npm - gramene-search - Versions diffs - 1.6.45 → 1.6.46 - Mend

gramene-search 1.6.45 → 1.6.46

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (11) hide show

package/.parcel-cache/83e7562660f7cc15-BundleGraph +0 -0
package/.parcel-cache/9a0d07555444f4da-AssetGraph +0 -0
package/.parcel-cache/d3a1b9507cb44047-AssetGraph +0 -0
package/.parcel-cache/data.mdb +0 -0
package/.parcel-cache/dc1da35000e13623-RequestGraph +0 -0
package/.parcel-cache/lock.mdb +0 -0
package/.parcel-cache/snapshot-dc1da35000e13623.txt +2 -2
package/dist/index.js +2 -1
package/dist/index.js.map +1 -1
package/package.json +1 -1
package/src/components/results/details/VEP.js +2 -1

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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const t = store.selectSuggestionsQuery().replaceAll(':',' ').trim();\n const g = store.selectGrameneGenomes();\n const q = `/suggest?q={!boost b=relevance}name:${t}^5 ids:${t}^5 ids:${t}^3 synonym:${t}^3 synonym:${t}^2 text:${t}^1`;\n // const promises = sites.map(site => fetch(`https://data.gramene.org/${site}${q}`));\n // return Promise.all(promises)\n return fetch(store.selectGrameneAPI() + q)\n .then(res => {\n return res.json()\n })\n .then(suggestions => {\n if (Object.keys(g.active).length > 0) {\n suggestions.grouped.category.groups.forEach(group => {\n group.doclist.docs.forEach(sugg => {\n sugg.num_genes = 0;\n sugg.taxon_id.forEach((id,idx) => {\n if (g.active[id] && !g.active[id].hidden) {\n sugg.num_genes += sugg.taxon_freq[idx]\n }\n })\n })\n })\n }\n return suggestions\n })\n }\n});\n\ngrameneSuggestions.reactGrameneSuggestions = createSelector(\n 'selectGrameneSuggestionsShouldUpdate',\n 'selectSuggestionsQuery',\n (shouldUpdate, queryString) => {\n if (shouldUpdate && queryString) {\n return { actionCreator: 'doFetchGrameneSuggestions' }\n }\n }\n);\n\ngrameneSuggestions.selectGrameneSuggestionsStatus = createSelector(\n 'selectGrameneSuggestionsShouldUpdate',\n 'selectGrameneSuggestionsIsLoading',\n 'selectGrameneSuggestionsRaw',\n 'selectSuggestionsQuery',\n (shouldUpdate, isLoading, suggestionsRaw, queryString) => {\n if (!queryString) return '';\n if (shouldUpdate) return 'update needed';\n if (isLoading) return 'loading';\n if (suggestionsRaw.data) return suggestionsRaw.data.grouped.category.matches + ' terms';\n console.error(suggestionsRaw)\n return 'error';\n }\n);\n\ngrameneSuggestions.selectGrameneSuggestionsReady = createSelector(\n 'selectGrameneSuggestionsStatus',\n (status) => {\n const regex = RegExp('terms$');\n return regex.test(status);\n }\n);\n\ngrameneSuggestions.doFocusFirstGrameneSuggestion = arg => ({dispatch, getState}) => {\n console.log('inside doFocusFirstGrameneSuggestion');\n};\n\nfunction compressLongTaxonName(node) {\n const fullName = node.name;\n const removedExtraineousWords = fullName.replace(/( Group$\| subsp\\.\| ssp\\.\| var\\.\| strain)/, '');\n let finalVersion;\n if (removedExtraineousWords.length > 20) {\n let words = removedExtraineousWords.split(' ');\n if (words.length === 2) {\n // abrreviate first word.\n finalVersion = removedExtraineousWords.replace(/^([A-Z])[a-z]+/, '$1.')\n }\n if (words.length > 2) {\n finalVersion = removedExtraineousWords.replace(/^([A-Z])[a-z]+\\s([a-z])[a-z]+/, '$1$2.')\n }\n }\n else {\n finalVersion = removedExtraineousWords;\n }\n node.short_name = finalVersion;\n}\n\nconst grameneTaxonomy = createAsyncResourceBundle({\n name: 'grameneTaxonomy',\n actionBaseType: 'GRAMENE_TAXONOMY',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/taxonomy?subset=gramene&rows=-1`)\n .then(res => res.json())\n .then(taxNodes => {\n let taxonomy = _.keyBy(taxNodes, '_id');\n taxNodes.forEach(t => {\n t._id = +t._id; // ensure taxonomy id is a number\n compressLongTaxonName(t);\n if (t.hasOwnProperty(\"is_a\")) {\n t.is_a.forEach(p_id => {\n const p = taxonomy[p_id];\n if (!p.hasOwnProperty('children')) p.children = [];\n p.children.push(t._id)\n })\n }\n });\n return taxonomy\n })\n }\n});\ngrameneTaxonomy.reactGrameneTaxonomy = createSelector(\n 'selectGrameneTaxonomyShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneTaxonomy' }\n }\n }\n);\nconst grameneMaps = createAsyncResourceBundle({\n name: 'grameneMaps',\n actionBaseType: 'GRAMENE_MAPS',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/maps?rows=-1`)\n .then(res => res.json())\n .then(maps => {\n maps.forEach(m => {\n m.regionLength = {};\n m.regions.names.forEach((rname,idx) => {\n m.regionLength[rname] = m.regions.lengths[idx]\n })\n })\n return _.keyBy(maps, 'taxon_id');\n })\n }\n});\ngrameneMaps.reactGrameneMaps = createSelector(\n 'selectGrameneMapsShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneMaps' }\n }\n }\n);\n\nconst expressionStudies = createAsyncResourceBundle( {\n name: 'expressionStudies',\n actionBaseType: 'EXPRESSION_STUDIES',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`)\n .then(res => res.json())\n .then(res => _.groupBy(res, 'taxon_id'))\n }\n});\nexpressionStudies.reactExpressionStudies = createSelector(\n 'selectExpressionStudiesShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchExpressionStudies' }\n }\n }\n);\n\nconst expressionSamples = createAsyncResourceBundle( {\n name: 'expressionSamples',\n actionBaseType: 'EXPRESSION_SAMPLES',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/assays?rows=-1`)\n .then(res => res.json())\n .then(samples => _.groupBy(samples, 'experiment'))\n .then(studies => 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grameneGermplasm = createAsyncResourceBundle( {\n name: 'grameneGermplasm',\n actionBaseType: 'GRAMENE_GERMPLASM',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/germplasm?rows=-1`)\n .then(res => res.json())\n .then(res => {\n res.forEach(g => {\n if (!g.subpop) {\n g.subpop = \"?\"\n }\n });\n return _.groupBy(res, 'ens_id')\n })\n }\n});\ngrameneGermplasm.reactGrameneGermplasm = createSelector(\n 'selectGrameneGermplasmShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneGermplasm' }\n }\n }\n);\n//\n// const grameneExpressionAssays = createAsyncResourceBundle( {\n// name: 'grameneExpressionAssays',\n// actionBaseType: 'GRAMENE_EXPRESSION_ASSAYS',\n// persist: true,\n// getPromise: ({store}) => {\n// return fetch(`${store.selectGrameneAPI()}/assays?rows=-1`)\n// .then(res => res.json())\n// .then(res => {\n// let expr={};\n// res.forEach(assay => {\n// if (!expr.hasOwnProperty(assay.taxon_id)) {\n// expr[assay.taxon_id] = {};\n// }\n// if (!expr[assay.taxon_id].hasOwnProperty(assay.experiment)) {\n// expr[assay.taxon_id][assay.experiment] = [];\n// }\n// assay.order = +assay.group.replace('g','');\n// expr[assay.taxon_id][assay.experiment].push(assay);\n// });\n// // sort each experiment\n// for (const tid in expr) {\n// for (const exp in expr[tid]) {\n// expr[tid][exp].sort((a,b) => a.order - b.order);\n// }\n// }\n// return expr;\n// })\n// }\n// });\n// grameneExpressionAssays.reactGrameneExpressionAssays = createSelector(\n// 'selectGrameneExpressionAssaysShouldUpdate',\n// (shouldUpdate) => {\n// if (shouldUpdate) {\n// return { actionCreator: 'doFetchGrameneExpressionAssays' }\n// }\n// }\n// );\n\nconst attribFacetFields = [\n \"{!facet.limit='10' facet.mincount='1' key='age'}panset_age_attr_s\",\n \"{!facet.limit='100' facet.mincount='1' key='taxa'}panset_ntaxa_attr_i\",\n \"{!facet.limit='100' facet.mincount='1' key='AED' type='range' start=0 end=1.0 gap=0.25}MAKER_AED_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI2' type='range' start=0 end=1.0 gap=0.25}MAKER_QI2_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI3' type='range' start=0 end=1.0 gap=0.25}MAKER_QI3_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI4' type='range' start=0 end=1.0 gap=0.25}MAKER_QI4_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI5' type='range' start=0 end=1.0 gap=0.25}MAKER_QI5_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI6' type='range' start=0 end=1.0 gap=0.25}MAKER_QI6_attr_f\"\n];\nconst attribFacets = {\n \"age\":{ \"type\": \"terms\", \"field\": \"panset_age_attr_s\" },\n \"nTaxa\": { \"type\": \"terms\", \"field\": \"panset_ntaxa_attr_i\", \"limit\": 100 },\n \"AED\":{ \"type\": \"range\", \"field\": \"MAKER_AED_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI2\":{ \"type\": \"range\", \"field\": \"MAKER_QI2_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI3\":{ \"type\": \"range\", \"field\": \"MAKER_QI3_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI4\":{ \"type\": \"range\", \"field\": \"MAKER_QI4_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI5\":{ \"type\": \"range\", \"field\": \"MAKER_QI5_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI6\":{ \"type\": \"range\", \"field\": \"MAKER_QI6_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"byAge\":{ \"type\": \"terms\", \"field\": \"panset_age_attr_s\", \"facet\": {\n \"nTaxa\": { \"type\": \"terms\", \"field\": \"panset_ntaxa_attr_i\", \"limit\": 100 },\n \"AED\":{ \"type\": \"range\", \"field\": \"MAKER_AED_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI2\":{ \"type\": \"range\", \"field\": \"MAKER_QI2_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI3\":{ \"type\": \"range\", \"field\": \"MAKER_QI3_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI4\":{ \"type\": \"range\", \"field\": \"MAKER_QI4_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI5\":{ \"type\": \"range\", \"field\": \"MAKER_QI5_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI6\":{ \"type\": \"range\", \"field\": \"MAKER_QI6_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 }\n }\n }\n}\nconst grameneGeneAttribs = createAsyncResourceBundle( {\n name: 'grameneGeneAttribs',\n actionBaseType: 'GRAMENE_GENE_ATTRIBS',\n persist: false,\n getPromise: ({store}) => {\n const g = store.selectGrameneGenomes();\n const taxa = Object.keys(g.active);\n let fq='';\n if (taxa.length) {\n console.log('search add a fq for ',taxa);\n fq = `&fq=taxon_id:(${taxa.join(' OR ')})`;\n }\n return fetch(`${store.selectGrameneAPI()}/search?q=${store.selectGrameneFiltersQueryString()}&json.facet=${JSON.stringify(attribFacets)}&rows=0${fq}`)\n // return fetch(`${store.selectGrameneAPI()}/search?rows=1&q=MAKER_AED_attr_f:&json.facet=${JSON.stringify(attribFacets)}`)\n .then(res => res.json())\n .then(res => {\n return res.facets\n })\n }\n});\ngrameneGeneAttribs.reactGrameneGeneAttribs = createSelector(\n 'selectGrameneGeneAttribsShouldUpdate',\n 'selectGrameneFiltersStatus',\n 'selectGrameneViews',\n (shouldUpdate, status, views) => {\n if (shouldUpdate && (status === 'finished' \|\| status === 'ready')) {\n const byId = _.keyBy(views.options,'id');\n if (byId.attribs.show === \"on\") {\n return { actionCreator: 'doFetchGrameneGeneAttribs' }\n }\n }\n }\n);\n\nconst grameneSearch = createAsyncResourceBundle({\n name: 'grameneSearch',\n actionBaseType: 'GRAMENE_SEARCH',\n persist: false,\n getPromise: ({store}) => {\n const offset = store.selectGrameneSearchOffset();\n const rows = store.selectGrameneSearchRows();\n const g = store.selectGrameneGenomes();\n const taxa = Object.keys(g.active).filter(tid => !g.active[tid].hidden);\n let fq='';\n if (taxa.length) {\n console.log('search add a fq for ',taxa);\n fq = `&fq=taxon_id:(${taxa.join(' OR ')})`;\n }\n return fetch(`${store.selectGrameneAPI()}/search?q=${store.selectGrameneFiltersQueryString()}&facet.field=${facets}&rows=${rows}&start=${offset}${fq}`)\n .then(res => res.json())\n .then(res => {\n res.response.docs.forEach(d => {\n d.can_show = {};\n d.capabilities.forEach(c => {\n d.can_show[c]=true;\n })\n });\n return res;\n })\n }\n});\ngrameneSearch.reactGrameneSearch = createSelector(\n 'selectGrameneSearchShouldUpdate',\n 'selectGrameneFiltersStatus',\n 'selectGrameneGenomes','selectGrameneMaps',\n (shouldUpdate, status, genomes, maps) => {\n if (shouldUpdate && status === 'search' && genomes && maps) {\n return { actionCreator: 'doFetchGrameneSearch' }\n }\n }\n);\n\nfunction formatFacetCountsForViz(a) {\n let res = {\n count: a.length/2,\n displayName: \"fixed_1000__bin\",\n data: {},\n sorted: []\n };\n let counts = [];\n for(let i=0;i<a.length;i+=2) {\n const fc = {\n id: +a[i],\n count: +a[i+1]\n };\n res.data[a[i]] = fc;\n counts.push(fc);\n }\n res.sorted = counts.sort((a,b) => a.id - b.id);\n return res;\n}\n\n// bundle to prepare data for the TaxDist component\nconst grameneTaxDist = {\n name: 'grameneTaxDist',\n getReducer: () => {\n const initialState = {};\n return (state = initialState, {type, payload}) => {\n return state;\n }\n },\n selectGrameneTaxDist: createSelector(\n 'selectGrameneSearch',\n 'selectGrameneTaxonomy',\n 'selectGrameneMaps',\n (grameneSearch,grameneTaxonomy,grameneMaps) => {\n if (grameneSearch && grameneTaxonomy && grameneMaps) {\n _.forIn(grameneMaps, (map, tid) => {\n grameneTaxonomy[tid].name = map.display_name;\n });\n const binnedResults = formatFacetCountsForViz(grameneSearch.facet_counts.facet_fields.fixed_1000__bin);\n let speciesTree = treesClient.taxonomy.tree(Object.values(grameneTaxonomy));\n let binMapper = binsClient.bins(grameneMaps);\n let taxDist = build(binMapper, speciesTree);\n taxDist.setBinType('fixed',1000);\n taxDist.setResults(binnedResults);\n return taxDist;\n }\n return null;\n }\n )\n};\n\n// this query will give the sorghum orthologs of AT1G01260\n// want to provide these on non-sorghum genes if available\n// http://data.gramene.org/search?q=homology__all_orthologs:AT1G01260&fq=taxon_id:4558&fl=id\nconst grameneOrthologs = {\n name: 'grameneOrthologs',\n getReducer: () => {\n const initialState = {};\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_ORTHOLOGS_REQUESTED':\n if (!state.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState[payload] = [];\n return newState;\n }\n break;\n case 'GRAMENE_ORTHOLOGS_RECEIVED':\n return Object.assign({}, state, payload);\n }\n return state;\n }\n },\n doRequestOrthologs: geneId => ({dispatch, store}) => {\n const orthologs = store.selectGrameneOrthologs();\n if (!orthologs.hasOwnProperty(geneId)) {\n dispatch({type: 'GRAMENE_ORTHOLOGS_REQUESTED', payload: geneId});\n const API = store.selectGrameneAPI();\n const taxonId = store.selectTargetTaxonId();\n fetch(`${API}/search?q=homology__all_orthologs:${geneId}&fq=taxon_id:${taxonId}&fl=id`)\n .then(res => res.json())\n .then(res => {\n let newOrthologs = {};\n newOrthologs[geneId] = res.response.docs.map(d => d.id);\n dispatch({type: 'GRAMENE_ORTHOLOGS_RECEIVED', payload: newOrthologs})\n })\n }\n },\n selectGrameneOrthologs: state => state.grameneOrthologs\n};\n\nconst grameneParalogs = {\n name: 'grameneParalogs',\n getReducer: () => {\n const initialState = {};\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_PARALOGS_REQUESTED':\n if (!state.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState[payload] = [];\n return newState;\n }\n break;\n case 'GRAMENE_PARALOGS_RECEIVED':\n return Object.assign({}, state, payload);\n }\n return state;\n }\n },\n doRequestParalogs: (geneId,supertree,taxon_id) => ({dispatch, store}) => {\n const paralogs = store.selectGrameneParalogs();\n if (!paralogs.hasOwnProperty(geneId)) {\n dispatch({type: 'GRAMENE_PARALOGS_REQUESTED', payload: geneId});\n const API = store.selectGrameneAPI();\n const q= supertree ? `supertree_attr_s:${supertree}` : `homology__within_species_paralog:${geneId}`;\n fetch(`${API}/search?q=${q}&rows=100&fq=taxon_id:${taxon_id}`)\n .then(res => res.json())\n .then(res => {\n let newParalogs = {};\n newParalogs[geneId] = res.response.docs.map(d => d.id);\n dispatch({type: 'GRAMENE_PARALOGS_RECEIVED', payload: newParalogs})\n })\n }\n },\n selectGrameneParalogs: state => state.grameneParalogs\n};\n\n// function selectFacetIDs(store, field) {\n// const path = `grameneGenes.data.facet_counts.facet_fields.${field}`;\n// if (_.has(store,path)) {\n// const flat_facets = _.get(store,path);\n// let idList = [];\n// if (isNaN(+flat_facets[0])) {\n// for (let i = 0; i < flat_facets.length; i += 2) {\n// idList.push(flat_facets[i])\n// }\n// }\n// else {\n// for (let i = 0; i < flat_facets.length; i += 2) {\n// idList.push(+flat_facets[i])\n// }\n// if (idList.length === 1) idList.push(0);\n// }\n// return idList;\n// }\n// }\n//\n// grameneGenes.selectDomainFacets = store => selectFacetIDs(store, 'domains');\n// grameneGenes.selectPathwayFacets = store => selectFacetIDs(store, 'pathways');\n// grameneGenes.selectTaxonomyFacets = store => selectFacetIDs(store, 'taxon_id');\n//\n// const grameneDomains = createAsyncResourceBundle({\n// name: 'grameneDomains',\n// actionBaseType: 'GRAMENE_DOMAINS',\n// persist: false,\n// getPromise: ({store}) =>\n// fetch(`${store.selectGrameneAPI()}/domains?rows=-1&idList=${store.selectDomainFacets().join(',')}`)\n// .then(res => res.json())\n// .then(docs => {return {domains: docs, numFound: docs.length}})\n// });\n//\n// const gramenePathways = createAsyncResourceBundle({\n// name: 'gramenePathways',\n// actionBaseType: 'GRAMENE_PATHWAYS',\n// persist: false,\n// getPromise: ({store}) =>\n// fetch(`${store.selectGrameneAPI()}/pathways?rows=-1&idList=${store.selectPathwayFacets().join(',')}`)\n// .then(res => res.json())\n// .then(docs => {return {pathways: docs, numFound: docs.length}})\n// });\n//\n// const grameneTaxonomy = createAsyncResourceBundle({\n// name: 'grameneTaxonomy',\n// actionBaseType: 'GRAMENE_TAXONOMY',\n// persist: false,\n// getPromise: ({store}) =>\n// fetch(`${store.selectGrameneAPI()}/taxonomy?rows=-1&idList=${store.selectTaxonomyFacets().join(',')}`)\n// .then(res => res.json())\n// .then(docs => {return {taxonomy: docs, numFound: docs.length}})\n// });\n\n\nexport default [grameneSuggestions, grameneSearch, grameneMaps, grameneTaxonomy, grameneTaxDist, grameneOrthologs, grameneParalogs, curatedGenes, grameneGermplasm, grameneGeneAttribs, expressionSamples, expressionStudies];\n","import {createSelector} from \"redux-bundler\";\nimport _ from 'lodash';\nimport ReactGA from 'react-ga4'\nconst MAX_IDLIST_LENGTH = 20;\n\nfunction findNodeWithLeftIdx(node, idx) {\n if (node.leftIdx === idx) {\n return node;\n }\n let result=null;\n if (node.leftIdx < idx && node.hasOwnProperty('children')) {\n node.children.forEach(child => {\n if (child.rightIdx > idx) {\n child.parentIdx = node.leftIdx;\n const res = findNodeWithLeftIdx(child, idx);\n if (res) result = res;\n }\n })\n }\n return result;\n}\n\nfunction markSubtree(node, source, invert) {\n node.marked = (node.leftIdx >= source.leftIdx && node.rightIdx <= source.rightIdx);\n if (invert) node.marked = !node.marked;\n if (node.hasOwnProperty('children')) {\n node.children.forEach(child => {\n markSubtree(child, source, invert);\n })\n }\n}\n\nfunction reindexTree(node, idx) {\n node.leftIdx = idx;\n idx++;\n if (node.hasOwnProperty('children')) {\n node.children.forEach(child => {\n idx = reindexTree(child, idx);\n });\n }\n node.rightIdx = idx;\n idx++;\n return idx;\n}\n\nconst grameneFilters = {\n name: 'grameneFilters',\n getReducer: () => {\n const initialState = {\n status: 'init', // others include 'search', 'waiting' and 'ready'\n operation: 'AND',\n negate: false,\n marked: false,\n leftIdx: 0,\n rightIdx: 1,\n children: [],\n showMarked: false,\n showMenu: false,\n moveCopyMode: '',\n searchOffset: 0,\n rows: 20\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_FILTERS_CLEARED': {\n newState = Object.assign({}, initialState, {\n status: 'search',\n children: []\n });\n return newState;\n }\n case 'GRAMENE_FILTER_ADDED': {\n const idx = state.rightIdx;\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n rightIdx: idx + 2,\n searchOffset: 0\n });\n let child = _.pick(payload, ['fq_field', 'fq_value', 'name', 'category']);\n child.leftIdx = idx;\n child.rightIdx = idx + 1;\n child.negate = false;\n child.showMenu = false;\n newState.children.push(child);\n markSubtree(newState, child, false);\n return newState;\n }\n case 'GRAMENE_FILTER_TREE_ADDED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n rightIdx: payload.rightIdx + 1,\n searchOffset: 0\n });\n newState.children.push(payload);\n markSubtree(newState, payload, false);\n return newState;\n }\n case 'GRAMENE_FILTER_SET_ADDED': {\n // create a filter with the payload.operation and children payload.filters\n let filter = {\n leftIdx: state.rightIdx,\n rightIdx: state.rightIdx + (payload.filters.length) * 2 + 1,\n operation: payload.operation,\n negate: false,\n showMenu: false,\n children: payload.filters\n };\n if (payload.warning) {\n filter.warning = payload.warning\n }\n let nextIdx = filter.leftIdx+1;\n payload.filters.forEach(f => {\n f.leftIdx = nextIdx++;\n f.rightIdx = nextIdx++;\n f.negate = false;\n f.showMenu = false;\n });\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0,\n rightIdx: filter.rightIdx + 1\n });\n newState.children.push(filter);\n markSubtree(newState, filter, false);\n return newState;\n }\n case 'GRAMENE_FILTER_NEGATED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0\n });\n let node = findNodeWithLeftIdx(newState, payload.leftIdx);\n if (node) {\n node.negate = !node.negate;\n markSubtree(newState, node, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_DELETED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0\n });\n let node = findNodeWithLeftIdx(newState, payload.leftIdx);\n if (node) {\n let parent = findNodeWithLeftIdx(newState, node.parentIdx);\n parent.children = parent.children.filter(child => child.leftIdx !== node.leftIdx);\n reindexTree(newState, 0);\n markSubtree(newState, parent, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_OPERATION_CHANGED': {\n if (payload.hasOwnProperty('operation')) {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0\n });\n let node = findNodeWithLeftIdx(newState, payload.leftIdx);\n node.operation = node.operation === 'AND' ? 'OR' : 'AND';\n markSubtree(newState, node, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_MOVED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n moveCopyMode: '',\n searchOffset: 0\n });\n let source = findNodeWithLeftIdx(newState, payload.source.leftIdx);\n let target = findNodeWithLeftIdx(newState, payload.target.leftIdx);\n if (source && target) {\n source.showMenu = false;\n let parent = findNodeWithLeftIdx(newState, source.parentIdx);\n parent.children = parent.children.filter(child => child.leftIdx !== source.leftIdx);\n target.showMenu = false;\n if (!target.hasOwnProperty('children')) {\n let targetCopy = Object.assign({}, target);\n target.children = [targetCopy];\n target.operation = 'OR';\n target.negate = false;\n delete target.fq_field;\n delete target.fq_value;\n delete target.name;\n delete target.category;\n }\n target.children.push(source);\n reindexTree(newState, 0);\n markSubtree(newState, target, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_COPIED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n moveCopyMode: '',\n searchOffset: 0\n });\n let source = findNodeWithLeftIdx(newState, payload.source.leftIdx);\n let target = findNodeWithLeftIdx(newState, payload.target.leftIdx);\n if (source && target) {\n source.showMenu = false;\n if (!target.hasOwnProperty('children')) {\n let targetCopy = Object.assign({}, target);\n target.children = [targetCopy];\n target.operation = 'OR';\n target.negate = false;\n delete target.fq_field;\n delete target.fq_value;\n delete target.name;\n delete target.category;\n }\n let sourceCopy = Object.assign({}, source);\n target.children.push(sourceCopy);\n reindexTree(newState, 0);\n markSubtree(newState, target, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_TARGETS_MARKED':\n newState = Object.assign({}, state, {\n showMarked: true,\n moveCopyMode: payload.mode,\n moveCopySource: payload.source\n });\n markSubtree(newState, payload.source, true);\n return newState;\n case 'GRAMENE_FILTER_TARGETS_UNMARKED':\n newState = Object.assign({}, state, {\n showMarked: false\n });\n return newState;\n case 'GRAMENE_FILTERS_REPLACED':\n payload.status = 'search';\n payload.searchOffset = 0;\n return payload;\n case 'GRAMENE_FILTERS_STATUS_CHANGED':\n if (!(state.status === 'ready' && payload === 'waiting')) {\n return Object.assign({}, state, {status: payload})\n }\n break;\n case 'GRAMENE_FILTERS_SET_SHOW_MARKED':\n return Object.assign({}, state, {showMarked: payload});\n case 'GRAMENE_FILTER_MENU_TOGGLED':\n payload.showMenu = !payload.showMenu;\n return Object.assign({}, state);\n case 'GRAMENE_SEARCH_PAGE_REQUESTED':\n return Object.assign({}, state, {status: 'search', searchOffset: payload * state.rows});\n case 'GRAMENE_SEARCH_FETCH_STARTED':\n return Object.assign({}, state, {status: 'loading'});\n case 'GRAMENE_SEARCH_FETCH_FINISHED':\n return Object.assign({}, state, {status: 'finished'});\n case 'GRAMENE_GENOMES_UPDATED':\n return Object.assign({}, state, {status: 'search'});\n case 'URL_UPDATED':\n if (state.status === 'ready') {\n return Object.assign({}, initialState, {children:[]})\n }\n break;\n case 'APP_IDLE':\n if (state.showMarked) {\n return Object.assign({}, state, {showMarked: false})\n }\n }\n return state;\n }\n },\n doNegateGrameneFilter: filter => ({dispatch, getState}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_NEGATED', payload: filter}\n ]\n })\n },\n doDeleteGrameneFilter: filter => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_TAXONOMY_CLEARED'},\n {type: 'GRAMENE_FILTER_DELETED', payload: filter}\n ]\n })\n },\n doChangeGrameneFilterOperation: filter => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_OPERATION_CHANGED', payload: filter}\n ]\n })\n },\n doMoveOrCopyGrameneFilter: (target) => ({dispatch, getState}) => {\n const state = getState();\n if (state.grameneFilters.moveCopyMode) {\n const source = state.grameneFilters.moveCopySource;\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: `GRAMENE_FILTER_${state.grameneFilters.moveCopyMode.toUpperCase()}D`, payload: {source, target}}\n ]\n })\n }\n },\n doCopyGrameneFilter: (source, target) => ({dispatch, getState}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_COPIED', payload: {source, target}}\n ]\n })\n },\n doMarkGrameneFilterTargets: (source, mode) => ({dispatch}) => {\n dispatch({type: 'GRAMENE_FILTER_TARGETS_MARKED', payload: {source:source, mode:mode}})\n },\n doUnmarkGrameneFilterTargets: () => ({dispatch}) => {\n dispatch({type: 'GRAMENE_FILTER_TARGETS_UNMARKED'})\n },\n doAcceptGrameneSuggestion: suggestion => ({dispatch, getState}) => {\n if (!suggestion.name) {\n suggestion.name = suggestion.display_name;\n }\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: suggestion}\n ]\n })\n },\n doAddGrameneRangeQuery: terms => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_SET_ADDED', payload: {operation: 'AND', filters: terms}}\n ]\n })\n },\n doToggleGrameneFilterMenu: node => ({dispatch}) => {\n dispatch({type: 'GRAMENE_FILTER_MENU_TOGGLED', payload: node})\n },\n doRequestResultsPage: page => ({dispatch}) => {\n dispatch(\n {type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_SEARCH_PAGE_REQUESTED', payload: page}\n ]\n })\n },\n doReplaceGrameneFilters: filters => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_REPLACED', payload: filters}\n ]\n })\n },\n doClearGrameneFilters: () => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_CLEARED'}\n ]\n })\n },\n selectGrameneFilters: state => state.grameneFilters,\n selectGrameneFiltersStatus: state => state.grameneFilters.status,\n selectGrameneFiltersQueryString: state => {\n const hasSpaces = new RegExp(/^[^\\[\\(].\\s/);\n const isQuery = new RegExp(/\\([a-zA-Z0-9_]+:[a-zA-Z0-9_]+\\s/);\n const isRegionQuery = new RegExp(/^\\(map:/);\n const idWithColon = new RegExp(/^[a-zA-Z0-9_]+:[a-zA-Z0-9_]+$/);\n function getQuery(node) {\n const negate = node.negate ? 'NOT ' : '';\n if (node.hasOwnProperty('children')) {\n // do some recursion\n return `${negate}(${node.children.map(c => getQuery(c)).sort().join(` ${node.operation} `)})`\n }\n else {\n // this node is a suggestion\n if (node.fq_field === 'location' && isRegionQuery.test(node.fq_value))\n return `${negate}${node.fq_value}`\n if (isQuery.test(node.fq_value))\n return `${negate}${node.fq_value.replace(/:/g,'\\\\:')}`;\n if (hasSpaces.test(node.fq_value))\n return `${negate}${node.fq_field}:\"${node.fq_value}\"`;\n else if (idWithColon.test(node.fq_value))\n return `${negate}${node.fq_field}:${node.fq_value.replace(/:/g,'\\\\:')}`;\n else\n return `${negate}${node.fq_field}:${node.fq_value}`\n }\n }\n if (state.grameneFilters.rightIdx === 1) {\n return ':';\n }\n return `:* AND (${getQuery(state.grameneFilters)})`;\n },\n selectGrameneSearchOffset: state => state.grameneFilters.searchOffset,\n selectGrameneSearchRows: state => state.grameneFilters.rows\n};\n\nconst handleIdList = (queryObject) => {\n let actions = [{type: 'GRAMENE_SEARCH_CLEARED'}];\n let ids = _.uniq(queryObject.idList.split(','));\n let warning = null;\n if (ids.length > MAX_IDLIST_LENGTH) {\n ids = _.slice(ids, 0, MAX_IDLIST_LENGTH);\n warning = `The idList query parameter is limited to ${MAX_IDLIST_LENGTH} genes`\n }\n let filters = ids.map((id,idx) => {\n return {\n category: 'Gene',\n name: id,\n fq_field: 'id',\n fq_value: id\n }\n });\n if (filters.length === 1) {\n actions.push({type: 'GRAMENE_FILTER_ADDED', payload: filters[0]})\n }\n else {\n let action = {type: 'GRAMENE_FILTER_SET_ADDED', payload: {operation: 'OR', filters:filters}};\n if (warning) {\n action.payload.warning = warning\n }\n actions.push(action)\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n};\n\ngrameneFilters.reactGrameneFilters = createSelector(\n 'selectQueryObject',\n 'selectGrameneFilters',\n 'selectActiveGenomes',\n 'selectUrlObject',\n (queryObject, filters, genomes, myUrl) => {\n if (filters.status === 'init') {\n if (queryObject.filters) {\n const newFilters = JSON.parse(queryObject.filters);\n let actions = [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_REPLACED', payload: newFilters}\n ];\n if (queryObject.genomes) {\n let active={};\n queryObject.genomes.split(',').forEach(t => {\n active[t]=true\n });\n actions.push({type: 'GRAMENE_GENOMES_UPDATED', payload: active});\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n }\n if (queryObject.hasOwnProperty('sugg')) {\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: JSON.parse(queryObject.sugg)}\n ]\n };\n }\n if (queryObject.hasOwnProperty('suggestion')) {\n const url = new URL(myUrl.href);\n url.search = '';\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'URL_UPDATED', payload: {url: url.href, replace:false}},\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'SUGGESTIONS_QUERY_CHANGED', payload: {query: queryObject.suggestion}}\n ]\n };\n }\n if (queryObject.hasOwnProperty('idList')) {\n return handleIdList(queryObject);\n }\n if (queryObject.hasOwnProperty('fq_field') && queryObject.hasOwnProperty('fq_value')\n && queryObject.hasOwnProperty('category') && queryObject.hasOwnProperty('name')) {\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: queryObject}\n ]\n };\n }\n const url = new URL(myUrl.href);\n if (url.pathname === '/genes') {\n return {type: 'GRAMENE_FILTERS_CLEARED'}\n }\n }\n if (filters.status === 'finished') {\n const url = new URL(myUrl.href);\n url.search = `filters=${JSON.stringify(Object.assign({}, filters, {status: 'init'}))}&genomes=${genomes.join(',')}`;\n ReactGA.event({\n category: \"Gene Search\",\n action: \"filter finished\",\n label: url.search\n });\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'URL_UPDATED', payload: {url: url.href, replace:false}},\n {type: 'GRAMENE_FILTERS_STATUS_CHANGED', payload: 'ready'}\n ]\n }\n }\n }\n);\n\nexport default grameneFilters;\n","const grameneViews = {\n name: 'grameneViews',\n getReducer: () => {\n const initialState = {\n options: [\n {\n id: 'help',\n name: 'Help / Demo',\n show: 'off',\n shouldScroll: false\n },\n {\n id: 'userLists',\n name: 'User Gene Lists',\n show: 'off',\n shouldScroll: false\n },\n {\n id: 'taxonomy',\n name: 'Taxonomic distribution',\n show: 'on',\n shouldScroll: false\n },\n {\n id: 'list',\n name: 'Gene list',\n show: 'on',\n shouldScroll: false\n },\n {\n id: 'expression',\n name: 'Gene expression',\n show: 'off',\n shouldScroll: false,\n desiredSamples: {}\n },\n {\n id: 'attribs',\n name: 'Gene attributes',\n show: 'disabled',\n shouldScroll: false\n }\n // {\n // id: 'domains',\n // name: 'Domains',\n // show: 'disabled'\n // },\n // {\n // id: 'go',\n // name: 'GO terms',\n // show: 'disabled'\n // }\n ]\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_VIEW_TOGGLED':\n newState = Object.assign({},state);\n newState.options.forEach(view => {\n view.shouldScroll = false;\n if (view.id === payload) {\n view.show = view.show === 'on' ? 'off' : 'on'\n view.shouldScroll = view.show === 'on';\n }\n });\n return newState;\n case 'GRAMENE_VIEW_CLICKED':\n newState = Object.assign({}, state);\n newState.options.forEach(view => {\n view.shouldScroll = false;\n if (view.id === payload) {\n view.show = view.show === 'on' ? 'on' : 'on';\n view.shouldScroll = view.show === 'on';\n }\n });\n return newState;\n case 'GRAMENE_VIEW_SCROLLED':\n newState = Object.assign({}, state);\n newState.options.forEach(v => v.shouldScroll = false)\n return newState;\n default:\n return state;\n }\n }\n },\n doToggleGrameneView: idx => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_VIEW_TOGGLED', payload: idx})\n },\n dontToggleGrameneView: idx => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_VIEW_CLICKED', payload: idx})\n },\n doCancelShouldScroll: () => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_VIEW_SCROLLED', payload: null})\n },\n selectGrameneViews: state => state.grameneViews\n};\n\nexport default grameneViews;\n","const grameneDocs = {\n name: 'grameneDocs',\n getReducer: () => {\n const initialState = {\n genes: {},\n trees: {},\n domains: {},\n pathways: {},\n expression: {},\n sequences: {},\n rnaSequences: {},\n pepSequences: {},\n studies: {},\n desiredSamples: {},\n consequences: {}\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_CONSEQUENCES_REQUESTED':\n if (!state.consequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.consequences[payload] = {};\n return newState;\n }\n break;\n case 'GRAMENE_CONSEQUENCES_RECEIVED':\n newState = Object.assign({}, state);\n newState.consequences = Object.assign({}, state.consequences, payload);\n return newState;\n case 'GRAMENE_GENE_REQUESTED':\n if (!state.genes.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.genes[payload] = {};\n return newState;\n }\n break;\n case 'GRAMENE_GENE_RECEIVED':\n newState = Object.assign({}, state);\n newState.genes = Object.assign({}, state.genes, payload);\n return newState;\n case 'GRAMENE_TREE_REQUESTED':\n if (!state.trees.