diff --git a/.github/workflows/node.yml b/.github/workflows/node.yml new file mode 100644 index 00000000..1b9d8ddf --- /dev/null +++ b/.github/workflows/node.yml @@ -0,0 +1,43 @@ +name: Unit tests + +on: + push: + branches: + - master + - develop + pull_request: + branches: + - master + - develop + release: + types: + - created + +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + node-version: [10.x, 14.x] + steps: + - uses: actions/checkout@v2 + - name: Use Node.js ${{ matrix.node-version }} + uses: actions/setup-node@v1 + with: + node-version: ${{ matrix.node-version }} + - name: Cache Node.js modules + uses: actions/cache@v2 + with: + # npm cache files are stored in `~/.npm` on Linux/macOS + path: ~/.npm + key: ${{ runner.OS }}-node-${{ hashFiles('**/package-lock.json') }} + restore-keys: | + ${{ runner.OS }}-node- + ${{ runner.OS }}- + - name: Build and test package + run: | + npm ci + npm run build + npm run test + env: + CI: true diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 188a0d95..00000000 --- a/.travis.yml +++ /dev/null @@ -1,22 +0,0 @@ -language: node_js -node_js: - - "lts/erbium" - - "lts/dubnium" -cache: - yarn: true - directories: - - node_modules -before_script: - - npm install -script: - - eslint . - - npm test -branches: - only: - - master - - develop -notifications: - email: - - abought@umich.edu - slack: - secure: 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 diff --git a/README.md b/README.md index dd0e5931..60a3d961 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ LocusZoom is a Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. -[![Build Status](https://api.travis-ci.org/statgen/locuszoom.svg?branch=master)](https://api.travis-ci.org/statgen/locuszoom) +![Build Status](https://github.com/statgen/locuszoom/workflows/Unit%20tests/badge.svg?branch=develop) See [github.com/statgen/locuszoom/wiki](https://github.com/statgen/locuszoom/wiki) for full documentation and API reference. diff --git a/assets/docs/layout_tutorial.md b/assets/docs/layout_tutorial.md index 3edf7bb3..99d4f244 100644 --- a/assets/docs/layout_tutorial.md +++ b/assets/docs/layout_tutorial.md @@ -364,7 +364,6 @@ existing_datasources .add("assoc_study3", ["AssociationLZ", {url: "/api/association/", params: { source: 3 }}]); const new_panel = existing_plot.addPanel(extra_panel_layout); // Adds the panel and redraws plot -new_panel.addBasicLoader(); // Add a nice "loading" indicator for UI ``` ### Common issues diff --git a/css/locuszoom.scss b/css/locuszoom.scss index f5d9650e..7bd4217e 100644 --- a/css/locuszoom.scss +++ b/css/locuszoom.scss @@ -220,10 +220,16 @@ svg.#{$namespace}-locuszoom { stroke-width: 1px; } - rect.#{$namespace}-data_layer-intervals.#{$namespace}-interval_rect { + g.#{$namespace}-data_layer-intervals { stroke-width: 0px; } + rect.#{$namespace}-data_layer-intervals-highlighted, rect.#{$namespace}-data_layer-intervals-selected { + stroke: #{$default_black}; + stroke-opacity: #{$default_black_opacity}; + stroke-width: 1px; + } + path.#{$namespace}-data_layer-forest { stroke: #{$default_black_shadow}; stroke-opacity: #{$default_black_shadow_opacity}; diff --git a/dist/ext/lz-aggregation-tests.min.js b/dist/ext/lz-aggregation-tests.min.js index 7c0f1983..fca6840d 100644 --- a/dist/ext/lz-aggregation-tests.min.js +++ b/dist/ext/lz-aggregation-tests.min.js @@ -1,3 +1,3 @@ -/*! Locuszoom 0.13.0-beta.2 */ -var LzAggregationTests=function(e){var t={};function n(r){if(t[r])return t[r].exports;var o=t[r]={i:r,l:!1,exports:{}};return e[r].call(o.exports,o,o.exports,n),o.l=!0,o.exports}return n.m=e,n.c=t,n.d=function(e,t,r){n.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:r})},n.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},n.t=function(e,t){if(1&t&&(e=n(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var r=Object.create(null);if(n.r(r),Object.defineProperty(r,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)n.d(r,o,function(t){return e[t]}.bind(null,o));return r},n.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return n.d(t,"a",t),t},n.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},n.p="",n(n.s=11)}({11:function(e,t,n){"use strict";n.r(t);var r=n(4),o=n(2);function a(e){return(a="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 i(e,t,n){return(i="undefined"!=typeof Reflect&&Reflect.get?Reflect.get:function(e,t,n){var r=function(e,t){for(;!Object.prototype.hasOwnProperty.call(e,t)&&null!==(e=d(e)););return e}(e,t);if(r){var o=Object.getOwnPropertyDescriptor(r,t);return o.get?o.get.call(n):o.value}})(e,t,n||e)}function u(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function c(e,t){for(var n=0;nt?1:0}))}}]),n}(t),l=function(e){f(n,e);var t=h(n);function n(){return u(this,n),t.apply(this,arguments)}return s(n,[{key:"_getRequiredSources",value:function(){return["gene_ns","aggregation_ns"]}},{key:"combineChainBody",value:function(e,t){var n=this._source_name_mapping.aggregation_ns,r=this._source_name_mapping.gene_ns,o=t.discrete[n],a=t.discrete[r],i={};return o.groups.forEach((function(e){Object.prototype.hasOwnProperty.call(i,e.group)||(i[e.group]=[]),i[e.group].push(e.pvalue)})),a.forEach((function(e){var t=e.gene_name,n=i[t];n&&(e.aggregation_best_pvalue=Math.min.apply(null,n))})),a}}]),n}(n);e.Adapters.add("AggregationTestSourceLZ",a),e.Adapters.add("AssocFromAggregationLZ",c),e.Adapters.add("GeneAggregationConnectorLZ",l)}"undefined"!=typeof LocusZoom&&LocusZoom.use(y),t.default=y},2:function(e,t,n){"use strict";function r(e,t){return function(e){if(Array.isArray(e))return e}(e)||function(e,t){if("undefined"==typeof Symbol||!(Symbol.iterator in Object(e)))return;var n=[],r=!0,o=!1,a=void 0;try{for(var i,u=e[Symbol.iterator]();!(r=(i=u.next()).done)&&(n.push(i.value),!t||n.length!==t);r=!0);}catch(e){o=!0,a=e}finally{try{r||null==u.return||u.return()}finally{if(o)throw a}}return n}(e,t)||function(e,t){if(!e)return;if("string"==typeof e)return o(e,t);var n=Object.prototype.toString.call(e).slice(8,-1);"Object"===n&&e.constructor&&(n=e.constructor.name);if("Map"===n||"Set"===n)return Array.from(e);if("Arguments"===n||/^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n))return o(e,t)}(e,t)||function(){throw new TypeError("Invalid attempt to destructure non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}()}function o(e,t){(null==t||t>e.length)&&(t=e.length);for(var n=0,r=new Array(t);n1&&(2!==t.length||!t.includes("isrefvar")))throw new Error("LD does not know how to get all fields: ".concat(t.join(", ")))}},{key:"findMergeFields",value:function(e){var t,n={id:this.params.id_field,position:this.params.position_field,pvalue:this.params.pvalue_field,_names_:null};if(e&&e.body&&e.body.length>0){var r=Object.keys(e.body[0]),o=(t=r,function(){for(var e=arguments,n=function(n){var r=e[n],o=t.filter((function(e){return e.match(r)}));if(o.length)return{v:o[0]}},r=0;rt}:function(e,t){return et.log_pvalue))for(var u=0;u{if(!e.ok)throw new Error(e.statusText);return e.text()}).then((function(e){const t="string"==typeof e?JSON.parse(e):e;if(t.error)throw new Error(t.error);return t}))}annotateData(e,t){if(!e.groups)return{groups:[],variants:[]};e.groups=e.groups.filter((function(e){return"GENE"===e.groupType}));const r=n.helpers.parsePortalJSON(e);let o=r[0];const s=r[1];o=o.byMask(t.header.aggregation_mask_ids);const i=t.header.aggregation_calcs;if(!i||0===Object.keys(i).length)return{variants:[],groups:[],results:[]};return new n.helpers.PortalTestRunner(o,s,i).toJSON().then((function(e){const r=t.header.aggregation_masks.reduce((function(e,t){return e[t.name]=t.description,e}),{});return e.data.groups.forEach((function(e){e.mask_name=r[e.mask]})),e.data})).catch((function(e){throw console.error(e),new Error("Failed to calculate aggregation test results")}))}normalizeResponse(e){return e}combineChainBody(e,t){return t.body}}e.Adapters.add("AggregationTestSourceLZ",s),e.Adapters.add("AssocFromAggregationLZ",class extends t{constructor(e){if(!e||!e.from)throw"Must specify the name of the source that contains association data";super(...arguments)}parseInit(e){super.parseInit(e),this._from=e.from}getRequest(e,t,r){if(t.discrete&&!t.discrete[this._from])throw`${this.constructor.SOURCE_NAME} cannot be used before loading required data for: ${this._from}`;return Promise.resolve(JSON.parse(JSON.stringify(t.discrete[this._from].variants)))}normalizeResponse(e){const t=new RegExp("(?:chr)?