltip', 'annotation_credible_set', {\n namespace: { 'assoc': 'assoc', 'credset': 'credset' },\n closable: true,\n show: { or: ['highlighted', 'selected'] },\n hide: { and: ['unhighlighted', 'unselected'] },\n html: '{{{{namespace[assoc]}}variant|htmlescape}}
'\n + 'P Value: {{{{namespace[assoc]}}log_pvalue|logtoscinotation|htmlescape}}
' +\n '
Posterior probability: {{{{namespace[credset]}}posterior_prob|scinotation|htmlescape}}',\n });\n\n LocusZoom.Layouts.add('data_layer', 'association_credible_set', function () {\n const base = LocusZoom.Layouts.get('data_layer', 'association_pvalues', {\n unnamespaced: true,\n id: 'associationcredibleset',\n namespace: { 'assoc': 'assoc', 'credset': 'credset', 'ld': 'ld' },\n fill_opacity: 0.7,\n tooltip: LocusZoom.Layouts.get('tooltip', 'association_credible_set', { unnamespaced: true }),\n fields: [\n '{{namespace[assoc]}}variant', '{{namespace[assoc]}}position',\n '{{namespace[assoc]}}log_pvalue', '{{namespace[assoc]}}log_pvalue|logtoscinotation',\n '{{namespace[assoc]}}ref_allele',\n '{{namespace[credset]}}posterior_prob', '{{namespace[credset]}}contrib_fraction',\n '{{namespace[credset]}}is_member',\n '{{namespace[ld]}}state', '{{namespace[ld]}}isrefvar',\n ],\n match: { send: '{{namespace[assoc]}}variant', receive: '{{namespace[assoc]}}variant' },\n });\n base.color.unshift({\n field: 'lz_highlight_match', // Special field name whose presence triggers custom rendering\n scale_function: 'if',\n parameters: {\n field_value: true,\n then: '#FFf000',\n },\n });\n return base;\n }());\n\n LocusZoom.Layouts.add('data_layer', 'annotation_credible_set', {\n namespace: { 'assoc': 'assoc', 'credset': 'credset' },\n id: 'annotationcredibleset',\n type: 'annotation_track',\n id_field: '{{namespace[assoc]}}variant',\n x_axis: {\n field: '{{namespace[assoc]}}position',\n },\n color: [\n {\n field: 'lz_highlight_match', // Special field name whose presence triggers custom rendering\n scale_function: 'if',\n parameters: {\n field_value: true,\n then: '#001cee',\n },\n },\n '#00CC00',\n ],\n fields: ['{{namespace[assoc]}}variant', '{{namespace[assoc]}}position', '{{namespace[assoc]}}log_pvalue', '{{namespace[credset]}}posterior_prob', '{{namespace[credset]}}contrib_fraction', '{{namespace[credset]}}is_member'],\n match: { send: '{{namespace[assoc]}}variant', receive: '{{namespace[assoc]}}variant' },\n filters: [\n // Specify which points to show on the track. Any selection must satisfy ALL filters\n { field: '{{namespace[credset]}}is_member', operator: '=', value: true },\n ],\n behaviors: {\n onmouseover: [\n { action: 'set', status: 'highlighted' },\n ],\n onmouseout: [\n { action: 'unset', status: 'highlighted' },\n ],\n onclick: [\n { action: 'toggle', status: 'selected', exclusive: true },\n ],\n onshiftclick: [\n { action: 'toggle', status: 'selected' },\n ],\n },\n tooltip: LocusZoom.Layouts.get('tooltip', 'annotation_credible_set', { unnamespaced: true }),\n tooltip_positioning: 'top',\n });\n\n LocusZoom.Layouts.add('panel', 'annotation_credible_set', {\n id: 'annotationcredibleset',\n title: { text: 'SNPs in 95% credible set', x: 50, style: { 'font-size': '14px' } },\n width: 800,\n height: 45,\n min_height: 45,\n proportional_width: 1,\n margin: { top: 25, right: 50, bottom: 0, left: 50 },\n inner_border: 'rgb(210, 210, 210)',\n toolbar: LocusZoom.Layouts.get('toolbar', 'standard_panel', { unnamespaced: true }),\n interaction: {\n drag_background_to_pan: true,\n scroll_to_zoom: true,\n x_linked: true,\n },\n data_layers: [\n LocusZoom.Layouts.get('data_layer', 'annotation_credible_set', { unnamespaced: true }),\n ],\n });\n\n LocusZoom.Layouts.add('panel', 