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.trees[payload] = {};\n return newState;\n }\n break;\n case 'GRAMENE_TREE_RECEIVED':\n newState = Object.assign({}, state);\n newState.trees = Object.assign({}, state.trees, payload);\n return newState;\n case 'GRAMENE_PATHWAYS_RECEIVED':\n newState = Object.assign({}, state);\n newState.pathways = Object.assign({}, state.pathways, payload);\n return newState;\n case 'ATLAS_STUDIES_RECEIVED':\n newState = Object.assign({}, state);\n newState.studies = Object.assign({}, state.studies, payload);\n return newState;\n case 'ATLAS_SAMPLES_REQUESTED':\n if (!state.studies.byID[payload].hasOwnProperty('samples')) {\n newState = Object.assign({},state);\n newState.studies.byID[payload].samples = [];\n return newState;\n }\n break;\n case 'ATLAS_SAMPLES_RECEIVED':\n newState = Object.assign({}, state);\n newState.studies.byID[payload.id].samples = payload.samples;\n return newState;\n case 'GENE_SEQUENCE_REQUESTED':\n if (!state.sequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.sequences[payload] = {};\n return newState;\n }\n break;\n case 'RNA_SEQUENCE_REQUESTED':\n if (!state.rnaSequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.rnaSequences[payload] = {};\n return newState;\n }\n break;\n case 'PEP_SEQUENCE_REQUESTED':\n if (!state.rnaSequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.pepSequences[payload] = {};\n return newState;\n }\n break;\n case 'GENE_SEQUENCE_RECEIVED':\n newState = Object.assign({}, state);\n newState.sequences = Object.assign({}, state.sequences);\n newState.sequences[payload.id] = payload.geneSeq;\n return newState;\n case 'RNA_SEQUENCE_RECEIVED':\n newState = Object.assign({}, state);\n newState.rnaSequences = Object.assign({}, state.rnaSequences);\n newState.rnaSequences[payload.id] = payload.RnaSeq;\n return newState;\n case 'PEP_SEQUENCE_RECEIVED':\n newState = Object.assign({}, state);\n newState.pepSequences = Object.assign({}, state.pepSequences);\n newState.pepSequences[payload.id] = payload.PepSeq;\n return newState;\n case 'PARALOG_EXPRESSION_REQUESTED':\n if (!state.expression.hasOwnProperty(payload)) {\n newState = Object.assign({},state);\n newState.expression[payload] = [];\n return newState;\n }\n break;\n case 'PARALOG_EXPRESSION_RECEIVED':\n newState = Object.assign({}, state);\n newState.expression = Object.assign({}, state.expression);\n newState.expression[payload.id] = payload.paralogs;\n return newState;\n case 'EXPRESSION_SAMPLE_TOGGLED':\n newState = Object.assign({}, state);\n newState.desiredSamples = Object.assign({}, state.desiredSamples);\n if (newState.desiredSamples.hasOwnProperty(payload)) {\n delete newState.desiredSamples[payload]\n }\n else {\n newState.desiredSamples[payload] = {status: 'need'}\n }\n }\n return state;\n }\n },\n doToggleExpressionSample: id => ({dispatch}) => {\n dispatch({type: 'EXPRESSION_SAMPLE_TOGGLED', payload: id});\n },\n doRequestVEP: id => ({dispatch, store}) => {\n const consequences = store.selectGrameneConsequences();\n if (!consequences.hasOwnProperty(id)) {\n dispatch({type: 'GRAMENE_CONSEQUENCES_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/search?q=id:${id}&fl=id,VEP__`)\n .then(res => res.json())\n .then(res => {\n let genes = {};\n res.response.docs.forEach(g => {\n genes[g.id] = g;\n });\n dispatch({type: 'GRAMENE_CONSEQUENCES_RECEIVED', payload: genes})\n })\n }\n },\n doRequestGrameneGene: id => ({dispatch, store}) => {\n const genes = store.selectGrameneGenes();\n if (!genes.hasOwnProperty(id)) {\n dispatch({type: 'GRAMENE_GENE_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/genes?idList=${id}`)\n .then(res => res.json())\n .then(res => {\n let genes = {};\n res.forEach(g => {\n genes[g._id] = g;\n });\n dispatch({type: 'GRAMENE_GENE_RECEIVED', payload: genes})\n })\n }\n },\n doRequestGrameneTree: id => ({dispatch, store}) => {\n const trees = store.selectGrameneTrees();\n const maps = store.selectGrameneMaps();\n if (!trees.hasOwnProperty(id)) {\n dispatch({type: 'GRAMENE_TREE_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/genetrees?idList=${id}`)\n .then(res => res.json())\n .then(res => {\n let trees = {};\n res.forEach(t => {\n function update_taxon_name(node) {\n if (maps.hasOwnProperty(node.taxon_id)) {\n node.taxon_name = maps[node.taxon_id].display_name\n }\n else if (node.taxon_id === 1100004558) {\n node.taxon_name = \"Sorghum bicolor\"\n }\n if (node.taxon_id === 45580023 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Sorghum bicolor\"\n }\n if (node.taxon_id === 45770001 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Zea mays\"\n }\n if (node.taxon_id === 297600009 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Vitis vinifera\"\n }\n if (node.hasOwnProperty('children')) {\n node.children.forEach(c => update_taxon_name(c))\n }\n }\n update_taxon_name(t);\n trees[t._id] = t;\n });\n dispatch({type: 'GRAMENE_TREE_RECEIVED', payload: trees})\n })\n }\n },\n doRequestGramenePathways: ids => ({dispatch, store}) => {\n const pathways = store.selectGramenePathways();\n let newIds = ids.filter(id => !pathways.hasOwnProperty(id));\n if (newIds) {\n dispatch({type: 'GRAMENE_PATHWAYS_REQUESTED', payload: newIds});\n if (newIds.length === 1) newIds.push(0);\n fetch(`${store.selectGrameneAPI()}/pathways?idList=${newIds.join(',')}`)\n .then(res => res.json())\n .then(res => {\n let pathways = {};\n res.forEach(p => {\n pathways[p._id] = p;\n });\n dispatch({type: 'GRAMENE_PATHWAYS_RECEIVED', payload: pathways})\n })\n }\n },\n doRequestExpressionStudies: id => ({dispatch, store}) => {\n fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`)\n .then(res => res.json())\n .then(res => {\n let studies = {byID:{},byTaxon:{}};\n res.forEach(s => {\n studies.byID[s._id] = s;\n if (! studies.byTaxon.hasOwnProperty(s.taxon_id)) {\n studies.byTaxon[s.taxon_id] = []\n }\n studies.byTaxon[s.taxon_id].push(s._id)\n })\n dispatch({type: 'ATLAS_STUDIES_RECEIVED', payload: studies})\n })\n },\n doRequestStudyMetadata: id => ({dispatch, store}) => {\n const studies = store.selectAtlasStudies();\n if (!studies.byID[id].hasOwnProperty('samples')) {\n dispatch({type: 'ATLAS_SAMPLES_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/assays?experiment=${id}&rows=-1`)\n .then(res => res.json())\n .then(samples => {\n dispatch({type: 'ATLAS_SAMPLES_RECEIVED', payload: {id, samples}})\n })\n }\n },\n doRequestGeneSequence: gene => ({dispatch, store}) => {\n const maps = store.selectGrameneMaps();\n const seqs = store.selectGeneSequences();\n const id = gene._id;\n const MAX_FLANK = 2000;\n if (!seqs.hasOwnProperty(id)) {\n dispatch({type: 'GENE_SEQUENCE_REQUESTED', payload: id});\n const start = gene.location.start > MAX_FLANK ? gene.location.start - MAX_FLANK : 1;\n const dnaLength = maps[gene.taxon_id].regionLength[gene.location.region];\n const end = gene.location.end + MAX_FLANK > dnaLength ? dnaLength : gene.location.end + MAX_FLANK;\n fetch(`${store.selectEnsemblAPI()}/sequence/region/${gene.system_name}/${gene.location.region}:${start}..${end}:${gene.location.strand}?content-type=application/json`)\n .then(res => res.json())\n .then(geneSeq => {\n const x = geneSeq.id.split(':');\n geneSeq.genome = x[1];\n geneSeq.start = +x[3];\n geneSeq.end = +x[4];\n dispatch({type: 'GENE_SEQUENCE_RECEIVED', payload: {id, geneSeq}});\n })\n }\n },\n doRequestRnaSequence: (id,gene) => ({dispatch, store}) => {\n const seqs = store.selectRnaSequences();\n if (!seqs.hasOwnProperty(id)) {\n dispatch({type: 'RNA_SEQUENCE_REQUESTED', payload: id});\n fetch(`${store.selectEnsemblAPI()}/sequence/id/${id}?species=${gene.system_name}&type=cdna&content-type=application/json`)\n .then(res => res.json())\n .then(RnaSeq => {\n dispatch({type: 'RNA_SEQUENCE_RECEIVED', payload: {id, RnaSeq}});\n })\n }\n },\n doRequestPepSequence: (id,gene) => ({dispatch, store}) => {\n const seqs = store.selectPepSequences();\n if (!seqs.hasOwnProperty(id)) {\n dispatch({type: 'PEP_SEQUENCE_REQUESTED', payload: id});\n fetch(`${store.selectEnsemblAPI()}/sequence/id/${id}?species=${gene.system_name}&type=protein&content-type=application/json`)\n .then(res => res.json())\n .then(PepSeq => {\n dispatch({type: 'PEP_SEQUENCE_RECEIVED', payload: {id, PepSeq}});\n })\n }\n },\n doRequestParalogExpression: id => ({dispatch, store}) => {\n const expr = store.selectParalogExpression();\n if (!expr.hasOwnProperty(id)) {\n dispatch({type: 'PARALOG_EXPRESSION_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/search?q=homology__within_species_paralog:${id}&fl=id,atlas_id,name,__expr&rows=100`)\n .then(res => res.json())\n .then(res => {\n const assay_re = /(.+)_g(\\d+)/;\n const paralogs = res.response.docs.map(d => {\n let p = {\n id: d.id,\n name: d.name,\n experiments: {},\n min:1000,\n max:0\n };\n if (d.atlas_id) {\n p.atlas_id = d.atlas_id;\n delete d.atlas_id;\n }\n delete d.id;\n delete d.name;\n Object.entries(d).forEach(assay => {\n const parsed = assay[0].match(assay_re);\n const expr = parsed[1].replace('_','-').replace('-tpms','');\n if (! p.experiments.hasOwnProperty(expr)) {\n p.experiments[expr] = [];\n }\n const g = parsed[2] - 1;\n const e = d[assay[0]];\n if (e < p.min) p.min = e;\n if (e > p.max) p.max = e;\n p.experiments[expr][g] = e;\n });\n return p;\n }).map(p => {\n for (const expr in p.experiments) {\n p.experiments[expr] = p.experiments[expr].filter(e => e >= 0);\n }\n return p;\n });\n dispatch({type: 'PARALOG_EXPRESSION_RECEIVED', payload: {id, paralogs}});\n })\n }\n },\n selectGrameneGenes: state => state.grameneDocs.genes,\n selectGrameneConsequences: state => state.grameneDocs.consequences,\n selectGrameneTrees: state => state.grameneDocs.trees,\n selectGramenePathways: state => state.grameneDocs.pathways,\n selectParalogExpression: state => state.grameneDocs.expression,\n selectGeneSequences: state => state.grameneDocs.sequences,\n selectRnaSequences: state => state.grameneDocs.rnaSequences,\n selectPepSequences: state => state.grameneDocs.pepSequences,\n selectAtlasStudies: state => state.grameneDocs.studies,\n selectDesiredSamples: state => state.grameneDocs.desiredSamples\n};\n\nexport default grameneDocs;\n","import {createSelector} from \"redux-bundler\";\nconst grameneGenomes = {\n name: 'grameneGenomes',\n getReducer: () => {\n const initialState = {\n show: false,\n active: {}\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_GENOMES_TOGGLED':\n newState = Object.assign({},state);\n newState.show = !newState.show;\n return newState;\n case 'GRAMENE_GENOMES_UPDATED':\n newState = Object.assign({}, state);\n newState.active = payload;\n return newState;\n case 'GRAMENE_MAPS_FETCH_FINISHED':\n newState = Object.assign({}, state);\n newState.active = payload;\n default:\n return state;\n }\n }\n },\n doShowGrameneGenomes: () => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_GENOMES_TOGGLED'})\n },\n doInitializeGrameneGenomes: genomes => ({dispatch, getState}) => {\n dispatch({type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_GENOMES_UPDATED', payload: genomes}]})\n },\n doUpdateGrameneGenomes: genomes => ({dispatch, getState}) => {\n dispatch({type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_GENOMES_TOGGLED'},\n {type: 'GRAMENE_GENOMES_UPDATED', payload: genomes}]})\n },\n doEnsureGrameneGenome: genome => ({dispatch, getState}) => {\n const state = getState();\n if (Object.keys(state.grameneGenomes.active).length > 0 && !state.grameneGenomes.active.hasOwnProperty(genome)) {\n let active = Object.assign({}, state.grameneGenomes.active);\n active[genome]=true;\n dispatch({type: 'GRAMENE_GENOMES_UPDATED', payload: active})\n }\n },\n selectGrameneGenomes: state => state.grameneGenomes,\n selectActiveGenomes: state => {\n return Object.keys(state.grameneGenomes.active)\n },\n selectActiveGenomeCount: createSelector(\n 'selectGrameneMaps',\n 'selectGrameneGenomes',\n (maps,genomes) => {\n if (maps && genomes) {\n return Object.keys(genomes.active).length \|\| Object.keys(maps).length;\n }\n return 0;\n }\n )\n};\n\nexport default grameneGenomes;","import {connect} from 'redux-bundler-react'\nimport React from 'react'\n\nconst Gene = ({gene}) => {\n return <div className=\"row\">{gene.id}</div>\n};\n\nconst Genes = (results, rows, doChangeQuantity) => {\n if (results && results.numFound > 0) {\n const moreButton = (results.numFound > rows)\n ? <button onClick={e => doChangeQuantity('Genes',20)}>more</button>\n : '';\n const fewerButton = (rows > 20)\n ? <button onClick={e => doChangeQuantity('Genes',-20)}>fewer</button>\n : '';\n const docsToShow = results.response.docs.slice(0,rows);\n return (\n <div id=\"Genes\" className=\"container mb40 anchor\">\n <div className=\"fancy-title mb40\">\n <h4>Genes</h4>\n </div>\n {docsToShow.map((doc,idx) => <Gene key={idx} gene={doc}/>)}\n {fewerButton}{moreButton}\n </div>\n );\n }\n};\n\nconst Pathway = ({pathway}) => {\n return <div className=\"row\">{pathway.name}</div>\n};\nconst Pathways = results => {\n if (results && results.numFound > 0) {\n return (\n <div id=\"Pathways\" className=\"container mb40 anchor\">\n <div className=\"fancy-title\">\n <h4>Pathways</h4>\n </div>\n {results.pathways.map((doc,idx) => (<Pathway key={idx} pathway={doc}/>))}\n </div>\n );\n }\n};\n\nconst Domain = ({domain}) => {\n return <div className=\"row\">{domain.id}</div>\n};\nconst Domains = results => {\n if (results && results.numFound > 0) {\n return (\n <div id=\"Domains\" className=\"container mb40 anchor\">\n <div className=\"fancy-title mb40\">\n <h4>Domains</h4>\n </div>\n {results.domains.map((doc,idx) => (<Domain key={idx} domain={doc}/>))}\n </div>\n );\n }\n};\n\nconst Taxon = ({taxon}) => {\n return <div className=\"row\">{taxon.id}</div>\n};\nconst Species = results => {\n if (results && results.numFound > 0) {\n return (\n <div id=\"Species\" className=\"container mb40 anchor\">\n <div className=\"fancy-title mb40\">\n <h4>Species</h4>\n </div>\n {results.taxonomy.map((doc,idx) => (<Taxon key={idx} taxon={doc}/>))}\n </div>\n );\n }\n};\n\nconst ResultList = ({grameneGenes, grameneDomains, gramenePathways, grameneTaxonomy, searchUI, searchUpdated, doChangeQuantity}) => {\n if (searchUI.Gramene) {\n return (\n <div id=\"gramene\" className=\"row\">\n <div className=\"fancy-title pt50\">\n <h3>Gramene search results</h3>\n </div>\n {searchUI.Genes && Genes(grameneGenes, searchUI.rows.Genes, doChangeQuantity)}\n {searchUI.Domains && Domains(grameneDomains)}\n {searchUI.Pathways && Pathways(gramenePathways)}\n {searchUI.Species && Species(grameneTaxonomy)}\n </div>\n )\n }\n else {\n return null;\n }\n};\n\nexport default connect(\n 'selectGrameneGenes',\n 'selectGrameneDomains',\n 'selectGramenePathways',\n 'selectGrameneTaxonomy',\n 'selectSearchUI',\n 'selectSearchUpdated',\n 'doChangeQuantity',\n ResultList\n);\n","import {connect} from 'redux-bundler-react'\nimport React from 'react'\n\nconst getStatus = (cat, results, isChecked, toggle) => {\n const tally = results ? results.numFound : <img src=\"/static/images/dna_spinner.svg\"/>;\n return (\n <li className='category-leaf'>\n <input type=\"checkbox\" checked={isChecked} onChange={e => toggle(cat)}/>\n <a data-scroll href={`#${cat}`} className=\"nav-link active\">{cat}<span style={{float:\"right\"}}>{tally}</span></a>\n </li>\n )\n};\n\nconst ResultSummary = ({grameneGenes, gramenePathways, grameneDomains, grameneTaxonomy, searchUI, searchUpdated, doToggleCategory}) => {\n const status = grameneGenes ?\n grameneGenes.numFound:\n<img src=\"/static/images/dna_spinner.svg\"/>;\n if (searchUI.Gramene) return (\n <li className=\"active category-expanded\">\n <a onClick={e => doToggleCategory('Gramene')}>\n Gramene Search<span style={{float:\"right\"}}>{status}</span>\n </a>\n <ul className=\"list-unstyled\">\n {getStatus('Genes', grameneGenes, searchUI.Genes, doToggleCategory)}\n {getStatus('Domains', grameneDomains, searchUI.Domains, doToggleCategory)}\n {getStatus('Pathways', gramenePathways, searchUI.Pathways, doToggleCategory)}\n {getStatus('Species', grameneTaxonomy, searchUI.Species, doToggleCategory)}\n</ul>\n </li>\n);\nelse return (\n <li className=\"active category-collapsed\">\n <a onClick={e => doToggleCategory('Gramene')}>\n Gramene Search<span\n style={{float:\"right\"}}>{status}</span>\n </a>\n </li>\n);\n};\n\nexport default connect(\n 'selectGrameneGenes',\n 'selectGramenePathways',\n 'selectGrameneDomains',\n 'selectGrameneTaxonomy',\n 'selectSearchUI',\n 'selectSearchUpdated',\n 'doToggleCategory',\n ResultSummary\n);\n","import {connect} from 'redux-bundler-react'\nimport React from 'react'\nimport ReactGA from 'react-ga4'\nimport { Button, Badge, Alert } from 'react-bootstrap'\nimport './styles.css'\n\nfunction showMatches(text, x) {\n let re = new RegExp(`(${x})`, 'ig');\n let match = text.split(re);\n return <span>\n {match.map((str, idx) => {\n if (idx % 2 === 1) {\n return <span key={idx} style={{fontWeight:'bolder'}}>{str}</span>\n }\n return <span key={idx}>{str}</span>\n })}\n </span>\n}\n\nfunction logAction(sugg) {\n ReactGA.event({\n category: 'Search',\n action: 'SetFilter',\n label: sugg.name\n })\n}\nfunction getLowestCommonAncestorName(tids, taxonomy) {\n let lca;\n tids.forEach(tid => {\n if (!lca) {\n lca = [...taxonomy[tid].ancestors];\n } else {\n let ancestors = new Set(taxonomy[tid].ancestors);\n while (!ancestors.has(lca[0])) {\n lca.shift();\n }\n }\n });\n return taxonomy[lca[0]].short_name;\n}\n\nconst TryPan = (props) => {\n const query = props.query;\n const pan = props.pan;\n return <div className=\"suggestion-panlink\">\n <a target=\"_blank\" href={pan.url + \"?suggestion=\" + query}>\n <img src={pan.svg} title={`Search at ${pan.name}`}/>\n </a>\n </div>;\n};\n\nconst TryAnotherSite = props => {\n const query = props.query;\n const config = props.config;\n let sites = Object.keys(config.panSite);\n return <div>\n <Alert variant={'info'}>Don't see what you're looking for? Search for <b>{query}</b> on one of our sister sites</Alert>\n {sites.map((p, idx) => <TryPan key={idx} query={query} pan={config.panSite[p]}/>)}\n </div>\n}\n\nconst Suggestions = props => {\n let suggestions = props.grameneSuggestions;\n if (suggestions && suggestions.grouped) {\n if (suggestions.grouped.category.matches === 0) {\n let sugg1 = {\n fq_field: 'text',\n fq_value: props.suggestionsQuery,\n name: `Genes containing \"${props.suggestionsQuery}\"`,\n category: 'Gene',\n };\n let sugg2 = {\n fq_field: 'text',\n fq_value: `${props.suggestionsQuery}`,\n name: `Genes matching \"${props.suggestionsQuery}\"`,\n category: 'Gene',\n };\n return (\n <div style={{margin: '10px', maxWidth: '820px'}}>\n <Alert variant={'info'}><em>No suggestions found.</em> You may still attempt a full text search, though it is unlikely to find any genes for you.</Alert>\n <Button id={'word'}\n size={'sm'}\n variant={'outline-secondary'}\n onClick={() => {logAction(sugg1); props.doAcceptSuggestion(sugg1); props.doAcceptGrameneSuggestion(sugg1)}}>\n {`All genes that contain the word \"${props.suggestionsQuery}\"`}\n </Button>\n <Button id={'word'}\n size={'sm'}\n variant={'outline-secondary'}\n onClick={() => {logAction(sugg2); props.doAcceptSuggestion(sugg2); props.doAcceptGrameneSuggestion(sugg2)}}>\n {`All genes that contain a word that starts with \"${props.suggestionsQuery}\"`}\n </Button>\n <TryAnotherSite query={props.suggestionsQuery} config={props.configuration}/>\n </div>\n );\n }\n else {\n return (\n <div style={{margin: '10px'}}>\n {suggestions.grouped.category.groups.map((g,idx) => {\n return <div key={idx} id='gramene-suggestion'>\n <h4 className=\"mt10\">{g.groupValue}</h4>\n {g.doclist.docs.map((sugg,jdx) =>\n <Button id={`${idx}-${jdx}`}\n key={jdx}\n disabled={sugg.num_genes === 0}\n size='sm'\n variant=\"outline-secondary\"\n onClick={() => {logAction(sugg); props.doAcceptSuggestion(sugg); props.doAcceptGrameneSuggestion(sugg)}}>\n {showMatches(sugg.display_name,props.suggestionsQuery)}{' '}\n <Badge bg=\"secondary\">{sugg.num_genes}</Badge>\n <i> {getLowestCommonAncestorName(sugg.taxon_id, props.grameneTaxonomy)}</i>\n </Button>\n )}\n </div>\n })}\n <TryAnotherSite query={props.suggestionsQuery} config={props.configuration}/>\n </div>\n );\n }\n }\n else {\n return <div></div>\n }\n}\n\nexport default connect(\n 'selectGrameneSuggestions',\n 'selectSuggestionsQuery',\n 'selectGrameneTaxonomy',\n 'selectConfiguration',\n 'doAcceptSuggestion',\n 'doAcceptGrameneSuggestion',\n Suggestions\n);\n","import React, { useRef, useEffect } from 'react'\nimport { connect } from 'redux-bundler-react'\nimport { Navbar, Nav, NavDropdown, Container, OverlayTrigger, Popover} from 'react-bootstrap'\nimport Switch from 'react-switch'\nimport { IoAlertCircle } from 'react-icons/io5'\nimport { BsGearFill,BsTrash } from 'react-icons/bs'\nimport GeneList from './results/GeneList'\nimport TaxDist from './results/TaxDist'\nimport HelpDemo from './results/HelpDemo'\nimport GeneAttribs from './results/GeneAttribs'\nimport TaxonomyModal from './TaxonomyModal'\nimport Expression from './results/Expression'\nimport UserGeneLists from './results/UserGeneLists'\nimport Auth from './Auth'\nimport ReactGA from 'react-ga4'\nimport './styles.css';\n\nconst inventory = {\n help: HelpDemo,\n list: GeneList,\n taxonomy: TaxDist,\n attribs: GeneAttribs,\n expression: Expression,\n userLists: UserGeneLists\n};\n\nconst StatusCmp = props => {\n let content = props.grameneFiltersStatus;\n // if (props.grameneFiltersStatus === 'init') {\n // props.doClearGrameneFilters();\n // }\n if (props.grameneFiltersStatus === 'ready') {\n let tally = <span>Ready</span>;\n if (props.grameneSearch) {\n let genes = props.grameneSearch.response.numFound;\n let genomes = props.grameneSearch.facet_counts.facet_fields.taxon_id.length / 2;\n tally = <span><b>{genes}</b> genes in <b>{genomes}</b> genomes</span>;\n }\n const popover = (\n <Popover>\n <Popover.Header as=\"h3\">Genomes Filter</Popover.Header>\n <Popover.Body>Searching {props.activeGenomeCount} genomes</Popover.Body>\n </Popover>\n );\n\n content = <span>\n {tally}\n <OverlayTrigger placement=\"auto\" overlay={popover}>\n <span style={{float:'right', cursor:'pointer'}} onClick={props.doShowGrameneGenomes}><BsGearFill/></span>\n </OverlayTrigger>\n <TaxonomyModal/>\n </span>;\n }\n return <div style={{padding:'5px', color:'cornsilk', fontSize:'small'}}>{content}</div>\n};\n\nconst Status = connect(\n 'selectGrameneSearch',\n 'selectGrameneFiltersStatus',\n 'selectActiveGenomeCount',\n 'doShowGrameneGenomes',\n 'doClearGrameneFilters',\n StatusCmp\n);\n\nconst handleClick = (e, moveCopyMode, showMarked, node, actions) => {\n if (!e) e = window.event;\n e.cancelBubble = true;\n if (e.stopPropagation) e.stopPropagation();\n\n if (showMarked && moveCopyMode) {\n if (node.marked) {\n actions.selectTarget(node);\n }\n else {\n actions.unmarkTargets()\n }\n }\n console.log(node, showMarked);\n};\nfunction logAction(action) {\n ReactGA.event({\n category: 'Search',\n action: action\n })\n}\nconst Filter = ({node,moveCopyMode,showMarked,actions}) => {\n let classes = 'gramene-filter gramene-filter';\n if (node.operation) {\n classes = `${classes}-${node.operation}`\n }\n if (node.negate) {\n classes = `${classes} gramene-filter-NOT`\n }\n if (showMarked && node.marked) {\n classes = `${classes} gramene-filter-marked`\n }\n let content = '';\n let menu = '';\n let children = [];\n\n if (node.showMenu) {\n let key=1;\n let menuItems = [];\n if (node.hasOwnProperty('operation')) {\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Change to ${node.operation}`); actions.changeOperation(node)}}>convert to <i>{node.operation === 'AND' ? 'OR' : 'AND'}</i></li>);\n }\n if (node.leftIdx > 0) {\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Delete filter`); actions.deleteNode(node)}}>delete</li>);\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Move filter`); actions.markTargets(node,'move')}}>move{node.isSource && ' select destination'}</li>);\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Copy filter`); actions.markTargets(node,'copy')}}>copy{node.isSource && ' select destination'}</li>)\n }\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Negate filter`); actions.negate(node)}}>negate</li>);\n menu = <div className='gramene-filter-menu'><ul>{menuItems}</ul></div>;\n }\n let warning;\n if (node.warning) {\n const popover = (\n <Popover>\n <Popover.Header as=\"h3\">Warning</Popover.Header>\n <Popover.Body>{node.warning}</Popover.Body>\n </Popover>\n );\n warning = (\n <OverlayTrigger placement=\"auto\" overlay={popover}><span style={{float:'right', color:'red', cursor:'pointer'}}><IoAlertCircle/></span></OverlayTrigger>\n )\n }\n if (node.operation) {\n children = node.children.map((child,idx) => <Filter key={idx} moveCopyMode={moveCopyMode} node={child} showMarked={showMarked} actions={actions}/>);\n content = (\n <div>\n <span className='gramene-filter-operation'\n onClick={()=>actions.toggleMenu(node)}>{node.operation}</span>\n {warning}\n </div>\n );\n }\n else {\n content = <span className='gramene-filter-text'\n onClick={()=>actions.toggleMenu(node)}>{node.category} \| {node.name}</span>;\n }\n return (\n <div key={node.leftIdx} className={classes} onClick={(e)=>handleClick(e,moveCopyMode, showMarked,node,actions)}>\n {content}{menu}{children}\n </div>\n )\n};\n\nconst FiltersCmp = props => {\n const actions = {\n negate: props.doNegateGrameneFilter,\n deleteNode: props.doDeleteGrameneFilter,\n changeOperation: props.doChangeGrameneFilterOperation,\n selectTarget: props.doMoveOrCopyGrameneFilter,\n markTargets: props.doMarkGrameneFilterTargets,\n unmarkTargets: props.doUnmarkGrameneFilterTargets,\n toggleMenu: props.doToggleGrameneFilterMenu\n };\n if (props.grameneFilters.rightIdx > 1) {\n return <div className={props.configuration.id === 'sorghum' ? 'sorghumbase-filter-container': 'gramene-filter-container'}>\n <b>Filters</b>\n <span style={{float:'right', cursor:'pointer'}} onClick={props.doClearGrameneFilters}><BsTrash/></span>\n <Filter node={props.grameneFilters}\n moveCopyMode={props.grameneFilters.moveCopyMode}\n showMarked={props.grameneFilters.showMarked}\n actions={actions}/>\n </div>\n }\n else {\n return <div className={props.configuration.id === 'sorghum' ? 'sorghumbase-filter-container': 'gramene-filter-container'}>\n <b>Filters</b>\n <div className='gramene-filter gramene-filter-AND'>No filters defined</div>\n </div>\n }\n};\n\nconst Filters = connect(\n 'selectGrameneFilters',\n 'selectConfiguration',\n 'doNegateGrameneFilter',\n 'doDeleteGrameneFilter',\n 'doChangeGrameneFilterOperation',\n 'doMoveOrCopyGrameneFilter',\n 'doMarkGrameneFilterTargets',\n 'doUnmarkGrameneFilterTargets',\n 'doToggleGrameneFilterMenu',\n 'doClearGrameneFilters',\n FiltersCmp\n);\n\nconst ResultsCmp = props => {\n let activeViews = props.grameneViews.options;\n return props.grameneFilters.rightIdx > 0 ? (\n <div>\n {activeViews.map((v,idx) => {\n let p = Object.assign({}, props);\n const divRef = useRef(null);\n useEffect(() => {\n if (v.shouldScroll) {\n const navBarHeight=0;\n const scrollPosition = divRef.current.offsetTop - navBarHeight;\n window.scrollTo({\n top: scrollPosition,\n behavior: 'smooth'\n })\n props.doCancelShouldScroll();\n }\n }, [v.shouldScroll]);\n return (\n <div key={idx} ref={divRef}>\n {v.show === 'on' && <div style={{borderTopWidth:'medium'}} className='gramene-view-header'>{v.name}</div>}\n {v.show === 'on' && React.createElement(inventory[v.id], p)}\n </div>\n )\n })}\n </div>\n ) : null;\n};\n\nconst Results = connect(\n 'selectGrameneFilters',\n 'selectGrameneViews',\n 'doCancelShouldScroll',\n ResultsCmp\n);\n\nconst ViewsCmp = props => (\n <div className={'gramene-view-container'}>\n <b>Views</b>\n {props.grameneViews.options.filter(view => view.show !== 'disabled').map((view,idx) => (\n <div style={{textWrap:'nowrap'}} key={idx}>\n <Switch onChange={()=>props.doToggleGrameneView(view.id)} checked={view.show === 'on'}\n height={18}\n width={30}\n handleDiameter={16}\n checkedIcon={false}\n uncheckedIcon={false}\n />\n <span className={`gramene-view-span-${view.show}`} onClick={(e) => {\n props.dontToggleGrameneView(view.id)\n }}>{view.name}</span>\n </div>\n ))}\n </div>\n);\n\nconst Views = connect(\n 'selectGrameneViews',\n 'doToggleGrameneView',\n 'dontToggleGrameneView',\n ViewsCmp\n);\n\nexport {Status, Filters, Results, Views, Auth};\n","import React from 'react'\nimport ReactGA from 'react-ga4'\nimport { connect } from 'redux-bundler-react'\nimport './genes.css'\nimport Expression from './details/Expression'\nimport Homology from './details/Homology'\nimport Location from './details/Location'\nimport Pathways from \"./details/Pathways\"\nimport VEP from \"./details/VEP\"\nimport Xrefs from \"./details/Xrefs\"\nimport Publications from \"./details/Publications\"\nimport Sequences from \"./details/Sequences\"\nimport {suggestionToFilters} from \"../utils\";\nimport {GrFormPrevious, GrFormNextLink, GrFormNext, GrHpe} from 'react-icons/gr'\nimport { Badge, OverlayTrigger, Tooltip } from 'react-bootstrap'\n\nlet external = <small title=\"This link opens a page from an external site\"> <i className=\"fa fa-external-link\"/></small>;\n\nlet inventory = {\n sequences: Sequences,\n location: Location,\n expression: Expression,\n homology: Homology,\n pathways: Pathways,\n VEP: VEP,\n xrefs: Xrefs,\n pubs: Publications\n};\n\nfunction renderTairSummary(searchResult) {\n const summary = searchResult.summary;\n if(summary && summary !== \"NULL\" && searchResult.system_name === \"arabidopsis_thaliana\") {\n return (\n <div className=\"gene-summary-tair\">\n {trimSummary(summary)}\n </div>\n )\n }\n}\n\nfunction trimSummary(summary) {\n if(summary.length > 160) {\n const start = summary.substr(0, 150);\n const rest = summary.substr(150);\n return <p>{start}<span className=\"ellipsis\">…</span><span className=\"rest\">{rest}</span></p>\n }\n else {\n return <p>{summary}</p>\n }\n}\nconst PanLink = (props) => {\n const gene = props.gene;\n const pan = props.pan;\n return <div className=\"gene-panlink\">\n <a target=\"_blank\" href={pan.url + \"?idList=\" + gene.id}>\n <img src={pan.svg} title={`View this gene at ${pan.name}`}/>\n </a>\n </div>;\n};\n\nconst CurationComponent1 = ({ curation }) => {\n return (\n <div className=\"gene-curation\">\n <span>Curated gene structure</span>\n {curation.okay > 0 && <span className=\"status\">✔️ {curation.okay}</span>}\n {curation.flagged > -10 && <span className=\"status\">⚠️ {curation.flagged}</span>}\n </div>\n );\n};\nconst CurationComponent = ({ curation, gene }) => {\n const total = curation.okay + curation.flagged;\n const okayRatio = (curation.okay / total);\n const flaggedRatio = (curation.flagged / total);\n const tooltip = (\n <Tooltip id=\"tooltip\">\n <strong>Gene structure</strong><br/>\n Okay: {curation.okay}  \n Flagged: {curation.flagged}\n </Tooltip>\n );\n return (\n <OverlayTrigger placement=\"left\" overlay={tooltip}>\n <a className=\"gene-curation\" target=\"_blank\" href={`https://devdata.gramene.org/curation/curations?idList=${gene.id}`}>\n <span className=\"okay\" style={{opacity: okayRatio}}>☑</span>\n <span className=\"flagged\" style={{opacity: flaggedRatio}}>⚠</span>\n </a>\n </OverlayTrigger>\n )\n};\n\nconst ClosestOrthologCmp = (props) => {\n let id, taxon_id, name, desc, species, className, identity;\n const gene = props.gene;\n\n if (gene.closest_rep_id) {\n name = gene.closest_rep_name \|\| gene.closest_rep_id;\n desc = gene.closest_rep_description;\n species = gene.closest_rep_species_name;\n id = gene.closest_rep_id;\n taxon_id = gene.closest_rep_taxon_id;\n className = \"closest-ortholog\";\n identity = gene.closest_rep_identity \|\| 0;\n }\n else if (gene.model_rep_id) {\n name = gene.model_rep_name \|\| gene.model_rep_id;\n desc = gene.model_rep_description;\n species = gene.model_rep_species_name;\n id = gene.model_rep_id;\n taxon_id = gene.model_rep_taxon_id;\n className = \"model-ortholog\";\n identity = gene.model_rep_identity \|\| 0;\n }\n var isZm = new RegExp(/^Zm00001e/);\n if (isZm.test(desc)) {\n desc='';\n }\n\n return (\n <div className={className} onClick={() => {\n props.doEnsureGrameneGenome(taxon_id);\n props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene',\n fq_field: 'id',\n fq_value: id,\n name: name\n }))\n }}>\n <div className=\"gene-species\">{species}</div>\n {identity > 0 && <div className=\"rep-identity\">{Math.round(identity100)}</div>}\n <h3 className=\"gene-id\">{name}</h3>\n <p>{desc}</p>\n </div>\n );\n};\n\nconst ClosestOrtholog = connect(\n 'doReplaceGrameneFilters','doEnsureGrameneGenome',\n ClosestOrthologCmp\n);\n\nfunction renderClosestOrtholog(gene) {\n\n if (shouldShowClosestOrtholog(gene)) {\n\n // we used to not add the closest ortholog to the DOM if the homology detail was visible.\n // however, that could cause the height of the result to change. Instead we set visibility:hidden\n // so that the renderer takes into account the height of the ortholog even if not shown.\n return (\n <ClosestOrtholog gene={gene}/>\n );\n }\n}\n\n// show closest ortholog prominently if we have data to show:-\n// a. either there's a closest ortholog (determined by traversing the gene tree until an id or description looks\n// curated) b. or there's a model ortholog (traverse tree to find an ortholog in arabidopsis)\nfunction shouldShowClosestOrtholog(searchResult) {\n return (\n searchResult.closest_rep_id \|\| (\n searchResult.model_rep_id &&\n searchResult.model_rep_id !== searchResult.id\n )\n );\n}\n\nconst allDetails = [\n {\n id: 'VEP',\n label: 'Germplasm',\n popup: 'Germplasm with protein truncating variants (PTVs)',\n available: false\n },\n {\n id: 'sequences',\n label: 'Sequences',\n popup: 'Gene/cDNA/protein fasta',\n available: true\n },\n {\n id: 'location',\n label: 'Location',\n popup: 'Genome Browser',\n available: false\n },\n {\n id: 'expression',\n label: 'Expression',\n popup: 'Gene Expression Atlas',\n available: false\n },\n {\n id: 'homology',\n label: 'Homology',\n popup: 'Gene Family Tree',\n available: false\n },\n {\n id: 'pathways',\n label: 'Pathways',\n popup: 'Plant Reactome Pathways',\n available: false\n },\n {\n id: 'pubs',\n label: 'Papers',\n popup: 'Curated Publications',\n available: false\n },\n {\n id: 'xrefs',\n label: 'Xrefs',\n popup: 'Database Cross-references',\n available: false\n }\n];\n\n\nclass Gene extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n details: allDetails.map(o => ({...o})).filter(d => props.config.details[d.id]),\n expandedDetail: props.expandedDetail\n };\n let hasData = {};\n props.searchResult.capabilities.forEach(c => {\n hasData[c] = true;\n if (c === 'PanOryza') {\n hasData.xrefs = true;\n }\n });\n this.state.details.forEach(d => d.available \|= hasData.hasOwnProperty(d.id));\n }\n getDetailStatus(d) {\n if (this.state.expandedDetail === d.id) return 'expanded';\n if (d.available) return 'closed'\n return d.id === \"pubs\" ? 'empty' : 'disabled';\n }\n setExpanded(d) {\n if (d.available \|\| d.id === \"pubs\") {\n if (this.state.expandedDetail === d.id) {\n this.setState({expandedDetail: null})\n }\n else {\n const geneId = this.props.searchResult.id;\n if (!(this.props.geneDocs && this.props.geneDocs.hasOwnProperty(geneId))) {\n this.props.requestGene(geneId)\n }\n ReactGA.event({\n category: 'Search',\n action: 'Details',\n label: d.label\n });\n this.setState({expandedDetail: d.id})\n }\n }\n }\n ensureGene(id) {\n if (!(this.props.geneDocs && this.props.geneDocs.hasOwnProperty(id))) {\n this.props.requestGene(id);\n return false;\n }\n return this.props.geneDocs[id].hasOwnProperty('taxon_id')\n }\n renderMetadata() {\n let gene = this.props.searchResult;\n if (gene.model_rep_taxon_id) {\n gene.model_rep_species_name = this.props.taxLut[gene.model_rep_taxon_id].short_name;\n }\n if (gene.closest_rep_taxon_id) {\n gene.closest_rep_species_name = this.props.taxLut[gene.closest_rep_taxon_id].short_name;\n }\n return renderTairSummary(gene) \|\| renderClosestOrtholog(gene);\n }\n render() {\n const panSite = this.props.config.panSite;\n const searchResult = this.props.searchResult;\n const taxName = this.props.taxName;\n const curation = this.props.curation;\n // let orthologs='';\n // if (this.props.orthologs && this.props.orthologs.hasOwnProperty(searchResult.id)) {\n // orthologs = this.props.orthologs[searchResult.id].join(', ');\n // }\n const numWordsInDescription = searchResult.description.split(' ').length;\n return (\n <div className=\"result-gene\">\n <div className=\"result-gene-summary\">\n <div className=\"result-gene-title-body\">\n {panSite.hasOwnProperty(searchResult.system_name) && <PanLink pan={panSite[searchResult.system_name]} gene={searchResult}/>}\n {curation && <CurationComponent curation={curation} gene={searchResult}/> }\n <div className=\"gene-title\">\n <div className=\"gene-species\">{taxName}</div>\n <h3 className=\"gene-name\">{searchResult.name}\n {searchResult.id !== searchResult.name && <small className=\"gene-id\"> {searchResult.id}</small>}\n </h3>\n </div>\n {searchResult.synonyms && <small className=\"gene-synonyms\">{searchResult.synonyms.join(', ')}</small>}\n {searchResult.description !== \"unknown\" && (numWordsInDescription > 1 \|\| searchResult.can_show.pubs) && <p className=\"gene-description\">{searchResult.description}</p>}\n </div>\n {this.renderMetadata()}\n </div>\n <div className=\"gene-detail-tabs\">\n {this.state.details.map((d,idx) => (\n <OverlayTrigger\n key={idx}\n placement={'bottom'}\n overlay={\n <Tooltip id={`tooltip`}>{d.popup}</Tooltip>\n }\n >\n <div key={idx}\n className={`col-md-1 text-center gene-detail-tab-${this.getDetailStatus(d)}`}\n onClick={()=>this.setExpanded(d)}\n >{d.label}</div>\n </OverlayTrigger>\n ))}\n </div>\n {this.state.expandedDetail && this.ensureGene(searchResult.id) && <div className=\"visible-detail\">{React.createElement(inventory[this.state.expandedDetail], this.props)}</div>}\n </div>\n )\n }\n}\n\nconst GeneList = props => {\n if (props.grameneSearch && props.grameneSearch.response && props.grameneTaxonomy) {\n let prev,page,next;\n const numFound = props.grameneSearch.response.numFound;\n if (numFound > props.grameneSearchRows) {\n const pageNum = props.grameneSearchOffset/props.grameneSearchRows;\n page = <span style={{padding:'10px'}}>page <b>{pageNum + 1}</b> of <b>{Math.ceil(numFound/props.grameneSearchRows)}</b></span>;\n prev = <GrHpe/>;\n if (pageNum > 0) {\n prev = <Badge onClick={()=>props.doRequestResultsPage(pageNum - 1)}><GrFormPrevious/></Badge>\n }\n next = <GrHpe/>;\n if (numFound > props.grameneSearchOffset + props.grameneSearchRows) {\n next = <Badge onClick={()=>props.doRequestResultsPage(pageNum + 1)}><GrFormNext/></Badge>\n }\n }\n return <div>\n <div>{prev}{page}{next}</div>\n {props.grameneSearch.response.docs.map((g,idx) => (\n <Gene key={idx}\n searchResult={g}\n config={props.configuration}\n taxName={props.grameneTaxonomy[g.taxon_id].name}\n geneDocs={props.grameneGenes}\n requestGene={props.doRequestGrameneGene}\n requestOrthologs={props.doRequestOrthologs}\n orthologs={props.grameneOrthologs}\n taxLut={props.grameneTaxonomy}\n curation={props.curatedGenes ? props.curatedGenes[g.id] : null}\n expandedDetail={props.grameneSearch.response.numFound === 1 && g.can_show.homology ? 