(.+):(\\d+)_?(\\w+)?/?([^_]+)?_?(.*)?");return e.map(e=>{const r=e.variant.match(t);return{variant:e.variant,chromosome:r[1],position:+r[2],ref_allele:r[3],ref_allele_freq:1-e.altFreq,log_pvalue:-Math.log10(e.pvalue)}}).sort((e,t)=>(e=e.variant)<(t=t.variant)?-1:e>t?1:0)}}),e.Adapters.add("GeneAggregationConnectorLZ",class extends r{_getRequiredSources(){return["gene_ns","aggregation_ns"]}combineChainBody(e,t){const r=this._source_name_mapping.aggregation_ns,n=this._source_name_mapping.gene_ns,o=t.discrete[r],s=t.discrete[n],i={};return o.groups.forEach((function(e){Object.prototype.hasOwnProperty.call(i,e.group)||(i[e.group]=[]),i[e.group].push(e.pvalue)})),s.forEach((function(e){const t=e.gene_name,r=i[t];r&&(e.aggregation_best_pvalue=Math.min.apply(null,r))})),s}})}"undefined"!=typeof LocusZoom&&LocusZoom.use(s),t.default=s},2:function(e,t,r){"use strict";function n(e,t,r){if(t&&r||!t&&!r)throw new Error(e+' must provide a parameter specifying either "build" or "source". It should not specify both.');if(t&&!["GRCh37","GRCh38"].includes(t))throw new Error(e+" must specify a valid genome build number")}r.r(t),r.d(t,"BaseAdapter",(function(){return o})),r.d(t,"BaseApiAdapter",(function(){return s})),r.d(t,"AssociationLZ",(function(){return i})),r.d(t,"ConnectorSource",(function(){return f})),r.d(t,"GeneConstraintLZ",(function(){return d})),r.d(t,"GeneLZ",(function(){return c})),r.d(t,"GwasCatalogLZ",(function(){return u})),r.d(t,"LDServer",(function(){return a})),r.d(t,"PheWASLZ",(function(){return p})),r.d(t,"RecombLZ",(function(){return l})),r.d(t,"StaticSource",(function(){return h}));class o{constructor(e){this._enableCache=!0,this._cachedKey=null,this.__dependentSource=!1,this.parseInit(e)}parseInit(e){this.params=e.params||{}}getCacheKey(e,t,r){return this.getURL(e,t,r)}getURL(e,t,r){return this.url}fetchRequest(e,t,r){const n=this.getURL(e,t,r);return fetch(n).then(e=>{if(!e.ok)throw new Error(e.statusText);return e.text()})}getRequest(e,t,r){let n;const o=this.getCacheKey(e,t,r);return this._enableCache&&void 0!==o&&o===this._cachedKey?n=Promise.resolve(this._cachedResponse):(n=this.fetchRequest(e,t,r),this._enableCache&&(this._cachedKey=o,this._cachedResponse=n)),n}normalizeResponse(e){if(Array.isArray(e))return e;const t=Object.keys(e),r=e[t[0]].length;if(!t.every((function(t){return e[t].length===r})))throw new Error(this.constructor.name+" expects a response in which all arrays of data are the same length");const n=[],o=Object.keys(e);for(let t=0;tPromise.resolve(this.annotateData(e,t))).then(e=>Promise.resolve(this.extractFields(e,r,n,o))).then(e=>(t.discrete[s]=e,Promise.resolve(this.combineChainBody(e,t,r,n,o)))).then(e=>({header:t.header||{},discrete:t.discrete,body:e}))}getData(e,t,r,n){if(this.preGetData){const o=this.preGetData(e,t,r,n);this.pre&&(e=o.state||e,t=o.fields||t,r=o.outnames||r,n=o.trans||n)}return o=>this.__dependentSource&&o&&o.body&&!o.body.length?Promise.resolve(o):this.getRequest(e,o,t).then(e=>this.parseResponse(e,o,t,r,n))}}class s extends o{parseInit(e){if(super.parseInit(e),this.url=e.url,!this.url)throw new Error("Source not initialized with required URL")}}class i extends s{preGetData(e,t,r,n){return[this.params.id_field||"id","position"].forEach((function(e){t.includes(e)||(t.unshift(e),r.unshift(e),n.unshift(null))})),{fields:t,outnames:r,trans:n}}getURL(e,t,r){const n=t.header.analysis||this.params.source||this.params.analysis;if(void 0===n)throw new Error("Association source must specify an analysis ID to plot");return`${this.url}results/?filter=analysis in ${n} and chromosome in '${e.chr}' and position ge ${e.start} and position le ${e.end}`}normalizeResponse(e){return e=super.normalizeResponse(e),this.params&&this.params.sort&&e.length&&e[0].position&&e.sort((function(e,t){return e.position-t.position})),e}}class a extends s{constructor(e){super(e),this.__dependentSource=!0}preGetData(e,t){if(t.length>1&&(2!==t.length||!t.includes("isrefvar")))throw new Error("LD does not know how to get all fields: "+t.join(", "))}findMergeFields(e){let t={id:this.params.id_field,position:this.params.position_field,pvalue:this.params.pvalue_field,_names_:null};if(e&&e.body&&e.body.length>0){const n=Object.keys(e.body[0]),o=(r=n,function(){const e=arguments;for(let t=0;tt}:function(e,t){return e{if(!e.ok)throw new Error(e.statusText);return e.text()}).then((function(e){return e=JSON.parse(e),Object.keys(e.data).forEach((function(t){o.data[t]=(o.data[t]||[]).concat(e.data[t])})),e.next?s(e.next):o}))};return s(n)}}class u extends s{constructor(e){super(e),this.__dependentSource=!0}getURL(e,t,r){const o=e.genome_build||this.params.build;n(this.constructor.name,o,null);const s="GRCh38"===o?5:6,i=this.params.source||s;return`${this.url}?format=objects&sort=pos&filter=id eq ${i} and chrom eq '${e.chr}' and pos ge ${e.start} and pos le ${e.end}`}findMergeFields(e){const t=Object.keys(e).find((function(e){return e.match(/\b(position|pos)\b/i)}));if(!t)throw new Error("Could not find data to align with GWAS catalog results");return{pos:t}}extractFields(e,t,r,n){return e}combineChainBody(e,t,r,n,o){if(!e.length)return t.body;const s=n[r.indexOf("log_pvalue")];function i(e,t,r,n,o){const i=e.n_catalog_matches||0;if(e.n_catalog_matches=i+1,!(e[s]&&e[s]>t.log_pvalue))for(let s=0;se.ok?e.text():[]).catch(e=>[])}combineChainBody(e,t,r,n,o){return e?(t.body.forEach((function(t){const r="_"+t.gene_name.replace(/[^A-Za-z0-9_]/g,"_"),n=e[r]&&e[r].gnomad_constraint;n&&Object.keys(n).forEach((function(e){let r=n[e];void 0===t[e]&&("number"==typeof r&&r.toString().includes(".")&&(r=parseFloat(r.toFixed(2))),t[e]=r)}))})),t.body):t}}class l extends s{getURL(e,t,r){const o=e.genome_build||this.params.build;let s=this.params.source;return n(this.constructor.SOURCE_NAME,o,s),o&&(s="GRCh38"===o?16:15),`${this.url}?filter=id in ${s} and chromosome eq '${e.chr}' and position le ${e.end} and position ge ${e.start}`}}class h extends o{parseInit(e){this._data=e}getRequest(e,t,r){return Promise.resolve(this._data)}}class p extends s{getURL(e,t,r){const n=(e.genome_build?[e.genome_build]:null)||this.params.build;if(!n||!Array.isArray(n)||!n.length)throw new Error(["Data source",this.constructor.SOURCE_NAME,"requires that you specify array of one or more desired genome build names"].join(" "));return[this.url,"?filter=variant eq '",encodeURIComponent(e.variant),"'&format=objects&",n.map((function(e){return"build="+encodeURIComponent(e)})).join("&")].join("")}}class f extends o{constructor(e){if(super(e),!e||!e.sources)throw new Error("Connectors must specify the data they require as init.sources = {internal_name: chain_source_id}} pairs");this._source_name_mapping=e.sources;const t=Object.keys(e.sources);this._getRequiredSources().forEach(e=>{if(!t.includes(e))throw new Error(`Configuration for 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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. 