'association_credible_set', function () {\n const l = LocusZoom.Layouts.get('panel', 'association', {\n unnamespaced: true,\n id: 'associationcrediblesets',\n namespace: { 'assoc': 'assoc', 'credset': 'credset' },\n data_layers: [\n LocusZoom.Layouts.get('data_layer', 'significance', { unnamespaced: true }),\n LocusZoom.Layouts.get('data_layer', 'recomb_rate', { unnamespaced: true }),\n LocusZoom.Layouts.get('data_layer', 'association_credible_set', { unnamespaced: true }),\n ],\n });\n // Add \"display options\" button to control how credible set coloring is overlaid on the standard association plot\n l.toolbar.widgets.push(\n {\n type: 'display_options',\n position: 'right',\n color: 'blue',\n // Below: special config specific to this widget\n button_html: 'Display options...',\n button_title: 'Control how plot items are displayed',\n layer_name: 'associationcredibleset',\n default_config_display_name: 'Linkage Disequilibrium (default)', // display name for the default plot color option (allow user to revert to plot defaults)\n\n options: [\n {\n // First dropdown menu item\n display_name: '95% credible set (boolean)', // Human readable representation of field name\n display: { // Specify layout directives that control display of the plot for this option\n point_shape: 'circle',\n point_size: 40,\n color: {\n field: '{{namespace[credset]}}is_member',\n scale_function: 'if',\n parameters: {\n field_value: true,\n then: '#00CC00',\n else: '#CCCCCC',\n },\n },\n legend: [ // Tells the legend how to represent this display option\n {\n shape: 'circle',\n color: '#00CC00',\n size: 40,\n label: 'In credible set',\n class: 'lz-data_layer-scatter',\n },\n {\n shape: 'circle',\n color: '#CCCCCC',\n size: 40,\n label: 'Not in credible set',\n class: 'lz-data_layer-scatter',\n },\n ],\n },\n },\n {\n // Second option. The same plot- or even the same field- can be colored in more than one way.\n display_name: '95% credible set (gradient by contribution)',\n display: {\n point_shape: 'circle',\n point_size: 40,\n color: [\n {\n field: '{{namespace[credset]}}contrib_fraction',\n scale_function: 'if',\n parameters: {\n field_value: 0,\n then: '#777777',\n },\n },\n {\n scale_function: 'interpolate',\n field: '{{namespace[credset]}}contrib_fraction',\n parameters: {\n breaks: [0, 1],\n values: ['#fafe87', '#9c0000'],\n },\n },\n ],\n legend: [\n {\n shape: 'circle',\n color: '#777777',\n size: 40,\n label: 'No contribution',\n class: 'lz-data_layer-scatter',\n },\n {\n shape: 'circle',\n color: '#fafe87',\n size: 40,\n label: 'Some contribution',\n class: 'lz-data_layer-scatter',\n },\n {\n shape: 'circle',\n color: '#9c0000',\n size: 40,\n label: 'Most contribution',\n class: 'lz-data_layer-scatter',\n },\n ],\n },\n },\n ],\n }\n );\n return l;\n }());\n\n LocusZoom.Layouts.add('plot', 'association_credible_set', {\n state: {},\n width: 800,\n height: 450,\n responsive_resize: true,\n min_region_scale: 20000,\n max_region_scale: 1000000,\n toolbar: LocusZoom.Layouts.get('toolbar', 'standard_association', { unnamespaced: true }),\n panels: [\n LocusZoom.Layouts.get('panel', 'association_credible_set', { unnamespaced: true }),\n LocusZoom.Layouts.get('panel', 'annotation_credible_set', { unnamespaced: true }),\n LocusZoom.Layouts.get('panel', 'genes', { unnamespaced: true }),\n ],\n });\n\n}\n\n\nif (typeof LocusZoom !== 'undefined') {\n // Auto-register the plugin when included as a script tag. 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'\n + 'P Value: {{{{namespace[assoc]}}log_pvalue|logtoscinotation|htmlescape}}
' +\n '
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