'homology' : null}\n />\n ))}\n {prev}{page}{next}\n </div>\n }\n return null;\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGrameneSearch',\n 'selectGrameneTaxonomy',\n 'selectGrameneGenes',\n 'selectGrameneOrthologs',\n 'selectGrameneSearchOffset',\n 'selectGrameneSearchRows',\n 'selectCuratedGenes',\n 'doRequestGrameneGene',\n 'doRequestOrthologs',\n 'doRequestResultsPage',\n GeneList);\n","import React, { useRef, useEffect, useState } from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport {Tabs, Tab, Form, Row, Col} from 'react-bootstrap';\nimport BAR, {haveBAR} from \"gramene-efp-browser\";\n\nfunction DynamicIframe(props) {\n // Create a ref for the iframe element\n const iframeRef = useRef(null);\n const [iframeHeight, setIframeHeight] = useState(500); // Default height\n\n useEffect(() => {\n const handleMessage = (event) => {\n if (event.data.type === 'heightChange') {\n setIframeHeight(event.data.height + 44);\n }\n };\n\n window.addEventListener(\"message\", handleMessage);\n\n return () => window.removeEventListener(\"message\", handleMessage);\n }, []);\n\n return (\n <iframe\n ref={iframeRef}\n src={props.url}\n title=\"Dynamic Iframe\"\n style={{ width: '100%', height: `${iframeHeight}px`, border: 'none' }}\n />\n );\n}\n\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n const [atlasExperiment, setAtlasExperiment] = useState(null);\n const [atlasExperimentList, setAtlasExperimentList] = useState([]);\n const [isLocal, setIsLocal] = useState(false);\n const [activeTab, setActiveTab] = useState('gene');\n\n const handleLocalAPIChange = (event) => {\n setIsLocal(event.target.checked);\n };\n useEffect(() => {\n const tid = Math.floor(gene.taxon_id / 1000);\n if (props.expressionStudies[tid]) {\n let eList = props.expressionStudies[tid].sort((a,b) => {\n const a_name = `${a.type}:${a.description \|\| a._id}`;\n const b_name = `${b.type}:${b.description \|\| b._id}`;\n return a_name < b_name ? -1 : 1;\n });\n if (props.searchResult.hasOwnProperty('expressed_in_gxa_attr_ss')) {\n const in_gxa = new Set(props.searchResult.expressed_in_gxa_attr_ss);\n eList = eList.filter(e => in_gxa.has(e._id))\n }\n setAtlasExperimentList(eList);\n\n let refExp = eList.filter(e => e.isRef);\n if (refExp.length === 1) {\n setAtlasExperiment(refExp[0]._id);\n } else {\n // no reference experiment - choose first\n setAtlasExperiment(eList[0]._id);\n }\n }\n }, [props.expressionStudies]);\n\n let paralogs_url;\n let gene_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${gene.atlas_id \|\| gene._id}&localAPI=${isLocal}`;\n let paralogs = [];\n if (props.grameneParalogs && props.grameneParalogs[gene._id]) {\n paralogs = props.grameneParalogs[gene._id];\n } else if(gene.homology) {\n props.doRequestParalogs(gene._id, gene.homology.supertree, gene.taxon_id);\n }\n // if (gene.homology && gene.homology.homologous_genes && gene.homology.homologous_genes.within_species_paralog) {\n // paralogs = gene.homology.homologous_genes.within_species_paralog;\n // }\n if (paralogs.length > 1 && atlasExperiment) {\n paralogs_url= `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;\n }\n return <Tabs activeKey={activeTab} onSelect={(k) => setActiveTab(k)}>\n {paralogs_url &&\n <Tab tabClassName=\"gxa\" eventKey=\"paralogs\" title={`Paralogs`} key=\"gxaparalogs\">\n <Form.Select aria-label='experiment selector'\n placeholder='Select experiment'\n onChange={(e) => setAtlasExperiment(e.target.value)}>\n { atlasExperimentList.map((e,idx) =>\n <option key={idx} value={e._id}>{e.type}: {e.description \|\| e._id}</option>\n )}\n </Form.Select>\n {activeTab === \"paralogs\" && <DynamicIframe url={paralogs_url}/> }\n </Tab>\n }\n <Tab tabClassName=\"gxa\" eventKey=\"gene\" title=\"All Studies\" key=\"gxa\">\n {/<Form.Check/}\n {/ type=\"switch\"/}\n {/ id=\"localAPI\"/}\n {/ label=\"Local API\"/}\n {/ checked={isLocal}/}\n {/ onChange={handleLocalAPIChange}/}\n {//>/}\n {activeTab === \"gene\" && <DynamicIframe url={gene_url}/> }\n </Tab>\n {haveBAR(gene) &&\n <Tab tabClassName=\"eFP\" eventKey=\"eFP\" title=\"eFP Browser\" key=\"bar\"><BAR gene={gene}/></Tab>\n }\n </Tabs>\n};\n\nexport default connect(\n 'selectGrameneParalogs',\n 'selectExpressionStudies',\n 'doRequestParalogs',\n //'doRequestParalogExpression',\n Detail\n);\n\n","import React from 'react'\nimport _ from 'lodash';\nimport {connect} from \"redux-bundler-react\";\nimport TreeVis from \"gramene-genetree-vis\";\nimport treesClient from \"gramene-trees-client\";\nimport {Detail, Title, Description, Content, Explore, Links} from \"./generic\";\nimport {suggestionToFilters} from \"../../utils\";\nimport {Spinner, Alert} from \"react-bootstrap\";\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/msa.less';\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/tree.less';\n\nclass Homology extends React.Component {\n constructor(props) {\n super(props);\n if (!props.geneDocs.hasOwnProperty(props.searchResult.id)) {\n props.requestGene(props.searchResult.id)\n }\n this.taxonomy = treesClient.taxonomy.tree(Object.values(props.grameneTaxonomy))\n }\n renderTreeVis() {\n return (\n <div className=\"gene-genetree\">\n <TreeVis genetree={this.tree}\n initialGeneOfInterest={this.gene}\n genomesOfInterest={this.props.grameneGenomes.active}\n taxonomy={this.taxonomy}\n allowGeneSelection={true}\n pivotTree={true}\n enableCuration={false}\n enablePhyloview={true}\n numberOfNeighbors={10}\n ensemblUrl={this.props.configuration.ensemblURL}/>\n </div>\n )\n }\n filterAllHomologs() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'gene_tree',\n fq_value: this.tree._id,\n name: `Homologs of ${this.gene.name}`\n }))\n }\n filterOrthologs() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'homology__all_orthologs',\n fq_value: this.gene._id,\n name: `Orthologs of ${this.gene.name}`\n }))\n }\n filterParalogs() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'homology__within_species_paralog',\n fq_value: this.gene._id,\n name: `Paralogs of ${this.gene.name}`\n }))\n }\n searchSupertree() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'supertree_attr_s',\n fq_value: this.gene.homology.supertree,\n name: this.gene.homology.supertree\n }))\n }\n orthologList() {\n return this.orthoParaList('ortholog');\n }\n\n paralogList() {\n return this.orthoParaList('within_species_paralog');\n }\n\n orthoParaList(type) {\n var homology, thisGeneId;\n homology = _.get(this.gene, 'homology.homologous_genes');\n thisGeneId = this.gene._id;\n\n if (homology) {\n var homologs = _(homology)\n .pickBy(function filterCategories(thing, name) {\n return name.indexOf(type) === 0;\n })\n .values()\n .flatten()\n .uniq()\n .value();\n\n if (!_.isEmpty(homologs)) {\n if (!homologs.includes(thisGeneId)) {\n console.log(\"add to homologs list\",thisGeneId);\n homologs.push(thisGeneId);\n }\n return homologs; // only return something if we have something. We're testing for truthiness later.\n }\n }\n }\n explorations() {\n let x = [{\n name: 'Homologs',\n category: 'Gene Tree',\n count: this.tree.geneCount,\n handleClick: this.filterAllHomologs.bind(this)\n }];\n if (this.orthologs) {\n x.push({\n name: 'Orthologs',\n category: 'Gene Tree',\n count: this.orthologs.length,\n handleClick: this.filterOrthologs.bind(this)\n });\n }\n if (this.paralogs) {\n x.push({\n name: 'Paralogs',\n category: 'Gene Tree',\n count: this.paralogs.length,\n handleClick: this.filterParalogs.bind(this)\n });\n }\n if (this.gene.homology.supertree) {\n x.push({\n name: `Supertree`,\n category: `Gene Tree`,\n count: this.gene.homology.supertree,\n handleClick: this.searchSupertree.bind(this)\n })\n }\n return x;\n }\n links() {\n let links = [\n {\n name: 'Ensembl Gene Tree view',\n url: `${this.props.configuration.ensemblURL}/${this.gene.system_name}/Gene/Compara_Tree?g=${this.gene._id}`\n }\n ];\n if (this.props.curation && this.props.curation.taxa.hasOwnProperty(this.gene.taxon_id)) {\n links.push({\n name: 'Curate',\n url: this.props.curation.url + this.gene._id\n })\n }\n return links;\n }\n render() {\n const id = this.props.searchResult.id;\n if (!this.props.geneDocs.hasOwnProperty(id)) {\n return <Spinner/>\n }\n this.gene = this.props.geneDocs[id];\n const treeId = this.gene.homology.gene_tree.id;\n if (! this.props.grameneTrees.hasOwnProperty(treeId)) {\n this.props.doRequestGrameneTree(treeId);\n }\n else {\n const tree = this.props.grameneTrees[treeId];\n if (tree.hasOwnProperty('taxon_id')) {\n this.tree = treesClient.genetree.tree([this.props.grameneTrees[treeId]]);\n this.orthologs = this.orthologList();\n this.paralogs = this.paralogList();\n }\n }\n let flagged=0;\n // if (this.props.curation && this.props.curation.taxa.hasOwnProperty(this.gene.taxon_id)) {\n // flagged = this.props.curatedGenes && this.props.curatedGenes[id] ? this.props.curatedGenes[id].flagged : 0;\n // }\n return (\n <Detail>\n <Title key=\"title\">Compara Gene Tree</Title>\n <Description key=\"description\">\n This phylogram shows the relationships between this gene and others similar to it, as determined by Ensembl Compara.\n {flagged > 1 && <Alert variant={'warning'}>This gene was flagged for potential gene structural annotation issues by {flagged} curators</Alert>}\n </Description>\n {this.tree && <Content key=\"content\">{this.renderTreeVis()}</Content>}\n {this.tree && <Explore key=\"explore\" explorations={this.explorations()}/>}\n <Links key=\"links\" links={this.links()}/>\n </Detail>\n )\n }\n}\n\nexport default connect(\n 'selectGrameneTaxonomy',\n 'selectGrameneTrees',\n 'selectGrameneGenomes',\n 'selectConfiguration',\n 'selectCuration',\n 'selectCuratedGenes',\n 'doRequestGrameneTree',\n 'doAcceptGrameneSuggestion',\n 'doReplaceGrameneFilters',\n Homology\n);\n\n","import React from 'react';\nimport keyBy from 'lodash/keyBy';\nimport _ from \"lodash\";\nimport ReactGA from \"react-ga4\";\nimport { BiLinkExternal } from \"react-icons/bi\";\nimport { Button, Badge } from \"react-bootstrap\";\n\nexport const Detail = props => {\n let subComponents = keyBy(props.children, 'key');\n return (\n <div className=\"detail\">\n <div className=\"intro\">\n {subComponents.title}\n {subComponents.description}\n </div>\n <div className=\"content-wrapper\">\n {subComponents.content}\n </div>\n <div className=\"actions\">\n <div className=\"action-wrapper\" xs={12} sm={5}>\n {subComponents.explore}\n </div>\n <div className=\"action-wrapper\" xs={12} sm={7}>\n {subComponents.links}\n </div>\n </div>\n </div>\n )\n};\n\nexport const Title = props => <h4>{props.children}</h4>;\nexport const Description = props => <p className=\"description\">{props.children}</p>;\nexport const Content = props => <div className=\"content\">{props.children}</div>;\n\nconst QueryTerm = props => {\n let category, name, badge;\n name = props.name;\n if (props.category) {\n category = props.category + ' \| ';\n }\n if (_.isNumber(props.count)) {\n badge = <Badge style={{marginLeft: \"0.5rem\"}} bg='secondary'>{props.count}</Badge>\n }\n return (\n <Button variant='outline-dark' onClick={props.handleClick}>\n {category}{name}{badge}\n </Button>\n )\n};\n\nfunction renderExplorations(explorations) {\n return explorations.map(\n (exploration, idx) =>\n <QueryTerm key={idx} {...exploration} />\n );\n}\nexport const Explore = props => (\n <div className=\"explore\">\n <h5>Search Filters</h5>\n <div>\n {renderExplorations(props.explorations)}\n </div>\n </div>\n);\n\nfunction renderLinks(links) {\n let external = <small title=\"This link opens a page from an external site\"> <BiLinkExternal/></small>;\n return links.map((link, idx) =>\n <li key={idx}>\n <a href={link.url} target=\"_blank\" className=\"external-link\" onClick={()=>{\n ReactGA.event({\n category: \"outbound link\", action: \"follow\", label: link.name\n })\n }}>{link.name}{external}</a>\n {/<ReactGA.OutboundLink/}\n {/ eventLabel={link.name}/}\n {/ to={link.url}/}\n {/ target=\"_blank\"/}\n {/ className=\"external-link\"/}\n {/>/}\n {/ {link.name}{external}/}\n {/</ReactGA.OutboundLink>/}\n </li>\n )\n}\n\nexport const Links = props => (\n <div className=\"links\">\n <h5>Links to other resources</h5>\n <ul>\n {renderLinks(props.links)}\n </ul>\n </div>\n);\n","import { initializeApp } from \"firebase/app\";\n\nconst firebaseConfig = {\n apiKey: \"AIzaSyCyTJmxfWgfuhI6-8uqocSiE9KOWUlkgkk\",\n authDomain: \"gramene-auth.firebaseapp.com\",\n projectId: \"gramene-auth\",\n storageBucket: \"gramene-auth.appspot.com\",\n messagingSenderId: \"590873346270\",\n appId: \"1:590873346270:web:f76a31a93619e69439824f\"\n};\n\nexport const firebaseApp = initializeApp(firebaseConfig);\n\nexport const suggestionToFilters = (suggestion) => {\n return {\n status: 'init',\n rows: 20,\n operation: 'AND',\n negate: false,\n leftIdx: 0,\n rightIdx: 3,\n children: [\n {\n fq_field: suggestion.fq_field,\n fq_value: suggestion.fq_value,\n name: suggestion.name,\n category: suggestion.category,\n leftIdx: 1,\n rightIdx: 2,\n negate: false,\n marked: false\n }\n ]\n }\n}\n","import React from 'react'\nimport getProp from 'lodash/get';\nimport isEqual from 'lodash/isEqual';\nimport {Button} from \"react-bootstrap\";\nimport Browser from \"./location/browser\";\nimport {connect} from \"redux-bundler-react\";\nimport {Detail, Title, Description, Content, Explore, Links} from \"./generic\";\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/msa.less';\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/tree.less';\n\nclass Location extends React.Component {\n constructor(props) {\n super(props);\n this.gene = this.props.geneDocs[this.props.searchResult.id];\n this.initRegion();\n this.state = {\n visibleRange: this.initVisibleRange()\n };\n }\n\n initVisibleRange() {\n var location, span, padding, result;\n location = this.gene.location;\n if(!location) {\n throw new Error(`Could not find the location of the gene in props.`);\n }\n\n span = location.end - location.start + 1;\n padding = Math.floor(.1 span);\n\n result = {\n chr: location.region,\n start: location.start - padding,\n end: location.end + padding\n };\n\n result.displayName = `${result.chr}:${result.start}-${result.end}`;\n\n return result;\n }\n\n initRegion() {\n var region, isChromosome, regionType, regionName;\n region = this.gene.location.region;\n if (region) {\n isChromosome = /^\\d+$/.test(region);\n if (isChromosome) {\n regionType = 'chromosome';\n regionName = 'Chromosome ' + region;\n }\n else {\n regionType = 'scaffold';\n regionName = region;\n }\n this.region = {\n isChromsome: isChromosome,\n name: regionName,\n type: regionType\n };\n }\n }\n\n\n handleViewChange(chr, start, end) {\n var visibleRange = {\n chr: chr,\n start: start,\n end: end,\n displayName: `${chr}:${start}-${end}`\n };\n\n if(!isEqual(visibleRange, this.state.visibleRange)) {\n this.setState({\n visibleRange: visibleRange\n });\n }\n }\n\n updateQuery(restrictToVisibleRange) {\n var location, geneName, visibleRange, filter, filterDisplayName, fq;\n location = this.gene.location;\n geneName = this.gene.name;\n // category: 'Gene Tree',\n // fq_field: 'gene_tree',\n // fq_value: this.tree._id,\n // name: `Homologs of ${this.gene.name}`\n\n let terms = [\n {\n category: \"Map\",\n name: location.map,\n fq_field: 'map',\n fq_value: location.map\n },\n {\n category: \"Region\",\n name: location.region,\n fq_field: 'region',\n fq_value: location.region\n }\n ];\n fq = `map:${location.map} AND region:${location.region}`;\n\n if (restrictToVisibleRange) {\n visibleRange = this.state.visibleRange;\n\n terms.push({\n category: \"Interval\",\n name: `${visibleRange.start}-${visibleRange.end}`,\n fq_field: 'start',\n fq_value: `[${visibleRange.start} TO ${visibleRange.end}]`\n });\n fq += ` AND (start:[${visibleRange.start} TO ${visibleRange.end}]`\n + ` OR end:[${visibleRange.start} TO ${visibleRange.end}])`;\n\n filterDisplayName = visibleRange.displayName;\n } else {\n filterDisplayName = \"Shares \" + this.region.type + \" with \" + geneName;\n }\n\n console.log(\"User asked to filter by location\");\n filter = {\n category: 'Location',\n id: fq,\n fq: fq,\n display_name: filterDisplayName\n };\n\n // QueryActions.removeAllFilters();\n // QueryActions.setFilter(filter);\n this.props.doAddGrameneRangeQuery(terms);\n if (this.props.closeModal) this.props.closeModal();\n }\n\n explorations() {\n var visible, result;\n visible = this.state.visibleRange;\n result = [\n {\n name: `All on ${this.region.name}`,\n handleClick: ()=>this.updateQuery(false)\n }\n ];\n if (visible) {\n result.push({\n name: `All within ${getProp(visible, 'displayName')}`,\n handleClick: ()=>this.updateQuery(true)\n });\n }\n return result;\n }\n\n links() {\n function jgiify(id) {\n return id.replace('SORBI_3','Sobic.').replace(/\\.v[0-9]\\.[0-9]$/,'');\n }\n var gene = this.gene;\n let links = [\n {name: 'Ensembl Browser', url: `${this.props.config.ensemblURL}/${gene.system_name}/Gene/Summary?g=${gene._id}`}\n ];\n if (gene.annotations.taxonomy.ancestors.includes(4557))\n links.push({name: 'Phytozome', url: `https://phytozome-next.jgi.doe.gov/report/gene/Sbicolor_v5_1/${jgiify(gene._id)}`})\n if (gene.taxon_id === 3702)\n links.push(\n {name: 'tair', url: `https://www.arabidopsis.org/servlets/TairObject?name=${gene._id}&type=locus`},\n {name: 'ThaleMine', url: `https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=${gene._id}&searchSubmit=search`}\n );\n if (gene.taxon_id === 39947)\n links.push({name: 'RAP-DB', url: `https://rapdb.dna.affrc.go.jp/locus/?name=${gene._id}`});\n const isMaize = new RegExp(/^Zm[0-9]+/);\n if (isMaize.test(gene._id))\n links.push({name: 'MaizeGDB', url: `http://www.maizegdb.org/gene_center/gene/${gene._id}`});\n return links;\n }\n\n render() {\n return (\n <Detail>\n {/<Title key=\"title\">Genome location: {this.renderGenePosition()}</Title>/}\n <Description key=\"description\">Currently viewing: {this.renderLocation()} {this.renderResetButton()}</Description>\n <Content key=\"content\">\n {this.renderBrowser()}\n </Content>\n <Explore key=\"explore\" explorations={this.explorations()}/>\n <Links key=\"links\" links={this.links()}/>\n </Detail>\n );\n }\n\n\n renderBrowser() {\n return (\n <Browser gene={this.gene} {...this.props} {...this.state} onViewChange={ this.handleViewChange.bind(this) }/>\n );\n }\n\n renderGenePosition() {\n var location = this.gene.location;\n return (\n <span className=\"location\">\n <span className=\"region\">{this.region.name}</span>:<span className=\"start\">{location.start}</span>-<span\n className=\"end\">{location.end}</span>\n </span>\n );\n }\n\n renderLocation() {\n var location = this.state.visibleRange;\n return (\n <span className=\"location\">\n <span className=\"region\">{location.chr}</span>:<span className=\"start\">{location.start}</span>-<span\n className=\"end\">{location.end}</span>\n </span>\n );\n }\n\n resetVisibleRange() {\n const {chr, start, end} = this.initVisibleRange();\n this.handleViewChange(chr, start, end);\n }\n\n renderResetButton() {\n // let active=isEqual(this.props.visibleRange, this.state.visibleRange);\n return (\n <Button\n size=\"sm\"\n variant=\"outline-dark\"\n onClick={() => this.resetVisibleRange()}>\n Reset\n </Button>\n )\n }\n}\n\nexport default connect('doAddGrameneRangeQuery',Location);\n\n","import React from \"react\";\nimport DallianceBrowser from \"./dallianceBrowser.js\";\n\nexport default class Browser extends React.Component {\n constructor(props) {\n super(props);\n }\n\n render() {\n return (\n <div className=\"location-browser\">\n <DallianceBrowser {...this.props} expanded={!!this.props.closeModal} />\n </div>\n )\n }\n\n}\n\n// Browser.propTypes = {\n// gene: React.PropTypes.object.isRequired,\n// expanded: React.PropTypes.bool,\n// visibleRange: React.PropTypes.object.isRequired,\n// onViewChange: React.PropTypes.func.isRequired\n// };","import React from \"react\";\nimport isEqual from \"lodash/isEqual\";\n\n// var ensemblREST = require('../../../../../package.json').gramene.ensemblREST;\n//const ensemblREST = 'http://data.gramene.org/ensembl63';\n// const ensemblREST = 'https://data.sorghumbase.org/ensembl2';\n// const ensemblREST = 'https://data.gramene.org/vitis-ensembl1';\n// const ensemblREST = 'https://data.gramene.org/pansite-ensembl';\n\n// calculate this once.\nconst PREFIX = '/static/gramene-dalliance/';\n\nexport default class DallianceBrowser extends React.Component {\n\n constructor(props) {\n super(props);\n this.initialVisibleRange = props.visibleRange;\n }\n\n shouldComponentUpdate(newProps) {\n // should we reset the view to initial state?\n if(isEqual(newProps.visibleRange, this.initialVisibleRange)) {\n this.browser.setLocation(newProps.visibleRange.chr, newProps.visibleRange.start, newProps.visibleRange.end);\n }\n\n return false;\n }\n\n biodallianceElementId() {\n return this.props.gene._id + 'Browser';\n }\n\n browser() {\n var g, view, start, end, browser;\n g = this.props.gene;\n view = this.props.visibleRange;\n start = view.start;\n end = view.end;\n\n this.browser = browser = new Browser(\n {\n pageName: this.biodallianceElementId(),\n chr: g.location.region,\n viewStart: start,\n viewEnd: end,\n cookieKey: g._id + 'BrowserCookie',\n prefix: PREFIX,\n\n coordSystem: {\n speciesName: g.system_name,\n taxon: g.taxon_id,\n auth: 'Gramene',\n version: '3',\n ucscName: 'IRGSP-1.0'\n },\n\n sources: [\n {\n name: 'DNA',\n ensemblURI: this.props.config.ensemblRest,\n species: g.system_name,\n tier_type: 'sequence'\n },\n {\n name: 'Genes',\n uri: this.props.config.ensemblRest,\n tier_type: 'ensembl',\n species: g.system_name,\n type: ['gene', 'transcript', 'exon', 'cds']\n }\n ],\n\n // hubs: ['/Track_Hubs/DRP000315/hub.txt'],\n disablePoweredBy: true,\n setDocumentTitle: false,\n noDefaultLabels: true,//!this.props.expanded,\n noPersist: true,\n noPersistView: true,\n maxWorkers: 2,\n noTitle: true,\n noLocationField: false,\n noLeapButtons: true,//!this.props.expanded,\n noZoomSlider: false, //!this.props.expanded,\n noTrackAdder: true,//!this.props.expanded,\n noTrackEditor: true,//!this.props.expanded,\n noExport: true,//!this.props.expanded,\n noOptions: true,//!this.props.expanded,\n noHelp: true,\n maxViewWidth: 1000000\n }\n );\n\n browser.addViewListener(this.props.onViewChange);\n }\n\n cancel() {\n if (typeof this.timeoutID == \"number\") {\n window.clearTimeout(this.timeoutID);\n delete this.timeoutID;\n }\n }\n\n componentDidMount() {\n // this.browser();\n this.cancel();\n var self = this;\n this.timeoutID = window.setTimeout(function () {self.browser();}, 0);\n }\n\n componentWillUnmount() {\n this.cancel();\n }\n\n render() {\n return (\n <div id={this.biodallianceElementId()}/>\n );\n }\n}\n\n// DallianceBrowser.propTypes = {\n// gene: React.PropTypes.object.isRequired,\n// visibleRange: React.PropTypes.object.isRequired,\n// expanded: React.PropTypes.bool,\n// onViewChange: React.PropTypes.func.isRequired\n// };\n","import React from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport FlatToNested from 'flat-to-nested';\nimport {Explore, Links} from \"./generic\";\nimport treesClient from \"gramene-trees-client\";\n// import {TreeMenu} from \"react-tree-menu\";\nimport TreeMenu from \"react-simple-tree-menu\";\nimport '../../../../node_modules/react-simple-tree-menu/dist/main.css';\n\nimport {Spinner} from \"react-bootstrap\";\nimport _ from 'lodash'\nimport \"./tree-view.css\"\n\nvar reactomeURL = \"https://plantreactome.gramene.org\";\n\nclass Pathways extends React.Component {\n constructor(props) {\n super(props);\n this.taxonomy = treesClient.taxonomy.tree(Object.values(props.grameneTaxonomy))\n this.gene = props.geneDocs[props.searchResult.id];\n this.holderId = 'displayHolder' + this.gene._id;\n this.state = {};\n }\n\n initDiagram() {\n this.diagram = Reactome.Diagram.create({\n proxyPrefix: reactomeURL, //'//plantreactome.gramene.org', //'//plantreactomedev.oicr.on.ca', ////cord3084-pc7.science.oregonstate.edu', // reactomedev.oicr.on.ca\n placeHolder: this.holderId,\n width: this.divWrapper.clientWidth - 350 - 1,\n height: 500\n });\n }\n\n stableId(dbId) {\n let prefix = this.taxonomy.indices.id[this.gene.taxon_id].model.reactomePrefix \|\| 'OSA';\n return `R-${prefix}-${dbId}`;\n }\n\n loadDiagram(pathwayId, reactionId) {\n if (!this.diagram) this.initDiagram();\n this.diagram.loadDiagram(pathwayId);\n\n this.diagram.onDiagramLoaded(function (loaded) {\n this.loadedDiagram = loaded;\n if (reactionId) {\n this.diagram.selectItem(reactionId);\n }\n // var xref = _.find(this.props.gene.xrefs,{db : 'Gramene_Plant_Reactome'}).ids[0];\n this.diagram.flagItems(this.gene._id);\n }.bind(this));\n }\n\n componentDidMount() {\n if (Reactome && Reactome.Diagram) {\n // this.initDiagram();\n }\n else {\n window.addEventListener('launchDiagram', function (e) {\n // this.initDiagram()\n }.bind(this));\n }\n }\n\n componentDidUpdate(prevProps, prevState) {\n if (this.state.hierarchy && ! this.state.selectedNode) {\n let node = this.state.hierarchy[0];\n let path = [0];\n let parent = node;\n while (node.nodes) {\n path.push(0);\n parent = node;\n node = node.nodes[0];\n }\n console.log(parent,node,path);\n this.loadNodes(path);\n }\n if (!this.state.hierarchy && this.pathwayIds) {\n const haveDocs = this.pathwayIds.filter(id => this.props.gramenePathways.hasOwnProperty(id));\n if (haveDocs.length === this.pathwayIds.length) {\n const docs = this.pathwayIds.map(id => this.props.gramenePathways[id]);\n this.getHierarchy(this.makeTaxonSpecific(docs,this.gene.taxon_id));\n }\n }\n }\n\n componentWillMount() {\n var pathways, reactionId, ancestorIds;\n pathways = this.gene.annotations.pathways;\n if(!pathways) {\n throw new Error(\"No pathway annotation present for \" + this.gene._id);\n }\n\n this.pathwayIds = _.clone(pathways.ancestors);\n pathways.entries.forEach(function(reaction) {\n let [r,speciesCode,id] = reaction.id.split('-');\n\n this.pathwayIds.push(+id);\n }.bind(this));\n\n this.props.doRequestGramenePathways(this.pathwayIds);\n\n // DocActions.needDocs('pathways', this.pathwayIds, (docs) => { return this.makeTaxonSpecific(docs,this.props.gene.taxon_id)}, this.getHierarchy);\n }\n\n makeTaxonSpecific(docs,taxon_id) {\n let lineageField = 'lineage_'+taxon_id;\n if (! docs[0].hasOwnProperty(lineageField)) {\n let tid = Math.floor(taxon_id / 1000);\n lineageField = 'lineage_'+tid;\n }\n let tsDocs = docs.map(function(doc) {\n let tsDoc = _.pick(doc,['_id','name','type']);\n tsDoc.lineage = doc[lineageField];\n return tsDoc;\n });\n console.log(tsDocs);\n return tsDocs;\n }\n\n componentWillUnmount() {\n // DocActions.noLongerNeedDocs('pathways', this.pathwayIds);\n if (this.diagram) this.diagram.detach();\n }\n\n getHierarchy(docs) {\n let pathways = _.keyBy(docs,'_id');\n let nodes = [];\n this.pathwayIds.forEach(function (pwyId) {\n if (pathways[pwyId]) {\n let pwy = pathways[pwyId];\n pwy.lineage.forEach(function(line) {\n let parentOffset = line.length - 2;\n nodes.push({\n id: pwyId,\n key: pwyId,\n label: pwy.name,\n type: pwy.type,\n checkbox: false,\n selected: false,\n parent: parentOffset >=0 ? line[parentOffset] : undefined\n });\n });\n }\n });\n\n let nested = new FlatToNested({\n children: 'nodes'\n }).convert(nodes);\n\n this.setState({hierarchy: [nested], selectedNode: undefined});\n }\n possiblyLoadNodes(node) {\n if (!node.selected) {\n let selectedNode = this.state.selectedNode;\n selectedNode.selected = false;\n node.selected = true;\n selectedNode = node;\n if (node.type === \"Pathway\") {\n let pathway = this.stableId(node.id);\n this.loadDiagram(pathway);\n }\n else {\n let reaction = this.stableId(node.id);\n let pathway = this.stableId(node.parent.split(\"/\").pop());\n if (this.loadedDiagram === pathway) {\n this.diagram.selectItem(reaction);\n }\n else {\n if (this.diagram) this.diagram.resetSelection();\n this.loadDiagram(pathway,reaction);\n }\n }\n this.setState({selectedNode})\n }\n }\n loadNodes(nodes) {\n let hierarchy = this.state.hierarchy;\n let selectedNode = this.state.selectedNode;\n let offset = nodes.shift();\n let nodeRef = hierarchy[offset];\n let lineage = [nodeRef];\n while (nodeRef.nodes) {\n nodeRef = nodeRef.nodes[0];\n lineage.unshift(nodeRef);\n }\n if (lineage[0].id !== 2894885) {\n let pathway = this.stableId(lineage[0].id);\n let reaction = undefined;\n if (lineage[0].type === \"Reaction\") {\n reaction = pathway;\n pathway = this.stableId(lineage[1].id);\n }\n if (lineage[0].selected) {\n selectedNode = undefined;\n lineage[0].selected = false;\n if (this.loadedDiagram === pathway) {\n this.diagram.resetSelection();\n }\n else {\n if (this.diagram) this.diagram.resetSelection();\n this.loadDiagram(pathway);\n }\n }\n else {\n if (selectedNode) {\n selectedNode.selected = false;\n }\n selectedNode = lineage[0];\n lineage[0].selected = true;\n if (this.loadedDiagram === pathway) {\n if (reaction) {\n this.diagram.selectItem(reaction);\n }\n else {\n this.diagram.resetSelection();\n }\n }\n else {\n if (this.diagram) this.diagram.resetSelection();\n if (reaction) {\n this.loadDiagram(pathway, reaction);\n }\n else {\n this.loadDiagram(pathway);\n }\n }\n }\n this.setState({hierarchy: hierarchy, selectedNode: selectedNode});\n }\n }\n\n renderHierarchy() {\n if (this.state.hierarchy) {\n let path = [];\n let allPaths = [];\n let nodes = this.state.hierarchy;\n while (nodes) {\n path.push(nodes[0].key);\n allPaths.push(path.join('/'));\n if (nodes[0].hasOwnProperty('nodes')) {\n nodes = nodes[0].nodes;\n }\n else {\n nodes = undefined;\n }\n }\n // console.log(path);\n return <TreeMenu\n data={this.state.hierarchy}\n hasSearch={false}\n onClickItem={(item) => this.possiblyLoadNodes(item)}\n onClickItemx={(item) => console.log('onClickItem', item)}\n initialActiveKey={path.join('/')}\n initialOpenNodes={allPaths}\n />;\n // return (\n // <TreeMenu\n // data={this.state.hierarchy}\n // expandIconClass=\"fa fa-chevron-right\"\n // collapseIconClass=\"fa fa-chevron-down\"\n // stateful={true}\n // collapsible={true}\n // onTreeNodeClick={this.loadNodes.bind(this)}\n // />\n // );\n }\n return <Spinner/>\n }\n\n updateQuery() {\n console.log(\"User asked to filter by \"+ this.state.selectedNode.type);\n\n this.props.doAcceptGrameneSuggestion({\n category: 'Plant Reactome',\n fq_field: 'pathways__ancestors',\n fq_value: this.state.selectedNode.id,\n name: this.state.selectedNode.label\n })\n }\n\n render() {\n let reactomeLink,searchFilter;\n\n if (this.state.selectedNode) {\n let xrefLUT = _.keyBy(this.gene.xrefs,'db');\n let links = [\n {name: 'Plant Reactome '+this.state.selectedNode.type, url: `${reactomeURL}/content/detail/${this.stableId(this.state.selectedNode.id)}`}\n ];\n if (xrefLUT.hasOwnProperty('notGramene_Plant_Reactome')) {\n links.push({name: 'Plant Reactome Gene', url: `${reactomeURL}/content/detail/${xrefLUT.notGramene_Plant_Reactome.ids[0]}`});\n }\n reactomeLink = <Links key=\"links\" links={links}/>;\n let filters = [\n {\n name: `All genes in this ${this.state.selectedNode.type}`,\n handleClick: ()=>this.updateQuery()\n }\n ];\n searchFilter = <Explore key=\"explore\" explorations={filters}/>;\n }\n return (\n <div ref={(div) => {this.divWrapper = div;}}>\n <div style={{width:350, height: 500, overflow:'scroll', float:'left'}}>{this.renderHierarchy()}</div>\n <div id={this.holderId}/>\n {searchFilter}\n {reactomeLink}\n </div>\n );\n }\n}\n\nexport default connect(\n 'selectGrameneTaxonomy',\n 'selectGramenePathways',\n 'doRequestGramenePathways',\n 'doAcceptGrameneSuggestion',\n Pathways\n);\n","import React, {useState, useEffect, useRef, useCallback} from 'react';\nimport {connect} from \"redux-bundler-react\";\nimport {Button} from 'react-bootstrap';\nimport { AgGridReact } from \"ag-grid-react\";\nimport _ from 'lodash';\nimport \"ag-grid-community/styles/ag-grid.css\";\nimport \"ag-grid-community/styles/ag-theme-quartz.css\";\nimport '@fortawesome/fontawesome-free/css/all.min.css';\nimport \"./VEP.css\";\n\nconst ggURL = {\n IRRI: 'https://gringlobal.irri.org/gringlobal/accessiondetail?id=',\n ARS: 'https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=',\n ICRISAT: 'https://genebank.icrisat.org/IND/PassportSummary?ID=',\n sorbmutdb: 'https://www.depts.ttu.edu/igcast/sorbmutdb.php',\n maizeGDB: 'https://wgs.maizegdb.org/',\n NCBI: 'https://www.ncbi.nlm.nih.gov/biosample/?term='\n};\n\nconst rice_studies = {'1': {label: 'Rice 3K', type: 'NAT'}};\nconst study_info = {\n 'sorghum_bicolor': {\n '1': {label: 'Purdue EMS', type: 'EMS'},\n '2': {label: 'USDA Lubbock EMS', type: 'EMS'},\n '3': {label: 'Lozano', type: 'NAT'},\n '4': {label: 'USDA Lubbock EMS', type: 'EMS'},\n '5': {label: 'Boatwright SAP', type: 'NAT'},\n '7': {label: 'Kumar BAP', type: 'NAT'},\n '8': {label: 'Lasky landraces', type: 'NAT'},\n '9': {label: 'Sorghum Genomics Toolbox', type: 'NAT'}\n },\n 'zea_maysb73': {\n '15': {label: 'MaizeGDB 2024', type: 'NAT'}\n },\n 'oryza_sativa': {\n '7': {label: 'Rice 3K', type: 'NAT'},\n '20': {label: '20K-RGP', type: 'NAT'},\n '29': {label: 'Rice USDA mini core', type: 'NAT'},\n '38': {label: 'RAPDB 2024', type: 'NAT'},\n },\n 'oryza_aus': { '20': {label: '20K-RGP', type: 'NAT'}},\n 'oryza_sativa117425': { '20': {label: '20K-RGP', type: 'NAT'}},\n 'oryza_sativair64rs2': { '20': {label: '20K-RGP', type: 'NAT'}},\n 'oryza_sativamh63': { '20': {label: '20K-RGP', type: 'NAT'}}\n};\nconst AccessionLink = ({germplasm, gene_id}) => {\n const genebank = germplasm.stock_center;\n const url = ggURL[genebank];\n if (germplasm.germplasm_dbid) { // link to stock center\n const germ_id = germplasm.germplasm_dbid;\n if (germ_id && url && germ_id !== \"0\") {\n return <a target=\"_blank\" href={`${url}${germ_id}`}>\n {germplasm.pub_id} ({genebank})</a>;\n }\n }\n if (genebank === \"sorbmutdb\") {\n return (\n <form id={germplasm.pub_id} action={url} method=\"post\" target=\"_blank\">\n <input type=\"hidden\" name=\"search\" value={gene_id.replace('SORBI_3','Sobic.')} />\n <input type=\"hidden\" name=\"submit\" value=\"Search\" />\n <button type=\"submit\" className=\"button-like-link\">SorbMutDB</button>\n </form>\n );\n }\n if (germplasm.pop_id === '15' && germplasm.stock_center === 'NOT FOUND') {\n return <a target=\"_blank\" href={ggURL['maizeGDB']}>{germplasm.pub_id} (SNPVersity)</a>\n }\n return <span>{germplasm.pub_id}</span>\n}\nfunction compareGermplasm(a, b) {\n const aSub = a?.germplasm?.subpop ?? '';\n const bSub = b?.germplasm?.subpop ?? '';\n const subCmp = aSub.localeCompare(bSub, 'en', { sensitivity: 'accent' });\n if (subCmp !== 0) return subCmp;\n\n const aPub = a?.germplasm?.pub_id ?? '';\n const bPub = b?.germplasm?.pub_id ?? '';\n return aPub.localeCompare(bPub, 'en', { sensitivity: 'accent' });\n}\nfunction group_germplasm(gene, germplasmLUT, vep_obj) {\n let accessionTable = [];\n Object.entries(vep_obj).forEach(([key,accessions]) => {\n const parts = key.split(\"__\");\n if (parts[0] === \"VEP\") {\n if (parts[1] !== \"merged\") {\n accessions.filter(ens_id => germplasmLUT.hasOwnProperty(ens_id)).forEach(ens_id => {\n const germplasm = germplasmLUT[ens_id][0];\n const pop = study_info[parts[3]][parts[4]];\n const conseq = parts[1].replaceAll(\"_\",\" \");\n const status = parts[2] === \"het\" ? \"heterozygous\" : \"homozygous\";\n const accInfo = {\n key: [pop.label,conseq,status].join('%%%'),\n germplasm: germplasm,\n pop: pop\n };\n accessionTable.push(accInfo);\n });\n }\n }\n });\n // group accessionTable by key field\n const groups = _.groupBy(accessionTable, 'key');\n let grouped = [];\n let id=0;\n Object.keys(groups).sort().forEach((group) => {\n const [pop,conseq,status] = group.split('%%%');\n id++;\n const tally = groups[group].length;\n grouped.push({\n id: id,\n group: group,\n summary: true,\n pop: pop,\n conseq: conseq,\n status: status,\n tally: tally\n });\n groups[group].sort(compareGermplasm).forEach(acc => {\n id++;\n grouped.push({\n id: id,\n group: group,\n summary: false,\n pop:pop,\n conseq: conseq,\n status: status,\n accession: acc,\n tally: tally\n })\n })\n })\n return grouped;\n}\nconst THRESHOLD = 5;\nconst GridWithGroups = ({groups,gene_id,doGrin}) => {\n const [rowData, setRowData] = useState(groups);\n\n const initialExpanded = {};\n rowData.forEach((row) => {\n if (row.summary) {\n initialExpanded[row.group] = (row.tally < THRESHOLD);\n }\n });\n const [expandedGroups, setExpandedGroups] = useState(initialExpanded);\n\n\n // Toggle group visibility\n const toggleGroup = (group) => {\n setExpandedGroups((prevExpandedGroups) => ({\n ...prevExpandedGroups,\n [group]: !prevExpandedGroups[group], // Toggle the group's state\n }));\n };\n\n // Filter the data to show/hide rows based on the expanded group state\n const getVisibleRowData = () => {\n const visibleRows = [];\n rowData.forEach((row) => {\n if (row.summary) {\n if (row.tally > 1) {\n visibleRows.push(row);\n }\n } else if (expandedGroups[row.group]) {\n visibleRows.push(row); // Show non-summary rows if the group is expanded\n }\n });\n return visibleRows;\n };\n\n // Define columns with a custom renderer for the summary rows\n const columnDefs = [\n { field: 'pop', headerName: 'Study/Population', flex: 1,\n cellRenderer: (params) => {\n if (params.data.summary \|\| params.data.tally === 1) {\n return params.value;\n }\n return null;\n }\n },\n { field: 'conseq', headerName: 'VEP consequence', flex: 1,\n cellRenderer: (params) => {\n if (params.data.summary \|\| params.data.tally === 1) {\n return params.value;\n }\n return null;\n }\n },\n { field: 'status', headerName: 'Allele status', flex: 1,\n cellRenderer: (params) => {\n if (params.data.summary \|\| params.data.tally === 1) {\n return params.value;\n }\n return null;\n }\n },\n { field: 'accession', headerName: doGrin ? 'Order Germplasm' : 'Accession', flex: 1,\n headerComponent: (props) => {\n return (\n <div style={{display: 'flex', alignItems: 'center'}}>\n {doGrin && <i className=\"fas fa-shopping-cart\"> </i>}\n <span>{props.displayName}</span>\n </div>\n );\n }, // Use the custom header with the shopping cart icon\n cellRenderer: (params) => {\n if (params.value) {\n return <AccessionLink germplasm={params.value.germplasm} gene_id={gene_id} />;\n }\n if (params.data.summary) {\n return (\n <span\n onClick={() => toggleGroup(params.data.group)}\n >\n {params.data.tally} Accessions {expandedGroups[params.data.group] ? '▼' : '▶'}\n </span>\n );\n }\n return null;\n }\n },\n { field: 'synonym', headerName: 'Synonym', filter:false, sortable:false, flex: 1, cellRenderer: (params) => {\n if (params.data.accession) {\n return params.data.accession.germplasm.ens_id\n }\n return null;\n }},\n { field: 'subpop', headerName: 'Subpopulation', filter:false, sortable: false, flex: 1, cellRenderer: (params) => {\n if (params.data.accession && params.data.accession.germplasm.subpop && params.data.accession.germplasm.subpop !