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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. 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12);\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). Using a separate connector allows us to add caching and run this front-end\n * calculation only once, while using it in many different places\n * @public\n */\n const BaseAdapter = LocusZoom.Adapters.get('BaseAdapter');\n const ConnectorSource = LocusZoom.Adapters.get('ConnectorSource');\n\n class AggregationTestSource extends BaseApiAdapter {\n getURL(state, chain, fields) {\n // Unlike most sources, calculations may require access to plot state data even after the initial request\n // This example source REQUIRES that the external UI widget would store the needed test definitions in a plot state\n // field called `aggregation_tests` (an object {masks: [], calcs: {})\n const required_info = state.aggregation_tests || {};\n\n if (!chain.header) {\n chain.header = {};\n }\n // All of these fields are required in order to use this datasource. TODO: Add validation?\n chain.header.aggregation_genoset_id = required_info.genoset_id || null; // Number\n chain.header.aggregation_genoset_build = required_info.genoset_build || null; // String\n chain.header.aggregation_phenoset_id = required_info.phenoset_id || null; // Number\n chain.header.aggregation_pheno = required_info.pheno || null; // String\n chain.header.aggregation_calcs = required_info.calcs || {}; // String[]\n const mask_data = required_info.masks || [];\n chain.header.aggregation_masks = mask_data; // {name:desc}[]\n chain.header.aggregation_mask_ids = mask_data.map(function (item) {\n return item.name;\n }); // Number[]\n return this.url;\n }\n\n getCacheKey(state, chain, fields) {\n this.getURL(state, chain, fields); // TODO: This just sets the chain.header fields\n return JSON.stringify({\n chrom: state.chr,\n start: state.start,\n stop: state.end,\n genotypeDataset: chain.header.aggregation_genoset_id,\n phenotypeDataset: chain.header.aggregation_phenoset_id,\n phenotype: chain.header.aggregation_pheno,\n samples: 'ALL',\n genomeBuild: chain.header.aggregation_genoset_build,\n masks: chain.header.aggregation_mask_ids,\n });\n }\n\n fetchRequest(state, chain, fields) {\n const url = this.getURL(state, chain, fields);\n const body = this.getCacheKey(state, chain, fields);\n const headers = {\n 'Content-Type': 'application/json',\n };\n\n return fetch(url, {method: 'POST', body: body, headers: headers}).then((response) => {\n if (!response.ok) {\n throw new Error(response.statusText);\n }\n return response.text();\n }).then(function (resp) {\n const json = typeof resp == 'string' ? 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: ${keys._names_})`);\n }\n refVar = chain.body[findExtremeValue(chain.body, keys.pvalue)][keys.id];\n }\n return refVar;\n }\n\n getURL(state, chain, fields) {\n // Accept the following params in this.params:\n // - method (r, rsquare, cov)\n // - source (aka panel)\n // - population (ALL, AFR, EUR, etc)\n // - build\n // The LD source/pop can be overridden from plot.state for dynamic layouts\n const build = state.genome_build || this.params.build || 'GRCh37';\n let source = state.ld_source || this.params.source || '1000G';\n const population = state.ld_pop || this.params.population || 'ALL'; // LDServer panels will always have an ALL\n const method = this.params.method || 'rsquare';\n\n if (source === '1000G' && build === 'GRCh38') {\n // For build 38 (only), there is a newer/improved 1000G LD panel available that uses WGS data. Auto upgrade by default.\n source = '1000G-FRZ09';\n }\n\n validateBuildSource(this.constructor.name, build, null); // LD doesn't need to validate `source` option\n\n let refVar = this.getRefvar(state, chain, fields);\n // Some datasets, notably the Portal, use a different marker format.\n // Coerce it into one that will work with the LDServer API. (CHROM:POS_REF/ALT)\n const REGEX_MARKER = /^(?:chr)?([a-zA-Z0-9]+?)[_:-](\\d+)[_:|-]?(\\w+)?[/_:|-]?([^_]+)?_?(.*)?/;\n const match = refVar && refVar.match(REGEX_MARKER);\n\n if (!match) {\n throw new Error('Could not request LD for a missing or incomplete marker format');\n }\n const [original, chrom, pos, ref, alt] = match;\n // Currently, the LD server only accepts full variant specs; it won't return LD w/o ref+alt. Allowing\n // a partial match at most leaves room for potential future features.\n refVar = `${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 ${state.start}`;\n }\n}\n\n/**\n * Data Source for static blobs of data as raw JS objects. This does not perform additional parsing, which is required\n * for some sources (eg when joining together LD and association data).\n *\n * Therefore it is the responsibility of the user to pass information in a format that can be read and\n * understood by the chosen plot- a StaticJSON source is rarely a drop-in replacement.\n *\n * This source is largely here for legacy reasons. More often, a convenient way to serve static data is as separate\n * JSON files to an existing source (with the JSON url in place of an API).\n * @public\n */\nclass StaticSource extends BaseAdapter {\n parseInit(data) {\n // Does not receive any config; the only argument is the raw data, embedded when source is created\n this._data = data;\n }\n getRequest(state, chain, fields) {\n return Promise.resolve(this._data);\n }\n}\n\n\n/**\n * Data source for PheWAS data retrieved from a LocusZoom/PortalDev compatible API\n * @public\n * @param {String[]} init.params.build This datasource expects to be provided the name of the genome build that will\n * be used to provide pheWAS results for this position. Note positions may not translate between builds.\n */\nclass PheWASLZ extends BaseApiAdapter {\n getURL(state, chain, fields) {\n const build = (state.genome_build ? [state.genome_build] : null) || this.params.build;\n if (!build || !Array.isArray(build) || !build.length) {\n throw new Error(['Data source', this.constructor.SOURCE_NAME, 'requires that you specify array of one or more desired genome build names'].join(' '));\n }\n const url = [\n this.url,\n \"?filter=variant eq '\", encodeURIComponent(state.variant), \"'&format=objects&\",\n build.map(function (item) {\n return `build=${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 f73f4c72..ef224835 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.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}}
P Value: {{{{namespace[assoc]}}log_pvalue|logtoscinotation|htmlescape}}