== \"?\") {\n return params.data.accession.germplasm.subpop\n }\n return null;\n }},\n { field: 'search', headerName: 'All LOF Genes', sortable:false, filter:false, flex: 1,\n cellRenderer: (params) => {\n if (params.data.accession) {\n const currentURL = new URL(window.location.href);\n const accession = params.data.accession;\n currentURL.search = '';\n currentURL.searchParams.set('category', 'Germplasm');\n currentURL.searchParams.set('fq_field', `VEP__merged__${accession.pop.type}__attr_ss`);\n currentURL.searchParams.set('fq_value', accession.germplasm.ens_id);\n currentURL.searchParams.set('name', accession.germplasm.ens_id);\n\n return <Button size='sm' href={currentURL.toString()}>Search</Button>\n\n }\n return null;\n }\n }\n ];\n\n const defaultColDef = {\n sortable: true,\n filter: \"agTextColumnFilter\",\n cellStyle: (params) => {\n if (params.data.summary) {\n return {cursor: 'pointer'};\n }\n return null;\n }\n };\n\n const nVisible = getVisibleRowData().length;\n const tableHeight = 50 + Math.min(nVisible, 10) * 42;\n return (\n <div\n className=\"ag-theme-quartz\"\n style={{ height: tableHeight, width: \"100%\", maxWidth: \"1200px\" }}\n >\n <AgGridReact\n rowData={getVisibleRowData()}\n columnDefs={columnDefs}\n getRowNodeId={(data) => data.id}\n animateRows={true}\n defaultColDef={defaultColDef}\n />\n </div>\n );\n};\n\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n if (props.grameneConsequences && props.grameneConsequences[gene._id] && props.grameneGermplasm) {\n const groups = group_germplasm(gene, props.grameneGermplasm, props.grameneConsequences[gene._id]);\n\n return <div>\n <h5>Predicted loss-of-function alleles were detected in these germplasm.</h5>\n <div >Explore other variants within this gene in the <a target=\"_blank\"\n href={`${props.configuration.ensemblURL}/${gene.system_name}/Gene/Variation_Gene/Image?db=core;g=${props.searchResult.id}`}>\n Variant image</a> page in the Ensembl genome browser.</div>\n <GridWithGroups groups={...groups} gene_id={gene._id} doGrin={!props.configuration.hasOwnProperty('noGRIN')}/>\n </div>\n } else {\n props.doRequestVEP(gene._id);\n return <pre>loading</pre>;\n }\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGrameneConsequences',\n 'selectGrameneGermplasm',\n 'doRequestVEP',\n Detail\n);\n\n","import React from 'react'\nimport ReactGA from 'react-ga4'\n// import {connect} from \"redux-bundler-react\";\nimport _ from 'lodash'\nimport dbxrefs from 'gramene-dbxrefs';\nimport {Detail, Title, Description, Content} from \"./generic\";\n\nconst HOW_MANY_TO_SHOW_BY_DEFAULT = 10;\n\nclass Xref extends React.Component {\n constructor(props) {\n super(props);\n this.state = {showAll: false};\n }\n\n toggleShowAll() {\n this.setState({showAll: !this.state.showAll});\n }\n\n possiblyTruncateList(vals) {\n var ellipsis, ellipsisChar, ellipsisTitle;\n\n if (vals.length > HOW_MANY_TO_SHOW_BY_DEFAULT) {\n if (this.state.showAll) {\n ellipsisChar = '^ show first ' + HOW_MANY_TO_SHOW_BY_DEFAULT;\n ellipsisTitle = 'Show less';\n }\n else {\n ellipsisChar = '… show all (' + (vals.length - HOW_MANY_TO_SHOW_BY_DEFAULT) + ' more)';\n ellipsisTitle = 'Show more';\n vals = vals.slice(0, HOW_MANY_TO_SHOW_BY_DEFAULT);\n }\n\n ellipsis = (\n <li key=\"showMore\" className=\"showAll\">\n <a title={ellipsisTitle} onClick={this.toggleShowAll.bind(this)}>{ellipsisChar}</a>\n </li>\n );\n\n vals.push(ellipsis);\n }\n\n return vals;\n }\n\n render() {\n var db = this.props.xref.label;\n var urlfcn = this.props.xref.url;\n\n var members = this.props.members.sort();\n\n var vals = members.map(function (item, idx) {\n var url = urlfcn(item),\n liClass = idx < HOW_MANY_TO_SHOW_BY_DEFAULT ? \"default\" : \"extra\";\n let external = <small title=\"This link opens a page from an external site\"> <i className=\"fa fa-external-link\"/></small>;\n return (\n <li key={idx} className={liClass}>\n <a href={url} target=\"_blank\" onClick={()=>{\n ReactGA.event({\n category: \"outbound link\", action: \"follow\", label: item\n })\n }}>{item}{external}</a>\n {/<ReactGA.OutboundLink/}\n {/* eventLabel={db}/}\n {/ to={url}/}\n {/ target=\"_blank\"/}\n {/>/}\n {/ {item}{external}/}\n {/</ReactGA.OutboundLink>/}\n </li>\n )\n })\n\n vals = this.possiblyTruncateList(vals);\n\n return (\n <tr>\n <td className=\"xref-name-col\">{db}</td>\n <td className=\"xref-value-col\">\n <ol className=\"xref-id-list\">{vals}</ol>\n </td>\n </tr>\n );\n }\n}\n\nfunction formatXrefsForGene(gene) {\n if(!gene \|\| !_.isArray(gene.xrefs)) {\n throw new Error(\"No xrefs for \" + _.get(gene._id));\n }\n return gene.xrefs\n .filter(xr => dbxrefs.isKnown(xr.db) && xr.db !== \"PUBMED\")\n .sort()\n .map((xr,idx) => {\n var xref = dbxrefs.fetch(xr.db);\n return (\n <Xref key={idx} xref={xref} members={xr.ids} source={xr.source} text={xr.text} />\n )\n })\n}\n\nconst Xrefs = ({searchResult, geneDocs}) => (\n <Detail>\n <Title key=\"title\">Cross-references</Title>\n <Description key=\"description\">References to this gene in other databases:</Description>\n <Content key=\"content\">\n <table className=\"xrefs table\">\n <thead>\n <tr>\n <th className=\"xref-name-col\">Database</th>\n <th className=\"xref-value-col\">IDs and links</th>\n </tr>\n </thead>\n <tbody>\n {formatXrefsForGene(geneDocs[searchResult.id])}\n </tbody>\n </table>\n </Content>\n </Detail>\n);\n\nexport default Xrefs;\n\n","import React from 'react'\nimport ReactGA from 'react-ga4'\n// import {connect} from \"redux-bundler-react\";\nimport _ from 'lodash'\nimport dbxrefs from 'gramene-dbxrefs';\nimport {Detail, Title, Description, Content} from \"./generic\";\n\nconst HOW_MANY_TO_SHOW_BY_DEFAULT = 10;\n\nclass Xref extends React.Component {\n constructor(props) {\n super(props);\n this.state = {showAll: false};\n }\n\n toggleShowAll() {\n this.setState({showAll: !this.state.showAll});\n }\n\n possiblyTruncateList(vals) {\n var ellipsis, ellipsisChar, ellipsisTitle;\n\n if (vals.length > HOW_MANY_TO_SHOW_BY_DEFAULT) {\n if (this.state.showAll) {\n ellipsisChar = '^ show first ' + HOW_MANY_TO_SHOW_BY_DEFAULT;\n ellipsisTitle = 'Show less';\n }\n else {\n ellipsisChar = '… show all (' + (vals.length - HOW_MANY_TO_SHOW_BY_DEFAULT) + ' more)';\n ellipsisTitle = 'Show more';\n vals = vals.slice(0, HOW_MANY_TO_SHOW_BY_DEFAULT);\n }\n\n ellipsis = (\n <li key=\"showMore\" className=\"showAll\">\n <a title={ellipsisTitle} onClick={this.toggleShowAll.bind(this)}>{ellipsisChar}</a>\n </li>\n );\n\n vals.push(ellipsis);\n }\n\n return vals;\n }\n\n render() {\n var db = this.props.xref.label;\n var urlfcn = this.props.xref.url;\n\n var members = this.props.members.sort();\n\n var vals = members.map(function (item, idx) {\n var url = urlfcn(item),\n liClass = idx < HOW_MANY_TO_SHOW_BY_DEFAULT ? \"default\" : \"extra\";\n let external = <small title=\"This link opens a page from an external site\"> <i className=\"fa fa-external-link\"/></small>;\n return (\n <li key={idx} className={liClass}>\n <a href={url} target=\"_blank\" onClick={()=>{\n ReactGA.event({\n category: \"outbound link\", action: \"follow\", label: item\n })\n }}>{item}{external}</a>\n {/<ReactGA.OutboundLink/}\n {/ eventLabel={db}/}\n {/ to={url}/}\n {/ target=\"_blank\"/}\n {/>/}\n {/ {item}{external}/}\n {/</ReactGA.OutboundLink>/}\n </li>\n )\n })\n\n vals = this.possiblyTruncateList(vals);\n\n return (\n <tr>\n {/<td className=\"xref-name-col\">{db}</td>/}\n <td className=\"xref-value-col\">\n <ol className=\"xref-id-list\">{vals}</ol>\n </td>\n <td className=\"xref-name-col\">{this.props.source}</td>\n <td className=\"xref-value-col\">{this.props.text}</td>\n </tr>\n );\n }\n}\n\nfunction formatPubsForGene(gene) {\n if(!gene \|\| !_.isArray(gene.xrefs)) {\n throw new Error(\"No xrefs for \" + _.get(gene._id));\n }\n let pubs = gene.xrefs.filter(xr => xr.db === \"PUBMED\");\n if (pubs.length === 0) {\n return <tr><td colSpan={3}>No publications found.</td></tr>\n }\n return pubs.sort((a,b) => {\n if (a.source) {\n if (b.source) {\n if (a.source < b.source) {\n return -1;\n }\n if (a.source > b.source) {\n return 1;\n }\n }\n else {\n return -1;\n }\n }\n else if (b.source) {\n return 1;\n }\n if (a.db < b.db) {\n return -1;\n }\n if (a.db > b.db) {\n return 1;\n }\n return 0;\n })\n .map((xr,idx) => {\n var xref = dbxrefs.fetch(xr.db);\n return (\n <Xref key={idx} xref={xref} members={xr.ids} source={xr.source} text={xr.text} />\n )\n })\n}\nconst formURL = 'https://docs.google.com/forms/d/e/1FAIpQLSey-xPyTysdd9c2phXT6kcbjEDeCppG4dLG7LjZCeLpx_KGog/viewform?usp=pp_url&entry.1266455249=';\nconst Publications = ({searchResult, geneDocs}) => (\n <Detail>\n <Title key=\"title\">Curated publications</Title>\n <Description key=\"description\">Functions described in the literature:</Description>\n <Content key=\"content\">\n <table className=\"xrefs table\">\n <thead>\n <tr>\n <th className=\"xref-10-col\">PubMed link</th>\n <th className=\"xref-10-col\">Curation source</th>\n <th className=\"xref-80-col\">Title/Description</th>\n </tr>\n </thead>\n <tbody>\n {formatPubsForGene(geneDocs[searchResult.id])}\n </tbody>\n <tfoot>\n <tr>\n <th colSpan={3}>Submit a gene function <a target=\"_blank\" href={formURL + searchResult.id}>here</a></th>\n </tr>\n </tfoot>\n </table>\n </Content>\n </Detail>\n);\n\nexport default Publications;\n\n","import React, { useState, useEffect } from 'react';\nimport {connect} from \"redux-bundler-react\";\nimport {Tabs, Tab, Form, Container, Row, Col, ToggleButton, ButtonGroup } from 'react-bootstrap';\nimport { AiOutlineCopy } from 'react-icons/ai';\nimport './sequences.css';\nimport keyBy from \"lodash/keyBy\";\n\nconst CodeBlock = props => {\n const plainFasta = `>${props.id}\\n${props.seq}`\n\n const [showNotification, setShowNotification] = useState(false);\n\n const copyCode = () => {\n // Use the Clipboard API to write text to the clipboard\n navigator.clipboard.writeText(plainFasta)\n .then(() => {\n setShowNotification(true);\n })\n .catch((err) => {\n console.error('Unable to copy to clipboard', err);\n });\n };\n\n useEffect(() => {\n if (showNotification) {\n const notificationTimeout = setTimeout(() => {\n setShowNotification(false);\n }, 2000); // Hide the notification after 2 seconds\n\n return () => clearTimeout(notificationTimeout);\n }\n }, [showNotification]);\n\n return (\n <div className=\"fasta-container\">\n <code className=\"fasta\"><span className=\"header\">>{props.id}</span><br/>{\n props.blocks.map((block,idx) =>\n <span key={idx} className={block.kind}>{block.seq}</span>\n )\n }</code>\n <p className=\"fasta-key\">\n <b>Key:</b> 5'UTR \n <span className=\"square-utr5\">  </span>\n  CDS \n <span className=\"square-cds\">  </span>\n  3'UTR \n <span className=\"square-utr3\">  </span>\n </p>\n <button className=\"copy-button\" onClick={copyCode}><AiOutlineCopy /></button>\n {showNotification && <div className=\"notification\">Sequence copied</div>}\n </div>\n );\n};\n\nconst decoratePeptide = (seq, transcript) => {\n let junctions = [];\n if (transcript.exon_junctions) {\n transcript.exon_junctions.forEach((ej, idx) => {\n if (ej > transcript.cds.start && ej <= transcript.cds.end) {\n junctions.push(Math.floor((ej - transcript.cds.start) / 3));\n }\n });\n }\n if (junctions.length === 0) {\n return [{kind:'cds', seq:seq}];\n }\n let offset = 0;\n let blocks = [];\n junctions.forEach((j, idx) => {\n let kind = idx % 2 === 0 ? \"cds\" : \"cds-other\";\n blocks.push({kind: kind, seq: seq.substring(offset, j)});\n offset = j;\n });\n blocks.push({kind: junctions.length % 2 === 0 ? \"cds\" : \"cds-other\", seq: seq.substring(junctions.pop())});\n return blocks;\n}\nconst decorateSeq = (geneSeq, gene, up, down, tid, mode) => {\n // return a list of blocks with kind and seq properties\n let blocks = [];\n const transcript = gene.gene_structure.transcripts.find(tr => tr.id === tid);\n const offset = gene.location.strand === 1\n ? gene.location.start - geneSeq.start\n : geneSeq.end - gene.location.end\n if (up > 0) {\n const TSS = gene.gene_structure.exons.find(exon => exon.id === transcript.exons[0]).start;\n blocks.push({\n kind:'upstream',\n seq: geneSeq.seq.substring(offset - up + TSS - 1, offset + TSS - 1).toLowerCase()\n })\n }\n // add exons and introns based on tid\n let pos_in_transcript = 0;\n let pos_in_gene = 0;\n let blockType = 'utr5';\n let extra = '';\n transcript.exons.forEach((eid, e_idx) => {\n const exon = gene.gene_structure.exons.find(exon => exon.id === eid);\n if (e_idx > 0 && mode === \"dna\") {\n blocks.push({\n kind: 'intron',\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + exon.start - 1).toLowerCase()\n });\n pos_in_gene = exon.start-1;\n }\n if (mode === \"rna\") {\n extra = e_idx % 2 === 1 ? '-other' : '';\n }\n let exon_length = exon.end - exon.start + 1;\n if (transcript.cds && pos_in_transcript < transcript.cds.start && pos_in_transcript + exon_length >= transcript.cds.start) {\n // CDS starts in this exon\n const utr5_len = transcript.cds.start - pos_in_transcript - 1;\n if (utr5_len > 0) {\n blocks.push({\n kind: blockType + extra,\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + utr5_len)\n });\n exon_length -= utr5_len;\n pos_in_gene += utr5_len;\n pos_in_transcript = transcript.cds.start - 1;\n }\n blockType = 'cds';\n }\n if (blockType === 'cds' && pos_in_transcript + exon_length >= transcript.cds.end) {\n // CDS ends in this exon\n const cds_len = transcript.cds.end - pos_in_transcript;\n if (cds_len > 0) {\n blocks.push({\n kind: blockType + extra,\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + cds_len)\n });\n exon_length -= cds_len;\n pos_in_gene += cds_len;\n pos_in_transcript = transcript.cds.end;\n }\n blockType = 'utr3';\n }\n if (exon_length > 0) {\n blocks.push({\n kind: blockType + extra,\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + exon_length)\n })\n }\n pos_in_gene = exon.end;\n pos_in_transcript += exon_length;\n })\n // check if there's more to the gene locus after end of transcript?\n // downstream is currently relative to end of transcript but upstream is relative to first TSS\n if (down > 0) {\n blocks.push({\n kind:'downstream',\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + down).toLowerCase()\n })\n }\n return blocks;\n};\nconst buildId = (gene, geneSeq, up, down) => {\n let gs = gene.location.strand === 1 ? gene.location.start - up : gene.location.start - down;\n let ge = gene.location.strand === 1 ? gene.location.end + down : gene.location.end + up;\n let extras = [];\n if (gene.location.strand === -1) {\n extras.push('reverse')\n }\n if (up > 0) {\n extras.push(`upstream=${up}`)\n }\n if (down > 0) {\n extras.push(`downstream=${down}`)\n }\n return `${geneSeq.genome}\|${gene._id}\|${gene.location.region}:${gs}..${ge} ${extras.join('\|')}`\n};\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n const [tab, setTab] = useState('dna');\n const [upstream, setUpstream] = useState(0);\n const [downstream, setDownstream] = useState(0);\n const [tid, setTid] = useState(gene.gene_structure.canonical_transcript);\n let geneSeq;\n let rnaSeq;\n let pepSeq;\n if (props.geneSequences && props.geneSequences[gene._id]) {\n geneSeq = props.geneSequences[gene._id];\n }\n else {\n props.doRequestGeneSequence(gene)\n return <pre>loading</pre>;\n }\n if (props.rnaSequences && props.rnaSequences[tid]) {\n rnaSeq = props.rnaSequences[tid]\n }\n else {\n props.doRequestRnaSequence(tid, gene)\n return <pre>loading</pre>;\n }\n const maxUp = gene.location.strand === 1 ? gene.location.start - geneSeq.start : geneSeq.end - gene.location.end;\n const maxDown = gene.location.strand === -1 ? gene.location.start - geneSeq.start : geneSeq.end - gene.location.end;\n const transcript = gene.gene_structure.transcripts.find(tr => tr.id === tid);\n let tl_id;\n if (transcript.translation) {\n tl_id = transcript.translation.id;\n if (props.pepSequences && props.pepSequences[tl_id]) {\n pepSeq = props.pepSequences[tl_id];\n }\n else {\n props.doRequestPepSequence(tl_id, gene);\n return <pre>loading</pre>;\n }\n }\n return <Tabs activeKey={tab}\n onSelect={(k) => setTab(k)}\n >\n <Tab tabClassName=\"dna\" eventKey=\"dna\" title=\"Genomic sequence\">\n <Container style={{ width: '100ch', marginLeft: 0}}>\n <Row>\n <Col><b><i>Show flanking sequence</i></b></Col>\n </Row>\n <Row>\n <Col style={{ maxWidth: '5ch', textAlign: 'right'}}>{upstream}</Col>\n <Col style={{maxWidth: '20ch'}}>\n <Form.Range\n className=\"reverse-slide\"\n value={upstream}\n onChange={(e) => setUpstream(e.target.value)}\n min={0}\n max={maxUp}\n step={10}\n /><div style={{textAlign:'right'}}>Upstream</div>\n </Col>\n <Col style={{maxWidth: '30ch'}}>\n <div className=\"styled-span\">\n <div className=\"vertical-line\"/>\n <div className=\"horizontal-line\"/>\n <span>Transcript (unspliced)</span>\n <div className=\"horizontal-line\"/>\n <div className=\"vertical-line\"/>\n </div>\n </Col>\n <Col style={{maxWidth: '20ch'}}>\n <Form.Range\n value={downstream}\n onChange={(e) => setDownstream(e.target.value)}\n min={0}\n max={maxDown}\n step={10}\n /><div style={{textAlign:'left'}}>Downstream</div>\n </Col>\n <Col style={{ maxWidth: '5ch', textAlign: 'left'}}>{downstream}</Col>\n </Row>\n {gene.gene_structure.transcripts.length > 1 &&\n <Row>\n <Col><b><i>Highlight transcript</i></b><br/>\n <ButtonGroup>{gene.gene_structure.transcripts.sort((a,b) => a.id.localeCompare(b.id)).map((tr, idx) => {\n let v = tr.id === gene.gene_structure.canonical_transcript ? 'primary' : 'secondary';\n if (tr.id !== tid) {\n v = `outline-${v}`\n }\n return <ToggleButton\n variant={v}\n key={idx}\n id={`radio-${idx}`}\n type=\"radio\"\n name={tr.id}\n value={tr.id}\n checked={tr.id === tid}\n onChange={e => setTid(e.currentTarget.value)}\n >{tr.id}</ToggleButton>\n })}</ButtonGroup>\n </Col>\n </Row>\n }\n </Container>\n {geneSeq && <CodeBlock id={buildId(gene,geneSeq,+upstream,+downstream)} seq={geneSeq.seq.substring(maxUp - +upstream, maxUp + gene.location.end - gene.location.start + 1 + +downstream)} blocks={decorateSeq(geneSeq,gene,+upstream,+downstream,tid,\"dna\")}/>}\n </Tab>\n <Tab tabClassName=\"rna\" eventKey=\"rna\" title=\"Transcript sequence\">\n <Container style={{ width: '100ch', marginLeft: 0}}>\n {gene.gene_structure.transcripts.length > 1 &&\n <Row>\n <Col><b><i>Select transcript</i></b><br/>\n <ButtonGroup>{gene.gene_structure.transcripts.sort((a,b) => a.id.localeCompare(b.id)).map((tr, idx) => {\n let v = tr.id === gene.gene_structure.canonical_transcript ? 'primary' : 'secondary';\n if (tr.id !== tid) {\n v = `outline-${v}`\n }\n return <ToggleButton\n variant={v}\n key={idx}\n id={`radio-${idx}`}\n type=\"radio\"\n name={tr.id}\n value={tr.id}\n checked={tr.id === tid}\n onChange={e => setTid(e.currentTarget.value)}\n >{tr.id}</ToggleButton>\n })}</ButtonGroup>\n </Col>\n </Row>\n }\n </Container>\n {geneSeq && <CodeBlock id={tid} seq={rnaSeq.seq} blocks={decorateSeq(geneSeq,gene,0,0,tid,\"rna\")}/>}\n </Tab>\n {gene.biotype === \"protein_coding\" &&\n <Tab tabClassName=\"pep\" eventKey=\"pep\" title=\"Peptide sequence\">\n <Container style={{ width: '100ch', marginLeft: 0}}>\n {gene.gene_structure.transcripts.length > 1 &&\n <Row>\n <Col><b><i>Select transcript</i></b><br/>\n <ButtonGroup>{gene.gene_structure.transcripts.sort((a,b) => a.id.localeCompare(b.id)).map((tr, idx) => {\n let v = tr.id === gene.gene_structure.canonical_transcript ? 'primary' : 'secondary';\n if (tr.id !== tid) {\n v = `outline-${v}`\n }\n return <ToggleButton\n variant={v}\n key={idx}\n id={`radio-${idx}`}\n type=\"radio\"\n name={tr.id}\n value={tr.id}\n checked={tr.id === tid}\n onChange={e => setTid(e.currentTarget.value)}\n >{tr.id}</ToggleButton>\n })}</ButtonGroup>\n </Col>\n </Row>\n }\n </Container>\n {geneSeq && <CodeBlock id={tl_id} seq={pepSeq.seq} blocks={decoratePeptide(pepSeq.seq,transcript)}/>}\n </Tab>}\n </Tabs>\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGeneSequences',\n 'selectRnaSequences',\n 'selectPepSequences',\n 'doRequestGeneSequence',\n 'doRequestRnaSequence',\n 'doRequestPepSequence',\n Detail\n);\n\n","import React from 'react'\nimport { connect } from 'redux-bundler-react'\nimport Vis from \"gramene-search-vis\"\nimport Selection from './selection.js'\nimport '../../../node_modules/gramene-search-vis/styles/main.less';\n\nclass TaxDist extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n collapseEmpties: true\n };\n }\n handleSelection(selections) {\n this.setState({selections})\n }\n handleHighlight(highlight) {\n this.setState({highlight})\n }\n handleFilter() {\n this.setState({selections:null})\n }\n toggleEmpties() {\n this.setState({collapseEmpties: !this.state.collapseEmpties})\n }\n render() {\n let selectedTaxa = {};\n if (this.props.grameneSearch && this.state.collapseEmpties) {\n this.props.grameneSearch.facet_counts.facet_fields.taxon_id.filter((tid,idx) => idx % 2 === 0).forEach(tid => {\n selectedTaxa[tid] = true;\n })\n }\n else {\n selectedTaxa = this.props.grameneGenomes.active\n }\n return (\n <div className=\"results-vis big-vis\">\n {this.props.grameneTaxDist && <button type=\"button\"\n className=\"btn btn-primary btn-sm\"\n onClick={this.toggleEmpties.bind(this)}>\n {this.state.collapseEmpties ? 'Expand' : 'Collapse'} empty branches\n </button>}\n {this.props.grameneTaxDist && <Vis taxonomy={this.props.grameneTaxDist}\n selectedTaxa={selectedTaxa}\n onSelection={this.handleSelection.bind(this)}\n onHighlight={this.handleHighlight.bind(this)}\n />}\n {this.renderSelection()}\n </div>\n );\n }\n renderSelection() {\n if (this.state.selections && this.props.grameneTaxDist) {\n return <Selection taxonomy={this.props.grameneTaxDist}\n selectedTaxa={{}}\n selections={this.state.selections}\n onFilter={this.handleFilter.bind(this)}/>\n }\n }\n}\n\nexport default connect(\n 'selectGrameneTaxDist',\n 'selectGrameneGenomes',\n 'selectGrameneSearch',\n TaxDist\n);\n","import React from 'react';\nimport numeral from 'numeral';\nimport _ from \"lodash\";\n\nimport {Table, Button, Badge} from 'react-bootstrap';\nimport {connect} from \"redux-bundler-react\";\n\nfunction selectionStats(selections, taxonomy) {\n const selectionData = getSelectionData(selections, taxonomy);\n const totalGeneResults = taxonomy.model.results.count;\n const fq = fqFromSelections(selections);\n\n return {\n selectedGenes: selectionData.resultsCount,\n totalGeneResults,\n fq,\n numSelectedBins: selectionData.binsCount,\n proportionGenesSelected: selectionData.resultsCount / totalGeneResults\n }\n}\n\nfunction getSelectionData(selection, taxonomy) {\n return _.reduce(selection, (countAcc, sel) => {\n const bins = taxonomy.getBins(sel.binFrom.idx, sel.binTo.idx);\n countAcc.binsCount += bins.length;\n countAcc.resultsCount += _.reduce(bins, (acc, bin) => acc + bin.results.count, 0);\n return countAcc;\n }, {resultsCount: 0, binsCount: 0});\n}\n\nconst selectionToSolrRange = (sel)=>`[${sel.binFrom.idx} TO ${sel.binTo.idx}]`;\n\nfunction fqFromSelections(selections) {\n const rangeStrings = selections.map(selectionToSolrRange);\n return `fixed_1000__bin:(${rangeStrings.join(' ')})`;\n}\n\nconst Selections = ({selections, taxonomy, doAcceptGrameneSuggestion, onFilter}) => {\n const stats = selectionStats(selections, taxonomy);\n\n const setFilter = () => {\n doAcceptGrameneSuggestion({\n category: 'Selections',\n fq_field: 'fixed_1000__bin',\n fq_value: `(${selections.map(selectionToSolrRange).join(' ')})`,\n name: `${selections.length} region${selections.length === 1 ? '':'s'}`\n });\n onFilter();\n };\n\n const formatProportion = (prop) => '(' + (_.isFinite(prop) ? numeral(prop).format('0.0%') : undefined) + ')';\n\n return (\n <div>\n <Table>\n <tbody>\n <tr>\n <th>Number of selected genes</th>\n <td>{stats.selectedGenes} {formatProportion(stats.proportionGenesSelected)}</td>\n <td><Button size='sm' onClick={setFilter}>selections \|<Badge>{stats.selectedGenes}</Badge></Button>\n </td>\n </tr>\n </tbody>\n </Table>\n </div>\n )\n};\n\nexport default connect(\n 'doAcceptGrameneSuggestion',\n Selections\n);\n","import React from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport {Alert, Container, Row, Card, CardGroup} from 'react-bootstrap'\nimport './genes.css'\n\nconst examples = [\n {\n subsite: {\n maize:1,\n sorghum:1,\n main:1,\n },\n text: \"What are the orthologs of Arabidopsis thaliana's PAD4 gene in Andropogoneae?\",\n filters: {\n status: 'init',\n rows: 20,\n operation: 'AND',\n negate: false,\n leftIdx: 0,\n rightIdx: 5,\n children: [\n {\n fq_field: 'homology__all_orthologs',\n fq_value: 'AT3G52430',\n name: 'Orthologs of PAD4',\n category: 'Gene Tree',\n leftIdx:1,\n rightIdx:2,\n negate: false,\n marked: false\n },\n {\n fq_field: 'taxonomy__ancestors',\n fq_value: 147429,\n name: 'Andropogoneae',\n category: 'Taxonomy',\n leftIdx:3,\n rightIdx:4,\n negate: false,\n marked: false\n }\n ]\n }\n },\n {\n subsite: {\n grapevine:1\n },\n text: \"What are the orthologs of Arabidopsis thaliana's PAD4 gene in rosids?\",\n filters: {\n status: 'init',\n rows: 20,\n operation: 'AND',\n negate: false,\n leftIdx: 0,\n rightIdx: 5,\n children: [\n {\n fq_field: 'homology__all_orthologs',\n fq_value: 'AT3G52430',\n name: 'Orthologs of PAD4',\n category: 'Gene Tree',\n leftIdx:1,\n rightIdx:2,\n negate: false,\n marked: false\n },\n {\n fq_field: 'taxonomy__ancestors',\n fq_value: 71275,\n name: 'rosids',\n category: 'Taxonomy',\n leftIdx:3,\n rightIdx:4,\n negate: false,\n marked: false\n }\n ]\n }\n }\n];\nconst HelpDemo = ({configuration,doReplaceGrameneFilters}) => (\n <Container fluid style={{padding: '40px'}}>\n <Row>\n <h3>Search Features</h3>\n </Row>\n <Row>\n <CardGroup style={{width:'80%'}}>\n <Card style={{'backgroundColor':'#f3f6f5', 'borderColor':'#DDE5E3'}}>\n <Card.Body>\n <Card.Title>Suggestions</Card.Title>\n <Card.Text>Matching terms are provided as you type:</Card.Text>\n <div className='gene-search-pic-sugg'/>\n </Card.Body>\n </Card>\n <Card style={{'backgroundColor':'#f3f6f5', 'borderColor':'#DDE5E3'}}>\n <Card.Body>\n <Card.Title>Visualization</Card.Title>\n <Card.Text>See the distribution of results across all genomes:</Card.Text>\n <div className='gene-search-pic-results'/>\n </Card.Body>\n </Card>\n <Card style={{'backgroundColor':'#f3f6f5', 'borderColor':'#DDE5E3'}}>\n <Card.Body>\n <Card.Title>Gene tree view</Card.Title>\n <Card.Text>Explore evolutionary history of a gene family:</Card.Text>\n <div className='gene-search-pic-genetree'/>\n </Card.Body>\n </Card>\n </CardGroup>\n </Row>\n <Row>\n <h4>For Example</h4>\n </Row>\n <Row>\n <small>\n You can ask sophisticated questions about the genes:<br/>\n <ul>\n {examples.filter(e => !!e.subsite[configuration.id]).map((e,idx) => (\n <li key={idx}><a onClick={() => doReplaceGrameneFilters(e.filters)}>{e.text}</a></li>\n ))}\n </ul>\n </small>\n </Row>\n </Container>\n);\n\nexport default connect(\n 'selectConfiguration',\n 'doReplaceGrameneFilters',\n HelpDemo\n);\n\n","import React from 'react'\nimport { connect } from 'redux-bundler-react'\n\nclass GeneAttribs extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n };\n }\n render() {\n return (\n <div className=\"gramene-attribs\">\n {this.props.grameneGeneAttribs && <pre>hi</pre>}\n </div>\n );\n }\n}\n\nexport default connect(\n 'selectGrameneGeneAttribs',\n GeneAttribs\n);\n","import React from \"react\";\nimport { connect } from 'redux-bundler-react'\nimport { Modal, Button } from \"react-bootstrap\";\n\nclass TaxonomyModal extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n genomes : Object.values(props.grameneMaps).sort((a,b) => a.left_index - b.left_index)\n };\n if (Object.keys(props.grameneGenomes.active).length === 0) {\n this.state.genomes.forEach(g => {\n g.selected = !g.hidden;\n })\n }\n else {\n this.state.genomes.forEach(g => {\n g.selected = !g.hidden && props.grameneGenomes.active[g.taxon_id];\n })\n }\n }\n getSelectedGenomes() {\n let selected = {};\n let notHidden = {};\n let somethingWasSelected = false;\n this.state.genomes.forEach(g => {\n if (!g.hidden) {\n notHidden[g.taxon_id] = true;\n if (g.selected) {\n selected[g.taxon_id] = true;\n somethingWasSelected = true;\n }\n }\n });\n return somethingWasSelected ? selected : notHidden;\n }\n handleChange(e) {\n const idx = +e.target.value;\n let newState = Object.assign({},this.state);\n newState.genomes[idx].selected = !newState.genomes[idx].selected;\n this.setState(newState);\n }\n handleClose() {\n this.props.doUpdateGrameneGenomes(this.getSelectedGenomes())\n }\n selectAll() {\n const genomes = this.state.genomes.map(g => {g.selected = true; return g});\n this.setState({genomes});\n }\n selectNone() {\n const genomes = this.state.genomes.map(g => {g.selected = false; return g});\n this.setState({genomes});\n }\n renderGenomes() {\n return (\n <div>\n {this.state.genomes.map((m,idx) => {\n if(m.hidden) return <></>\n return (\n <div key={idx}>\n <input checked={m.selected}\n onChange={this.handleChange.bind(this)}\n type=\"checkbox\"\n value={idx}\n />\n {' '}{m.display_name}\n </div>\n )\n })}\n <Button onClick={this.handleClose.bind(this)}>Submit</Button>\n </div>\n )\n }\n render() {\n return (\n <Modal\n show={this.props.grameneGenomes.show}\n onHide={this.handleClose.bind(this)}\n size='lg'\n >\n <Modal.Header closeButton>\n <Modal.Title>Select Genomes of Interest</Modal.Title>\n </Modal.Header>\n <Modal.Body>\n <Button variant=\"outline-secondary\" onClick={this.selectAll.bind(this)}>All</Button>{' '}\n <Button variant=\"outline-secondary\" onClick={this.selectNone.bind(this)}>None</Button>\n {this.renderGenomes()}\n </Modal.Body>\n </Modal>\n )\n }\n};\n\nexport default connect(\n 'selectGrameneGenomes',\n 'selectGrameneMaps',\n 'doUpdateGrameneGenomes',\n TaxonomyModal\n)\n","import React, { useState, Suspense } from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport { Accordion, Button } from 'react-bootstrap';\nimport \"./expression.css\";\nconst LazyStudy = React.lazy(() => import('./Study'));\n\nconst StudyList = props => {\n return <Accordion alwaysOpen defaultActiveKey={props.studies.length === 1 ? \"study_0\" : undefined}>\n {props.studies.map((study, idx) => {\n return (\n <Accordion.Item key={idx} eventKey={'study_'+idx}>\n <Accordion.Header>{study.description}</Accordion.Header>\n <Accordion.Body>\n <Suspense fallback={<div>Loading...</div>}>\n <LazyStudy id={study._id}/>\n </Suspense>\n {/<Study id={study._id} />/}\n </Accordion.Body>\n </Accordion.Item>\n )\n })}\n </Accordion>\n};\n\nconst Expression = props => {\n let searchTaxa = {};\n if (props.grameneSearch) {\n const taxon_id_facet = props.grameneSearch.facet_counts.facet_fields.taxon_id;\n taxon_id_facet.filter((tid, idx) => idx % 2 === 0).forEach(tid => searchTaxa[tid] = true);\n }\n const availableTaxa = Object.keys(props.expressionStudies)\n .filter(tid => searchTaxa[tid] \|\| searchTaxa[tid + '001'])\n .sort((a,b) => props.grameneMaps[a + '001'].left_index - props.grameneMaps[b + '001'].left_index);\n return availableTaxa && props.grameneTaxonomy &&\n <div>\n <div>This is where you can launch a component for the selected samples. props.desiredSamples lists them.\n This component can request the data from the API\n organize samples by factor metadata? One big table with all the studies?\n <Button>Show Samples ({Object.keys(props.desiredSamples).length} selected)</Button>\n </div>\n <Accordion alwaysOpen defaultActiveKey={availableTaxa.length === 1 ? \"tax_0\" : undefined}>\n {availableTaxa.map((tid, idx) => {\n const n = props.expressionStudies[tid].length;\n return <Accordion.Item key={idx} eventKey={'tax_'+idx}>\n <Accordion.Header>{props.grameneTaxonomy[tid].name} - {n} {n === 1 ? 'study' : 'studies'}</Accordion.Header>\n <Accordion.Body><StudyList studies={props.expressionStudies[tid]}/></Accordion.Body>\n </Accordion.Item>\n })}\n </Accordion>\n </div>\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGrameneSearch',\n 'selectGrameneTaxonomy',\n 'selectGrameneMaps',\n 'selectExpressionStudies',\n 'selectDesiredSamples', // current set of samples to fetch expression data for\n Expression\n);\n","import {connect} from \"redux-bundler-react\";\nimport React, { useEffect, useState } from 'react';\nimport {Table, Form, Button, Alert, Spinner, Container, Row, Col} from 'react-bootstrap';\nimport { firebaseApp } from \"../utils\";\nimport {getAuth, onAuthStateChanged} from \"firebase/auth\";\n\nconst auth = getAuth(firebaseApp);\n\nconst MAX_GENE_IDS = 1000; // Define the maximum number of gene IDs allowed\n\nconst GeneListDisplayComponent = props => {\n const [publicGeneLists, setPublicGeneLists] = useState([]);\n const [privateGeneLists, setPrivateGeneLists] = useState([]);\n const [error, setError] = useState(null);\n const [user, setUser] = useState({});\n onAuthStateChanged(auth, (user) => setUser(user));\n\n const fetchPrivateGeneLists = async () => {\n try {\n const token = await user.getIdToken();\n // Replace this with actual fetch from your backend or storage\n const response = await fetch(`${props.api}/gene_lists?site=${props.site}&isPublic=false`, {\n method: 'GET',\n headers: {\n \"Content-Type\": \"application/json\",\n \"Authorization\": `Bearer ${token}`\n }\n });\n const result = await response.json();\n\n if (response.ok) {\n setError(null);\n setPrivateGeneLists(result); // array of saved gene lists\n } else {\n setError('Error fetching gene lists.');\n }\n } catch (err) {\n setError('Failed to fetch private gene lists. Please try again later.');\n }\n };\n // Fetch saved gene lists from a backend or local storage\n const fetchPublicGeneLists = async () => {\n try {\n // Replace this with actual fetch from your backend or storage\n const response = await fetch(`${props.api}/gene_lists?site=${props.site}&isPublic=true`);\n const result = await response.json();\n\n if (response.ok) {\n setPublicGeneLists(result); // array of saved gene lists\n } else {\n setError('Error fetching gene lists.');\n }\n } catch (err) {\n setError('Failed to fetch gene lists. Please try again later.');\n }\n };\n\n // Fetch data when the component is mounted\n useEffect(() => {\n fetchPublicGeneLists();\n }, []);\n useEffect(() => {\n fetchPrivateGeneLists();\n }, [user]);\n\n return (\n <div className=\"gene-list-display-component\">\n <h4>Saved Gene Lists</h4>\n\n {error && (\n <Alert variant=\"danger\">\n {error}\n </Alert>\n )}\n\n {privateGeneLists.length > 0 && (\n <Table striped bordered hover className=\"mt-4\">\n <thead>\n <tr>\n <th>List Name</th>\n <th>Number of Genes</th>\n <th>Actions</th>\n </tr>\n </thead>\n <tbody>\n {privateGeneLists.map((list, index) => (\n <tr key={index}>\n <td>{list.label}</td>\n <td>{list.hash}</td>\n <td>\n <Button variant=\"info\" onClick={() => viewGeneList(list)}>\n View\n </Button>\n <Button variant=\"danger\" onClick={() => deleteGeneList(props.api, list._id)} className=\"ml-2\">\n Delete\n </Button>\n </td>\n </tr>\n ))}\n </tbody>\n </Table>\n )}\n\n {publicGeneLists.length > 0 ? (\n <Table striped bordered hover className=\"mt-4\">\n <thead>\n <tr>\n <th>List Name</th>\n <th>Number of Genes</th>\n <th>Actions</th>\n </tr>\n </thead>\n <tbody>\n {publicGeneLists.map((list, index) => (\n <tr key={index}>\n <td>{list.label}</td>\n <td>{list.hash}</td>\n <td>\n <Button variant=\"info\" onClick={() => viewGeneList(list)}>\n View\n </Button>\n <Button variant=\"danger\" onClick={() => deleteGeneList(props.api, list._id)} className=\"ml-2\">\n Delete\n </Button>\n </td>\n </tr>\n ))}\n </tbody>\n </Table>\n ) : (\n <Alert variant=\"warning\" className=\"mt-4\">\n No saved gene lists found.\n </Alert>\n )}\n </div>\n );\n};\n\n// Example functions for viewing and deleting lists\nconst viewGeneList = (list) => {\n alert(`Viewing gene list: ${list.name}\\nGenes: ${list.genes.join(', ')}`);\n};\n\nconst deleteGeneList = async (api,listId) => {\n if (window.confirm('Are you sure you want to delete this gene list?')) {\n // Replace with the actual delete request\n try {\n await fetch(`${api}/gene_lists/${listId}`, {\n method: 'DELETE',\n });\n alert('Gene list deleted!');\n // Optionally refetch the updated list\n } catch (err) {\n alert('Failed to delete gene list.');\n }\n }\n};\n\n\nconst GeneListComponent = props => {\n const [geneList, setGeneList] = useState('');\n const [listHash, setListHash] = useState(null);\n const [validationError, setValidationError] = useState([]);\n const [listName, setListName] = useState('');\n const [listIsPublic, setListIsPublic] = useState(false);\n const [validatedList, setValidatedList] = useState([]);\n const [errorMessage, setErrorMessage] = useState('');\n const [loading, setLoading] = useState(false); // New loading state\n const [user, setUser] = useState({});\n onAuthStateChanged(auth, (user) => setUser(user));\n\n // Function to handle gene list input\n const handleGeneListChange = (event) => {\n setGeneList(event.target.value);\n };\n\n // Function to handle drag and drop of gene list\n const handleDrop = (event) => {\n event.preventDefault();\n const geneData = event.dataTransfer.getData('text');\n setGeneList(geneData);\n };\n\n // Function to handle drag over (needed for drop)\n const handleDragOver = (event) => {\n event.preventDefault();\n };\n\n // Function to submit gene list for validation\n const handleSubmit = async () => {\n const geneArray = geneList.split('\\n').filter(Boolean); // Convert the gene list into an array and filter out empty values\n\n if (geneArray.length > MAX_GENE_IDS) {\n setErrorMessage(`You have exceeded the maximum limit of ${MAX_GENE_IDS} gene IDs.