Posterior probability: {{{{namespace[credset]}}posterior_prob|scinotation|htmlescape}}"}),e.Layouts.add("data_layer","association_credible_set",((a=e.Layouts.get("data_layer","association_pvalues",{unnamespaced:!0,id:"associationcredibleset",namespace:{assoc:"assoc",credset:"credset",ld:"ld"},fill_opacity:.7,tooltip:e.Layouts.get("tooltip","association_credible_set",{unnamespaced:!0}),fields:["{{namespace[assoc]}}variant","{{namespace[assoc]}}position","{{namespace[assoc]}}log_pvalue","{{namespace[assoc]}}log_pvalue|logtoscinotation","{{namespace[assoc]}}ref_allele","{{namespace[credset]}}posterior_prob","{{namespace[credset]}}contrib_fraction","{{namespace[credset]}}is_member","{{namespace[ld]}}state","{{namespace[ld]}}isrefvar"],match:{send:"{{namespace[assoc]}}variant",receive:"{{namespace[assoc]}}variant"}})).color.unshift({field:"lz_highlight_match",scale_function:"if",parameters:{field_value:!0,then:"#FFf000"}}),a)),e.Layouts.add("data_layer","annotation_credible_set",{namespace:{assoc:"assoc",credset:"credset"},id:"annotationcredibleset",type:"annotation_track",id_field:"{{namespace[assoc]}}variant",x_axis:{field:"{{namespace[assoc]}}position"},color:[{field:"lz_highlight_match",scale_function:"if",parameters:{field_value:!0,then:"#001cee"}},"#00CC00"],fields:["{{namespace[assoc]}}variant","{{namespace[assoc]}}position","{{namespace[assoc]}}log_pvalue","{{namespace[credset]}}posterior_prob","{{namespace[credset]}}contrib_fraction","{{namespace[credset]}}is_member"],match:{send:"{{namespace[assoc]}}variant",receive:"{{namespace[assoc]}}variant"},filters:[{field:"{{namespace[credset]}}is_member",operator:"=",value:!0}],behaviors:{onmouseover:[{action:"set",status:"highlighted"}],onmouseout:[{action:"unset",status:"highlighted"}],onclick:[{action:"toggle",status:"selected",exclusive:!0}],onshiftclick:[{action:"toggle",status:"selected"}]},tooltip:e.Layouts.get("tooltip","annotation_credible_set",{unnamespaced:!0}),tooltip_positioning:"top"}),e.Layouts.add("panel","annotation_credible_set",{id:"annotationcredibleset",title:{text:"SNPs in 95% credible set",x:50,style:{"font-size":"14px"}},width:800,height:45,min_height:45,proportional_width:1,margin:{top:25,right:50,bottom:0,left:50},inner_border:"rgb(210, 210, 210)",toolbar:e.Layouts.get("toolbar","standard_panel",{unnamespaced:!0}),interaction:{drag_background_to_pan:!0,scroll_to_zoom:!0,x_linked:!0},data_layers:[e.Layouts.get("data_layer","annotation_credible_set",{unnamespaced:!0})]}),e.Layouts.add("panel","association_credible_set",function(){var t=e.Layouts.get("panel","association",{unnamespaced:!0,id:"associationcrediblesets",namespace:{assoc:"assoc",credset:"credset"},data_layers:[e.Layouts.get("data_layer","significance",{unnamespaced:!0}),e.Layouts.get("data_layer","recomb_rate",{unnamespaced:!0}),e.Layouts.get("data_layer","association_credible_set",{unnamespaced:!0})]});return t.toolbar.widgets.push({type:"display_options",position:"right",color:"blue",button_html:"Display options...",button_title:"Control how plot items are displayed",layer_name:"associationcredibleset",default_config_display_name:"Linkage Disequilibrium (default)",options:[{display_name:"95% credible set (boolean)",display:{point_shape:"circle",point_size:40,color:{field:"{{namespace[credset]}}is_member",scale_function:"if",parameters:{field_value:!0,then:"#00CC00",else:"#CCCCCC"}},legend:[{shape:"circle",color:"#00CC00",size:40,label:"In credible set",class:"lz-data_layer-scatter"},{shape:"circle",color:"#CCCCCC",size:40,label:"Not in credible set",class:"lz-data_layer-scatter"}]}},{display_name:"95% credible set (gradient by contribution)",display:{point_shape:"circle",point_size:40,color:[{field:"{{namespace[credset]}}contrib_fraction",scale_function:"if",parameters:{field_value:0,then:"#777777"}},{scale_function:"interpolate",field:"{{namespace[credset]}}contrib_fraction",parameters:{breaks:[0,1],values:["#fafe87","#9c0000"]}}],legend:[{shape:"circle",color:"#777777",size:40,label:"No contribution",class:"lz-data_layer-scatter"},{shape:"circle",color:"#fafe87",size:40,label:"Some contribution",class:"lz-data_layer-scatter"},{shape:"circle",color:"#9c0000",size:40,label:"Most contribution",class:"lz-data_layer-scatter"}]}}]}),t}()),e.Layouts.add("plot","association_credible_set",{state:{},width:800,height:450,responsive_resize:!0,min_region_scale:2e4,max_region_scale:1e6,toolbar:e.Layouts.get("toolbar","standard_association",{unnamespaced:!0}),panels:[e.Layouts.get("panel","association_credible_set",{unnamespaced:!0}),e.Layouts.get("panel","annotation_credible_set",{unnamespaced:!0}),e.Layouts.get("panel","genes",{unnamespaced:!0})]})}"undefined"!=typeof LocusZoom&&LocusZoom.use(d),t.default=d}}).default; +/*! Locuszoom 0.13.0-beta.3 */ +var LzCredibleSets=function(e){var t={};function a(s){if(t[s])return t[s].exports;var o=t[s]={i:s,l:!1,exports:{}};return e[s].call(o.exports,o,o.exports,a),o.l=!0,o.exports}return a.m=e,a.c=t,a.d=function(e,t,s){a.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:s})},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 s=Object.create(null);if(a.r(s),Object.defineProperty(s,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)a.d(s,o,function(t){return e[t]}.bind(null,o));return s},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 s=a(3);function o(e){const t=e.Adapters.get("BaseAdapter");e.Adapters.add("CredibleSetLZ",class extends t{constructor(e){super(...arguments),this.dependentSource=!0}parseInit(e){if(super.parseInit(...arguments),!this.params.fields||!this.params.fields.log_pvalue)throw new Error(`Source config for ${this.constructor.SOURCE_NAME} must specify how to find 'fields.log_pvalue'`);this.params=Object.assign({threshold:.95,significance_threshold:7.301},this.params)}getCacheKey(e,t,a){return[e.credible_set_threshold||this.params.threshold,e.chr,e.start,e.end].join("_")}fetchRequest(e,t){if(!t.body.length)return Promise.resolve([]);const a=this,o=e.credible_set_threshold||this.params.threshold;if(void 0===t.body[0][a.params.fields.log_pvalue])throw new Error("Credible set source could not locate the required fields from a previous request.");const i=t.body.map(e=>e[a.params.fields.log_pvalue]);if(!i.some(e=>e>=a.params.significance_threshold))return Promise.resolve([]);const r=[];try{const e=s.scoring.bayesFactors(i),a=s.scoring.normalizeProbabilities(e),n=s.marking.findCredibleSet(a,o),c=s.marking.rescaleCredibleSet(n),l=s.marking.markBoolean(n);for(let e=0;e{{{{namespace[assoc]}}variant|htmlescape}}
P Value: {{{{namespace[assoc]}}log_pvalue|logtoscinotation|htmlescape}}
{{#if {{namespace[credset]}}posterior_prob}}
Posterior probability: {{{{namespace[credset]}}posterior_prob|scinotation|htmlescape}}{{/if}}"}),e.Layouts.add("data_layer","association_credible_set",function(){const t=e.Layouts.get("data_layer","association_pvalues",{unnamespaced:!0,id:"associationcredibleset",namespace:{assoc:"assoc",credset:"credset",ld:"ld"},fill_opacity:.7,tooltip:e.Layouts.get("tooltip","association_credible_set",{unnamespaced:!0}),fields:["{{namespace[assoc]}}variant","{{namespace[assoc]}}position","{{namespace[assoc]}}log_pvalue","{{namespace[assoc]}}log_pvalue|logtoscinotation","{{namespace[assoc]}}ref_allele","{{namespace[credset]}}posterior_prob","{{namespace[credset]}}contrib_fraction","{{namespace[credset]}}is_member","{{namespace[ld]}}state","{{namespace[ld]}}isrefvar"],match:{send:"{{namespace[assoc]}}variant",receive:"{{namespace[assoc]}}variant"}});return t.color.unshift({field:"lz_highlight_match",scale_function:"if",parameters:{field_value:!0,then:"#FFf000"}}),t}()),e.Layouts.add("data_layer","annotation_credible_set",{namespace:{assoc:"assoc",credset:"credset"},id:"annotationcredibleset",type:"annotation_track",id_field:"{{namespace[assoc]}}variant",x_axis:{field:"{{namespace[assoc]}}position"},color:[{field:"lz_highlight_match",scale_function:"if",parameters:{field_value:!0,then:"#001cee"}},"#00CC00"],fields:["{{namespace[assoc]}}variant","{{namespace[assoc]}}position","{{namespace[assoc]}}log_pvalue","{{namespace[credset]}}posterior_prob","{{namespace[credset]}}contrib_fraction","{{namespace[credset]}}is_member"],match:{send:"{{namespace[assoc]}}variant",receive:"{{namespace[assoc]}}variant"},filters:[{field:"{{namespace[credset]}}is_member",operator:"=",value:!0}],behaviors:{onmouseover:[{action:"set",status:"highlighted"}],onmouseout:[{action:"unset",status:"highlighted"}],onclick:[{action:"toggle",status:"selected",exclusive:!0}],onshiftclick:[{action:"toggle",status:"selected"}]},tooltip:e.Layouts.get("tooltip","annotation_credible_set",{unnamespaced:!0}),tooltip_positioning:"top"}),e.Layouts.add("panel","annotation_credible_set",{id:"annotationcredibleset",title:{text:"SNPs in 95% credible set",x:50,style:{"font-size":"14px"}},width:800,height:45,min_height:45,proportional_width:1,margin:{top:25,right:50,bottom:0,left:50},inner_border:"rgb(210, 210, 210)",toolbar:e.Layouts.get("toolbar","standard_panel",{unnamespaced:!0}),interaction:{drag_background_to_pan:!0,scroll_to_zoom:!0,x_linked:!0},data_layers:[e.Layouts.get("data_layer","annotation_credible_set",{unnamespaced:!0})]}),e.Layouts.add("panel","association_credible_set",function(){const t=e.Layouts.get("panel","association",{unnamespaced:!0,id:"associationcrediblesets",namespace:{assoc:"assoc",credset:"credset"},data_layers:[e.Layouts.get("data_layer","significance",{unnamespaced:!0}),e.Layouts.get("data_layer","recomb_rate",{unnamespaced:!0}),e.Layouts.get("data_layer","association_credible_set",{unnamespaced:!0})]});return t.toolbar.widgets.push({type:"display_options",position:"right",color:"blue",button_html:"Display options...",button_title:"Control how plot items are displayed",layer_name:"associationcredibleset",default_config_display_name:"Linkage Disequilibrium (default)",options:[{display_name:"95% credible set (boolean)",display:{point_shape:"circle",point_size:40,color:{field:"{{namespace[credset]}}is_member",scale_function:"if",parameters:{field_value:!0,then:"#00CC00",else:"#CCCCCC"}},legend:[{shape:"circle",color:"#00CC00",size:40,label:"In credible set",class:"lz-data_layer-scatter"},{shape:"circle",color:"#CCCCCC",size:40,label:"Not in credible set",class:"lz-data_layer-scatter"}]}},{display_name:"95% credible set (gradient by contribution)",display:{point_shape:"circle",point_size:40,color:[{field:"{{namespace[credset]}}contrib_fraction",scale_function:"if",parameters:{field_value:0,then:"#777777"}},{scale_function:"interpolate",field:"{{namespace[credset]}}contrib_fraction",parameters:{breaks:[0,1],values:["#fafe87","#9c0000"]}}],legend:[{shape:"circle",color:"#777777",size:40,label:"No 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'\n + 'P Value: {{{{namespace[assoc]}}log_pvalue|logtoscinotation|htmlescape}}
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(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}}
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'\n + 'P Value: {{{{namespace[assoc]}}log_pvalue|logtoscinotation|htmlescape}}
' +\n '{{#if {{namespace[credset]}}posterior_prob}}
Posterior probability: {{{{namespace[credset]}}posterior_prob|scinotation|htmlescape}}{{/if}}',\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. 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6);\n","/**\n * Optional LocusZoom extension: must be included separately, and after LocusZoom has been loaded\n *\n * This plugin exports helper functions, but does not modify the global registry. It does not require `LocusZoom.use`.\n *\n * Demonstrates a mechanism by which the plot can be loaded to a specific initial state based on the URL query string\n * (and, optionally, to update the URL bar when the plot state changes, with back button support)\n *\n * This makes it possible to create \"direct links\" to a particular plot of interest (and go back to a previous state\n * as the user interacts with the page). Optionally, there is support for custom callbacks to connect the URL to\n * arbitrarily complex plot behaviors.\n * @module\n */\n\nfunction _serializeQueryParams(paramsObj) {\n // Serialize an object of parameter values into a query string\n // TODO: Improve support for array values v[]=1&v[]=2\n return `?${\n Object.keys(paramsObj).map(function(key) {\n return `${encodeURIComponent(key)}=${encodeURIComponent(paramsObj[key])}`;\n }).join('&')}`;\n}\n\nfunction _parseQueryParams(queryString) {\n // Parse a query string into an object of parameter values.\n // Does not attempt any type coercion; all values are, therefore, strings.\n // TODO future: Support arrays / params that specify more than one value\n const query = {};\n if (queryString) {\n const pairs = (queryString[0] === '?' ? queryString.substr(1) : queryString).split('&');\n for (let i = 0; i < pairs.length; i++) {\n const pair = pairs[i].split('=');\n query[decodeURIComponent(pair[0])] = decodeURIComponent(pair[1] || '');\n }\n }\n return query;\n}\n\n// A useful helper function for serializing values from a provided object\nfunction _extractValues(data, mapping, reverse) {\n // Use the mapping to convert between {stateField: urlParam} (or the reverse). Any fields not referenced in\n // the \"key\" side of the mapping will be omitted from the return value.\n // Likewise, will omit any requested keys that the source side of the mapping has no information for\n reverse = reverse || false;\n\n const ret = {};\n let newMapping = mapping;\n if (reverse) {\n newMapping = {};\n Object.keys(mapping).forEach(function(k) {\n newMapping[mapping[k]] = k;\n });\n }\n\n Object.keys(newMapping).forEach(function(k) {\n const asName = newMapping[k];\n if (Object.prototype.hasOwnProperty.call(data, k)) {\n ret[asName] = data[k];\n }\n\n });\n return ret;\n}\n\nfunction _setStateFromUrlHandler(plot, stateData) {\n // A default way to deal with URL changes: push all the params as state into plot and rerender\n // More complex handlers are possible- example, URL parameters could be used to add or remove data layers\n plot.applyState(stateData);\n}\n\nfunction _setUrlFromStateHandler(plot, mapping) {\n // Serialize and return basic query params based solely on information from plot.state\n // More complex handlers are possible- the serializer can extract any information desired because it is given\n // a direct reference to the plot object\n\n // This default method does not use the eventContext data, because so many things change plot.state without\n // officially triggering an event.\n return _extractValues(plot.state, mapping);\n}\n\n/**\n * Extract plot parameters from the URL query string. Very useful for setting up the plot on initial page load.\n * @param {object} mapping How to map elements of plot state to URL param fields. Hash of\n * {plotFieldName: urlParamName} entries (both values should be unique)\n * @param {string} [queryString='window.location.search'] The query string to parse\n * @returns {object} Plot parameter values\n */\nfunction paramsFromUrl(mapping, queryString) {\n // Internal helper function: second argument only used for unit testing\n queryString = queryString || window.location.search;\n const queryParams = _parseQueryParams(queryString);\n return _extractValues(queryParams, mapping, true);\n}\n\n/**\n * Allows the plot to monitor changes in the URL and take action when the URL changes.\n *\n * For example, this enables using the browser back button to jump to a previous plot after user interaction.\n *\n * @param {Plot} plot A reference to the LZ plot\n * @param {object} mapping How to map elements of plot state to URL param fields. Hash of\n * {plotFieldName: urlParamName} entries (both values should be unique)\n * @param {function} [callback] Specify how the plot acts on information read in from query params.