`);\n return;\n }\n\n setErrorMessage(''); // Reset error message if validation passes\n setLoading(true); // Set loading state to true to show progress\n\n try {\n const response = await fetch(`${props.api}/gene_lists/validate`, {\n method: 'POST',\n headers: {\n 'Content-Type': 'application/json',\n },\n body: JSON.stringify(geneArray),\n });\n\n const result = await response.json();\n\n if (result.hash) {\n setListHash(result.hash);\n setValidatedList(result.ids);\n setValidationError(result.missing);\n } else {\n // Handle errors from validation\n alert('Error during validation.');\n }\n } catch (error) {\n alert('There was an error with the validation service.',error);\n } finally {\n setLoading(false); // Set loading to false when the request is complete\n }\n };\n\n // Function to save the validated gene list\n const handleSaveList = async () => {\n const queryParams = {\n label: listName,\n hash: listHash,\n site: props.site,\n isPublic: listIsPublic\n };\n const queryString = new URLSearchParams(queryParams).toString();\n\n const token = await user.getIdToken();\n try {\n const response = await fetch(`${props.api}/gene_lists?${queryString}`, {\n method: 'POST',\n headers: {\n \"Content-Type\": \"application/json\",\n \"Authorization\": `Bearer ${token}`\n }\n });\n if (!response.ok) {\n throw new Error('Failed to save list');\n }\n const result = await response.json();\n console.log(result);\n\n } catch (error) {\n console.error(\"There was an problem with fetch\", error)\n }\n };\n\n return (\n <div className=\"gene-list-component\">\n <h4>Gene List Validator</h4>\n\n <Form>\n {/ Input for Gene List /}\n <Form.Group controlId=\"geneList\">\n <Form.Label>Paste or drop your gene list here:</Form.Label>\n <Form.Control\n as=\"textarea\"\n rows={10}\n value={geneList}\n onChange={handleGeneListChange}\n placeholder={`Paste or drop your gene list here (Maximum: ${MAX_GENE_IDS} IDs)`}\n onDrop={handleDrop}\n onDragOver={handleDragOver}\n />\n </Form.Group>\n\n {/ Display error if gene list exceeds limit /}\n {errorMessage && (\n <Alert variant=\"danger\">\n {errorMessage}\n </Alert>\n )}\n\n {/ Button to submit for validation /}\n <Button variant=\"primary\" onClick={handleSubmit}>\n Validate Gene List\n </Button>\n </Form>\n\n {/ Display validation in progress /}\n {loading && (\n <div className=\"validation-summary mt-4\">\n <h3>Validation in Progress...</h3>\n <Spinner animation=\"border\" role=\"status\">\n <span className=\"sr-only\">Validating...</span>\n </Spinner>\n </div>\n )}\n\n\n {/ Display validation summary /}\n {!loading && listHash && (\n <div className=\"validation-summary mt-4\">\n <h3>Validation Summary</h3>\n <Alert variant=\"info\">\n <p>hash: <code>{listHash}</code></p>\n <p>Items Validated: {validatedList.length}</p>\n <p>Items Not Validated: {validationError.length}</p>\n </Alert>\n <ul>\n {validationError.map((errorItem, index) => (\n <li key={index}>{errorItem}</li>\n ))}\n </ul>\n </div>\n )}\n\n {/ Input for saving validated gene list */}\n {!loading && validatedList.length > 0 && (\n <div className=\"save-list mt-4\">\n <Form.Group controlId=\"listName\">\n <Form.Label>Save Validated Gene List</Form.Label>\n <Form.Control\n type=\"text\"\n value={listName}\n onChange={(e) => setListName(e.target.value)}\n placeholder=\"Enter list name\"\n />\n <Form.Check\n type='switch'\n id='listIsPublic'\n label='Public'\n onChange={(e) => setListIsPublic(!listIsPublic)}\n />\n </Form.Group>\n {user ?\n <Button variant=\"success\" onClick={handleSaveList}>\n Save Gene List\n </Button>\n : <Button variant=\"dark\" disabled>Login Required</Button> }\n </div>\n )}\n </div>\n );\n};\n\nconst UserGeneListsComponent = props => {\n return (\n <Container fluid>\n <Row>\n <Col><GeneListComponent api={props.configuration.grameneData} site={props.configuration.id}/></Col>\n <Col><GeneListDisplayComponent api={props.configuration.grameneData} site={props.configuration.id}/></Col>\n </Row>\n </Container>\n )\n}\n\nexport default connect(\n 'selectConfiguration',\n UserGeneListsComponent\n);\n","import React, { useState } from 'react'\nimport { Button, Modal } from 'react-bootstrap'\nimport { connect } from \"redux-bundler-react\";\nimport { firebaseApp } from \"./utils\";\nimport { getAuth, onAuthStateChanged, signOut, GoogleAuthProvider, signInWithPopup } from \"firebase/auth\";\n\nconst auth = getAuth(firebaseApp);\n\nconst provider = new GoogleAuthProvider();\n\nconst Auth = props => {\n const [user, setUser] = useState({});\n onAuthStateChanged(auth, (user) => setUser(user));\n\n function handleLogin() {\n signInWithPopup(auth, provider)\n .then((result) => {\n setUser(result.user)\n }).catch((err) => {\n console.log(err)\n });\n }\n function handleLogout() {\n signOut(auth)\n .then(() => {\n setUser(null);\n }).catch((err) => {\n console.log(err)\n });\n }\n return (\n <div className={props.configuration.id === 'sorghum' ? 'sorghumbase-auth-container': 'gramene-auth-container'}>\n <b>Account</b>\n <div>\n {user\n ? <Button size=\"sm\" variant=\"success\" onClick={handleLogout}>{user.displayName}</Button>\n : <Button size=\"sm\" variant=\"success\" onClick={handleLogin}>Login</Button>\n }\n </div>\n </div>\n )\n}\n\nexport default connect(\n 'selectConfiguration',\n Auth\n)\n"],"names":[],"version":3,"file":"index.js.map"}
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const t = store.selectSuggestionsQuery().replaceAll(':',' ').trim();\n const g = store.selectGrameneGenomes();\n const q = `/suggest?q={!boost b=relevance}name:${t}^5 ids:${t}^5 ids:${t}^3 synonym:${t}^3 synonym:${t}^2 text:${t}^1`;\n // const promises = sites.map(site => fetch(`https://data.gramene.org/${site}${q}`));\n // return Promise.all(promises)\n return fetch(store.selectGrameneAPI() + q)\n .then(res => {\n return res.json()\n })\n .then(suggestions => {\n if (Object.keys(g.active).length > 0) {\n suggestions.grouped.category.groups.forEach(group => {\n group.doclist.docs.forEach(sugg => {\n sugg.num_genes = 0;\n sugg.taxon_id.forEach((id,idx) => {\n if (g.active[id] && !g.active[id].hidden) {\n sugg.num_genes += sugg.taxon_freq[idx]\n }\n })\n })\n })\n }\n return suggestions\n })\n }\n});\n\ngrameneSuggestions.reactGrameneSuggestions = createSelector(\n 'selectGrameneSuggestionsShouldUpdate',\n 'selectSuggestionsQuery',\n (shouldUpdate, queryString) => {\n if (shouldUpdate && queryString) {\n return { actionCreator: 'doFetchGrameneSuggestions' }\n }\n }\n);\n\ngrameneSuggestions.selectGrameneSuggestionsStatus = createSelector(\n 'selectGrameneSuggestionsShouldUpdate',\n 'selectGrameneSuggestionsIsLoading',\n 'selectGrameneSuggestionsRaw',\n 'selectSuggestionsQuery',\n (shouldUpdate, isLoading, suggestionsRaw, queryString) => {\n if (!queryString) return '';\n if (shouldUpdate) return 'update needed';\n if (isLoading) return 'loading';\n if (suggestionsRaw.data) return suggestionsRaw.data.grouped.category.matches + ' terms';\n console.error(suggestionsRaw)\n return 'error';\n }\n);\n\ngrameneSuggestions.selectGrameneSuggestionsReady = createSelector(\n 'selectGrameneSuggestionsStatus',\n (status) => {\n const regex = RegExp('terms$');\n return regex.test(status);\n }\n);\n\ngrameneSuggestions.doFocusFirstGrameneSuggestion = arg => ({dispatch, getState}) => {\n console.log('inside doFocusFirstGrameneSuggestion');\n};\n\nfunction compressLongTaxonName(node) {\n const fullName = node.name;\n const removedExtraineousWords = fullName.replace(/( Group$\| subsp\\.\| ssp\\.\| var\\.\| strain)/, '');\n let finalVersion;\n if (removedExtraineousWords.length > 20) {\n let words = removedExtraineousWords.split(' ');\n if (words.length === 2) {\n // abrreviate first word.\n finalVersion = removedExtraineousWords.replace(/^([A-Z])[a-z]+/, '$1.')\n }\n if (words.length > 2) {\n finalVersion = removedExtraineousWords.replace(/^([A-Z])[a-z]+\\s([a-z])[a-z]+/, '$1$2.')\n }\n }\n else {\n finalVersion = removedExtraineousWords;\n }\n node.short_name = finalVersion;\n}\n\nconst grameneTaxonomy = createAsyncResourceBundle({\n name: 'grameneTaxonomy',\n actionBaseType: 'GRAMENE_TAXONOMY',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/taxonomy?subset=gramene&rows=-1`)\n .then(res => res.json())\n .then(taxNodes => {\n let taxonomy = _.keyBy(taxNodes, '_id');\n taxNodes.forEach(t => {\n t._id = +t._id; // ensure taxonomy id is a number\n compressLongTaxonName(t);\n if (t.hasOwnProperty(\"is_a\")) {\n t.is_a.forEach(p_id => {\n const p = taxonomy[p_id];\n if (!p.hasOwnProperty('children')) p.children = [];\n p.children.push(t._id)\n })\n }\n });\n return taxonomy\n })\n }\n});\ngrameneTaxonomy.reactGrameneTaxonomy = createSelector(\n 'selectGrameneTaxonomyShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneTaxonomy' }\n }\n }\n);\nconst grameneMaps = createAsyncResourceBundle({\n name: 'grameneMaps',\n actionBaseType: 'GRAMENE_MAPS',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/maps?rows=-1`)\n .then(res => res.json())\n .then(maps => {\n maps.forEach(m => {\n m.regionLength = {};\n m.regions.names.forEach((rname,idx) => {\n m.regionLength[rname] = m.regions.lengths[idx]\n })\n })\n return _.keyBy(maps, 'taxon_id');\n })\n }\n});\ngrameneMaps.reactGrameneMaps = createSelector(\n 'selectGrameneMapsShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneMaps' }\n }\n }\n);\n\nconst expressionStudies = createAsyncResourceBundle( {\n name: 'expressionStudies',\n actionBaseType: 'EXPRESSION_STUDIES',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`)\n .then(res => res.json())\n .then(res => _.groupBy(res, 'taxon_id'))\n }\n});\nexpressionStudies.reactExpressionStudies = createSelector(\n 'selectExpressionStudiesShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchExpressionStudies' }\n }\n }\n);\n\nconst expressionSamples = createAsyncResourceBundle( {\n name: 'expressionSamples',\n actionBaseType: 'EXPRESSION_SAMPLES',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/assays?rows=-1`)\n .then(res => res.json())\n .then(samples => _.groupBy(samples, 'experiment'))\n .then(studies => 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grameneGermplasm = createAsyncResourceBundle( {\n name: 'grameneGermplasm',\n actionBaseType: 'GRAMENE_GERMPLASM',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/germplasm?rows=-1`)\n .then(res => res.json())\n .then(res => {\n res.forEach(g => {\n if (!g.subpop) {\n g.subpop = \"?\"\n }\n });\n return _.groupBy(res, 'ens_id')\n })\n }\n});\ngrameneGermplasm.reactGrameneGermplasm = createSelector(\n 'selectGrameneGermplasmShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneGermplasm' }\n }\n }\n);\n//\n// const grameneExpressionAssays = createAsyncResourceBundle( {\n// name: 'grameneExpressionAssays',\n// actionBaseType: 'GRAMENE_EXPRESSION_ASSAYS',\n// persist: true,\n// getPromise: ({store}) => {\n// return fetch(`${store.selectGrameneAPI()}/assays?rows=-1`)\n// .then(res => res.json())\n// .then(res => {\n// let expr={};\n// res.forEach(assay => {\n// if (!expr.hasOwnProperty(assay.taxon_id)) {\n// expr[assay.taxon_id] = {};\n// }\n// if (!expr[assay.taxon_id].hasOwnProperty(assay.experiment)) {\n// expr[assay.taxon_id][assay.experiment] = [];\n// }\n// assay.order = +assay.group.replace('g','');\n// expr[assay.taxon_id][assay.experiment].push(assay);\n// });\n// // sort each experiment\n// for (const tid in expr) {\n// for (const exp in expr[tid]) {\n// expr[tid][exp].sort((a,b) => a.order - b.order);\n// }\n// }\n// return expr;\n// })\n// }\n// });\n// grameneExpressionAssays.reactGrameneExpressionAssays = createSelector(\n// 'selectGrameneExpressionAssaysShouldUpdate',\n// (shouldUpdate) => {\n// if (shouldUpdate) {\n// return { actionCreator: 'doFetchGrameneExpressionAssays' }\n// }\n// }\n// );\n\nconst attribFacetFields = [\n \"{!facet.limit='10' facet.mincount='1' key='age'}panset_age_attr_s\",\n \"{!facet.limit='100' facet.mincount='1' key='taxa'}panset_ntaxa_attr_i\",\n \"{!facet.limit='100' facet.mincount='1' key='AED' type='range' start=0 end=1.0 gap=0.25}MAKER_AED_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI2' type='range' start=0 end=1.0 gap=0.25}MAKER_QI2_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI3' type='range' start=0 end=1.0 gap=0.25}MAKER_QI3_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI4' type='range' start=0 end=1.0 gap=0.25}MAKER_QI4_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI5' type='range' start=0 end=1.0 gap=0.25}MAKER_QI5_attr_f\",\n \"{!facet.limit='100' facet.mincount='1' key='QI6' type='range' start=0 end=1.0 gap=0.25}MAKER_QI6_attr_f\"\n];\nconst attribFacets = {\n \"age\":{ \"type\": \"terms\", \"field\": \"panset_age_attr_s\" },\n \"nTaxa\": { \"type\": \"terms\", \"field\": \"panset_ntaxa_attr_i\", \"limit\": 100 },\n \"AED\":{ \"type\": \"range\", \"field\": \"MAKER_AED_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI2\":{ \"type\": \"range\", \"field\": \"MAKER_QI2_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI3\":{ \"type\": \"range\", \"field\": \"MAKER_QI3_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI4\":{ \"type\": \"range\", \"field\": \"MAKER_QI4_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI5\":{ \"type\": \"range\", \"field\": \"MAKER_QI5_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI6\":{ \"type\": \"range\", \"field\": \"MAKER_QI6_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"byAge\":{ \"type\": \"terms\", \"field\": \"panset_age_attr_s\", \"facet\": {\n \"nTaxa\": { \"type\": \"terms\", \"field\": \"panset_ntaxa_attr_i\", \"limit\": 100 },\n \"AED\":{ \"type\": \"range\", \"field\": \"MAKER_AED_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI2\":{ \"type\": \"range\", \"field\": \"MAKER_QI2_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI3\":{ \"type\": \"range\", \"field\": \"MAKER_QI3_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI4\":{ \"type\": \"range\", \"field\": \"MAKER_QI4_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI5\":{ \"type\": \"range\", \"field\": \"MAKER_QI5_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 },\n \"QI6\":{ \"type\": \"range\", \"field\": \"MAKER_QI6_attr_f\", \"start\": 0.0, \"end\": 1.0, \"gap\": 0.25 }\n }\n }\n}\nconst grameneGeneAttribs = createAsyncResourceBundle( {\n name: 'grameneGeneAttribs',\n actionBaseType: 'GRAMENE_GENE_ATTRIBS',\n persist: false,\n getPromise: ({store}) => {\n const g = store.selectGrameneGenomes();\n const taxa = Object.keys(g.active);\n let fq='';\n if (taxa.length) {\n console.log('search add a fq for ',taxa);\n fq = `&fq=taxon_id:(${taxa.join(' OR ')})`;\n }\n return fetch(`${store.selectGrameneAPI()}/search?q=${store.selectGrameneFiltersQueryString()}&json.facet=${JSON.stringify(attribFacets)}&rows=0${fq}`)\n // return fetch(`${store.selectGrameneAPI()}/search?rows=1&q=MAKER_AED_attr_f:&json.facet=${JSON.stringify(attribFacets)}`)\n .then(res => res.json())\n .then(res => {\n return res.facets\n })\n }\n});\ngrameneGeneAttribs.reactGrameneGeneAttribs = createSelector(\n 'selectGrameneGeneAttribsShouldUpdate',\n 'selectGrameneFiltersStatus',\n 'selectGrameneViews',\n (shouldUpdate, status, views) => {\n if (shouldUpdate && (status === 'finished' \|\| status === 'ready')) {\n const byId = _.keyBy(views.options,'id');\n if (byId.attribs.show === \"on\") {\n return { actionCreator: 'doFetchGrameneGeneAttribs' }\n }\n }\n }\n);\n\nconst grameneSearch = createAsyncResourceBundle({\n name: 'grameneSearch',\n actionBaseType: 'GRAMENE_SEARCH',\n persist: false,\n getPromise: ({store}) => {\n const offset = store.selectGrameneSearchOffset();\n const rows = store.selectGrameneSearchRows();\n const g = store.selectGrameneGenomes();\n const taxa = Object.keys(g.active).filter(tid => !g.active[tid].hidden);\n let fq='';\n if (taxa.length) {\n console.log('search add a fq for ',taxa);\n fq = `&fq=taxon_id:(${taxa.join(' OR ')})`;\n }\n return fetch(`${store.selectGrameneAPI()}/search?q=${store.selectGrameneFiltersQueryString()}&facet.field=${facets}&rows=${rows}&start=${offset}${fq}`)\n .then(res => res.json())\n .then(res => {\n res.response.docs.forEach(d => {\n d.can_show = {};\n d.capabilities.forEach(c => {\n d.can_show[c]=true;\n })\n });\n return res;\n })\n }\n});\ngrameneSearch.reactGrameneSearch = createSelector(\n 'selectGrameneSearchShouldUpdate',\n 'selectGrameneFiltersStatus',\n 'selectGrameneGenomes','selectGrameneMaps',\n (shouldUpdate, status, genomes, maps) => {\n if (shouldUpdate && status === 'search' && genomes && maps) {\n return { actionCreator: 'doFetchGrameneSearch' }\n }\n }\n);\n\nfunction formatFacetCountsForViz(a) {\n let res = {\n count: a.length/2,\n displayName: \"fixed_1000__bin\",\n data: {},\n sorted: []\n };\n let counts = [];\n for(let i=0;i<a.length;i+=2) {\n const fc = {\n id: +a[i],\n count: +a[i+1]\n };\n res.data[a[i]] = fc;\n counts.push(fc);\n }\n res.sorted = counts.sort((a,b) => a.id - b.id);\n return res;\n}\n\n// bundle to prepare data for the TaxDist component\nconst grameneTaxDist = {\n name: 'grameneTaxDist',\n getReducer: () => {\n const initialState = {};\n return (state = initialState, {type, payload}) => {\n return state;\n }\n },\n selectGrameneTaxDist: createSelector(\n 'selectGrameneSearch',\n 'selectGrameneTaxonomy',\n 'selectGrameneMaps',\n (grameneSearch,grameneTaxonomy,grameneMaps) => {\n if (grameneSearch && grameneTaxonomy && grameneMaps) {\n _.forIn(grameneMaps, (map, tid) => {\n grameneTaxonomy[tid].name = map.display_name;\n });\n const binnedResults = formatFacetCountsForViz(grameneSearch.facet_counts.facet_fields.fixed_1000__bin);\n let speciesTree = treesClient.taxonomy.tree(Object.values(grameneTaxonomy));\n let binMapper = binsClient.bins(grameneMaps);\n let taxDist = build(binMapper, speciesTree);\n taxDist.setBinType('fixed',1000);\n taxDist.setResults(binnedResults);\n return taxDist;\n }\n return null;\n }\n )\n};\n\n// this query will give the sorghum orthologs of AT1G01260\n// want to provide these on non-sorghum genes if available\n// http://data.gramene.org/search?q=homology__all_orthologs:AT1G01260&fq=taxon_id:4558&fl=id\nconst grameneOrthologs = {\n name: 'grameneOrthologs',\n getReducer: () => {\n const initialState = {};\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_ORTHOLOGS_REQUESTED':\n if (!state.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState[payload] = [];\n return newState;\n }\n break;\n case 'GRAMENE_ORTHOLOGS_RECEIVED':\n return Object.assign({}, state, payload);\n }\n return state;\n }\n },\n doRequestOrthologs: geneId => ({dispatch, store}) => {\n const orthologs = store.selectGrameneOrthologs();\n if (!orthologs.hasOwnProperty(geneId)) {\n dispatch({type: 'GRAMENE_ORTHOLOGS_REQUESTED', payload: geneId});\n const API = store.selectGrameneAPI();\n const taxonId = store.selectTargetTaxonId();\n fetch(`${API}/search?q=homology__all_orthologs:${geneId}&fq=taxon_id:${taxonId}&fl=id`)\n .then(res => res.json())\n .then(res => {\n let newOrthologs = {};\n newOrthologs[geneId] = res.response.docs.map(d => d.id);\n dispatch({type: 'GRAMENE_ORTHOLOGS_RECEIVED', payload: newOrthologs})\n })\n }\n },\n selectGrameneOrthologs: state => state.grameneOrthologs\n};\n\nconst grameneParalogs = {\n name: 'grameneParalogs',\n getReducer: () => {\n const initialState = {};\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_PARALOGS_REQUESTED':\n if (!state.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState[payload] = [];\n return newState;\n }\n break;\n case 'GRAMENE_PARALOGS_RECEIVED':\n return Object.assign({}, state, payload);\n }\n return state;\n }\n },\n doRequestParalogs: (geneId,supertree,taxon_id) => ({dispatch, store}) => {\n const paralogs = store.selectGrameneParalogs();\n if (!paralogs.hasOwnProperty(geneId)) {\n dispatch({type: 'GRAMENE_PARALOGS_REQUESTED', payload: geneId});\n const API = store.selectGrameneAPI();\n const q= supertree ? `supertree_attr_s:${supertree}` : `homology__within_species_paralog:${geneId}`;\n fetch(`${API}/search?q=${q}&rows=100&fq=taxon_id:${taxon_id}`)\n .then(res => res.json())\n .then(res => {\n let newParalogs = {};\n newParalogs[geneId] = res.response.docs.map(d => d.id);\n dispatch({type: 'GRAMENE_PARALOGS_RECEIVED', payload: newParalogs})\n })\n }\n },\n selectGrameneParalogs: state => state.grameneParalogs\n};\n\n// function selectFacetIDs(store, field) {\n// const path = `grameneGenes.data.facet_counts.facet_fields.${field}`;\n// if (_.has(store,path)) {\n// const flat_facets = _.get(store,path);\n// let idList = [];\n// if (isNaN(+flat_facets[0])) {\n// for (let i = 0; i < flat_facets.length; i += 2) {\n// idList.push(flat_facets[i])\n// }\n// }\n// else {\n// for (let i = 0; i < flat_facets.length; i += 2) {\n// idList.push(+flat_facets[i])\n// }\n// if (idList.length === 1) idList.push(0);\n// }\n// return idList;\n// }\n// }\n//\n// grameneGenes.selectDomainFacets = store => selectFacetIDs(store, 'domains');\n// grameneGenes.selectPathwayFacets = store => selectFacetIDs(store, 'pathways');\n// grameneGenes.selectTaxonomyFacets = store => selectFacetIDs(store, 'taxon_id');\n//\n// const grameneDomains = createAsyncResourceBundle({\n// name: 'grameneDomains',\n// actionBaseType: 'GRAMENE_DOMAINS',\n// persist: false,\n// getPromise: ({store}) =>\n// fetch(`${store.selectGrameneAPI()}/domains?rows=-1&idList=${store.selectDomainFacets().join(',')}`)\n// .then(res => res.json())\n// .then(docs => {return {domains: docs, numFound: docs.length}})\n// });\n//\n// const gramenePathways = createAsyncResourceBundle({\n// name: 'gramenePathways',\n// actionBaseType: 'GRAMENE_PATHWAYS',\n// persist: false,\n// getPromise: ({store}) =>\n// fetch(`${store.selectGrameneAPI()}/pathways?rows=-1&idList=${store.selectPathwayFacets().join(',')}`)\n// .then(res => res.json())\n// .then(docs => {return {pathways: docs, numFound: docs.length}})\n// });\n//\n// const grameneTaxonomy = createAsyncResourceBundle({\n// name: 'grameneTaxonomy',\n// actionBaseType: 'GRAMENE_TAXONOMY',\n// persist: false,\n// getPromise: ({store}) =>\n// fetch(`${store.selectGrameneAPI()}/taxonomy?rows=-1&idList=${store.selectTaxonomyFacets().join(',')}`)\n// .then(res => res.json())\n// .then(docs => {return {taxonomy: docs, numFound: docs.length}})\n// });\n\n\nexport default [grameneSuggestions, grameneSearch, grameneMaps, grameneTaxonomy, grameneTaxDist, grameneOrthologs, grameneParalogs, curatedGenes, grameneGermplasm, grameneGeneAttribs, expressionSamples, expressionStudies];\n","import {createSelector} from \"redux-bundler\";\nimport _ from 'lodash';\nimport ReactGA from 'react-ga4'\nconst MAX_IDLIST_LENGTH = 20;\n\nfunction findNodeWithLeftIdx(node, idx) {\n if (node.leftIdx === idx) {\n return node;\n }\n let result=null;\n if (node.leftIdx < idx && node.hasOwnProperty('children')) {\n node.children.forEach(child => {\n if (child.rightIdx > idx) {\n child.parentIdx = node.leftIdx;\n const res = findNodeWithLeftIdx(child, idx);\n if (res) result = res;\n }\n })\n }\n return result;\n}\n\nfunction markSubtree(node, source, invert) {\n node.marked = (node.leftIdx >= source.leftIdx && node.rightIdx <= source.rightIdx);\n if (invert) node.marked = !node.marked;\n if (node.hasOwnProperty('children')) {\n node.children.forEach(child => {\n markSubtree(child, source, invert);\n })\n }\n}\n\nfunction reindexTree(node, idx) {\n node.leftIdx = idx;\n idx++;\n if (node.hasOwnProperty('children')) {\n node.children.forEach(child => {\n idx = reindexTree(child, idx);\n });\n }\n node.rightIdx = idx;\n idx++;\n return idx;\n}\n\nconst grameneFilters = {\n name: 'grameneFilters',\n getReducer: () => {\n const initialState = {\n status: 'init', // others include 'search', 'waiting' and 'ready'\n operation: 'AND',\n negate: false,\n marked: false,\n leftIdx: 0,\n rightIdx: 1,\n children: [],\n showMarked: false,\n showMenu: false,\n moveCopyMode: '',\n searchOffset: 0,\n rows: 20\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_FILTERS_CLEARED': {\n newState = Object.assign({}, initialState, {\n status: 'search',\n children: []\n });\n return newState;\n }\n case 'GRAMENE_FILTER_ADDED': {\n const idx = state.rightIdx;\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n rightIdx: idx + 2,\n searchOffset: 0\n });\n let child = _.pick(payload, ['fq_field', 'fq_value', 'name', 'category']);\n child.leftIdx = idx;\n child.rightIdx = idx + 1;\n child.negate = false;\n child.showMenu = false;\n newState.children.push(child);\n markSubtree(newState, child, false);\n return newState;\n }\n case 'GRAMENE_FILTER_TREE_ADDED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n rightIdx: payload.rightIdx + 1,\n searchOffset: 0\n });\n newState.children.push(payload);\n markSubtree(newState, payload, false);\n return newState;\n }\n case 'GRAMENE_FILTER_SET_ADDED': {\n // create a filter with the payload.operation and children payload.filters\n let filter = {\n leftIdx: state.rightIdx,\n rightIdx: state.rightIdx + (payload.filters.length) * 2 + 1,\n operation: payload.operation,\n negate: false,\n showMenu: false,\n children: payload.filters\n };\n if (payload.warning) {\n filter.warning = payload.warning\n }\n let nextIdx = filter.leftIdx+1;\n payload.filters.forEach(f => {\n f.leftIdx = nextIdx++;\n f.rightIdx = nextIdx++;\n f.negate = false;\n f.showMenu = false;\n });\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0,\n rightIdx: filter.rightIdx + 1\n });\n newState.children.push(filter);\n markSubtree(newState, filter, false);\n return newState;\n }\n case 'GRAMENE_FILTER_NEGATED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0\n });\n let node = findNodeWithLeftIdx(newState, payload.leftIdx);\n if (node) {\n node.negate = !node.negate;\n markSubtree(newState, node, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_DELETED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0\n });\n let node = findNodeWithLeftIdx(newState, payload.leftIdx);\n if (node) {\n let parent = findNodeWithLeftIdx(newState, node.parentIdx);\n parent.children = parent.children.filter(child => child.leftIdx !== node.leftIdx);\n reindexTree(newState, 0);\n markSubtree(newState, parent, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_OPERATION_CHANGED': {\n if (payload.hasOwnProperty('operation')) {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n searchOffset: 0\n });\n let node = findNodeWithLeftIdx(newState, payload.leftIdx);\n node.operation = node.operation === 'AND' ? 'OR' : 'AND';\n markSubtree(newState, node, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_MOVED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n moveCopyMode: '',\n searchOffset: 0\n });\n let source = findNodeWithLeftIdx(newState, payload.source.leftIdx);\n let target = findNodeWithLeftIdx(newState, payload.target.leftIdx);\n if (source && target) {\n source.showMenu = false;\n let parent = findNodeWithLeftIdx(newState, source.parentIdx);\n parent.children = parent.children.filter(child => child.leftIdx !== source.leftIdx);\n target.showMenu = false;\n if (!target.hasOwnProperty('children')) {\n let targetCopy = Object.assign({}, target);\n target.children = [targetCopy];\n target.operation = 'OR';\n target.negate = false;\n delete target.fq_field;\n delete target.fq_value;\n delete target.name;\n delete target.category;\n }\n target.children.push(source);\n reindexTree(newState, 0);\n markSubtree(newState, target, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_COPIED': {\n newState = Object.assign({}, state, {\n status: 'search',\n showMarked: true,\n moveCopyMode: '',\n searchOffset: 0\n });\n let source = findNodeWithLeftIdx(newState, payload.source.leftIdx);\n let target = findNodeWithLeftIdx(newState, payload.target.leftIdx);\n if (source && target) {\n source.showMenu = false;\n if (!target.hasOwnProperty('children')) {\n let targetCopy = Object.assign({}, target);\n target.children = [targetCopy];\n target.operation = 'OR';\n target.negate = false;\n delete target.fq_field;\n delete target.fq_value;\n delete target.name;\n delete target.category;\n }\n let sourceCopy = Object.assign({}, source);\n target.children.push(sourceCopy);\n reindexTree(newState, 0);\n markSubtree(newState, target, false);\n return newState;\n }\n break;\n }\n case 'GRAMENE_FILTER_TARGETS_MARKED':\n newState = Object.assign({}, state, {\n showMarked: true,\n moveCopyMode: payload.mode,\n moveCopySource: payload.source\n });\n markSubtree(newState, payload.source, true);\n return newState;\n case 'GRAMENE_FILTER_TARGETS_UNMARKED':\n newState = Object.assign({}, state, {\n showMarked: false\n });\n return newState;\n case 'GRAMENE_FILTERS_REPLACED':\n payload.status = 'search';\n payload.searchOffset = 0;\n return payload;\n case 'GRAMENE_FILTERS_STATUS_CHANGED':\n if (!(state.status === 'ready' && payload === 'waiting')) {\n return Object.assign({}, state, {status: payload})\n }\n break;\n case 'GRAMENE_FILTERS_SET_SHOW_MARKED':\n return Object.assign({}, state, {showMarked: payload});\n case 'GRAMENE_FILTER_MENU_TOGGLED':\n payload.showMenu = !payload.showMenu;\n return Object.assign({}, state);\n case 'GRAMENE_SEARCH_PAGE_REQUESTED':\n return Object.assign({}, state, {status: 'search', searchOffset: payload * state.rows});\n case 'GRAMENE_SEARCH_FETCH_STARTED':\n return Object.assign({}, state, {status: 'loading'});\n case 'GRAMENE_SEARCH_FETCH_FINISHED':\n return Object.assign({}, state, {status: 'finished'});\n case 'GRAMENE_GENOMES_UPDATED':\n return Object.assign({}, state, {status: 'search'});\n case 'URL_UPDATED':\n if (state.status === 'ready') {\n return Object.assign({}, initialState, {children:[]})\n }\n break;\n case 'APP_IDLE':\n if (state.showMarked) {\n return Object.assign({}, state, {showMarked: false})\n }\n }\n return state;\n }\n },\n doNegateGrameneFilter: filter => ({dispatch, getState}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_NEGATED', payload: filter}\n ]\n })\n },\n doDeleteGrameneFilter: filter => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_TAXONOMY_CLEARED'},\n {type: 'GRAMENE_FILTER_DELETED', payload: filter}\n ]\n })\n },\n doChangeGrameneFilterOperation: filter => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_OPERATION_CHANGED', payload: filter}\n ]\n })\n },\n doMoveOrCopyGrameneFilter: (target) => ({dispatch, getState}) => {\n const state = getState();\n if (state.grameneFilters.moveCopyMode) {\n const source = state.grameneFilters.moveCopySource;\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: `GRAMENE_FILTER_${state.grameneFilters.moveCopyMode.toUpperCase()}D`, payload: {source, target}}\n ]\n })\n }\n },\n doCopyGrameneFilter: (source, target) => ({dispatch, getState}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_COPIED', payload: {source, target}}\n ]\n })\n },\n doMarkGrameneFilterTargets: (source, mode) => ({dispatch}) => {\n dispatch({type: 'GRAMENE_FILTER_TARGETS_MARKED', payload: {source:source, mode:mode}})\n },\n doUnmarkGrameneFilterTargets: () => ({dispatch}) => {\n dispatch({type: 'GRAMENE_FILTER_TARGETS_UNMARKED'})\n },\n doAcceptGrameneSuggestion: suggestion => ({dispatch, getState}) => {\n if (!suggestion.name) {\n suggestion.name = suggestion.display_name;\n }\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: suggestion}\n ]\n })\n },\n doAddGrameneRangeQuery: terms => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_SET_ADDED', payload: {operation: 'AND', filters: terms}}\n ]\n })\n },\n doToggleGrameneFilterMenu: node => ({dispatch}) => {\n dispatch({type: 'GRAMENE_FILTER_MENU_TOGGLED', payload: node})\n },\n doRequestResultsPage: page => ({dispatch}) => {\n dispatch(\n {type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_SEARCH_PAGE_REQUESTED', payload: page}\n ]\n })\n },\n doReplaceGrameneFilters: filters => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_REPLACED', payload: filters}\n ]\n })\n },\n doClearGrameneFilters: () => ({dispatch}) => {\n dispatch({\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_CLEARED'}\n ]\n })\n },\n selectGrameneFilters: state => state.grameneFilters,\n selectGrameneFiltersStatus: state => state.grameneFilters.status,\n selectGrameneFiltersQueryString: state => {\n const hasSpaces = new RegExp(/^[^\\[\\(].\\s/);\n const isQuery = new RegExp(/\\([a-zA-Z0-9_]+:[a-zA-Z0-9_]+\\s/);\n const isRegionQuery = new RegExp(/^\\(map:/);\n const idWithColon = new RegExp(/^[a-zA-Z0-9_]+:[a-zA-Z0-9_]+$/);\n function getQuery(node) {\n const negate = node.negate ? 'NOT ' : '';\n if (node.hasOwnProperty('children')) {\n // do some recursion\n return `${negate}(${node.children.map(c => getQuery(c)).sort().join(` ${node.operation} `)})`\n }\n else {\n // this node is a suggestion\n if (node.fq_field === 'location' && isRegionQuery.test(node.fq_value))\n return `${negate}${node.fq_value}`\n if (isQuery.test(node.fq_value))\n return `${negate}${node.fq_value.replace(/:/g,'\\\\:')}`;\n if (hasSpaces.test(node.fq_value))\n return `${negate}${node.fq_field}:\"${node.fq_value}\"`;\n else if (idWithColon.test(node.fq_value))\n return `${negate}${node.fq_field}:${node.fq_value.replace(/:/g,'\\\\:')}`;\n else\n return `${negate}${node.fq_field}:${node.fq_value}`\n }\n }\n if (state.grameneFilters.rightIdx === 1) {\n return ':';\n }\n return `:* AND (${getQuery(state.grameneFilters)})`;\n },\n selectGrameneSearchOffset: state => state.grameneFilters.searchOffset,\n selectGrameneSearchRows: state => state.grameneFilters.rows\n};\n\nconst handleIdList = (queryObject) => {\n let actions = [{type: 'GRAMENE_SEARCH_CLEARED'}];\n let ids = _.uniq(queryObject.idList.split(','));\n let warning = null;\n if (ids.length > MAX_IDLIST_LENGTH) {\n ids = _.slice(ids, 0, MAX_IDLIST_LENGTH);\n warning = `The idList query parameter is limited to ${MAX_IDLIST_LENGTH} genes`\n }\n let filters = ids.map((id,idx) => {\n return {\n category: 'Gene',\n name: id,\n fq_field: 'id',\n fq_value: id\n }\n });\n if (filters.length === 1) {\n actions.push({type: 'GRAMENE_FILTER_ADDED', payload: filters[0]})\n }\n else {\n let action = {type: 'GRAMENE_FILTER_SET_ADDED', payload: {operation: 'OR', filters:filters}};\n if (warning) {\n action.payload.warning = warning\n }\n actions.push(action)\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n};\n\ngrameneFilters.reactGrameneFilters = createSelector(\n 'selectQueryObject',\n 'selectGrameneFilters',\n 'selectActiveGenomes',\n 'selectUrlObject',\n (queryObject, filters, genomes, myUrl) => {\n if (filters.status === 'init') {\n if (queryObject.filters) {\n const newFilters = JSON.parse(queryObject.filters);\n let actions = [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_REPLACED', payload: newFilters}\n ];\n if (queryObject.genomes) {\n let active={};\n queryObject.genomes.split(',').forEach(t => {\n active[t]=true\n });\n actions.push({type: 'GRAMENE_GENOMES_UPDATED', payload: active});\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n }\n if (queryObject.hasOwnProperty('sugg')) {\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: JSON.parse(queryObject.sugg)}\n ]\n };\n }\n if (queryObject.hasOwnProperty('suggestion')) {\n const url = new URL(myUrl.href);\n url.search = '';\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'URL_UPDATED', payload: {url: url.href, replace:false}},\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'SUGGESTIONS_QUERY_CHANGED', payload: {query: queryObject.suggestion}}\n ]\n };\n }\n if (queryObject.hasOwnProperty('idList')) {\n return handleIdList(queryObject);\n }\n if (queryObject.hasOwnProperty('fq_field') && queryObject.hasOwnProperty('fq_value')\n && queryObject.hasOwnProperty('category') && queryObject.hasOwnProperty('name')) {\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: queryObject}\n ]\n };\n }\n const url = new URL(myUrl.href);\n if (url.pathname === '/genes') {\n return {type: 'GRAMENE_FILTERS_CLEARED'}\n }\n }\n if (filters.status === 'finished') {\n const url = new URL(myUrl.href);\n url.search = `filters=${JSON.stringify(Object.assign({}, filters, {status: 'init'}))}&genomes=${genomes.join(',')}`;\n ReactGA.event({\n category: \"Gene Search\",\n action: \"filter finished\",\n label: url.search\n });\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'URL_UPDATED', payload: {url: url.href, replace:false}},\n {type: 'GRAMENE_FILTERS_STATUS_CHANGED', payload: 'ready'}\n ]\n }\n }\n }\n);\n\nexport default grameneFilters;\n","const grameneViews = {\n name: 'grameneViews',\n getReducer: () => {\n const initialState = {\n options: [\n {\n id: 'help',\n name: 'Help / Demo',\n show: 'off',\n shouldScroll: false\n },\n {\n id: 'userLists',\n name: 'User Gene Lists',\n show: 'off',\n shouldScroll: false\n },\n {\n id: 'taxonomy',\n name: 'Taxonomic distribution',\n show: 'on',\n shouldScroll: false\n },\n {\n id: 'list',\n name: 'Gene list',\n show: 'on',\n shouldScroll: false\n },\n {\n id: 'expression',\n name: 'Gene expression',\n show: 'off',\n shouldScroll: false,\n desiredSamples: {}\n },\n {\n id: 'attribs',\n name: 'Gene attributes',\n show: 'disabled',\n shouldScroll: false\n }\n // {\n // id: 'domains',\n // name: 'Domains',\n // show: 'disabled'\n // },\n // {\n // id: 'go',\n // name: 'GO terms',\n // show: 'disabled'\n // }\n ]\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_VIEW_TOGGLED':\n newState = Object.assign({},state);\n newState.options.forEach(view => {\n view.shouldScroll = false;\n if (view.id === payload) {\n view.show = view.show === 'on' ? 