\n * The default behavior is to push the data into `plot.state`\n * Signature is function(plot, plotDataFromQueryString)\n * @returns {function} The function handle for the new listener (allows cleanup if plot is removed later)\n */\nfunction plotWatchesUrl(plot, mapping, callback) {\n callback = callback || _setStateFromUrlHandler;\n\n const listener = function (event) {\n const urlData = paramsFromUrl(mapping);\n // Tell the plot what to do with the params extracted from the URL\n callback(plot, urlData);\n };\n window.addEventListener('popstate', listener);\n plot.trackExternalListener(window, 'popstate', listener);\n return listener;\n}\n\n/**\n * Update the URL whenever the plot state changes\n * @param {Plot} plot A reference to the LZ plot\n * @param {object} mapping How to map elements of plot state to URL param fields. Hash of\n * {plotFieldName: urlParamName} entries (both values should be unique)\n * @param {function} [callback] Specify how plot data will be serialized into query params\n * The default behavior is to extract all the URL params from plot.state as the only source.\n * Signature is function(plot, mapping, eventContext)\n * @returns {function} The function handle for the new listener (allows cleanup if plot is removed later)\n */\nfunction plotUpdatesUrl(plot, mapping, callback) {\n callback = callback || _setUrlFromStateHandler;\n // Note: this event only fires when applyState receives *new* information that would trigger a rerender.\n // Plot state is sometimes changed without the event being fired.\n const listener = function (eventContext) {\n const oldParams = _parseQueryParams(window.location.search);\n // Apply custom serialization to convert plot data to URL params\n const serializedPlotData = callback(plot, mapping, eventContext);\n const newParams = Object.assign({}, oldParams, serializedPlotData);\n\n const update = Object.keys(newParams).some(function (k) {\n // Not every state change would affect the URL. Allow type coercion since query is a string.\n // eslint-disable-next-line eqeqeq\n return (oldParams[k] != newParams[k]);\n });\n if (update) {\n const queryString = _serializeQueryParams(newParams);\n\n if (Object.keys(oldParams).length) {\n history.pushState({}, document.title, queryString);\n } else {\n // Prevent broken back behavior on first page load: the first time query params are set,\n // we don't generate a separate history entry\n history.replaceState({}, document.title, queryString);\n }\n\n }\n };\n plot.on('state_changed', listener);\n return listener;\n}\n\n// Slight build quirk: we use a single webpack file for all modules, but `libraryTarget` expects the entire\n// module to be exported as `default` in diff --git a/examples/interval_annotations.html b/examples/interval_annotations.html index 1686d410..2f2b9b3c 100644 --- a/examples/interval_annotations.html +++ b/examples/interval_annotations.html @@ -11,7 +11,7 @@ - + LocusZoom.js ~ Interval Annotations Example @@ -115,11 +115,6 @@

Top Hits

// Generate the LocusZoom plot var plot = LocusZoom.populate("#plot", data_sources, layout); - // Add a basic loader to each panel (one that shows when data is requested and hides when one rendering) - plot.layout.panels.forEach(function(panel){ - plot.panels[panel.id].addBasicLoader(); - }); - // Create a method to parse a region string into a 600Kb genome range and load it function jumpTo(region) { var target = region.split(":"); diff --git a/examples/js/aggregation-tests-example-page.js b/examples/js/aggregation-tests-example-page.js index 84e30dd5..a40771f2 100644 --- a/examples/js/aggregation-tests-example-page.js +++ b/examples/js/aggregation-tests-example-page.js @@ -221,10 +221,6 @@ function createDisplayWidgets(label_store, context) { layout = customizePlotLayout(layout); const plot = LocusZoom.populate('#lz-plot', data_sources, layout); - // Add a basic loader to each panel (one that shows when data is requested and hides when one rendering) - plot.layout.panels.forEach(function(panel) { - plot.panels[panel.id].addBasicLoader(); - }); // Changes in the plot can be reflected in the URL, and vice versa (eg browser back button can go back to // a previously viewed region) diff --git a/examples/misc/covariates_model.html b/examples/misc/covariates_model.html index 1f1d5707..0138d2d6 100644 --- a/examples/misc/covariates_model.html +++ b/examples/misc/covariates_model.html @@ -101,11 +101,6 @@

Top Hits

// Generate the LocusZoom plot var plot = LocusZoom.populate("#plot", data_sources, layout); - // Add a basic loader to each panel (one that shows when data is requested and hides when one rendering) - plot.layout.panels.forEach(function(panel){ - plot.panels[panel.id].addBasicLoader(); - }); - // Create a method to parse a region string into a 600Kb genome range and load it function jumpTo(region) { var target = region.split(":"); diff --git a/examples/multiple_phenotypes_layered.html b/examples/multiple_phenotypes_layered.html index e81f3bd5..1102634c 100644 --- a/examples/multiple_phenotypes_layered.html +++ b/examples/multiple_phenotypes_layered.html @@ -133,11 +133,6 @@

Top Hits

// Generate the LocusZoom plot var plot = LocusZoom.populate("#plot", data_sources, layout); - // Add a basic loader to each panel (one that shows when data is requested and hides when one rendering) - plot.layout.panels.forEach(function(panel){ - plot.panels[panel.id].addBasicLoader(); - }); - // Create a method to parse a region string into a 600Kb genome range and load it function jumpTo(region) { var target = region.split(":"); diff --git a/examples/phewas_forest.html b/examples/phewas_forest.html index 0791c523..20d0e6d1 100644 --- a/examples/phewas_forest.html +++ b/examples/phewas_forest.html @@ -1,5 +1,5 @@ - + @@ -7,9 +7,11 @@ + - + + LocusZoom.js ~ PheWAS (Forest) Example diff --git a/index.html b/index.html index dc612c61..cb319ccc 100644 --- a/index.html +++ b/index.html @@ -76,7 +76,7 @@

Get LocusZoom.js

CSS
- https://cdn.jsdelivr.net/npm/locuszoom@0.13.0-beta.2/dist/locuszoom.css + https://cdn.jsdelivr.net/npm/locuszoom@0.13.0-beta.3/dist/locuszoom.css
All CSS classes are namespaced to avoid collisions
@@ -96,7 +96,7 @@
Dependencies
Javascript
- https://cdn.jsdelivr.net/npm/locuszoom@0.13.0-beta.2 + https://cdn.jsdelivr.net/npm/locuszoom@0.13.0-beta.3
@@ -244,11 +244,6 @@
Multiple Phenotypes (Layered)
LzDynamicUrls.plotUpdatesUrl(plot, stateUrlMapping); LzDynamicUrls.plotWatchesUrl(plot, stateUrlMapping); - // Add a basic loader to each panel (one that shows when data is requested and hides when one rendering) - plot.layout.panels.forEach(function(panel){ - plot.panels[panel.id].addBasicLoader(); - }); - // Create a method to parse a region string into a 600Kb genome range and load it function jumpTo(region) { var target = region.split(":"); diff --git a/package-lock.json b/package-lock.json index 92689c08..3d6b280c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "locuszoom", - "version": "0.13.0-beta.2", + "version": "0.13.0-beta.3", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -14,69 +14,60 @@ } }, "@babel/compat-data": { - "version": "7.11.0", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.11.0.tgz", - "integrity": "sha512-TPSvJfv73ng0pfnEOh17bYMPQbI95+nGWc71Ss4vZdRBHTDqmM9Z8ZV4rYz8Ks7sfzc95n30k6ODIq5UGnXcYQ==", - 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"version": "15.0.1", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-15.0.1.tgz", - "integrity": "sha512-0OAMV2mAZQrs3FkNpDQcBk1x5HXb8X4twADss4S0Iuk+2dGnLOE/fRHrsYm542GduMveyA77OF4wrNJuanRCWw==", - "dev": true, - "requires": { - "camelcase": "^5.0.0", - "decamelize": "^1.2.0" - } } } + }, + "yocto-queue": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", + "dev": true } } } diff --git a/package.json b/package.json index 892511e1..18411c54 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "locuszoom", - "version": "0.13.0-beta.2", + "version": "0.13.0-beta.3", "main": "dist/locuszoom.app.min.js", "module": "esm/index.js", "sideEffects": true, @@ -42,25 +42,25 @@ "d3": "^5.16.0" }, "devDependencies": { - "@babel/core": "^7.11.1", - "@babel/preset-env": "^7.11.0", - "@babel/register": "^7.10.5", - "babel-loader": "^8.1.0", + "@babel/core": "^7.12.10", + "@babel/preset-env": "^7.12.0", + "@babel/register": "^7.12.10", + "babel-loader": "^8.2.2", "babel-plugin-module-resolver": "^4.0.0", "chai": "^4.2.0", "clean-webpack-plugin": "^3.0.0", - "eslint": "^7.6.0", - "eslint-loader": "^4.0.2", + "eslint": "^7.15.0", + "eslint-webpack-plugin": "^2.4.1", "friendly-errors-webpack-plugin": "^1.7.0", - "jsdoc": "^3.6.5", + "jsdoc": "^3.6.6", "jsdom": "^16.4.0", "jsdom-global": "^3.0.2", - "mocha": "~8.1.3", + "mocha": "~8.2.1", "nyc": "^15.1.0", - "sass": "^1.26.10", - "sass-loader": "^8.0.2", + "sass": "^1.30.0", + "sass-loader": "^10.1.0", "sinon": "^6.3.5", - "source-map-loader": "^1.0.1", + "source-map-loader": "^1.1.3", "webpack": "^4.44.1", "webpack-cli": "^3.3.12", "webpack-merge": "^4.2.2" diff --git a/test/unit/components/test_datalayer.js b/test/unit/components/test_datalayer.js index d14d5d91..5b0e9755 100644 --- a/test/unit/components/test_datalayer.js +++ b/test/unit/components/test_datalayer.js @@ -1,5 +1,6 @@ import {assert} from 'chai'; import * as d3 from 'd3'; +import sinon from 'sinon'; import { SCALABLE } from '../../../esm/registry'; import BaseDataLayer from '../../../esm/components/data_layer/base'; @@ -584,9 +585,8 @@ describe('LocusZoom.DataLayer', function () { }); }); - describe('Tool tip functions', function () { + describe('Tool tip display', function () { beforeEach(function () { - this.plot = null; this.layout = { panels: [ { @@ -671,7 +671,6 @@ describe('LocusZoom.DataLayer', function () { d.unselectElement(b); assert.isUndefined(d.tooltips[b_id]); }); - it('should allow tooltip open/close state to be tracked separately from element selection', function () { // Regression test for zombie tooltips returning after re-render const layer = this.plot.panels.p.data_layers.d; @@ -709,6 +708,96 @@ describe('LocusZoom.DataLayer', function () { }); }); + describe('data element behaviors', function () { + beforeEach(function() { + const data_sources = new DataSources() + .add('d', ['StaticJSON', [{ id: 'a', x: 1, y: 2 }, { id: 'b', x: 2, y:0 }, { id: 'c', x: 3, y:1 }]]); + + const layout = { + panels: [ + { + id: 'p', + data_layers: [ + { + id: 'd', + type: 'scatter', + fields: ['d:id', 'd:x', 'd:y'], + id_field: 'd:id', + x_axis: { field: 'd:x' }, + y_axis: { field: 'd:y'}, + behaviors: { + onclick: [{ action: 'link', href: 'https://dev.example/{{d:id}}', target: '_blank' }], + onmouseover: [{ action: 'set', status: 'highlighted', exclusive: true }], + onmouseout: [{ action: 'unset', status: 'highlighted' }], + onshiftclick: [{ action: 'toggle', status: 'selected' }], + }, + }, + ], + }, + ], + }; + d3.select('body').append('div').attr('id', 'plot'); + this.plot = populate('#plot', data_sources, layout); + }); + it('can link to an external website', function () { + // NOTE: Not all variants of this behavior are tested. This only tests opening links in another window. + // This is because JSDom sometimes has issues mocking window.location. + return this.plot.applyState().then(() => { + const openStub = sinon.stub(window, 'open'); + + // Select the first data element + const datapoint = this.plot.panels.p.data_layers.d.svg.group.select('.lz-data_layer-scatter'); + + assert.notEqual(datapoint.size(), 0, 'nodes are rendered'); + datapoint.dispatch('click', { bubbles: true} ); + + assert.ok(openStub.calledOnce, 'window.open was called with the specified location and target'); + assert.ok(openStub.calledWith('https://dev.example/a', '_blank'), 'The URL can incorporate parameters from the specified data element'); + }); + }); + it('applies status-based styles when an item receives mouse events', function () { + // Since sequence is important, this test exercises multiple scenarios in a specific order + return this.plot.applyState().then(() => { + // Select the first and second data points + const first = this.plot.panels.p.data_layers.d.svg.group.select('.lz-data_layer-scatter'); + const second = this.plot.panels.p.data_layers.d.svg.group.selectAll('.lz-data_layer-scatter').filter((d, i) => i === 1); + + assert.notEqual(first.size(), 0, 'nodes are rendered'); + assert.notEqual(second.size(), 0, 'nodes are rendered'); + first.dispatch('mouseover', { bubbles: true} ); + + assert.ok(first.node().classList.contains('lz-data_layer-scatter-highlighted'), 'Style is applied appropriately'); + assert.notOk(second.node().classList.contains('lz-data_layer-scatter-highlighted'), 'Style is only applied to the requested node'); + + // When a different element receives mouseover, check that exclusivity and styling are applied correctly + second.dispatch('mouseover', { bubbles: true} ); + assert.notOk(first.node().classList.contains('lz-data_layer-scatter-highlighted'), 'Style is removed from other nodes'); + assert.ok(second.node().classList.contains('lz-data_layer-scatter-highlighted'), 'Style is applied to the new mouseover node'); + + // On mouse out, styles are removed + second.dispatch('mouseout', { bubbles: true} ); + assert.notOk(second.node().classList.contains('lz-data_layer-scatter-highlighted'), 'Style is removed on mouseout'); + }); + }); + it('recognizes keyboard modifiers as distinct events', function () { + return this.plot.applyState().then(() => { + const openStub = sinon.stub(window, 'open'); + + // Select the first data element + const datapoint = this.plot.panels.p.data_layers.d.svg.group.select('.lz-data_layer-scatter'); + + assert.notEqual(datapoint.size(), 0, 'nodes are rendered'); + datapoint.node().dispatchEvent(new MouseEvent('click', {bubbles: true, shiftKey: true})); + + assert.ok(openStub.notCalled, 'The basic click event did not fire because a modifier key was used'); + assert.ok(datapoint.node().classList.contains('lz-data_layer-scatter-selected'), 'Style is applied appropriately'); + }); + }); + afterEach(function () { + sinon.restore(); + }); + }); + describe('Filtering operations', function () { it('can filter numeric data', function () { const layer = new BaseDataLayer({id: 'test', id_field: 'a'}); diff --git a/test/unit/components/test_panel.js b/test/unit/components/test_panel.js index 6e5bc63b..38c4ac24 100644 --- a/test/unit/components/test_panel.js +++ b/test/unit/components/test_panel.js @@ -280,32 +280,36 @@ describe('Panel', function() { }); it('should have a loader object with show/update/animate/setPercentCompleted/hide methods, a showing boolean, and selectors', function() { - const loader = this.panel.loader; - assert.isObject(this.panel.loader); - assert.isFalse(loader.showing); - assert.isNull(loader.selector); - assert.isNull(loader.content_selector); - assert.isNull(loader.progress_selector); + return this.plot.applyState().then(() => { + const loader = this.panel.loader; + assert.isObject(this.panel.loader); + assert.isFalse(loader.showing); + assert.isNull(loader.selector); + assert.isNull(loader.content_selector); + assert.isNull(loader.progress_selector); + }); }); it('should show/hide/update on command and track shown status', function() { - const loader = this.panel.loader; - assert.isFalse(loader.showing); - assert.isNull(loader.selector); - assert.isNull(loader.content_selector); - assert.isNull(loader.progress_selector); - - loader.show('test content'); - assert.isTrue(loader.showing); - assert.isFalse(loader.selector.empty()); - assert.isFalse(loader.content_selector.empty()); - assert.equal(loader.content_selector.html(), 