'off' : 'on'\n view.shouldScroll = view.show === 'on';\n }\n });\n return newState;\n case 'GRAMENE_VIEW_CLICKED':\n newState = Object.assign({}, state);\n newState.options.forEach(view => {\n view.shouldScroll = false;\n if (view.id === payload) {\n view.show = view.show === 'on' ? 'on' : 'on';\n view.shouldScroll = view.show === 'on';\n }\n });\n return newState;\n case 'GRAMENE_VIEW_SCROLLED':\n newState = Object.assign({}, state);\n newState.options.forEach(v => v.shouldScroll = false)\n return newState;\n default:\n return state;\n }\n }\n },\n doToggleGrameneView: idx => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_VIEW_TOGGLED', payload: idx})\n },\n dontToggleGrameneView: idx => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_VIEW_CLICKED', payload: idx})\n },\n doCancelShouldScroll: () => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_VIEW_SCROLLED', payload: null})\n },\n selectGrameneViews: state => state.grameneViews\n};\n\nexport default grameneViews;\n","const grameneDocs = {\n name: 'grameneDocs',\n getReducer: () => {\n const initialState = {\n genes: {},\n trees: {},\n domains: {},\n pathways: {},\n expression: {},\n sequences: {},\n rnaSequences: {},\n pepSequences: {},\n studies: {},\n desiredSamples: {},\n consequences: {}\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_CONSEQUENCES_REQUESTED':\n if (!state.consequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.consequences[payload] = {};\n return newState;\n }\n break;\n case 'GRAMENE_CONSEQUENCES_RECEIVED':\n newState = Object.assign({}, state);\n newState.consequences = Object.assign({}, state.consequences, payload);\n return newState;\n case 'GRAMENE_GENE_REQUESTED':\n if (!state.genes.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.genes[payload] = {};\n return newState;\n }\n break;\n case 'GRAMENE_GENE_RECEIVED':\n newState = Object.assign({}, state);\n newState.genes = Object.assign({}, state.genes, payload);\n return newState;\n case 'GRAMENE_TREE_REQUESTED':\n if (!state.trees.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.trees[payload] = {};\n return newState;\n }\n break;\n case 'GRAMENE_TREE_RECEIVED':\n newState = Object.assign({}, state);\n newState.trees = Object.assign({}, state.trees, payload);\n return newState;\n case 'GRAMENE_PATHWAYS_RECEIVED':\n newState = Object.assign({}, state);\n newState.pathways = Object.assign({}, state.pathways, payload);\n return newState;\n case 'ATLAS_STUDIES_RECEIVED':\n newState = Object.assign({}, state);\n newState.studies = Object.assign({}, state.studies, payload);\n return newState;\n case 'ATLAS_SAMPLES_REQUESTED':\n if (!state.studies.byID[payload].hasOwnProperty('samples')) {\n newState = Object.assign({},state);\n newState.studies.byID[payload].samples = [];\n return newState;\n }\n break;\n case 'ATLAS_SAMPLES_RECEIVED':\n newState = Object.assign({}, state);\n newState.studies.byID[payload.id].samples = payload.samples;\n return newState;\n case 'GENE_SEQUENCE_REQUESTED':\n if (!state.sequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.sequences[payload] = {};\n return newState;\n }\n break;\n case 'RNA_SEQUENCE_REQUESTED':\n if (!state.rnaSequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.rnaSequences[payload] = {};\n return newState;\n }\n break;\n case 'PEP_SEQUENCE_REQUESTED':\n if (!state.rnaSequences.hasOwnProperty(payload)) {\n newState = Object.assign({}, state);\n newState.pepSequences[payload] = {};\n return newState;\n }\n break;\n case 'GENE_SEQUENCE_RECEIVED':\n newState = Object.assign({}, state);\n newState.sequences = Object.assign({}, state.sequences);\n newState.sequences[payload.id] = payload.geneSeq;\n return newState;\n case 'RNA_SEQUENCE_RECEIVED':\n newState = Object.assign({}, state);\n newState.rnaSequences = Object.assign({}, state.rnaSequences);\n newState.rnaSequences[payload.id] = payload.RnaSeq;\n return newState;\n case 'PEP_SEQUENCE_RECEIVED':\n newState = Object.assign({}, state);\n newState.pepSequences = Object.assign({}, state.pepSequences);\n newState.pepSequences[payload.id] = payload.PepSeq;\n return newState;\n case 'PARALOG_EXPRESSION_REQUESTED':\n if (!state.expression.hasOwnProperty(payload)) {\n newState = Object.assign({},state);\n newState.expression[payload] = [];\n return newState;\n }\n break;\n case 'PARALOG_EXPRESSION_RECEIVED':\n newState = Object.assign({}, state);\n newState.expression = Object.assign({}, state.expression);\n newState.expression[payload.id] = payload.paralogs;\n return newState;\n case 'EXPRESSION_SAMPLE_TOGGLED':\n newState = Object.assign({}, state);\n newState.desiredSamples = Object.assign({}, state.desiredSamples);\n if (newState.desiredSamples.hasOwnProperty(payload)) {\n delete newState.desiredSamples[payload]\n }\n else {\n newState.desiredSamples[payload] = {status: 'need'}\n }\n }\n return state;\n }\n },\n doToggleExpressionSample: id => ({dispatch}) => {\n dispatch({type: 'EXPRESSION_SAMPLE_TOGGLED', payload: id});\n },\n doRequestVEP: id => ({dispatch, store}) => {\n const consequences = store.selectGrameneConsequences();\n if (!consequences.hasOwnProperty(id)) {\n dispatch({type: 'GRAMENE_CONSEQUENCES_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/search?q=id:${id}&fl=id,VEP__`)\n .then(res => res.json())\n .then(res => {\n let genes = {};\n res.response.docs.forEach(g => {\n genes[g.id] = g;\n });\n dispatch({type: 'GRAMENE_CONSEQUENCES_RECEIVED', payload: genes})\n })\n }\n },\n doRequestGrameneGene: id => ({dispatch, store}) => {\n const genes = store.selectGrameneGenes();\n if (!genes.hasOwnProperty(id)) {\n dispatch({type: 'GRAMENE_GENE_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/genes?idList=${id}`)\n .then(res => res.json())\n .then(res => {\n let genes = {};\n res.forEach(g => {\n genes[g._id] = g;\n });\n dispatch({type: 'GRAMENE_GENE_RECEIVED', payload: genes})\n })\n }\n },\n doRequestGrameneTree: id => ({dispatch, store}) => {\n const trees = store.selectGrameneTrees();\n const maps = store.selectGrameneMaps();\n if (!trees.hasOwnProperty(id)) {\n dispatch({type: 'GRAMENE_TREE_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/genetrees?idList=${id}`)\n .then(res => res.json())\n .then(res => {\n let trees = {};\n res.forEach(t => {\n function update_taxon_name(node) {\n if (maps.hasOwnProperty(node.taxon_id)) {\n node.taxon_name = maps[node.taxon_id].display_name\n }\n else if (node.taxon_id === 1100004558) {\n node.taxon_name = \"Sorghum bicolor\"\n }\n if (node.taxon_id === 45580023 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Sorghum bicolor\"\n }\n if (node.taxon_id === 45770001 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Zea mays\"\n }\n if (node.taxon_id === 297600009 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Vitis vinifera\"\n }\n if (node.hasOwnProperty('children')) {\n node.children.forEach(c => update_taxon_name(c))\n }\n }\n update_taxon_name(t);\n trees[t._id] = t;\n });\n dispatch({type: 'GRAMENE_TREE_RECEIVED', payload: trees})\n })\n }\n },\n doRequestGramenePathways: ids => ({dispatch, store}) => {\n const pathways = store.selectGramenePathways();\n let newIds = ids.filter(id => !pathways.hasOwnProperty(id));\n if (newIds) {\n dispatch({type: 'GRAMENE_PATHWAYS_REQUESTED', payload: newIds});\n if (newIds.length === 1) newIds.push(0);\n fetch(`${store.selectGrameneAPI()}/pathways?idList=${newIds.join(',')}`)\n .then(res => res.json())\n .then(res => {\n let pathways = {};\n res.forEach(p => {\n pathways[p._id] = p;\n });\n dispatch({type: 'GRAMENE_PATHWAYS_RECEIVED', payload: pathways})\n })\n }\n },\n doRequestExpressionStudies: id => ({dispatch, store}) => {\n fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`)\n .then(res => res.json())\n .then(res => {\n let studies = {byID:{},byTaxon:{}};\n res.forEach(s => {\n studies.byID[s._id] = s;\n if (! studies.byTaxon.hasOwnProperty(s.taxon_id)) {\n studies.byTaxon[s.taxon_id] = []\n }\n studies.byTaxon[s.taxon_id].push(s._id)\n })\n dispatch({type: 'ATLAS_STUDIES_RECEIVED', payload: studies})\n })\n },\n doRequestStudyMetadata: id => ({dispatch, store}) => {\n const studies = store.selectAtlasStudies();\n if (!studies.byID[id].hasOwnProperty('samples')) {\n dispatch({type: 'ATLAS_SAMPLES_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/assays?experiment=${id}&rows=-1`)\n .then(res => res.json())\n .then(samples => {\n dispatch({type: 'ATLAS_SAMPLES_RECEIVED', payload: {id, samples}})\n })\n }\n },\n doRequestGeneSequence: gene => ({dispatch, store}) => {\n const maps = store.selectGrameneMaps();\n const seqs = store.selectGeneSequences();\n const id = gene._id;\n const MAX_FLANK = 2000;\n if (!seqs.hasOwnProperty(id)) {\n dispatch({type: 'GENE_SEQUENCE_REQUESTED', payload: id});\n const start = gene.location.start > MAX_FLANK ? gene.location.start - MAX_FLANK : 1;\n const dnaLength = maps[gene.taxon_id].regionLength[gene.location.region];\n const end = gene.location.end + MAX_FLANK > dnaLength ? dnaLength : gene.location.end + MAX_FLANK;\n fetch(`${store.selectEnsemblAPI()}/sequence/region/${gene.system_name}/${gene.location.region}:${start}..${end}:${gene.location.strand}?content-type=application/json`)\n .then(res => res.json())\n .then(geneSeq => {\n const x = geneSeq.id.split(':');\n geneSeq.genome = x[1];\n geneSeq.start = +x[3];\n geneSeq.end = +x[4];\n dispatch({type: 'GENE_SEQUENCE_RECEIVED', payload: {id, geneSeq}});\n })\n }\n },\n doRequestRnaSequence: (id,gene) => ({dispatch, store}) => {\n const seqs = store.selectRnaSequences();\n if (!seqs.hasOwnProperty(id)) {\n dispatch({type: 'RNA_SEQUENCE_REQUESTED', payload: id});\n fetch(`${store.selectEnsemblAPI()}/sequence/id/${id}?species=${gene.system_name}&type=cdna&content-type=application/json`)\n .then(res => res.json())\n .then(RnaSeq => {\n dispatch({type: 'RNA_SEQUENCE_RECEIVED', payload: {id, RnaSeq}});\n })\n }\n },\n doRequestPepSequence: (id,gene) => ({dispatch, store}) => {\n const seqs = store.selectPepSequences();\n if (!seqs.hasOwnProperty(id)) {\n dispatch({type: 'PEP_SEQUENCE_REQUESTED', payload: id});\n fetch(`${store.selectEnsemblAPI()}/sequence/id/${id}?species=${gene.system_name}&type=protein&content-type=application/json`)\n .then(res => res.json())\n .then(PepSeq => {\n dispatch({type: 'PEP_SEQUENCE_RECEIVED', payload: {id, PepSeq}});\n })\n }\n },\n doRequestParalogExpression: id => ({dispatch, store}) => {\n const expr = store.selectParalogExpression();\n if (!expr.hasOwnProperty(id)) {\n dispatch({type: 'PARALOG_EXPRESSION_REQUESTED', payload: id});\n fetch(`${store.selectGrameneAPI()}/search?q=homology__within_species_paralog:${id}&fl=id,atlas_id,name,__expr&rows=100`)\n .then(res => res.json())\n .then(res => {\n const assay_re = /(.+)_g(\\d+)/;\n const paralogs = res.response.docs.map(d => {\n let p = {\n id: d.id,\n name: d.name,\n experiments: {},\n min:1000,\n max:0\n };\n if (d.atlas_id) {\n p.atlas_id = d.atlas_id;\n delete d.atlas_id;\n }\n delete d.id;\n delete d.name;\n Object.entries(d).forEach(assay => {\n const parsed = assay[0].match(assay_re);\n const expr = parsed[1].replace('_','-').replace('-tpms','');\n if (! p.experiments.hasOwnProperty(expr)) {\n p.experiments[expr] = [];\n }\n const g = parsed[2] - 1;\n const e = d[assay[0]];\n if (e < p.min) p.min = e;\n if (e > p.max) p.max = e;\n p.experiments[expr][g] = e;\n });\n return p;\n }).map(p => {\n for (const expr in p.experiments) {\n p.experiments[expr] = p.experiments[expr].filter(e => e >= 0);\n }\n return p;\n });\n dispatch({type: 'PARALOG_EXPRESSION_RECEIVED', payload: {id, paralogs}});\n })\n }\n },\n selectGrameneGenes: state => state.grameneDocs.genes,\n selectGrameneConsequences: state => state.grameneDocs.consequences,\n selectGrameneTrees: state => state.grameneDocs.trees,\n selectGramenePathways: state => state.grameneDocs.pathways,\n selectParalogExpression: state => state.grameneDocs.expression,\n selectGeneSequences: state => state.grameneDocs.sequences,\n selectRnaSequences: state => state.grameneDocs.rnaSequences,\n selectPepSequences: state => state.grameneDocs.pepSequences,\n selectAtlasStudies: state => state.grameneDocs.studies,\n selectDesiredSamples: state => state.grameneDocs.desiredSamples\n};\n\nexport default grameneDocs;\n","import {createSelector} from \"redux-bundler\";\nconst grameneGenomes = {\n name: 'grameneGenomes',\n getReducer: () => {\n const initialState = {\n show: false,\n active: {}\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\n case 'GRAMENE_GENOMES_TOGGLED':\n newState = Object.assign({},state);\n newState.show = !newState.show;\n return newState;\n case 'GRAMENE_GENOMES_UPDATED':\n newState = Object.assign({}, state);\n newState.active = payload;\n return newState;\n case 'GRAMENE_MAPS_FETCH_FINISHED':\n newState = Object.assign({}, state);\n newState.active = payload;\n default:\n return state;\n }\n }\n },\n doShowGrameneGenomes: () => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_GENOMES_TOGGLED'})\n },\n doInitializeGrameneGenomes: genomes => ({dispatch, getState}) => {\n dispatch({type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_GENOMES_UPDATED', payload: genomes}]})\n },\n doUpdateGrameneGenomes: genomes => ({dispatch, getState}) => {\n dispatch({type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_GENOMES_TOGGLED'},\n {type: 'GRAMENE_GENOMES_UPDATED', payload: genomes}]})\n },\n doEnsureGrameneGenome: genome => ({dispatch, getState}) => {\n const state = getState();\n if (Object.keys(state.grameneGenomes.active).length > 0 && !state.grameneGenomes.active.hasOwnProperty(genome)) {\n let active = Object.assign({}, state.grameneGenomes.active);\n active[genome]=true;\n dispatch({type: 'GRAMENE_GENOMES_UPDATED', payload: active})\n }\n },\n selectGrameneGenomes: state => state.grameneGenomes,\n selectActiveGenomes: state => {\n return Object.keys(state.grameneGenomes.active)\n },\n selectActiveGenomeCount: createSelector(\n 'selectGrameneMaps',\n 'selectGrameneGenomes',\n (maps,genomes) => {\n if (maps && genomes) {\n return Object.keys(genomes.active).length \|\| Object.keys(maps).length;\n }\n return 0;\n }\n )\n};\n\nexport default grameneGenomes;","import {connect} from 'redux-bundler-react'\nimport React from 'react'\n\nconst Gene = ({gene}) => {\n return <div className=\"row\">{gene.id}</div>\n};\n\nconst Genes = (results, rows, doChangeQuantity) => {\n if (results && results.numFound > 0) {\n const moreButton = (results.numFound > rows)\n ? <button onClick={e => doChangeQuantity('Genes',20)}>more</button>\n : '';\n const fewerButton = (rows > 20)\n ? <button onClick={e => doChangeQuantity('Genes',-20)}>fewer</button>\n : '';\n const docsToShow = results.response.docs.slice(0,rows);\n return (\n <div id=\"Genes\" className=\"container mb40 anchor\">\n <div className=\"fancy-title mb40\">\n <h4>Genes</h4>\n </div>\n {docsToShow.map((doc,idx) => <Gene key={idx} gene={doc}/>)}\n {fewerButton}{moreButton}\n </div>\n );\n }\n};\n\nconst Pathway = ({pathway}) => {\n return <div className=\"row\">{pathway.name}</div>\n};\nconst Pathways = results => {\n if (results && results.numFound > 0) {\n return (\n <div id=\"Pathways\" className=\"container mb40 anchor\">\n <div className=\"fancy-title\">\n <h4>Pathways</h4>\n </div>\n {results.pathways.map((doc,idx) => (<Pathway key={idx} pathway={doc}/>))}\n </div>\n );\n }\n};\n\nconst Domain = ({domain}) => {\n return <div className=\"row\">{domain.id}</div>\n};\nconst Domains = results => {\n if (results && results.numFound > 0) {\n return (\n <div id=\"Domains\" className=\"container mb40 anchor\">\n <div className=\"fancy-title mb40\">\n <h4>Domains</h4>\n </div>\n {results.domains.map((doc,idx) => (<Domain key={idx} domain={doc}/>))}\n </div>\n );\n }\n};\n\nconst Taxon = ({taxon}) => {\n return <div className=\"row\">{taxon.id}</div>\n};\nconst Species = results => {\n if (results && results.numFound > 0) {\n return (\n <div id=\"Species\" className=\"container mb40 anchor\">\n <div className=\"fancy-title mb40\">\n <h4>Species</h4>\n </div>\n {results.taxonomy.map((doc,idx) => (<Taxon key={idx} taxon={doc}/>))}\n </div>\n );\n }\n};\n\nconst ResultList = ({grameneGenes, grameneDomains, gramenePathways, grameneTaxonomy, searchUI, searchUpdated, doChangeQuantity}) => {\n if (searchUI.Gramene) {\n return (\n <div id=\"gramene\" className=\"row\">\n <div className=\"fancy-title pt50\">\n <h3>Gramene search results</h3>\n </div>\n {searchUI.Genes && Genes(grameneGenes, searchUI.rows.Genes, doChangeQuantity)}\n {searchUI.Domains && Domains(grameneDomains)}\n {searchUI.Pathways && Pathways(gramenePathways)}\n {searchUI.Species && Species(grameneTaxonomy)}\n </div>\n )\n }\n else {\n return null;\n }\n};\n\nexport default connect(\n 'selectGrameneGenes',\n 'selectGrameneDomains',\n 'selectGramenePathways',\n 'selectGrameneTaxonomy',\n 'selectSearchUI',\n 'selectSearchUpdated',\n 'doChangeQuantity',\n ResultList\n);\n","import {connect} from 'redux-bundler-react'\nimport React from 'react'\n\nconst getStatus = (cat, results, isChecked, toggle) => {\n const tally = results ? results.numFound : <img src=\"/static/images/dna_spinner.svg\"/>;\n return (\n <li className='category-leaf'>\n <input type=\"checkbox\" checked={isChecked} onChange={e => toggle(cat)}/>\n <a data-scroll href={`#${cat}`} className=\"nav-link active\">{cat}<span style={{float:\"right\"}}>{tally}</span></a>\n </li>\n )\n};\n\nconst ResultSummary = ({grameneGenes, gramenePathways, grameneDomains, grameneTaxonomy, searchUI, searchUpdated, doToggleCategory}) => {\n const status = grameneGenes ?\n grameneGenes.numFound:\n<img src=\"/static/images/dna_spinner.svg\"/>;\n if (searchUI.Gramene) return (\n <li className=\"active category-expanded\">\n <a onClick={e => doToggleCategory('Gramene')}>\n Gramene Search<span style={{float:\"right\"}}>{status}</span>\n </a>\n <ul className=\"list-unstyled\">\n {getStatus('Genes', grameneGenes, searchUI.Genes, doToggleCategory)}\n {getStatus('Domains', grameneDomains, searchUI.Domains, doToggleCategory)}\n {getStatus('Pathways', gramenePathways, searchUI.Pathways, doToggleCategory)}\n {getStatus('Species', grameneTaxonomy, searchUI.Species, doToggleCategory)}\n</ul>\n </li>\n);\nelse return (\n <li className=\"active category-collapsed\">\n <a onClick={e => doToggleCategory('Gramene')}>\n Gramene Search<span\n style={{float:\"right\"}}>{status}</span>\n </a>\n </li>\n);\n};\n\nexport default connect(\n 'selectGrameneGenes',\n 'selectGramenePathways',\n 'selectGrameneDomains',\n 'selectGrameneTaxonomy',\n 'selectSearchUI',\n 'selectSearchUpdated',\n 'doToggleCategory',\n ResultSummary\n);\n","import {connect} from 'redux-bundler-react'\nimport React from 'react'\nimport ReactGA from 'react-ga4'\nimport { Button, Badge, Alert } from 'react-bootstrap'\nimport './styles.css'\n\nfunction showMatches(text, x) {\n let re = new RegExp(`(${x})`, 'ig');\n let match = text.split(re);\n return <span>\n {match.map((str, idx) => {\n if (idx % 2 === 1) {\n return <span key={idx} style={{fontWeight:'bolder'}}>{str}</span>\n }\n return <span key={idx}>{str}</span>\n })}\n </span>\n}\n\nfunction logAction(sugg) {\n ReactGA.event({\n category: 'Search',\n action: 'SetFilter',\n label: sugg.name\n })\n}\nfunction getLowestCommonAncestorName(tids, taxonomy) {\n let lca;\n tids.forEach(tid => {\n if (!lca) {\n lca = [...taxonomy[tid].ancestors];\n } else {\n let ancestors = new Set(taxonomy[tid].ancestors);\n while (!ancestors.has(lca[0])) {\n lca.shift();\n }\n }\n });\n return taxonomy[lca[0]].short_name;\n}\n\nconst TryPan = (props) => {\n const query = props.query;\n const pan = props.pan;\n return <div className=\"suggestion-panlink\">\n <a target=\"_blank\" href={pan.url + \"?suggestion=\" + query}>\n <img src={pan.svg} title={`Search at ${pan.name}`}/>\n </a>\n </div>;\n};\n\nconst TryAnotherSite = props => {\n const query = props.query;\n const config = props.config;\n let sites = Object.keys(config.panSite);\n return <div>\n <Alert variant={'info'}>Don't see what you're looking for? Search for <b>{query}</b> on one of our sister sites</Alert>\n {sites.map((p, idx) => <TryPan key={idx} query={query} pan={config.panSite[p]}/>)}\n </div>\n}\n\nconst Suggestions = props => {\n let suggestions = props.grameneSuggestions;\n if (suggestions && suggestions.grouped) {\n if (suggestions.grouped.category.matches === 0) {\n let sugg1 = {\n fq_field: 'text',\n fq_value: props.suggestionsQuery,\n name: `Genes containing \"${props.suggestionsQuery}\"`,\n category: 'Gene',\n };\n let sugg2 = {\n fq_field: 'text',\n fq_value: `${props.suggestionsQuery}`,\n name: `Genes matching \"${props.suggestionsQuery}\"`,\n category: 'Gene',\n };\n return (\n <div style={{margin: '10px', maxWidth: '820px'}}>\n <Alert variant={'info'}><em>No suggestions found.</em> You may still attempt a full text search, though it is unlikely to find any genes for you.</Alert>\n <Button id={'word'}\n size={'sm'}\n variant={'outline-secondary'}\n onClick={() => {logAction(sugg1); props.doAcceptSuggestion(sugg1); props.doAcceptGrameneSuggestion(sugg1)}}>\n {`All genes that contain the word \"${props.suggestionsQuery}\"`}\n </Button>\n <Button id={'word'}\n size={'sm'}\n variant={'outline-secondary'}\n onClick={() => {logAction(sugg2); props.doAcceptSuggestion(sugg2); props.doAcceptGrameneSuggestion(sugg2)}}>\n {`All genes that contain a word that starts with \"${props.suggestionsQuery}\"`}\n </Button>\n <TryAnotherSite query={props.suggestionsQuery} config={props.configuration}/>\n </div>\n );\n }\n else {\n return (\n <div style={{margin: '10px'}}>\n {suggestions.grouped.category.groups.map((g,idx) => {\n return <div key={idx} id='gramene-suggestion'>\n <h4 className=\"mt10\">{g.groupValue}</h4>\n {g.doclist.docs.map((sugg,jdx) =>\n <Button id={`${idx}-${jdx}`}\n key={jdx}\n disabled={sugg.num_genes === 0}\n size='sm'\n variant=\"outline-secondary\"\n onClick={() => {logAction(sugg); props.doAcceptSuggestion(sugg); props.doAcceptGrameneSuggestion(sugg)}}>\n {showMatches(sugg.display_name,props.suggestionsQuery)}{' '}\n <Badge bg=\"secondary\">{sugg.num_genes}</Badge>\n <i> {getLowestCommonAncestorName(sugg.taxon_id, props.grameneTaxonomy)}</i>\n </Button>\n )}\n </div>\n })}\n <TryAnotherSite query={props.suggestionsQuery} config={props.configuration}/>\n </div>\n );\n }\n }\n else {\n return <div></div>\n }\n}\n\nexport default connect(\n 'selectGrameneSuggestions',\n 'selectSuggestionsQuery',\n 'selectGrameneTaxonomy',\n 'selectConfiguration',\n 'doAcceptSuggestion',\n 'doAcceptGrameneSuggestion',\n Suggestions\n);\n","import React, { useRef, useEffect } from 'react'\nimport { connect } from 'redux-bundler-react'\nimport { Navbar, Nav, NavDropdown, Container, OverlayTrigger, Popover} from 'react-bootstrap'\nimport Switch from 'react-switch'\nimport { IoAlertCircle } from 'react-icons/io5'\nimport { BsGearFill,BsTrash } from 'react-icons/bs'\nimport GeneList from './results/GeneList'\nimport TaxDist from './results/TaxDist'\nimport HelpDemo from './results/HelpDemo'\nimport GeneAttribs from './results/GeneAttribs'\nimport TaxonomyModal from './TaxonomyModal'\nimport Expression from './results/Expression'\nimport UserGeneLists from './results/UserGeneLists'\nimport Auth from './Auth'\nimport ReactGA from 'react-ga4'\nimport './styles.css';\n\nconst inventory = {\n help: HelpDemo,\n list: GeneList,\n taxonomy: TaxDist,\n attribs: GeneAttribs,\n expression: Expression,\n userLists: UserGeneLists\n};\n\nconst StatusCmp = props => {\n let content = props.grameneFiltersStatus;\n // if (props.grameneFiltersStatus === 'init') {\n // props.doClearGrameneFilters();\n // }\n if (props.grameneFiltersStatus === 'ready') {\n let tally = <span>Ready</span>;\n if (props.grameneSearch) {\n let genes = props.grameneSearch.response.numFound;\n let genomes = props.grameneSearch.facet_counts.facet_fields.taxon_id.length / 2;\n tally = <span><b>{genes}</b> genes in <b>{genomes}</b> genomes</span>;\n }\n const popover = (\n <Popover>\n <Popover.Header as=\"h3\">Genomes Filter</Popover.Header>\n <Popover.Body>Searching {props.activeGenomeCount} genomes</Popover.Body>\n </Popover>\n );\n\n content = <span>\n {tally}\n <OverlayTrigger placement=\"auto\" overlay={popover}>\n <span style={{float:'right', cursor:'pointer'}} onClick={props.doShowGrameneGenomes}><BsGearFill/></span>\n </OverlayTrigger>\n <TaxonomyModal/>\n </span>;\n }\n return <div style={{padding:'5px', color:'cornsilk', fontSize:'small'}}>{content}</div>\n};\n\nconst Status = connect(\n 'selectGrameneSearch',\n 'selectGrameneFiltersStatus',\n 'selectActiveGenomeCount',\n 'doShowGrameneGenomes',\n 'doClearGrameneFilters',\n StatusCmp\n);\n\nconst handleClick = (e, moveCopyMode, showMarked, node, actions) => {\n if (!e) e = window.event;\n e.cancelBubble = true;\n if (e.stopPropagation) e.stopPropagation();\n\n if (showMarked && moveCopyMode) {\n if (node.marked) {\n actions.selectTarget(node);\n }\n else {\n actions.unmarkTargets()\n }\n }\n console.log(node, showMarked);\n};\nfunction logAction(action) {\n ReactGA.event({\n category: 'Search',\n action: action\n })\n}\nconst Filter = ({node,moveCopyMode,showMarked,actions}) => {\n let classes = 'gramene-filter gramene-filter';\n if (node.operation) {\n classes = `${classes}-${node.operation}`\n }\n if (node.negate) {\n classes = `${classes} gramene-filter-NOT`\n }\n if (showMarked && node.marked) {\n classes = `${classes} gramene-filter-marked`\n }\n let content = '';\n let menu = '';\n let children = [];\n\n if (node.showMenu) {\n let key=1;\n let menuItems = [];\n if (node.hasOwnProperty('operation')) {\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Change to ${node.operation}`); actions.changeOperation(node)}}>convert to <i>{node.operation === 'AND' ? 'OR' : 'AND'}</i></li>);\n }\n if (node.leftIdx > 0) {\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Delete filter`); actions.deleteNode(node)}}>delete</li>);\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Move filter`); actions.markTargets(node,'move')}}>move{node.isSource && ' select destination'}</li>);\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Copy filter`); actions.markTargets(node,'copy')}}>copy{node.isSource && ' select destination'}</li>)\n }\n menuItems.push(<li key={key++} onClick={()=>{logAction(`Negate filter`); actions.negate(node)}}>negate</li>);\n menu = <div className='gramene-filter-menu'><ul>{menuItems}</ul></div>;\n }\n let warning;\n if (node.warning) {\n const popover = (\n <Popover>\n <Popover.Header as=\"h3\">Warning</Popover.Header>\n <Popover.Body>{node.warning}</Popover.Body>\n </Popover>\n );\n warning = (\n <OverlayTrigger placement=\"auto\" overlay={popover}><span style={{float:'right', color:'red', cursor:'pointer'}}><IoAlertCircle/></span></OverlayTrigger>\n )\n }\n if (node.operation) {\n children = node.children.map((child,idx) => <Filter key={idx} moveCopyMode={moveCopyMode} node={child} showMarked={showMarked} actions={actions}/>);\n content = (\n <div>\n <span className='gramene-filter-operation'\n onClick={()=>actions.toggleMenu(node)}>{node.operation}</span>\n {warning}\n </div>\n );\n }\n else {\n content = <span className='gramene-filter-text'\n onClick={()=>actions.toggleMenu(node)}>{node.category} \| {node.name}</span>;\n }\n return (\n <div key={node.leftIdx} className={classes} onClick={(e)=>handleClick(e,moveCopyMode, showMarked,node,actions)}>\n {content}{menu}{children}\n </div>\n )\n};\n\nconst FiltersCmp = props => {\n const actions = {\n negate: props.doNegateGrameneFilter,\n deleteNode: props.doDeleteGrameneFilter,\n changeOperation: props.doChangeGrameneFilterOperation,\n selectTarget: props.doMoveOrCopyGrameneFilter,\n markTargets: props.doMarkGrameneFilterTargets,\n unmarkTargets: props.doUnmarkGrameneFilterTargets,\n toggleMenu: props.doToggleGrameneFilterMenu\n };\n if (props.grameneFilters.rightIdx > 1) {\n return <div className={props.configuration.id === 'sorghum' ? 'sorghumbase-filter-container': 'gramene-filter-container'}>\n <b>Filters</b>\n <span style={{float:'right', cursor:'pointer'}} onClick={props.doClearGrameneFilters}><BsTrash/></span>\n <Filter node={props.grameneFilters}\n moveCopyMode={props.grameneFilters.moveCopyMode}\n showMarked={props.grameneFilters.showMarked}\n actions={actions}/>\n </div>\n }\n else {\n return <div className={props.configuration.id === 'sorghum' ? 'sorghumbase-filter-container': 'gramene-filter-container'}>\n <b>Filters</b>\n <div className='gramene-filter gramene-filter-AND'>No filters defined</div>\n </div>\n }\n};\n\nconst Filters = connect(\n 'selectGrameneFilters',\n 'selectConfiguration',\n 'doNegateGrameneFilter',\n 'doDeleteGrameneFilter',\n 'doChangeGrameneFilterOperation',\n 'doMoveOrCopyGrameneFilter',\n 'doMarkGrameneFilterTargets',\n 'doUnmarkGrameneFilterTargets',\n 'doToggleGrameneFilterMenu',\n 'doClearGrameneFilters',\n FiltersCmp\n);\n\nconst ResultsCmp = props => {\n let activeViews = props.grameneViews.options;\n return props.grameneFilters.rightIdx > 0 ? (\n <div>\n {activeViews.map((v,idx) => {\n let p = Object.assign({}, props);\n const divRef = useRef(null);\n useEffect(() => {\n if (v.shouldScroll) {\n const navBarHeight=0;\n const scrollPosition = divRef.current.offsetTop - navBarHeight;\n window.scrollTo({\n top: scrollPosition,\n behavior: 'smooth'\n })\n props.doCancelShouldScroll();\n }\n }, [v.shouldScroll]);\n return (\n <div key={idx} ref={divRef}>\n {v.show === 'on' && <div style={{borderTopWidth:'medium'}} className='gramene-view-header'>{v.name}</div>}\n {v.show === 'on' && React.createElement(inventory[v.id], p)}\n </div>\n )\n })}\n </div>\n ) : null;\n};\n\nconst Results = connect(\n 'selectGrameneFilters',\n 'selectGrameneViews',\n 'doCancelShouldScroll',\n ResultsCmp\n);\n\nconst ViewsCmp = props => (\n <div className={'gramene-view-container'}>\n <b>Views</b>\n {props.grameneViews.options.filter(view => view.show !== 'disabled').map((view,idx) => (\n <div style={{textWrap:'nowrap'}} key={idx}>\n <Switch onChange={()=>props.doToggleGrameneView(view.id)} checked={view.show === 'on'}\n height={18}\n width={30}\n handleDiameter={16}\n checkedIcon={false}\n uncheckedIcon={false}\n />\n <span className={`gramene-view-span-${view.show}`} onClick={(e) => {\n props.dontToggleGrameneView(view.id)\n }}>{view.name}</span>\n </div>\n ))}\n </div>\n);\n\nconst Views = connect(\n 'selectGrameneViews',\n 'doToggleGrameneView',\n 'dontToggleGrameneView',\n ViewsCmp\n);\n\nexport {Status, Filters, Results, Views, Auth};\n","import React from 'react'\nimport ReactGA from 'react-ga4'\nimport { connect } from 'redux-bundler-react'\nimport './genes.css'\nimport Expression from './details/Expression'\nimport Homology from './details/Homology'\nimport Location from './details/Location'\nimport Pathways from \"./details/Pathways\"\nimport VEP from \"./details/VEP\"\nimport Xrefs from \"./details/Xrefs\"\nimport Publications from \"./details/Publications\"\nimport Sequences from \"./details/Sequences\"\nimport {suggestionToFilters} from \"../utils\";\nimport {GrFormPrevious, GrFormNextLink, GrFormNext, GrHpe} from 'react-icons/gr'\nimport { Badge, OverlayTrigger, Tooltip } from 'react-bootstrap'\n\nlet external = <small title=\"This link opens a page from an external site\"> <i className=\"fa fa-external-link\"/></small>;\n\nlet inventory = {\n sequences: Sequences,\n location: Location,\n expression: Expression,\n homology: Homology,\n pathways: Pathways,\n VEP: VEP,\n xrefs: Xrefs,\n pubs: Publications\n};\n\nfunction renderTairSummary(searchResult) {\n const summary = searchResult.summary;\n if(summary && summary !== \"NULL\" && searchResult.system_name === \"arabidopsis_thaliana\") {\n return (\n <div className=\"gene-summary-tair\">\n {trimSummary(summary)}\n </div>\n )\n }\n}\n\nfunction trimSummary(summary) {\n if(summary.length > 160) {\n const start = summary.substr(0, 150);\n const rest = summary.substr(150);\n return <p>{start}<span className=\"ellipsis\">…</span><span className=\"rest\">{rest}</span></p>\n }\n else {\n return <p>{summary}</p>\n }\n}\nconst PanLink = (props) => {\n const gene = props.gene;\n const pan = props.pan;\n return <div className=\"gene-panlink\">\n <a target=\"_blank\" href={pan.url + \"?idList=\" + gene.id}>\n <img src={pan.svg} title={`View this gene at ${pan.name}`}/>\n </a>\n </div>;\n};\n\nconst CurationComponent1 = ({ curation }) => {\n return (\n <div className=\"gene-curation\">\n <span>Curated gene structure</span>\n {curation.okay > 0 && <span className=\"status\">✔️ {curation.okay}</span>}\n {curation.flagged > -10 && <span className=\"status\">⚠️ {curation.flagged}</span>}\n </div>\n );\n};\nconst CurationComponent = ({ curation, gene }) => {\n const total = curation.okay + curation.flagged;\n const okayRatio = (curation.okay / total);\n const flaggedRatio = (curation.flagged / total);\n const tooltip = (\n <Tooltip id=\"tooltip\">\n <strong>Gene structure</strong><br/>\n Okay: {curation.okay}  \n Flagged: {curation.flagged}\n </Tooltip>\n );\n return (\n <OverlayTrigger placement=\"left\" overlay={tooltip}>\n <a className=\"gene-curation\" target=\"_blank\" href={`https://devdata.gramene.org/curation/curations?idList=${gene.id}`}>\n <span className=\"okay\" style={{opacity: okayRatio}}>☑</span>\n <span className=\"flagged\" style={{opacity: flaggedRatio}}>⚠</span>\n </a>\n </OverlayTrigger>\n )\n};\n\nconst ClosestOrthologCmp = (props) => {\n let id, taxon_id, name, desc, species, className, identity;\n const gene = props.gene;\n\n if (gene.closest_rep_id) {\n name = gene.closest_rep_name \|\| gene.closest_rep_id;\n desc = gene.closest_rep_description;\n species = gene.closest_rep_species_name;\n id = gene.closest_rep_id;\n taxon_id = gene.closest_rep_taxon_id;\n className = \"closest-ortholog\";\n identity = gene.closest_rep_identity \|\| 0;\n }\n else if (gene.model_rep_id) {\n name = gene.model_rep_name \|\| gene.model_rep_id;\n desc = gene.model_rep_description;\n species = gene.model_rep_species_name;\n id = gene.model_rep_id;\n taxon_id = gene.model_rep_taxon_id;\n className = \"model-ortholog\";\n identity = gene.model_rep_identity \|\| 0;\n }\n var isZm = new RegExp(/^Zm00001e/);\n if (isZm.test(desc)) {\n desc='';\n }\n\n return (\n <div className={className} onClick={() => {\n props.doEnsureGrameneGenome(taxon_id);\n props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene',\n fq_field: 'id',\n fq_value: id,\n name: name\n }))\n }}>\n <div className=\"gene-species\">{species}</div>\n {identity > 0 && <div className=\"rep-identity\">{Math.round(identity100)}</div>}\n <h3 className=\"gene-id\">{name}</h3>\n <p>{desc}</p>\n </div>\n );\n};\n\nconst ClosestOrtholog = connect(\n 'doReplaceGrameneFilters','doEnsureGrameneGenome',\n ClosestOrthologCmp\n);\n\nfunction renderClosestOrtholog(gene) {\n\n if (shouldShowClosestOrtholog(gene)) {\n\n // we used to not add the closest ortholog to the DOM if the homology detail was visible.\n // however, that could cause the height of the result to change. Instead we set visibility:hidden\n // so that the renderer takes into account the height of the ortholog even if not shown.\n return (\n <ClosestOrtholog gene={gene}/>\n );\n }\n}\n\n// show closest ortholog prominently if we have data to show:-\n// a. either there's a closest ortholog (determined by traversing the gene tree until an id or description looks\n// curated) b. or there's a model ortholog (traverse tree to find an ortholog in arabidopsis)\nfunction shouldShowClosestOrtholog(searchResult) {\n return (\n searchResult.closest_rep_id \|\| (\n searchResult.model_rep_id &&\n searchResult.model_rep_id !== searchResult.id\n )\n );\n}\n\nconst allDetails = [\n {\n id: 'VEP',\n label: 'Germplasm',\n popup: 'Germplasm with protein truncating variants (PTVs)',\n available: false\n },\n {\n id: 'sequences',\n label: 'Sequences',\n popup: 'Gene/cDNA/protein fasta',\n available: true\n },\n {\n id: 'location',\n label: 'Location',\n popup: 'Genome Browser',\n available: false\n },\n {\n id: 'expression',\n label: 'Expression',\n popup: 'Gene Expression Atlas',\n available: false\n },\n {\n id: 'homology',\n label: 'Homology',\n popup: 'Gene Family Tree',\n available: false\n },\n {\n id: 'pathways',\n label: 'Pathways',\n popup: 'Plant Reactome Pathways',\n available: false\n },\n {\n id: 'pubs',\n label: 'Papers',\n popup: 'Curated Publications',\n available: false\n },\n {\n id: 'xrefs',\n label: 'Xrefs',\n popup: 'Database Cross-references',\n available: false\n }\n];\n\n\nclass Gene extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n details: allDetails.map(o => ({...o})).filter(d => props.config.details[d.id]),\n expandedDetail: props.expandedDetail\n };\n let hasData = {};\n props.searchResult.capabilities.forEach(c => {\n hasData[c] = true;\n if (c === 'PanOryza') {\n hasData.xrefs = true;\n }\n });\n this.state.details.forEach(d => d.available \|= hasData.hasOwnProperty(d.id));\n }\n getDetailStatus(d) {\n if (this.state.expandedDetail === d.id) return 'expanded';\n if (d.available) return 'closed'\n return d.id === \"pubs\" ? 