'test content'); - assert.isFalse(loader.progress_selector.empty()); - loader.hide(); - assert.isFalse(loader.showing); - assert.isNull(loader.selector); - assert.isNull(loader.content_selector); - assert.isNull(loader.progress_selector); + return this.plot.applyState().then(() => { + const loader = this.panel.loader; + assert.isFalse(loader.showing); + assert.isNull(loader.selector); + assert.isNull(loader.content_selector); + assert.isNull(loader.progress_selector); + + loader.show('test content'); + assert.isTrue(loader.showing); + assert.isFalse(loader.selector.empty()); + assert.isFalse(loader.content_selector.empty()); + assert.equal(loader.content_selector.html(), 'test content'); + assert.isFalse(loader.progress_selector.empty()); + loader.hide(); + assert.isFalse(loader.showing); + assert.isNull(loader.selector); + assert.isNull(loader.content_selector); + assert.isNull(loader.progress_selector); + }); }); it('should allow for animating or showing discrete percentages of completion', function() { diff --git a/test/unit/ext/test_ext_intervals-track.js b/test/unit/ext/test_ext_intervals-track.js index 6dc51502..ac591172 100644 --- a/test/unit/ext/test_ext_intervals-track.js +++ b/test/unit/ext/test_ext_intervals-track.js @@ -1,8 +1,12 @@ import {assert} from 'chai'; +import sinon from 'sinon'; import LocusZoom from 'locuszoom'; import {DATA_LAYERS, LAYOUTS} from '../../../esm/registry'; import intervals_plugin from '../../../esm/ext/lz-intervals-track'; +import DataSources from '../../../esm/data'; +import * as d3 from 'd3'; +import {populate} from '../../../esm/helpers/display'; /** * Interval annotation track @@ -122,4 +126,82 @@ describe('Interval annotation track', function () { ); }); }); + + describe('collision detection and category grouping', function () { + beforeEach(function() { + this.plot = null; + const data_sources = new DataSources() + .add('intervals', ['StaticJSON', [ + { start: 100, end: 200, state_id: 'thing1', state_name: 'redfish', itemRgb: '255,0,0' }, + ]]); + + const layout = { + panels: [ LAYOUTS.get('panel', 'intervals') ], + state: { chr: 'X', start: 1, end: 500 }, + width: 800, height: 550, + }; + layout.panels[0].data_layers[0].split_tracks = true; + + d3.select('body').append('div').attr('id', 'plot'); + this.plot = populate('#plot', data_sources, layout); + this._intervals_source = data_sources.get('intervals'); + this._intervals_layer = this.plot.panels.intervals.data_layers.intervals; + }); + + it('re-renders the y-axis when categories change', function () { + return this.plot.applyState().then(() => { + assert.deepEqual(this._intervals_layer._categories, ['redfish'], 'Correct initial categories'); + + const renderSpy = sinon.spy(this._intervals_layer, 'updateSplitTrackAxis'); + + // Replace the original data and trigger a synchronous re-render (no new data fetching) + this._intervals_layer.data = [{ 'intervals:start': 100, 'intervals:end': 200, 'intervals:state_id': 'thing1', 'intervals:state_name': 'bluefish', 'intervals:itemRgb': '0,0,255' }]; + this._intervals_layer.render(); + + assert.ok(renderSpy.called, 'Axis was updated'); + assert.ok(renderSpy.calledWith(['bluefish']), 'Correct new categories were received'); + assert.deepEqual(this._intervals_layer._categories, ['bluefish'], 'Correct final categories'); + }); + }); + + it('does not re-render the y-axis when categories stay the same', function () { + return this.plot.applyState().then(() => { + assert.deepEqual(this._intervals_layer._categories, ['redfish'], 'Correct initial categories'); + + const renderSpy = sinon.spy(this._intervals_layer, 'updateSplitTrackAxis'); + + // Replace the original data and trigger a synchronous re-render (no new data fetching) + this._intervals_layer.data = [ // Same number of categories as original, different # of items + { 'intervals:start': 100, 'intervals:end': 200, 'intervals:state_id': 'thing1', 'intervals:state_name': 'redfish', 'intervals:itemRgb': '255,0,0' }, + { 'intervals:start': 101, 'intervals:end': 201, 'intervals:state_id': 'thing2', 'intervals:state_name': 'redfish', 'intervals:itemRgb': '255,0,0' }, + ]; + this._intervals_layer.render(); + + assert.ok(renderSpy.notCalled, 'Axis was not updated'); + assert.deepEqual(this._intervals_layer._categories, ['redfish'], 'Correct final categories'); + }); + }); + + it('draw status nodes only when relevant', function () { + return this.plot.applyState().then(() => { + const status_nodes = this._intervals_layer._statusnodes_group.node(); + assert.equal(status_nodes.childElementCount, 1, 'In split mode, 1 category means 1 status node'); + + // Selecting an element should also trigger a nice display for the associated "status node" background rectangle + const element = this._intervals_layer.data[0]; + assert.notOk(status_nodes.children[0].classList.contains('lz-data_layer-intervals-statusnode-selected'), 'Unselected elements are not styled as highlighted'); + this._intervals_layer.setElementStatus('selected', element, true, true); + assert.ok(status_nodes.children[0].classList.contains('lz-data_layer-intervals-statusnode-selected'), 'Selected elements get a highlighted style'); + + // Switch to merged tracks mode and count again + this._intervals_layer.layout.split_tracks = false; + this._intervals_layer.render(); + assert.equal(status_nodes.childElementCount, 0, 'No status nodes are rendered in merged tracks mode'); + }); + }); + + afterEach(function () { + sinon.restore(); + }); + }); }); diff --git a/webpack.common.cjs b/webpack.common.cjs index 2e52e59f..d749d406 100644 --- a/webpack.common.cjs +++ b/webpack.common.cjs @@ -1,8 +1,11 @@ /* eslint-env node */ const path = require('path'); const webpack = require('webpack'); -const FriendlyErrorsWebpackPlugin = require('friendly-errors-webpack-plugin'); + const { CleanWebpackPlugin } = require('clean-webpack-plugin'); +const ESLintPlugin = require('eslint-webpack-plugin'); +const FriendlyErrorsWebpackPlugin = require('friendly-errors-webpack-plugin'); + const PACKAGE = require('./package.json'); @@ -14,6 +17,7 @@ const FILENAMES = { LocusZoom: 'locuszoom.app.min.js', LzDynamicUrls: 'ext/lz-dynamic-urls.min.js', LzWidgetAddons: 'ext/lz-widget-addons.min.js', + LzForestTrack: 'ext/lz-forest-track.min.js', LzIntervalsTrack: 'ext/lz-intervals-track.min.js', LzCredibleSets: 'ext/lz-credible-sets.min.js', LzTabix: 'ext/lz-tabix-source.min.js', @@ -27,6 +31,7 @@ module.exports = { LocusZoom: path.resolve(srcPath, 'index.js'), LzDynamicUrls: path.resolve(srcPath, 'ext', 'lz-dynamic-urls.js'), LzWidgetAddons: path.resolve(srcPath, 'ext', 'lz-widget-addons.js'), + LzForestTrack: path.resolve(srcPath, 'ext', 'lz-forest-track.js'), LzIntervalsTrack: path.resolve(srcPath, 'ext', 'lz-intervals-track.js'), LzCredibleSets: path.resolve(srcPath, 'ext', 'lz-credible-sets.js'), LzTabix: path.resolve(srcPath, 'ext', 'lz-tabix-source.js'), @@ -39,28 +44,21 @@ module.exports = { }), new webpack.BannerPlugin(`Locuszoom ${PACKAGE.version}`), // add after uglify step new FriendlyErrorsWebpackPlugin(), + new ESLintPlugin(), ], resolve: { modules: [ - 'node_modules' + 'node_modules', ], }, module: { rules: [ - { - test: /\.m?js$/, - exclude: (file) => (/node_modules/.test(file)), - use: [ - { loader: 'babel-loader', options: { presets: ['@babel/preset-env'] } }, - 'eslint-loader' - ] - }, { test: /\.js$/, use: ['source-map-loader'], enforce: 'pre', }, - ] + ], }, output: { path: outputPath, @@ -83,5 +81,5 @@ module.exports = { 'gwas-credible-sets': 'gwasCredibleSets', 'tabix-reader': 'tabix', 'raremetal.js': 'raremetal', - } + }, };