'empty' : 'disabled';\n }\n setExpanded(d) {\n if (d.available \|\| d.id === \"pubs\") {\n if (this.state.expandedDetail === d.id) {\n this.setState({expandedDetail: null})\n }\n else {\n const geneId = this.props.searchResult.id;\n if (!(this.props.geneDocs && this.props.geneDocs.hasOwnProperty(geneId))) {\n this.props.requestGene(geneId)\n }\n ReactGA.event({\n category: 'Search',\n action: 'Details',\n label: d.label\n });\n this.setState({expandedDetail: d.id})\n }\n }\n }\n ensureGene(id) {\n if (!(this.props.geneDocs && this.props.geneDocs.hasOwnProperty(id))) {\n this.props.requestGene(id);\n return false;\n }\n return this.props.geneDocs[id].hasOwnProperty('taxon_id')\n }\n renderMetadata() {\n let gene = this.props.searchResult;\n if (gene.model_rep_taxon_id) {\n gene.model_rep_species_name = this.props.taxLut[gene.model_rep_taxon_id].short_name;\n }\n if (gene.closest_rep_taxon_id) {\n gene.closest_rep_species_name = this.props.taxLut[gene.closest_rep_taxon_id].short_name;\n }\n return renderTairSummary(gene) \|\| renderClosestOrtholog(gene);\n }\n render() {\n const panSite = this.props.config.panSite;\n const searchResult = this.props.searchResult;\n const taxName = this.props.taxName;\n const curation = this.props.curation;\n // let orthologs='';\n // if (this.props.orthologs && this.props.orthologs.hasOwnProperty(searchResult.id)) {\n // orthologs = this.props.orthologs[searchResult.id].join(', ');\n // }\n const numWordsInDescription = searchResult.description.split(' ').length;\n return (\n <div className=\"result-gene\">\n <div className=\"result-gene-summary\">\n <div className=\"result-gene-title-body\">\n {panSite.hasOwnProperty(searchResult.system_name) && <PanLink pan={panSite[searchResult.system_name]} gene={searchResult}/>}\n {curation && <CurationComponent curation={curation} gene={searchResult}/> }\n <div className=\"gene-title\">\n <div className=\"gene-species\">{taxName}</div>\n <h3 className=\"gene-name\">{searchResult.name}\n {searchResult.id !== searchResult.name && <small className=\"gene-id\"> {searchResult.id}</small>}\n </h3>\n </div>\n {searchResult.synonyms && <small className=\"gene-synonyms\">{searchResult.synonyms.join(', ')}</small>}\n {searchResult.description !== \"unknown\" && (numWordsInDescription > 1 \|\| searchResult.can_show.pubs) && <p className=\"gene-description\">{searchResult.description}</p>}\n </div>\n {this.renderMetadata()}\n </div>\n <div className=\"gene-detail-tabs\">\n {this.state.details.map((d,idx) => (\n <OverlayTrigger\n key={idx}\n placement={'bottom'}\n overlay={\n <Tooltip id={`tooltip`}>{d.popup}</Tooltip>\n }\n >\n <div key={idx}\n className={`col-md-1 text-center gene-detail-tab-${this.getDetailStatus(d)}`}\n onClick={()=>this.setExpanded(d)}\n >{d.label}</div>\n </OverlayTrigger>\n ))}\n </div>\n {this.state.expandedDetail && this.ensureGene(searchResult.id) && <div className=\"visible-detail\">{React.createElement(inventory[this.state.expandedDetail], this.props)}</div>}\n </div>\n )\n }\n}\n\nconst GeneList = props => {\n if (props.grameneSearch && props.grameneSearch.response && props.grameneTaxonomy) {\n let prev,page,next;\n const numFound = props.grameneSearch.response.numFound;\n if (numFound > props.grameneSearchRows) {\n const pageNum = props.grameneSearchOffset/props.grameneSearchRows;\n page = <span style={{padding:'10px'}}>page <b>{pageNum + 1}</b> of <b>{Math.ceil(numFound/props.grameneSearchRows)}</b></span>;\n prev = <GrHpe/>;\n if (pageNum > 0) {\n prev = <Badge onClick={()=>props.doRequestResultsPage(pageNum - 1)}><GrFormPrevious/></Badge>\n }\n next = <GrHpe/>;\n if (numFound > props.grameneSearchOffset + props.grameneSearchRows) {\n next = <Badge onClick={()=>props.doRequestResultsPage(pageNum + 1)}><GrFormNext/></Badge>\n }\n }\n return <div>\n <div>{prev}{page}{next}</div>\n {props.grameneSearch.response.docs.map((g,idx) => (\n <Gene key={idx}\n searchResult={g}\n config={props.configuration}\n taxName={props.grameneTaxonomy[g.taxon_id].name}\n geneDocs={props.grameneGenes}\n requestGene={props.doRequestGrameneGene}\n requestOrthologs={props.doRequestOrthologs}\n orthologs={props.grameneOrthologs}\n taxLut={props.grameneTaxonomy}\n curation={props.curatedGenes ? props.curatedGenes[g.id] : null}\n expandedDetail={props.grameneSearch.response.numFound === 1 && g.can_show.homology ? 'homology' : null}\n />\n ))}\n {prev}{page}{next}\n </div>\n }\n return null;\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGrameneSearch',\n 'selectGrameneTaxonomy',\n 'selectGrameneGenes',\n 'selectGrameneOrthologs',\n 'selectGrameneSearchOffset',\n 'selectGrameneSearchRows',\n 'selectCuratedGenes',\n 'doRequestGrameneGene',\n 'doRequestOrthologs',\n 'doRequestResultsPage',\n GeneList);\n","import React, { useRef, useEffect, useState } from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport {Tabs, Tab, Form, Row, Col} from 'react-bootstrap';\nimport BAR, {haveBAR} from \"gramene-efp-browser\";\n\nfunction DynamicIframe(props) {\n // Create a ref for the iframe element\n const iframeRef = useRef(null);\n const [iframeHeight, setIframeHeight] = useState(500); // Default height\n\n useEffect(() => {\n const handleMessage = (event) => {\n if (event.data.type === 'heightChange') {\n setIframeHeight(event.data.height + 44);\n }\n };\n\n window.addEventListener(\"message\", handleMessage);\n\n return () => window.removeEventListener(\"message\", handleMessage);\n }, []);\n\n return (\n <iframe\n ref={iframeRef}\n src={props.url}\n title=\"Dynamic Iframe\"\n style={{ width: '100%', height: `${iframeHeight}px`, border: 'none' }}\n />\n );\n}\n\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n const [atlasExperiment, setAtlasExperiment] = useState(null);\n const [atlasExperimentList, setAtlasExperimentList] = useState([]);\n const [isLocal, setIsLocal] = useState(false);\n const [activeTab, setActiveTab] = useState('gene');\n\n const handleLocalAPIChange = (event) => {\n setIsLocal(event.target.checked);\n };\n useEffect(() => {\n const tid = Math.floor(gene.taxon_id / 1000);\n if (props.expressionStudies[tid]) {\n let eList = props.expressionStudies[tid].sort((a,b) => {\n const a_name = `${a.type}:${a.description \|\| a._id}`;\n const b_name = `${b.type}:${b.description \|\| b._id}`;\n return a_name < b_name ? -1 : 1;\n });\n if (props.searchResult.hasOwnProperty('expressed_in_gxa_attr_ss')) {\n const in_gxa = new Set(props.searchResult.expressed_in_gxa_attr_ss);\n eList = eList.filter(e => in_gxa.has(e._id))\n }\n setAtlasExperimentList(eList);\n\n let refExp = eList.filter(e => e.isRef);\n if (refExp.length === 1) {\n setAtlasExperiment(refExp[0]._id);\n } else {\n // no reference experiment - choose first\n setAtlasExperiment(eList[0]._id);\n }\n }\n }, [props.expressionStudies]);\n\n let paralogs_url;\n let gene_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${gene.atlas_id \|\| gene._id}&localAPI=${isLocal}`;\n let paralogs = [];\n if (props.grameneParalogs && props.grameneParalogs[gene._id]) {\n paralogs = props.grameneParalogs[gene._id];\n } else if(gene.homology) {\n props.doRequestParalogs(gene._id, gene.homology.supertree, gene.taxon_id);\n }\n // if (gene.homology && gene.homology.homologous_genes && gene.homology.homologous_genes.within_species_paralog) {\n // paralogs = gene.homology.homologous_genes.within_species_paralog;\n // }\n if (paralogs.length > 1 && atlasExperiment) {\n paralogs_url= `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;\n }\n return <Tabs activeKey={activeTab} onSelect={(k) => setActiveTab(k)}>\n {paralogs_url &&\n <Tab tabClassName=\"gxa\" eventKey=\"paralogs\" title={`Paralogs`} key=\"gxaparalogs\">\n <Form.Select aria-label='experiment selector'\n placeholder='Select experiment'\n onChange={(e) => setAtlasExperiment(e.target.value)}>\n { atlasExperimentList.map((e,idx) =>\n <option key={idx} value={e._id}>{e.type}: {e.description \|\| e._id}</option>\n )}\n </Form.Select>\n {activeTab === \"paralogs\" && <DynamicIframe url={paralogs_url}/> }\n </Tab>\n }\n <Tab tabClassName=\"gxa\" eventKey=\"gene\" title=\"All Studies\" key=\"gxa\">\n {/<Form.Check/}\n {/ type=\"switch\"/}\n {/ id=\"localAPI\"/}\n {/ label=\"Local API\"/}\n {/ checked={isLocal}/}\n {/ onChange={handleLocalAPIChange}/}\n {//>/}\n {activeTab === \"gene\" && <DynamicIframe url={gene_url}/> }\n </Tab>\n {haveBAR(gene) &&\n <Tab tabClassName=\"eFP\" eventKey=\"eFP\" title=\"eFP Browser\" key=\"bar\"><BAR gene={gene}/></Tab>\n }\n </Tabs>\n};\n\nexport default connect(\n 'selectGrameneParalogs',\n 'selectExpressionStudies',\n 'doRequestParalogs',\n //'doRequestParalogExpression',\n Detail\n);\n\n","import React from 'react'\nimport _ from 'lodash';\nimport {connect} from \"redux-bundler-react\";\nimport TreeVis from \"gramene-genetree-vis\";\nimport treesClient from \"gramene-trees-client\";\nimport {Detail, Title, Description, Content, Explore, Links} from \"./generic\";\nimport {suggestionToFilters} from \"../../utils\";\nimport {Spinner, Alert} from \"react-bootstrap\";\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/msa.less';\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/tree.less';\n\nclass Homology extends React.Component {\n constructor(props) {\n super(props);\n if (!props.geneDocs.hasOwnProperty(props.searchResult.id)) {\n props.requestGene(props.searchResult.id)\n }\n this.taxonomy = treesClient.taxonomy.tree(Object.values(props.grameneTaxonomy))\n }\n renderTreeVis() {\n return (\n <div className=\"gene-genetree\">\n <TreeVis genetree={this.tree}\n initialGeneOfInterest={this.gene}\n genomesOfInterest={this.props.grameneGenomes.active}\n taxonomy={this.taxonomy}\n allowGeneSelection={true}\n pivotTree={true}\n enableCuration={false}\n enablePhyloview={true}\n numberOfNeighbors={10}\n ensemblUrl={this.props.configuration.ensemblURL}/>\n </div>\n )\n }\n filterAllHomologs() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'gene_tree',\n fq_value: this.tree._id,\n name: `Homologs of ${this.gene.name}`\n }))\n }\n filterOrthologs() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'homology__all_orthologs',\n fq_value: this.gene._id,\n name: `Orthologs of ${this.gene.name}`\n }))\n }\n filterParalogs() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'homology__within_species_paralog',\n fq_value: this.gene._id,\n name: `Paralogs of ${this.gene.name}`\n }))\n }\n searchSupertree() {\n this.props.doReplaceGrameneFilters(suggestionToFilters({\n category: 'Gene Tree',\n fq_field: 'supertree_attr_s',\n fq_value: this.gene.homology.supertree,\n name: this.gene.homology.supertree\n }))\n }\n orthologList() {\n return this.orthoParaList('ortholog');\n }\n\n paralogList() {\n return this.orthoParaList('within_species_paralog');\n }\n\n orthoParaList(type) {\n var homology, thisGeneId;\n homology = _.get(this.gene, 'homology.homologous_genes');\n thisGeneId = this.gene._id;\n\n if (homology) {\n var homologs = _(homology)\n .pickBy(function filterCategories(thing, name) {\n return name.indexOf(type) === 0;\n })\n .values()\n .flatten()\n .uniq()\n .value();\n\n if (!_.isEmpty(homologs)) {\n if (!homologs.includes(thisGeneId)) {\n console.log(\"add to homologs list\",thisGeneId);\n homologs.push(thisGeneId);\n }\n return homologs; // only return something if we have something. We're testing for truthiness later.\n }\n }\n }\n explorations() {\n let x = [{\n name: 'Homologs',\n category: 'Gene Tree',\n count: this.tree.geneCount,\n handleClick: this.filterAllHomologs.bind(this)\n }];\n if (this.orthologs) {\n x.push({\n name: 'Orthologs',\n category: 'Gene Tree',\n count: this.orthologs.length,\n handleClick: this.filterOrthologs.bind(this)\n });\n }\n if (this.paralogs) {\n x.push({\n name: 'Paralogs',\n category: 'Gene Tree',\n count: this.paralogs.length,\n handleClick: this.filterParalogs.bind(this)\n });\n }\n if (this.gene.homology.supertree) {\n x.push({\n name: `Supertree`,\n category: `Gene Tree`,\n count: this.gene.homology.supertree,\n handleClick: this.searchSupertree.bind(this)\n })\n }\n return x;\n }\n links() {\n let links = [\n {\n name: 'Ensembl Gene Tree view',\n url: `${this.props.configuration.ensemblURL}/${this.gene.system_name}/Gene/Compara_Tree?g=${this.gene._id}`\n }\n ];\n if (this.props.curation && this.props.curation.taxa.hasOwnProperty(this.gene.taxon_id)) {\n links.push({\n name: 'Curate',\n url: this.props.curation.url + this.gene._id\n })\n }\n return links;\n }\n render() {\n const id = this.props.searchResult.id;\n if (!this.props.geneDocs.hasOwnProperty(id)) {\n return <Spinner/>\n }\n this.gene = this.props.geneDocs[id];\n const treeId = this.gene.homology.gene_tree.id;\n if (! this.props.grameneTrees.hasOwnProperty(treeId)) {\n this.props.doRequestGrameneTree(treeId);\n }\n else {\n const tree = this.props.grameneTrees[treeId];\n if (tree.hasOwnProperty('taxon_id')) {\n this.tree = treesClient.genetree.tree([this.props.grameneTrees[treeId]]);\n this.orthologs = this.orthologList();\n this.paralogs = this.paralogList();\n }\n }\n let flagged=0;\n // if (this.props.curation && this.props.curation.taxa.hasOwnProperty(this.gene.taxon_id)) {\n // flagged = this.props.curatedGenes && this.props.curatedGenes[id] ? this.props.curatedGenes[id].flagged : 0;\n // }\n return (\n <Detail>\n <Title key=\"title\">Compara Gene Tree</Title>\n <Description key=\"description\">\n This phylogram shows the relationships between this gene and others similar to it, as determined by Ensembl Compara.\n {flagged > 1 && <Alert variant={'warning'}>This gene was flagged for potential gene structural annotation issues by {flagged} curators</Alert>}\n </Description>\n {this.tree && <Content key=\"content\">{this.renderTreeVis()}</Content>}\n {this.tree && <Explore key=\"explore\" explorations={this.explorations()}/>}\n <Links key=\"links\" links={this.links()}/>\n </Detail>\n )\n }\n}\n\nexport default connect(\n 'selectGrameneTaxonomy',\n 'selectGrameneTrees',\n 'selectGrameneGenomes',\n 'selectConfiguration',\n 'selectCuration',\n 'selectCuratedGenes',\n 'doRequestGrameneTree',\n 'doAcceptGrameneSuggestion',\n 'doReplaceGrameneFilters',\n Homology\n);\n\n","import React from 'react';\nimport keyBy from 'lodash/keyBy';\nimport _ from \"lodash\";\nimport ReactGA from \"react-ga4\";\nimport { BiLinkExternal } from \"react-icons/bi\";\nimport { Button, Badge } from \"react-bootstrap\";\n\nexport const Detail = props => {\n let subComponents = keyBy(props.children, 'key');\n return (\n <div className=\"detail\">\n <div className=\"intro\">\n {subComponents.title}\n {subComponents.description}\n </div>\n <div className=\"content-wrapper\">\n {subComponents.content}\n </div>\n <div className=\"actions\">\n <div className=\"action-wrapper\" xs={12} sm={5}>\n {subComponents.explore}\n </div>\n <div className=\"action-wrapper\" xs={12} sm={7}>\n {subComponents.links}\n </div>\n </div>\n </div>\n )\n};\n\nexport const Title = props => <h4>{props.children}</h4>;\nexport const Description = props => <p className=\"description\">{props.children}</p>;\nexport const Content = props => <div className=\"content\">{props.children}</div>;\n\nconst QueryTerm = props => {\n let category, name, badge;\n name = props.name;\n if (props.category) {\n category = props.category + ' \| ';\n }\n if (_.isNumber(props.count)) {\n badge = <Badge style={{marginLeft: \"0.5rem\"}} bg='secondary'>{props.count}</Badge>\n }\n return (\n <Button variant='outline-dark' onClick={props.handleClick}>\n {category}{name}{badge}\n </Button>\n )\n};\n\nfunction renderExplorations(explorations) {\n return explorations.map(\n (exploration, idx) =>\n <QueryTerm key={idx} {...exploration} />\n );\n}\nexport const Explore = props => (\n <div className=\"explore\">\n <h5>Search Filters</h5>\n <div>\n {renderExplorations(props.explorations)}\n </div>\n </div>\n);\n\nfunction renderLinks(links) {\n let external = <small title=\"This link opens a page from an external site\"> <BiLinkExternal/></small>;\n return links.map((link, idx) =>\n <li key={idx}>\n <a href={link.url} target=\"_blank\" className=\"external-link\" onClick={()=>{\n ReactGA.event({\n category: \"outbound link\", action: \"follow\", label: link.name\n })\n }}>{link.name}{external}</a>\n {/<ReactGA.OutboundLink/}\n {/ eventLabel={link.name}/}\n {/ to={link.url}/}\n {/ target=\"_blank\"/}\n {/ className=\"external-link\"/}\n {/>/}\n {/ {link.name}{external}/}\n {/</ReactGA.OutboundLink>/}\n </li>\n )\n}\n\nexport const Links = props => (\n <div className=\"links\">\n <h5>Links to other resources</h5>\n <ul>\n {renderLinks(props.links)}\n </ul>\n </div>\n);\n","import { initializeApp } from \"firebase/app\";\n\nconst firebaseConfig = {\n apiKey: \"AIzaSyCyTJmxfWgfuhI6-8uqocSiE9KOWUlkgkk\",\n authDomain: \"gramene-auth.firebaseapp.com\",\n projectId: \"gramene-auth\",\n storageBucket: \"gramene-auth.appspot.com\",\n messagingSenderId: \"590873346270\",\n appId: \"1:590873346270:web:f76a31a93619e69439824f\"\n};\n\nexport const firebaseApp = initializeApp(firebaseConfig);\n\nexport const suggestionToFilters = (suggestion) => {\n return {\n status: 'init',\n rows: 20,\n operation: 'AND',\n negate: false,\n leftIdx: 0,\n rightIdx: 3,\n children: [\n {\n fq_field: suggestion.fq_field,\n fq_value: suggestion.fq_value,\n name: suggestion.name,\n category: suggestion.category,\n leftIdx: 1,\n rightIdx: 2,\n negate: false,\n marked: false\n }\n ]\n }\n}\n","import React from 'react'\nimport getProp from 'lodash/get';\nimport isEqual from 'lodash/isEqual';\nimport {Button} from \"react-bootstrap\";\nimport Browser from \"./location/browser\";\nimport {connect} from \"redux-bundler-react\";\nimport {Detail, Title, Description, Content, Explore, Links} from \"./generic\";\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/msa.less';\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/tree.less';\n\nclass Location extends React.Component {\n constructor(props) {\n super(props);\n this.gene = this.props.geneDocs[this.props.searchResult.id];\n this.initRegion();\n this.state = {\n visibleRange: this.initVisibleRange()\n };\n }\n\n initVisibleRange() {\n var location, span, padding, result;\n location = this.gene.location;\n if(!location) {\n throw new Error(`Could not find the location of the gene in props.`);\n }\n\n span = location.end - location.start + 1;\n padding = Math.floor(.1 span);\n\n result = {\n chr: location.region,\n start: location.start - padding,\n end: location.end + padding\n };\n\n result.displayName = `${result.chr}:${result.start}-${result.end}`;\n\n return result;\n }\n\n initRegion() {\n var region, isChromosome, regionType, regionName;\n region = this.gene.location.region;\n if (region) {\n isChromosome = /^\\d+$/.test(region);\n if (isChromosome) {\n regionType = 'chromosome';\n regionName = 'Chromosome ' + region;\n }\n else {\n regionType = 'scaffold';\n regionName = region;\n }\n this.region = {\n isChromsome: isChromosome,\n name: regionName,\n type: regionType\n };\n }\n }\n\n\n handleViewChange(chr, start, end) {\n var visibleRange = {\n chr: chr,\n start: start,\n end: end,\n displayName: `${chr}:${start}-${end}`\n };\n\n if(!isEqual(visibleRange, this.state.visibleRange)) {\n this.setState({\n visibleRange: visibleRange\n });\n }\n }\n\n updateQuery(restrictToVisibleRange) {\n var location, geneName, visibleRange, filter, filterDisplayName, fq;\n location = this.gene.location;\n geneName = this.gene.name;\n // category: 'Gene Tree',\n // fq_field: 'gene_tree',\n // fq_value: this.tree._id,\n // name: `Homologs of ${this.gene.name}`\n\n let terms = [\n {\n category: \"Map\",\n name: location.map,\n fq_field: 'map',\n fq_value: location.map\n },\n {\n category: \"Region\",\n name: location.region,\n fq_field: 'region',\n fq_value: location.region\n }\n ];\n fq = `map:${location.map} AND region:${location.region}`;\n\n if (restrictToVisibleRange) {\n visibleRange = this.state.visibleRange;\n\n terms.push({\n category: \"Interval\",\n name: `${visibleRange.start}-${visibleRange.end}`,\n fq_field: 'start',\n fq_value: `[${visibleRange.start} TO ${visibleRange.end}]`\n });\n fq += ` AND (start:[${visibleRange.start} TO ${visibleRange.end}]`\n + ` OR end:[${visibleRange.start} TO ${visibleRange.end}])`;\n\n filterDisplayName = visibleRange.displayName;\n } else {\n filterDisplayName = \"Shares \" + this.region.type + \" with \" + geneName;\n }\n\n console.log(\"User asked to filter by location\");\n filter = {\n category: 'Location',\n id: fq,\n fq: fq,\n display_name: filterDisplayName\n };\n\n // QueryActions.removeAllFilters();\n // QueryActions.setFilter(filter);\n this.props.doAddGrameneRangeQuery(terms);\n if (this.props.closeModal) this.props.closeModal();\n }\n\n explorations() {\n var visible, result;\n visible = this.state.visibleRange;\n result = [\n {\n name: `All on ${this.region.name}`,\n handleClick: ()=>this.updateQuery(false)\n }\n ];\n if (visible) {\n result.push({\n name: `All within ${getProp(visible, 'displayName')}`,\n handleClick: ()=>this.updateQuery(true)\n });\n }\n return result;\n }\n\n links() {\n function jgiify(id) {\n return id.replace('SORBI_3','Sobic.').replace(/\\.v[0-9]\\.[0-9]$/,'');\n }\n var gene = this.gene;\n let links = [\n {name: 'Ensembl Browser', url: `${this.props.config.ensemblURL}/${gene.system_name}/Gene/Summary?g=${gene._id}`}\n ];\n if (gene.annotations.taxonomy.ancestors.includes(4557))\n links.push({name: 'Phytozome', url: `https://phytozome-next.jgi.doe.gov/report/gene/Sbicolor_v5_1/${jgiify(gene._id)}`})\n if (gene.taxon_id === 3702)\n links.push(\n {name: 'tair', url: `https://www.arabidopsis.org/servlets/TairObject?name=${gene._id}&type=locus`},\n {name: 'ThaleMine', url: `https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=${gene._id}&searchSubmit=search`}\n );\n if (gene.taxon_id === 39947)\n links.push({name: 'RAP-DB', url: `https://rapdb.dna.affrc.go.jp/locus/?name=${gene._id}`});\n const isMaize = new RegExp(/^Zm[0-9]+/);\n if (isMaize.test(gene._id))\n links.push({name: 'MaizeGDB', url: `http://www.maizegdb.org/gene_center/gene/${gene._id}`});\n return links;\n }\n\n render() {\n return (\n <Detail>\n {/<Title key=\"title\">Genome location: {this.renderGenePosition()}</Title>/}\n <Description key=\"description\">Currently viewing: {this.renderLocation()} {this.renderResetButton()}</Description>\n <Content key=\"content\">\n {this.renderBrowser()}\n </Content>\n <Explore key=\"explore\" explorations={this.explorations()}/>\n <Links key=\"links\" links={this.links()}/>\n </Detail>\n );\n }\n\n\n renderBrowser() {\n return (\n <Browser gene={this.gene} {...this.props} {...this.state} onViewChange={ this.handleViewChange.bind(this) }/>\n );\n }\n\n renderGenePosition() {\n var location = this.gene.location;\n return (\n <span className=\"location\">\n <span className=\"region\">{this.region.name}</span>:<span className=\"start\">{location.start}</span>-<span\n className=\"end\">{location.end}</span>\n </span>\n );\n }\n\n renderLocation() {\n var location = this.state.visibleRange;\n return (\n <span className=\"location\">\n <span className=\"region\">{location.chr}</span>:<span className=\"start\">{location.start}</span>-<span\n className=\"end\">{location.end}</span>\n </span>\n );\n }\n\n resetVisibleRange() {\n const {chr, start, end} = this.initVisibleRange();\n this.handleViewChange(chr, start, end);\n }\n\n renderResetButton() {\n // let active=isEqual(this.props.visibleRange, this.state.visibleRange);\n return (\n <Button\n size=\"sm\"\n variant=\"outline-dark\"\n onClick={() => this.resetVisibleRange()}>\n Reset\n </Button>\n )\n }\n}\n\nexport default connect('doAddGrameneRangeQuery',Location);\n\n","import React from \"react\";\nimport DallianceBrowser from \"./dallianceBrowser.js\";\n\nexport default class Browser extends React.Component {\n constructor(props) {\n super(props);\n }\n\n render() {\n return (\n <div className=\"location-browser\">\n <DallianceBrowser {...this.props} expanded={!!this.props.closeModal} />\n </div>\n )\n }\n\n}\n\n// Browser.propTypes = {\n// gene: React.PropTypes.object.isRequired,\n// expanded: React.PropTypes.bool,\n// visibleRange: React.PropTypes.object.isRequired,\n// onViewChange: React.PropTypes.func.isRequired\n// };","import React from \"react\";\nimport isEqual from \"lodash/isEqual\";\n\n// var ensemblREST = require('../../../../../package.json').gramene.ensemblREST;\n//const ensemblREST = 'http://data.gramene.org/ensembl63';\n// const ensemblREST = 'https://data.sorghumbase.org/ensembl2';\n// const ensemblREST = 'https://data.gramene.org/vitis-ensembl1';\n// const ensemblREST = 'https://data.gramene.org/pansite-ensembl';\n\n// calculate this once.\nconst PREFIX = '/static/gramene-dalliance/';\n\nexport default class DallianceBrowser extends React.Component {\n\n constructor(props) {\n super(props);\n this.initialVisibleRange = props.visibleRange;\n }\n\n shouldComponentUpdate(newProps) {\n // should we reset the view to initial state?\n if(isEqual(newProps.visibleRange, this.initialVisibleRange)) {\n this.browser.setLocation(newProps.visibleRange.chr, newProps.visibleRange.start, newProps.visibleRange.end);\n }\n\n return false;\n }\n\n biodallianceElementId() {\n return this.props.gene._id + 'Browser';\n }\n\n browser() {\n var g, view, start, end, browser;\n g = this.props.gene;\n view = this.props.visibleRange;\n start = view.start;\n end = view.end;\n\n this.browser = browser = new Browser(\n {\n pageName: this.biodallianceElementId(),\n chr: g.location.region,\n viewStart: start,\n viewEnd: end,\n cookieKey: g._id + 'BrowserCookie',\n prefix: PREFIX,\n\n coordSystem: {\n speciesName: g.system_name,\n taxon: g.taxon_id,\n auth: 'Gramene',\n version: '3',\n ucscName: 'IRGSP-1.0'\n },\n\n sources: [\n {\n name: 'DNA',\n ensemblURI: this.props.config.ensemblRest,\n species: g.system_name,\n tier_type: 'sequence'\n },\n {\n name: 'Genes',\n uri: this.props.config.ensemblRest,\n tier_type: 'ensembl',\n species: g.system_name,\n type: ['gene', 'transcript', 'exon', 'cds']\n }\n ],\n\n // hubs: ['/Track_Hubs/DRP000315/hub.txt'],\n disablePoweredBy: true,\n setDocumentTitle: false,\n noDefaultLabels: true,//!this.props.expanded,\n noPersist: true,\n noPersistView: true,\n maxWorkers: 2,\n noTitle: true,\n noLocationField: false,\n noLeapButtons: true,//!this.props.expanded,\n noZoomSlider: false, //!this.props.expanded,\n noTrackAdder: true,//!this.props.expanded,\n noTrackEditor: true,//!this.props.expanded,\n noExport: true,//!this.props.expanded,\n noOptions: true,//!this.props.expanded,\n noHelp: true,\n maxViewWidth: 1000000\n }\n );\n\n browser.addViewListener(this.props.onViewChange);\n }\n\n cancel() {\n if (typeof this.timeoutID == \"number\") {\n window.clearTimeout(this.timeoutID);\n delete this.timeoutID;\n }\n }\n\n componentDidMount() {\n // this.browser();\n this.cancel();\n var self = this;\n this.timeoutID = window.setTimeout(function () {self.browser();}, 0);\n }\n\n componentWillUnmount() {\n this.cancel();\n }\n\n render() {\n return (\n <div id={this.biodallianceElementId()}/>\n );\n }\n}\n\n// DallianceBrowser.propTypes = {\n// gene: React.PropTypes.object.isRequired,\n// visibleRange: React.PropTypes.object.isRequired,\n// expanded: React.PropTypes.bool,\n// onViewChange: React.PropTypes.func.isRequired\n// };\n","import React from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport FlatToNested from 'flat-to-nested';\nimport {Explore, Links} from \"./generic\";\nimport treesClient from \"gramene-trees-client\";\n// import {TreeMenu} from \"react-tree-menu\";\nimport TreeMenu from \"react-simple-tree-menu\";\nimport '../../../../node_modules/react-simple-tree-menu/dist/main.css';\n\nimport {Spinner} from \"react-bootstrap\";\nimport _ from 'lodash'\nimport \"./tree-view.css\"\n\nvar reactomeURL = \"https://plantreactome.gramene.org\";\n\nclass Pathways extends React.Component {\n constructor(props) {\n super(props);\n this.taxonomy = treesClient.taxonomy.tree(Object.values(props.grameneTaxonomy))\n this.gene = props.geneDocs[props.searchResult.id];\n this.holderId = 'displayHolder' + this.gene._id;\n this.state = {};\n }\n\n initDiagram() {\n this.diagram = Reactome.Diagram.create({\n proxyPrefix: reactomeURL, //'//plantreactome.gramene.org', //'//plantreactomedev.oicr.on.ca', ////cord3084-pc7.science.oregonstate.edu', // reactomedev.oicr.on.ca\n placeHolder: this.holderId,\n width: this.divWrapper.clientWidth - 350 - 1,\n height: 500\n });\n }\n\n stableId(dbId) {\n let prefix = this.taxonomy.indices.id[this.gene.taxon_id].model.reactomePrefix \|\| 'OSA';\n return `R-${prefix}-${dbId}`;\n }\n\n loadDiagram(pathwayId, reactionId) {\n if (!this.diagram) this.initDiagram();\n this.diagram.loadDiagram(pathwayId);\n\n this.diagram.onDiagramLoaded(function (loaded) {\n this.loadedDiagram = loaded;\n if (reactionId) {\n this.diagram.selectItem(reactionId);\n }\n // var xref = _.find(this.props.gene.xrefs,{db : 'Gramene_Plant_Reactome'}).ids[0];\n this.diagram.flagItems(this.gene._id);\n }.bind(this));\n }\n\n componentDidMount() {\n if (Reactome && Reactome.Diagram) {\n // this.initDiagram();\n }\n else {\n window.addEventListener('launchDiagram', function (e) {\n // this.initDiagram()\n }.bind(this));\n }\n }\n\n componentDidUpdate(prevProps, prevState) {\n if (this.state.hierarchy && ! this.state.selectedNode) {\n let node = this.state.hierarchy[0];\n let path = [0];\n let parent = node;\n while (node.nodes) {\n path.push(0);\n parent = node;\n node = node.nodes[0];\n }\n console.log(parent,node,path);\n this.loadNodes(path);\n }\n if (!this.state.hierarchy && this.pathwayIds) {\n const haveDocs = this.pathwayIds.filter(id => this.props.gramenePathways.hasOwnProperty(id));\n if (haveDocs.length === this.pathwayIds.length) {\n const docs = this.pathwayIds.map(id => this.props.gramenePathways[id]);\n this.getHierarchy(this.makeTaxonSpecific(docs,this.gene.taxon_id));\n }\n }\n }\n\n componentWillMount() {\n var pathways, reactionId, ancestorIds;\n pathways = this.gene.annotations.pathways;\n if(!pathways) {\n throw new Error(\"No pathway annotation present for \" + this.gene._id);\n }\n\n this.pathwayIds = _.clone(pathways.ancestors);\n pathways.entries.forEach(function(reaction) {\n let [r,speciesCode,id] = reaction.id.split('-');\n\n this.pathwayIds.push(+id);\n }.bind(this));\n\n this.props.doRequestGramenePathways(this.pathwayIds);\n\n // DocActions.needDocs('pathways', this.pathwayIds, (docs) => { return this.makeTaxonSpecific(docs,this.props.gene.taxon_id)}, this.getHierarchy);\n }\n\n makeTaxonSpecific(docs,taxon_id) {\n let lineageField = 'lineage_'+taxon_id;\n if (! docs[0].hasOwnProperty(lineageField)) {\n let tid = Math.floor(taxon_id / 1000);\n lineageField = 'lineage_'+tid;\n }\n let tsDocs = docs.map(function(doc) {\n let tsDoc = _.pick(doc,['_id','name','type']);\n tsDoc.lineage = doc[lineageField];\n return tsDoc;\n });\n console.log(tsDocs);\n return tsDocs;\n }\n\n componentWillUnmount() {\n // DocActions.noLongerNeedDocs('pathways', this.pathwayIds);\n if (this.diagram) this.diagram.detach();\n }\n\n getHierarchy(docs) {\n let pathways = _.keyBy(docs,'_id');\n let nodes = [];\n this.pathwayIds.forEach(function (pwyId) {\n if (pathways[pwyId]) {\n let pwy = pathways[pwyId];\n pwy.lineage.forEach(function(line) {\n let parentOffset = line.length - 2;\n nodes.push({\n id: pwyId,\n key: pwyId,\n label: pwy.name,\n type: pwy.type,\n checkbox: false,\n selected: false,\n parent: parentOffset >=0 ? line[parentOffset] : undefined\n });\n });\n }\n });\n\n let nested = new FlatToNested({\n children: 'nodes'\n }).convert(nodes);\n\n this.setState({hierarchy: [nested], selectedNode: undefined});\n }\n possiblyLoadNodes(node) {\n if (!node.selected) {\n let selectedNode = this.state.selectedNode;\n selectedNode.selected = false;\n node.selected = true;\n selectedNode = node;\n if (node.type === \"Pathway\") {\n let pathway = this.stableId(node.id);\n this.loadDiagram(pathway);\n }\n else {\n let reaction = this.stableId(node.id);\n let pathway = this.stableId(node.parent.split(\"/\").pop());\n if (this.loadedDiagram === pathway) {\n this.diagram.selectItem(reaction);\n }\n else {\n if (this.diagram) this.diagram.resetSelection();\n this.loadDiagram(pathway,reaction);\n }\n }\n this.setState({selectedNode})\n }\n }\n loadNodes(nodes) {\n let hierarchy = this.state.hierarchy;\n let selectedNode = this.state.selectedNode;\n let offset = nodes.shift();\n let nodeRef = hierarchy[offset];\n let lineage = [nodeRef];\n while (nodeRef.nodes) {\n nodeRef = nodeRef.nodes[0];\n lineage.unshift(nodeRef);\n }\n if (lineage[0].id !== 2894885) {\n let pathway = this.stableId(lineage[0].id);\n let reaction = undefined;\n if (lineage[0].type === \"Reaction\") {\n reaction = pathway;\n pathway = this.stableId(lineage[1].id);\n }\n if (lineage[0].selected) {\n selectedNode = undefined;\n lineage[0].selected = false;\n if (this.loadedDiagram === pathway) {\n this.diagram.resetSelection();\n }\n else {\n if (this.diagram) this.diagram.resetSelection();\n this.loadDiagram(pathway);\n }\n }\n else {\n if (selectedNode) {\n selectedNode.selected = false;\n }\n selectedNode = lineage[0];\n lineage[0].selected = true;\n if (this.loadedDiagram === pathway) {\n if (reaction) {\n this.diagram.selectItem(reaction);\n }\n else {\n this.diagram.resetSelection();\n }\n }\n else {\n if (this.diagram) this.diagram.resetSelection();\n if (reaction) {\n this.loadDiagram(pathway, reaction);\n }\n else {\n this.loadDiagram(pathway);\n }\n }\n }\n this.setState({hierarchy: hierarchy, selectedNode: selectedNode});\n }\n }\n\n renderHierarchy() {\n if (this.state.hierarchy) {\n let path = [];\n let allPaths = [];\n let nodes = this.state.hierarchy;\n while (nodes) {\n path.push(nodes[0].key);\n allPaths.push(path.join('/'));\n if (nodes[0].hasOwnProperty('nodes')) {\n nodes = nodes[0].nodes;\n }\n else {\n nodes = undefined;\n }\n }\n // console.log(path);\n return <TreeMenu\n data={this.state.hierarchy}\n hasSearch={false}\n onClickItem={(item) => this.possiblyLoadNodes(item)}\n onClickItemx={(item) => console.log('onClickItem', item)}\n initialActiveKey={path.join('/')}\n initialOpenNodes={allPaths}\n />;\n // return (\n // <TreeMenu\n // data={this.state.hierarchy}\n // expandIconClass=\"fa fa-chevron-right\"\n // collapseIconClass=\"fa fa-chevron-down\"\n // stateful={true}\n // collapsible={true}\n // onTreeNodeClick={this.loadNodes.bind(this)}\n // />\n // );\n }\n return <Spinner/>\n }\n\n updateQuery() {\n console.log(\"User asked to filter by \"+ this.state.selectedNode.type);\n\n this.props.doAcceptGrameneSuggestion({\n category: 'Plant Reactome',\n fq_field: 'pathways__ancestors',\n fq_value: this.state.selectedNode.id,\n name: this.state.selectedNode.label\n })\n }\n\n render() {\n let reactomeLink,searchFilter;\n\n if (this.state.selectedNode) {\n let xrefLUT = _.keyBy(this.gene.xrefs,'db');\n let links = [\n {name: 'Plant Reactome '+this.state.selectedNode.type, url: `${reactomeURL}/content/detail/${this.stableId(this.state.selectedNode.id)}`}\n ];\n if (xrefLUT.hasOwnProperty('notGramene_Plant_Reactome')) {\n links.push({name: 'Plant Reactome Gene', url: `${reactomeURL}/content/detail/${xrefLUT.notGramene_Plant_Reactome.ids[0]}`});\n }\n reactomeLink = <Links key=\"links\" links={links}/>;\n let filters = [\n {\n name: `All genes in this ${this.state.selectedNode.type}`,\n handleClick: ()=>this.updateQuery()\n }\n ];\n searchFilter = <Explore key=\"explore\" explorations={filters}/>;\n }\n return (\n <div ref={(div) => {this.divWrapper = div;}}>\n <div style={{width:350, height: 500, overflow:'scroll', float:'left'}}>{this.renderHierarchy()}</div>\n <div id={this.holderId}/>\n {searchFilter}\n {reactomeLink}\n </div>\n );\n }\n}\n\nexport default connect(\n 'selectGrameneTaxonomy',\n 'selectGramenePathways',\n 'doRequestGramenePathways',\n 'doAcceptGrameneSuggestion',\n Pathways\n);\n","import React, {useState, useEffect, useRef, useCallback} from 'react';\nimport {connect} from \"redux-bundler-react\";\nimport {Button} from 'react-bootstrap';\nimport { AgGridReact } from \"ag-grid-react\";\nimport _ from 'lodash';\nimport \"ag-grid-community/styles/ag-grid.css\";\nimport \"ag-grid-community/styles/ag-theme-quartz.css\";\nimport '@fortawesome/fontawesome-free/css/all.min.css';\nimport \"./VEP.css\";\n\nconst ggURL = {\n xIRRI: 'https://gringlobal.irri.org/gringlobal/accessiondetail?id=',\n IRRI: 'https://www.irri.org/genesys-rice#/a/',\n ARS: 'https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=',\n ICRISAT: 'https://genebank.icrisat.org/IND/PassportSummary?ID=',\n sorbmutdb: 'https://www.depts.ttu.edu/igcast/sorbmutdb.php',\n maizeGDB: 'https://wgs.maizegdb.org/',\n NCBI: 'https://www.ncbi.nlm.nih.gov/biosample/?term='\n};\n\nconst rice_studies = {'1': {label: 'Rice 3K', type: 'NAT'}};\nconst study_info = {\n 'sorghum_bicolor': {\n '1': {label: 'Purdue EMS', type: 'EMS'},\n '2': {label: 'USDA Lubbock EMS', type: 'EMS'},\n '3': {label: 'Lozano', type: 'NAT'},\n '4': {label: 'USDA Lubbock EMS', type: 'EMS'},\n '5': {label: 'Boatwright SAP', type: 'NAT'},\n '7': {label: 'Kumar BAP', type: 'NAT'},\n '8': {label: 'Lasky landraces', type: 'NAT'},\n '9': {label: 'Sorghum Genomics Toolbox', type: 'NAT'}\n },\n 'zea_maysb73': {\n '15': {label: 'MaizeGDB 2024', type: 'NAT'}\n },\n 'oryza_sativa': {\n '7': {label: 'Rice 3K', type: 'NAT'},\n '20': {label: '20K-RGP', type: 'NAT'},\n '29': {label: 'Rice USDA mini core', type: 'NAT'},\n '38': {label: 'RAPDB 2024', type: 'NAT'},\n },\n 'oryza_aus': { '20': {label: '20K-RGP', type: 'NAT'}},\n 'oryza_sativa117425': { '20': {label: '20K-RGP', type: 'NAT'}},\n 'oryza_sativair64rs2': { '20': {label: '20K-RGP', type: 'NAT'}},\n 'oryza_sativamh63': { '20': {label: '20K-RGP', type: 'NAT'}}\n};\nconst AccessionLink = ({germplasm, gene_id}) => {\n const genebank = germplasm.stock_center;\n const url = ggURL[genebank];\n if (germplasm.germplasm_dbid) { // link to stock center\n const germ_id = germplasm.germplasm_dbid;\n if (germ_id && url && germ_id !== \"0\") {\n return <a target=\"_blank\" href={`${url}${germ_id}`}>\n {germplasm.pub_id} ({genebank})</a>;\n }\n }\n if (genebank === \"sorbmutdb\") {\n return (\n <form id={germplasm.pub_id} action={url} method=\"post\" target=\"_blank\">\n <input type=\"hidden\" name=\"search\" value={gene_id.replace('SORBI_3','Sobic.')} />\n <input type=\"hidden\" name=\"submit\" value=\"Search\" />\n <button type=\"submit\" className=\"button-like-link\">SorbMutDB</button>\n </form>\n );\n }\n if (germplasm.pop_id === '15' && germplasm.stock_center === 'NOT FOUND') {\n return <a target=\"_blank\" href={ggURL['maizeGDB']}>{germplasm.pub_id} (SNPVersity)</a>\n }\n return <span>{germplasm.pub_id}</span>\n}\nfunction compareGermplasm(a, b) {\n const aSub = a?.germplasm?.subpop ?? '';\n const bSub = b?.germplasm?.subpop ?? '';\n const subCmp = aSub.localeCompare(bSub, 'en', { sensitivity: 'accent' });\n if (subCmp !== 0) return subCmp;\n\n const aPub = a?.germplasm?.pub_id ?? '';\n const bPub = b?.germplasm?.pub_id ?? '';\n return aPub.localeCompare(bPub, 'en', { sensitivity: 'accent' });\n}\nfunction group_germplasm(gene, germplasmLUT, vep_obj) {\n let accessionTable = [];\n Object.entries(vep_obj).forEach(([key,accessions]) => {\n const parts = key.split(\"__\");\n if (parts[0] === \"VEP\") {\n if (parts[1] !== \"merged\") {\n accessions.filter(ens_id => germplasmLUT.hasOwnProperty(ens_id)).forEach(ens_id => {\n const germplasm = germplasmLUT[ens_id][0];\n const pop = study_info[parts[3]][parts[4]];\n const conseq = parts[1].replaceAll(\"_\",\" \");\n const status = parts[2] === \"het\" ? \"heterozygous\" : \"homozygous\";\n const accInfo = {\n key: [pop.label,conseq,status].join('%%%'),\n germplasm: germplasm,\n pop: pop\n };\n accessionTable.push(accInfo);\n });\n }\n }\n });\n // group accessionTable by key field\n const groups = _.groupBy(accessionTable, 'key');\n let grouped = [];\n let id=0;\n Object.keys(groups).sort().forEach((group) => {\n const [pop,conseq,status] = group.split('%%%');\n id++;\n const tally = groups[group].length;\n grouped.push({\n id: id,\n group: group,\n summary: true,\n pop: pop,\n conseq: conseq,\n status: status,\n tally: tally\n });\n groups[group].sort(compareGermplasm).forEach(acc => {\n id++;\n grouped.push({\n id: id,\n group: group,\n summary: false,\n pop:pop,\n conseq: conseq,\n status: status,\n accession: acc,\n tally: tally\n })\n })\n })\n return grouped;\n}\nconst THRESHOLD = 5;\nconst GridWithGroups = ({groups,gene_id,doGrin}) => {\n const [rowData, setRowData] = useState(groups);\n\n const initialExpanded = {};\n rowData.forEach((row) => {\n if (row.summary) {\n initialExpanded[row.group] = (row.tally < THRESHOLD);\n }\n });\n const [expandedGroups, setExpandedGroups] = useState(initialExpanded);\n\n\n // Toggle group visibility\n const toggleGroup = (group) => {\n setExpandedGroups((prevExpandedGroups) => ({\n ...prevExpandedGroups,\n [group]: !prevExpandedGroups[group], // Toggle the group's state\n }));\n };\n\n // Filter the data to show/hide rows based on the expanded group state\n const getVisibleRowData = () => {\n const visibleRows = [];\n rowData.forEach((row) => {\n if (row.summary) {\n if (row.tally > 1) {\n visibleRows.push(row);\n }\n } else if (expandedGroups[row.group]) {\n visibleRows.push(row); // Show non-summary rows if the group is expanded\n }\n });\n return visibleRows;\n };\n\n // Define columns with a custom renderer for the summary rows\n const columnDefs = [\n { field: 'pop', headerName: 'Study/Population', flex: 1,\n cellRenderer: (params) => {\n if (params.data.summary \|\| params.data.tally === 1) {\n return params.value;\n }\n return null;\n }\n },\n { field: 'conseq', headerName: 'VEP consequence', flex: 1,\n cellRenderer: (params) => {\n if (params.data.summary \|\| params.data.tally === 1) {\n return params.value;\n }\n return null;\n }\n },\n { field: 'status', headerName: 'Allele status', flex: 1,\n cellRenderer: (params) => {\n if (params.data.summary \|\| params.data.tally === 1) {\n return params.value;\n }\n return null;\n }\n },\n { field: 'accession', headerName: doGrin ? 'Order Germplasm' : 'Accession', flex: 1,\n headerComponent: (props) => {\n return (\n <div style={{display: 'flex', alignItems: 'center'}}>\n {doGrin && <i className=\"fas fa-shopping-cart\"> </i>}\n <span>{props.displayName}</span>\n </div>\n );\n }, // Use the custom header with the shopping cart icon\n cellRenderer: (params) => {\n if (params.value) {\n return <AccessionLink germplasm={params.value.germplasm} gene_id={gene_id} />;\n }\n if (params.data.summary) {\n return (\n <span\n onClick={() => toggleGroup(params.data.group)}\n >\n {params.data.tally} Accessions {expandedGroups[params.data.group] ? '▼' : '▶'}\n </span>\n );\n }\n return null;\n }\n },\n { field: 'synonym', headerName: 'Synonym', filter:false, sortable:false, flex: 1, cellRenderer: (params) => {\n if (params.data.accession) {\n return params.data.accession.germplasm.ens_id\n }\n return null;\n }},\n { field: 'subpop', headerName: 'Subpopulation', filter:false, sortable: false, flex: 1, cellRenderer: (params) => {\n if (params.data.accession && params.data.accession.germplasm.subpop && params.data.accession.germplasm.subpop !== \"?\") {\n return params.data.accession.germplasm.subpop\n }\n return null;\n }},\n { field: 'search', headerName: 'All LOF Genes', sortable:false, filter:false, flex: 1,\n cellRenderer: (params) => {\n if (params.data.accession) {\n const currentURL = new URL(window.location.href);\n const accession = params.data.accession;\n currentURL.search = '';\n currentURL.searchParams.set('category', 'Germplasm');\n currentURL.searchParams.set('fq_field', `VEP__merged__${accession.pop.type}__attr_ss`);\n currentURL.searchParams.set('fq_value', accession.germplasm.ens_id);\n currentURL.searchParams.set('name', accession.germplasm.ens_id);\n\n return <Button size='sm' href={currentURL.toString()}>Search</Button>\n\n }\n return null;\n }\n }\n ];\n\n const defaultColDef = {\n sortable: true,\n filter: \"agTextColumnFilter\",\n cellStyle: (params) => {\n if (params.data.summary) {\n return {cursor: 'pointer'};\n }\n return null;\n }\n };\n\n const nVisible = getVisibleRowData().length;\n const tableHeight = 50 + Math.min(nVisible, 10) * 42;\n return (\n <div\n className=\"ag-theme-quartz\"\n style={{ height: tableHeight, width: \"100%\", maxWidth: \"1200px\" }}\n >\n <AgGridReact\n rowData={getVisibleRowData()}\n columnDefs={columnDefs}\n getRowNodeId={(data) => data.id}\n animateRows={true}\n defaultColDef={defaultColDef}\n />\n </div>\n );\n};\n\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n if (props.grameneConsequences && props.grameneConsequences[gene._id] && props.grameneGermplasm) {\n const groups = group_germplasm(gene, props.grameneGermplasm, props.grameneConsequences[gene._id]);\n\n return <div>\n <h5>Predicted loss-of-function alleles were detected in these germplasm.</h5>\n <div >Explore other variants within this gene in the <a target=\"_blank\"\n href={`${props.configuration.ensemblURL}/${gene.system_name}/Gene/Variation_Gene/Image?db=core;g=${props.searchResult.id}`}>\n Variant image</a> page in the Ensembl genome browser.</div>\n <GridWithGroups groups={...groups} gene_id={gene._id} doGrin={!props.configuration.hasOwnProperty('noGRIN')}/>\n </div>\n } else {\n props.doRequestVEP(gene._id);\n return <pre>loading</pre>;\n }\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGrameneConsequences',\n 'selectGrameneGermplasm',\n 'doRequestVEP',\n Detail\n);\n\n","import React from 'react'\nimport ReactGA from 'react-ga4'\n// import {connect} from \"redux-bundler-react\";\nimport _ from 'lodash'\nimport dbxrefs from 'gramene-dbxrefs';\nimport {Detail, Title, Description, Content} from \"./generic\";\n\nconst HOW_MANY_TO_SHOW_BY_DEFAULT = 10;\n\nclass Xref extends React.Component {\n constructor(props) {\n super(props);\n this.state = {showAll: false};\n }\n\n toggleShowAll() {\n this.setState({showAll: !this.state.showAll});\n }\n\n possiblyTruncateList(vals) {\n var ellipsis, ellipsisChar, ellipsisTitle;\n\n if (vals.length > HOW_MANY_TO_SHOW_BY_DEFAULT) {\n if (this.state.showAll) {\n ellipsisChar = '^ show first ' + HOW_MANY_TO_SHOW_BY_DEFAULT;\n ellipsisTitle = 'Show less';\n }\n else {\n ellipsisChar = '… show all (' + (vals.length - HOW_MANY_TO_SHOW_BY_DEFAULT) + ' more)';\n ellipsisTitle = 'Show more';\n vals = vals.slice(0, HOW_MANY_TO_SHOW_BY_DEFAULT);\n }\n\n ellipsis = (\n <li key=\"showMore\" className=\"showAll\">\n <a title={ellipsisTitle} onClick={this.toggleShowAll.bind(this)}>{ellipsisChar}</a>\n </li>\n );\n\n vals.push(ellipsis);\n }\n\n return vals;\n }\n\n render() {\n var db = this.props.xref.label;\n var urlfcn = this.props.xref.url;\n\n var members = this.props.members.sort();\n\n var vals = members.map(function (item, idx) {\n var url = urlfcn(item),\n liClass = idx < HOW_MANY_TO_SHOW_BY_DEFAULT ? \"default\" : \"extra\";\n let external = <small title=\"This link opens a page from an external site\"> <i className=\"fa fa-external-link\"/></small>;\n return (\n <li key={idx} className={liClass}>\n <a href={url} target=\"_blank\" onClick={()=>{\n ReactGA.event({\n category: \"outbound link\", action: \"follow\", label: item\n })\n }}>{item}{external}</a>\n {/<ReactGA.OutboundLink/}\n {/* eventLabel={db}/}\n {/ to={url}/}\n {/ target=\"_blank\"/}\n {/>/}\n {/ {item}{external}/}\n {/</ReactGA.OutboundLink>/}\n </li>\n )\n })\n\n vals = this.possiblyTruncateList(vals);\n\n return (\n <tr>\n <td className=\"xref-name-col\">{db}</td>\n <td className=\"xref-value-col\">\n <ol className=\"xref-id-list\">{vals}</ol>\n </td>\n </tr>\n );\n }\n}\n\nfunction formatXrefsForGene(gene) {\n if(!gene \|\| !_.isArray(gene.xrefs)) {\n throw new Error(\"No xrefs for \" + _.get(gene._id));\n }\n return gene.xrefs\n .filter(xr => dbxrefs.isKnown(xr.db) && xr.db !== \"PUBMED\")\n .sort()\n .map((xr,idx) => {\n var xref = dbxrefs.fetch(xr.db);\n return (\n <Xref key={idx} xref={xref} members={xr.ids} source={xr.source} text={xr.text} />\n )\n })\n}\n\nconst Xrefs = ({searchResult, geneDocs}) => (\n <Detail>\n <Title key=\"title\">Cross-references</Title>\n <Description key=\"description\">References to this gene in other databases:</Description>\n <Content key=\"content\">\n <table className=\"xrefs table\">\n <thead>\n <tr>\n <th className=\"xref-name-col\">Database</th>\n <th className=\"xref-value-col\">IDs and links</th>\n </tr>\n </thead>\n <tbody>\n {formatXrefsForGene(geneDocs[searchResult.id])}\n </tbody>\n </table>\n </Content>\n </Detail>\n);\n\nexport default Xrefs;\n\n","import React from 'react'\nimport ReactGA from 'react-ga4'\n// import {connect} from \"redux-bundler-react\";\nimport _ from 'lodash'\nimport dbxrefs from 'gramene-dbxrefs';\nimport {Detail, Title, Description, Content} from \"./generic\";\n\nconst HOW_MANY_TO_SHOW_BY_DEFAULT = 10;\n\nclass Xref extends React.Component {\n constructor(props) {\n super(props);\n this.state = {showAll: false};\n }\n\n toggleShowAll() {\n this.setState({showAll: !this.state.showAll});\n }\n\n possiblyTruncateList(vals) {\n var ellipsis, ellipsisChar, ellipsisTitle;\n\n if (vals.length > HOW_MANY_TO_SHOW_BY_DEFAULT) {\n if (this.state.showAll) {\n ellipsisChar = '^ show first ' + HOW_MANY_TO_SHOW_BY_DEFAULT;\n ellipsisTitle = 'Show less';\n }\n else {\n ellipsisChar = '… show all (' + (vals.length - HOW_MANY_TO_SHOW_BY_DEFAULT) + ' more)';\n ellipsisTitle = 'Show more';\n vals = vals.slice(0, HOW_MANY_TO_SHOW_BY_DEFAULT);\n }\n\n ellipsis = (\n <li key=\"showMore\" className=\"showAll\">\n <a title={ellipsisTitle} onClick={this.toggleShowAll.bind(this)}>{ellipsisChar}</a>\n </li>\n );\n\n vals.push(ellipsis);\n }\n\n return vals;\n }\n\n render() {\n var db = this.props.xref.label;\n var urlfcn = this.props.xref.url;\n\n var members = this.props.members.sort();\n\n var vals = members.map(function (item, idx) {\n var url = urlfcn(item),\n liClass = idx < HOW_MANY_TO_SHOW_BY_DEFAULT ? \"default\" : \"extra\";\n let external = <small title=\"This link opens a page from an external site\"> <i className=\"fa fa-external-link\"/></small>;\n return (\n <li key={idx} className={liClass}>\n <a href={url} target=\"_blank\" onClick={()=>{\n ReactGA.event({\n category: \"outbound link\", action: \"follow\", label: item\n })\n }}>{item}{external}</a>\n {/<ReactGA.OutboundLink/}\n {/ eventLabel={db}/}\n {/ to={url}/}\n {/ target=\"_blank\"/}\n {/>/}\n {/ {item}{external}/}\n {/</ReactGA.OutboundLink>/}\n </li>\n )\n })\n\n vals = this.possiblyTruncateList(vals);\n\n return (\n <tr>\n {/<td className=\"xref-name-col\">{db}</td>/}\n <td className=\"xref-value-col\">\n <ol className=\"xref-id-list\">{vals}</ol>\n </td>\n <td className=\"xref-name-col\">{this.props.source}</td>\n <td className=\"xref-value-col\">{this.props.text}</td>\n </tr>\n );\n }\n}\n\nfunction formatPubsForGene(gene) {\n if(!gene \|\| !_.isArray(gene.xrefs)) {\n throw new Error(\"No xrefs for \" + _.get(gene._id));\n }\n let pubs = gene.xrefs.filter(xr => xr.db === \"PUBMED\");\n if (pubs.length === 0) {\n return <tr><td colSpan={3}>No publications found.</td></tr>\n }\n return pubs.sort((a,b) => {\n if (a.source) {\n if (b.source) {\n if (a.source < b.source) {\n return -1;\n }\n if (a.source > b.source) {\n return 1;\n }\n }\n else {\n return -1;\n }\n }\n else if (b.source) {\n return 1;\n }\n if (a.db < b.db) {\n return -1;\n }\n if (a.db > b.db) {\n return 1;\n }\n return 0;\n })\n .map((xr,idx) => {\n var xref = dbxrefs.fetch(xr.db);\n return (\n <Xref key={idx} xref={xref} members={xr.ids} source={xr.source} text={xr.text} />\n )\n })\n}\nconst formURL = 'https://docs.google.com/forms/d/e/1FAIpQLSey-xPyTysdd9c2phXT6kcbjEDeCppG4dLG7LjZCeLpx_KGog/viewform?usp=pp_url&entry.1266455249=';\nconst Publications = ({searchResult, geneDocs}) => (\n <Detail>\n <Title key=\"title\">Curated publications</Title>\n <Description key=\"description\">Functions described in the literature:</Description>\n <Content key=\"content\">\n <table className=\"xrefs table\">\n <thead>\n <tr>\n <th className=\"xref-10-col\">PubMed link</th>\n <th className=\"xref-10-col\">Curation source</th>\n <th className=\"xref-80-col\">Title/Description</th>\n </tr>\n </thead>\n <tbody>\n {formatPubsForGene(geneDocs[searchResult.id])}\n </tbody>\n <tfoot>\n <tr>\n <th colSpan={3}>Submit a gene function <a target=\"_blank\" href={formURL + searchResult.id}>here</a></th>\n </tr>\n </tfoot>\n </table>\n </Content>\n </Detail>\n);\n\nexport default Publications;\n\n","import React, { useState, useEffect } from 'react';\nimport {connect} from \"redux-bundler-react\";\nimport {Tabs, Tab, Form, Container, Row, Col, ToggleButton, ButtonGroup } from 'react-bootstrap';\nimport { AiOutlineCopy } from 'react-icons/ai';\nimport './sequences.css';\nimport keyBy from \"lodash/keyBy\";\n\nconst CodeBlock = props => {\n const plainFasta = `>${props.id}\\n${props.seq}`\n\n const [showNotification, setShowNotification] = useState(false);\n\n const copyCode = () => {\n // Use the Clipboard API to write text to the clipboard\n navigator.clipboard.writeText(plainFasta)\n .then(() => {\n setShowNotification(true);\n })\n .catch((err) => {\n console.error('Unable to copy to clipboard', err);\n });\n };\n\n useEffect(() => {\n if (showNotification) {\n const notificationTimeout = setTimeout(() => {\n setShowNotification(false);\n }, 2000); // Hide the notification after 2 seconds\n\n return () => clearTimeout(notificationTimeout);\n }\n }, [showNotification]);\n\n return (\n <div className=\"fasta-container\">\n <code className=\"fasta\"><span className=\"header\">>{props.id}</span><br/>{\n props.blocks.map((block,idx) =>\n <span key={idx} className={block.kind}>{block.seq}</span>\n )\n }</code>\n <p className=\"fasta-key\">\n <b>Key:</b> 5'UTR \n <span className=\"square-utr5\">  </span>\n  CDS \n <span className=\"square-cds\">  </span>\n  3'UTR \n <span className=\"square-utr3\">  </span>\n </p>\n <button className=\"copy-button\" onClick={copyCode}><AiOutlineCopy /></button>\n {showNotification && <div className=\"notification\">Sequence copied</div>}\n </div>\n );\n};\n\nconst decoratePeptide = (seq, transcript) => {\n let junctions = [];\n if (transcript.exon_junctions) {\n transcript.exon_junctions.forEach((ej, idx) => {\n if (ej > transcript.cds.start && ej <= transcript.cds.end) {\n junctions.push(Math.floor((ej - transcript.cds.start) / 3));\n }\n });\n }\n if (junctions.length === 0) {\n return [{kind:'cds', seq:seq}];\n }\n let offset = 0;\n let blocks = [];\n junctions.forEach((j, idx) => {\n let kind = idx % 2 === 0 ? \"cds\" : \"cds-other\";\n blocks.push({kind: kind, seq: seq.substring(offset, j)});\n offset = j;\n });\n blocks.push({kind: junctions.length % 2 === 0 ? \"cds\" : \"cds-other\", seq: seq.substring(junctions.pop())});\n return blocks;\n}\nconst decorateSeq = (geneSeq, gene, up, down, tid, mode) => {\n // return a list of blocks with kind and seq properties\n let blocks = [];\n const transcript = gene.gene_structure.transcripts.find(tr => tr.id === tid);\n const offset = gene.location.strand === 1\n ? gene.location.start - geneSeq.start\n : geneSeq.end - gene.location.end\n if (up > 0) {\n const TSS = gene.gene_structure.exons.find(exon => exon.id === transcript.exons[0]).start;\n blocks.push({\n kind:'upstream',\n seq: geneSeq.seq.substring(offset - up + TSS - 1, offset + TSS - 1).toLowerCase()\n })\n }\n // add exons and introns based on tid\n let pos_in_transcript = 0;\n let pos_in_gene = 0;\n let blockType = 'utr5';\n let extra = '';\n transcript.exons.forEach((eid, e_idx) => {\n const exon = gene.gene_structure.exons.find(exon => exon.id === eid);\n if (e_idx > 0 && mode === \"dna\") {\n blocks.push({\n kind: 'intron',\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + exon.start - 1).toLowerCase()\n });\n pos_in_gene = exon.start-1;\n }\n if (mode === \"rna\") {\n extra = e_idx % 2 === 1 ? '-other' : '';\n }\n let exon_length = exon.end - exon.start + 1;\n if (transcript.cds && pos_in_transcript < transcript.cds.start && pos_in_transcript + exon_length >= transcript.cds.start) {\n // CDS starts in this exon\n const utr5_len = transcript.cds.start - pos_in_transcript - 1;\n if (utr5_len > 0) {\n blocks.push({\n kind: blockType + extra,\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + utr5_len)\n });\n exon_length -= utr5_len;\n pos_in_gene += utr5_len;\n pos_in_transcript = transcript.cds.start - 1;\n }\n blockType = 'cds';\n }\n if (blockType === 'cds' && pos_in_transcript + exon_length >= transcript.cds.end) {\n // CDS ends in this exon\n const cds_len = transcript.cds.end - pos_in_transcript;\n if (cds_len > 0) {\n blocks.push({\n kind: blockType + extra,\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + cds_len)\n });\n exon_length -= cds_len;\n pos_in_gene += cds_len;\n pos_in_transcript = transcript.cds.end;\n }\n blockType = 'utr3';\n }\n if (exon_length > 0) {\n blocks.push({\n kind: blockType + extra,\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + exon_length)\n })\n }\n pos_in_gene = exon.end;\n pos_in_transcript += exon_length;\n })\n // check if there's more to the gene locus after end of transcript?\n // downstream is currently relative to end of transcript but upstream is relative to first TSS\n if (down > 0) {\n blocks.push({\n kind:'downstream',\n seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + down).toLowerCase()\n })\n }\n return blocks;\n};\nconst buildId = (gene, geneSeq, up, down) => {\n let gs = gene.location.strand === 1 ? gene.location.start - up : gene.location.start - down;\n let ge = gene.location.strand === 1 ? gene.location.end + down : gene.location.end + up;\n let extras = [];\n if (gene.location.strand === -1) {\n extras.push('reverse')\n }\n if (up > 0) {\n extras.push(`upstream=${up}`)\n }\n if (down > 0) {\n extras.push(`downstream=${down}`)\n }\n return `${geneSeq.genome}\|${gene._id}\|${gene.location.region}:${gs}..${ge} ${extras.join('\|')}`\n};\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n const [tab, setTab] = useState('dna');\n const [upstream, setUpstream] = useState(0);\n const [downstream, setDownstream] = useState(0);\n const [tid, setTid] = useState(gene.gene_structure.canonical_transcript);\n let geneSeq;\n let rnaSeq;\n let pepSeq;\n if (props.geneSequences && props.geneSequences[gene._id]) {\n geneSeq = props.geneSequences[gene._id];\n }\n else {\n props.doRequestGeneSequence(gene)\n return <pre>loading</pre>;\n }\n if (props.rnaSequences && props.rnaSequences[tid]) {\n rnaSeq = props.rnaSequences[tid]\n }\n else {\n props.doRequestRnaSequence(tid, gene)\n return <pre>loading</pre>;\n }\n const maxUp = gene.location.strand === 1 ? gene.location.start - geneSeq.start : geneSeq.end - gene.location.end;\n const maxDown = gene.location.strand === -1 ? gene.location.start - geneSeq.start : geneSeq.end - gene.location.end;\n const transcript = gene.gene_structure.transcripts.find(tr => tr.id === tid);\n let tl_id;\n if (transcript.translation) {\n tl_id = transcript.translation.id;\n if (props.pepSequences && props.pepSequences[tl_id]) {\n pepSeq = props.pepSequences[tl_id];\n }\n else {\n props.doRequestPepSequence(tl_id, gene);\n return <pre>loading</pre>;\n }\n }\n return <Tabs activeKey={tab}\n onSelect={(k) => setTab(k)}\n >\n <Tab tabClassName=\"dna\" eventKey=\"dna\" title=\"Genomic sequence\">\n <Container style={{ width: '100ch', marginLeft: 0}}>\n <Row>\n <Col><b><i>Show flanking sequence</i></b></Col>\n </Row>\n <Row>\n <Col style={{ maxWidth: '5ch', textAlign: 'right'}}>{upstream}</Col>\n <Col style={{maxWidth: '20ch'}}>\n <Form.Range\n className=\"reverse-slide\"\n value={upstream}\n onChange={(e) => setUpstream(e.target.value)}\n min={0}\n max={maxUp}\n step={10}\n /><div style={{textAlign:'right'}}>Upstream</div>\n </Col>\n <Col style={{maxWidth: '30ch'}}>\n <div className=\"styled-span\">\n <div className=\"vertical-line\"/>\n <div className=\"horizontal-line\"/>\n <span>Transcript (unspliced)</span>\n <div className=\"horizontal-line\"/>\n <div className=\"vertical-line\"/>\n </div>\n </Col>\n <Col style={{maxWidth: '20ch'}}>\n <Form.Range\n value={downstream}\n onChange={(e) => setDownstream(e.target.value)}\n min={0}\n max={maxDown}\n step={10}\n /><div style={{textAlign:'left'}}>Downstream</div>\n </Col>\n <Col style={{ maxWidth: '5ch', textAlign: 'left'}}>{downstream}</Col>\n </Row>\n {gene.gene_structure.transcripts.length > 1 &&\n <Row>\n <Col><b><i>Highlight transcript</i></b><br/>\n <ButtonGroup>{gene.gene_structure.transcripts.sort((a,b) => a.id.localeCompare(b.id)).map((tr, idx) => {\n let v = tr.id === gene.gene_structure.canonical_transcript ? 'primary' : 'secondary';\n if (tr.id !== tid) {\n v = `outline-${v}`\n }\n return <ToggleButton\n variant={v}\n key={idx}\n id={`radio-${idx}`}\n type=\"radio\"\n name={tr.id}\n value={tr.id}\n checked={tr.id === tid}\n onChange={e => setTid(e.currentTarget.value)}\n >{tr.id}</ToggleButton>\n })}</ButtonGroup>\n </Col>\n </Row>\n }\n </Container>\n {geneSeq && <CodeBlock id={buildId(gene,geneSeq,+upstream,+downstream)} seq={geneSeq.seq.substring(maxUp - +upstream, maxUp + gene.location.end - gene.location.start + 1 + +downstream)} blocks={decorateSeq(geneSeq,gene,+upstream,+downstream,tid,\"dna\")}/>}\n </Tab>\n <Tab tabClassName=\"rna\" eventKey=\"rna\" title=\"Transcript sequence\">\n <Container style={{ width: '100ch', marginLeft: 0}}>\n {gene.gene_structure.transcripts.length > 1 &&\n <Row>\n <Col><b><i>Select transcript</i></b><br/>\n <ButtonGroup>{gene.gene_structure.transcripts.sort((a,b) => a.id.localeCompare(b.id)).map((tr, idx) => {\n let v = tr.id === gene.gene_structure.canonical_transcript ? 'primary' : 'secondary';\n if (tr.id !== tid) {\n v = `outline-${v}`\n }\n return <ToggleButton\n variant={v}\n key={idx}\n id={`radio-${idx}`}\n type=\"radio\"\n name={tr.id}\n value={tr.id}\n checked={tr.id === tid}\n onChange={e => setTid(e.currentTarget.value)}\n >{tr.id}</ToggleButton>\n })}</ButtonGroup>\n </Col>\n </Row>\n }\n </Container>\n {geneSeq && <CodeBlock id={tid} seq={rnaSeq.seq} blocks={decorateSeq(geneSeq,gene,0,0,tid,\"rna\")}/>}\n </Tab>\n {gene.biotype === \"protein_coding\" &&\n <Tab tabClassName=\"pep\" eventKey=\"pep\" title=\"Peptide sequence\">\n <Container style={{ width: '100ch', marginLeft: 0}}>\n {gene.gene_structure.transcripts.length > 1 &&\n <Row>\n <Col><b><i>Select transcript</i></b><br/>\n <ButtonGroup>{gene.gene_structure.transcripts.sort((a,b) => a.id.localeCompare(b.id)).map((tr, idx) => {\n let v = tr.id === gene.gene_structure.canonical_transcript ? 'primary' : 'secondary';\n if (tr.id !== tid) {\n v = `outline-${v}`\n }\n return <ToggleButton\n variant={v}\n key={idx}\n id={`radio-${idx}`}\n type=\"radio\"\n name={tr.id}\n value={tr.id}\n checked={tr.id === tid}\n onChange={e => setTid(e.currentTarget.value)}\n >{tr.id}</ToggleButton>\n })}</ButtonGroup>\n </Col>\n </Row>\n }\n </Container>\n {geneSeq && <CodeBlock id={tl_id} seq={pepSeq.seq} blocks={decoratePeptide(pepSeq.seq,transcript)}/>}\n </Tab>}\n </Tabs>\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGeneSequences',\n 'selectRnaSequences',\n 'selectPepSequences',\n 'doRequestGeneSequence',\n 'doRequestRnaSequence',\n 'doRequestPepSequence',\n Detail\n);\n\n","import React from 'react'\nimport { connect } from 'redux-bundler-react'\nimport Vis from \"gramene-search-vis\"\nimport Selection from './selection.js'\nimport '../../../node_modules/gramene-search-vis/styles/main.less';\n\nclass TaxDist extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n collapseEmpties: true\n };\n }\n handleSelection(selections) {\n this.setState({selections})\n }\n handleHighlight(highlight) {\n this.setState({highlight})\n }\n handleFilter() {\n this.setState({selections:null})\n }\n toggleEmpties() {\n this.setState({collapseEmpties: !this.state.collapseEmpties})\n }\n render() {\n let selectedTaxa = {};\n if (this.props.grameneSearch && this.state.collapseEmpties) {\n this.props.grameneSearch.facet_counts.facet_fields.taxon_id.filter((tid,idx) => idx % 2 === 0).forEach(tid => {\n selectedTaxa[tid] = true;\n })\n }\n else {\n selectedTaxa = this.props.grameneGenomes.active\n }\n return (\n <div className=\"results-vis big-vis\">\n {this.props.grameneTaxDist && <button type=\"button\"\n className=\"btn btn-primary btn-sm\"\n onClick={this.toggleEmpties.bind(this)}>\n {this.state.collapseEmpties ? 'Expand' : 'Collapse'} empty branches\n </button>}\n {this.props.grameneTaxDist && <Vis taxonomy={this.props.grameneTaxDist}\n selectedTaxa={selectedTaxa}\n onSelection={this.handleSelection.bind(this)}\n onHighlight={this.handleHighlight.bind(this)}\n />}\n {this.renderSelection()}\n </div>\n );\n }\n renderSelection() {\n if (this.state.selections && this.props.grameneTaxDist) {\n return <Selection taxonomy={this.props.grameneTaxDist}\n selectedTaxa={{}}\n selections={this.state.selections}\n onFilter={this.handleFilter.bind(this)}/>\n }\n }\n}\n\nexport default connect(\n 'selectGrameneTaxDist',\n 'selectGrameneGenomes',\n 'selectGrameneSearch',\n TaxDist\n);\n","import React from 'react';\nimport numeral from 'numeral';\nimport _ from \"lodash\";\n\nimport {Table, Button, Badge} from 'react-bootstrap';\nimport {connect} from \"redux-bundler-react\";\n\nfunction selectionStats(selections, taxonomy) {\n const selectionData = getSelectionData(selections, taxonomy);\n const totalGeneResults = taxonomy.model.results.count;\n const fq = fqFromSelections(selections);\n\n return {\n selectedGenes: selectionData.resultsCount,\n totalGeneResults,\n fq,\n numSelectedBins: selectionData.binsCount,\n proportionGenesSelected: selectionData.resultsCount / totalGeneResults\n }\n}\n\nfunction getSelectionData(selection, taxonomy) {\n return _.reduce(selection, (countAcc, sel) => {\n const bins = taxonomy.getBins(sel.binFrom.idx, sel.binTo.idx);\n countAcc.binsCount += bins.length;\n countAcc.resultsCount += _.reduce(bins, (acc, bin) => acc + bin.results.count, 0);\n return countAcc;\n }, {resultsCount: 0, binsCount: 0});\n}\n\nconst selectionToSolrRange = (sel)=>`[${sel.binFrom.idx} TO ${sel.binTo.idx}]`;\n\nfunction fqFromSelections(selections) {\n const rangeStrings = selections.map(selectionToSolrRange);\n return `fixed_1000__bin:(${rangeStrings.join(' ')})`;\n}\n\nconst Selections = ({selections, taxonomy, doAcceptGrameneSuggestion, onFilter}) => {\n const stats = selectionStats(selections, taxonomy);\n\n const setFilter = () => {\n doAcceptGrameneSuggestion({\n category: 'Selections',\n fq_field: 'fixed_1000__bin',\n fq_value: `(${selections.map(selectionToSolrRange).join(' ')})`,\n name: `${selections.length} region${selections.length === 1 ? '':'s'}`\n });\n onFilter();\n };\n\n const formatProportion = (prop) => '(' + (_.isFinite(prop) ? numeral(prop).format('0.0%') : undefined) + ')';\n\n return (\n <div>\n <Table>\n <tbody>\n <tr>\n <th>Number of selected genes</th>\n <td>{stats.selectedGenes} {formatProportion(stats.proportionGenesSelected)}</td>\n <td><Button size='sm' onClick={setFilter}>selections \|<Badge>{stats.selectedGenes}</Badge></Button>\n </td>\n </tr>\n </tbody>\n </Table>\n </div>\n )\n};\n\nexport default connect(\n 'doAcceptGrameneSuggestion',\n Selections\n);\n","import React from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport {Alert, Container, Row, Card, CardGroup} from 'react-bootstrap'\nimport './genes.css'\n\nconst examples = [\n {\n subsite: {\n maize:1,\n sorghum:1,\n main:1,\n },\n text: \"What are the orthologs of Arabidopsis thaliana's PAD4 gene in Andropogoneae?\",\n filters: {\n status: 'init',\n rows: 20,\n operation: 'AND',\n negate: false,\n leftIdx: 0,\n rightIdx: 5,\n children: [\n {\n fq_field: 'homology__all_orthologs',\n fq_value: 'AT3G52430',\n name: 'Orthologs of PAD4',\n category: 'Gene Tree',\n leftIdx:1,\n rightIdx:2,\n negate: false,\n marked: false\n },\n {\n fq_field: 'taxonomy__ancestors',\n fq_value: 147429,\n name: 'Andropogoneae',\n category: 'Taxonomy',\n leftIdx:3,\n rightIdx:4,\n negate: false,\n marked: false\n }\n ]\n }\n },\n {\n subsite: {\n grapevine:1\n },\n text: \"What are the orthologs of Arabidopsis thaliana's PAD4 gene in rosids?\",\n filters: {\n status: 'init',\n rows: 20,\n operation: 'AND',\n negate: false,\n leftIdx: 0,\n rightIdx: 5,\n children: [\n {\n fq_field: 'homology__all_orthologs',\n fq_value: 'AT3G52430',\n name: 'Orthologs of PAD4',\n category: 'Gene Tree',\n leftIdx:1,\n rightIdx:2,\n negate: false,\n marked: false\n },\n {\n fq_field: 'taxonomy__ancestors',\n fq_value: 71275,\n name: 'rosids',\n category: 'Taxonomy',\n leftIdx:3,\n rightIdx:4,\n negate: false,\n marked: false\n }\n ]\n }\n }\n];\nconst HelpDemo = ({configuration,doReplaceGrameneFilters}) => (\n <Container fluid style={{padding: '40px'}}>\n <Row>\n <h3>Search Features</h3>\n </Row>\n <Row>\n <CardGroup style={{width:'80%'}}>\n <Card style={{'backgroundColor':'#f3f6f5', 'borderColor':'#DDE5E3'}}>\n <Card.Body>\n <Card.Title>Suggestions</Card.Title>\n <Card.Text>Matching terms are provided as you type:</Card.Text>\n <div className='gene-search-pic-sugg'/>\n </Card.Body>\n </Card>\n <Card style={{'backgroundColor':'#f3f6f5', 'borderColor':'#DDE5E3'}}>\n <Card.Body>\n <Card.Title>Visualization</Card.Title>\n <Card.Text>See the distribution of results across all genomes:</Card.Text>\n <div className='gene-search-pic-results'/>\n </Card.Body>\n </Card>\n <Card style={{'backgroundColor':'#f3f6f5', 'borderColor':'#DDE5E3'}}>\n <Card.Body>\n <Card.Title>Gene tree view</Card.Title>\n <Card.Text>Explore evolutionary history of a gene family:</Card.Text>\n <div className='gene-search-pic-genetree'/>\n </Card.Body>\n </Card>\n </CardGroup>\n </Row>\n <Row>\n <h4>For Example</h4>\n </Row>\n <Row>\n <small>\n You can ask sophisticated questions about the genes:<br/>\n <ul>\n {examples.filter(e => !!e.subsite[configuration.id]).map((e,idx) => (\n <li key={idx}><a onClick={() => doReplaceGrameneFilters(e.filters)}>{e.text}</a></li>\n ))}\n </ul>\n </small>\n </Row>\n </Container>\n);\n\nexport default connect(\n 'selectConfiguration',\n 'doReplaceGrameneFilters',\n HelpDemo\n);\n\n","import React from 'react'\nimport { connect } from 'redux-bundler-react'\n\nclass GeneAttribs extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n };\n }\n render() {\n return (\n <div className=\"gramene-attribs\">\n {this.props.grameneGeneAttribs && <pre>hi</pre>}\n </div>\n );\n }\n}\n\nexport default connect(\n 'selectGrameneGeneAttribs',\n GeneAttribs\n);\n","import React from \"react\";\nimport { connect } from 'redux-bundler-react'\nimport { Modal, Button } from \"react-bootstrap\";\n\nclass TaxonomyModal extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n genomes : Object.values(props.grameneMaps).sort((a,b) => a.left_index - b.left_index)\n };\n if (Object.keys(props.grameneGenomes.active).length === 0) {\n this.state.genomes.forEach(g => {\n g.selected = !g.hidden;\n })\n }\n else {\n this.state.genomes.forEach(g => {\n g.selected = !g.hidden && props.grameneGenomes.active[g.taxon_id];\n })\n }\n }\n getSelectedGenomes() {\n let selected = {};\n let notHidden = {};\n let somethingWasSelected = false;\n this.state.genomes.forEach(g => {\n if (!g.hidden) {\n notHidden[g.taxon_id] = true;\n if (g.selected) {\n selected[g.taxon_id] = true;\n somethingWasSelected = true;\n }\n }\n });\n return somethingWasSelected ? selected : notHidden;\n }\n handleChange(e) {\n const idx = +e.target.value;\n let newState = Object.assign({},this.state);\n newState.genomes[idx].selected = !newState.genomes[idx].selected;\n this.setState(newState);\n }\n handleClose() {\n this.props.doUpdateGrameneGenomes(this.getSelectedGenomes())\n }\n selectAll() {\n const genomes = this.state.genomes.map(g => {g.selected = true; return g});\n this.setState({genomes});\n }\n selectNone() {\n const genomes = this.state.genomes.map(g => {g.selected = false; return g});\n this.setState({genomes});\n }\n renderGenomes() {\n return (\n <div>\n {this.state.genomes.map((m,idx) => {\n if(m.hidden) return <></>\n return (\n <div key={idx}>\n <input checked={m.selected}\n onChange={this.handleChange.bind(this)}\n type=\"checkbox\"\n value={idx}\n />\n {' '}{m.display_name}\n </div>\n )\n })}\n <Button onClick={this.handleClose.bind(this)}>Submit</Button>\n </div>\n )\n }\n render() {\n return (\n <Modal\n show={this.props.grameneGenomes.show}\n onHide={this.handleClose.bind(this)}\n size='lg'\n >\n <Modal.Header closeButton>\n <Modal.Title>Select Genomes of Interest</Modal.Title>\n </Modal.Header>\n <Modal.Body>\n <Button variant=\"outline-secondary\" onClick={this.selectAll.bind(this)}>All</Button>{' '}\n <Button variant=\"outline-secondary\" onClick={this.selectNone.bind(this)}>None</Button>\n {this.renderGenomes()}\n </Modal.Body>\n </Modal>\n )\n }\n};\n\nexport default connect(\n 'selectGrameneGenomes',\n 'selectGrameneMaps',\n 'doUpdateGrameneGenomes',\n TaxonomyModal\n)\n","import React, { useState, Suspense } from 'react'\nimport {connect} from \"redux-bundler-react\";\nimport { Accordion, Button } from 'react-bootstrap';\nimport \"./expression.css\";\nconst LazyStudy = React.lazy(() => import('./Study'));\n\nconst StudyList = props => {\n return <Accordion alwaysOpen defaultActiveKey={props.studies.length === 1 ? \"study_0\" : undefined}>\n {props.studies.map((study, idx) => {\n return (\n <Accordion.Item key={idx} eventKey={'study_'+idx}>\n <Accordion.Header>{study.description}</Accordion.Header>\n <Accordion.Body>\n <Suspense fallback={<div>Loading...</div>}>\n <LazyStudy id={study._id}/>\n </Suspense>\n {/<Study id={study._id} />/}\n </Accordion.Body>\n </Accordion.Item>\n )\n })}\n </Accordion>\n};\n\nconst Expression = props => {\n let searchTaxa = {};\n if (props.grameneSearch) {\n const taxon_id_facet = props.grameneSearch.facet_counts.facet_fields.taxon_id;\n taxon_id_facet.filter((tid, idx) => idx % 2 === 0).forEach(tid => searchTaxa[tid] = true);\n }\n const availableTaxa = Object.keys(props.expressionStudies)\n .filter(tid => searchTaxa[tid] \|\| searchTaxa[tid + '001'])\n .sort((a,b) => props.grameneMaps[a + '001'].left_index - props.grameneMaps[b + '001'].left_index);\n return availableTaxa && props.grameneTaxonomy &&\n <div>\n <div>This is where you can launch a component for the selected samples. props.desiredSamples lists them.\n This component can request the data from the API\n organize samples by factor metadata? One big table with all the studies?\n <Button>Show Samples ({Object.keys(props.desiredSamples).length} selected)</Button>\n </div>\n <Accordion alwaysOpen defaultActiveKey={availableTaxa.length === 1 ? \"tax_0\" : undefined}>\n {availableTaxa.map((tid, idx) => {\n const n = props.expressionStudies[tid].length;\n return <Accordion.Item key={idx} eventKey={'tax_'+idx}>\n <Accordion.Header>{props.grameneTaxonomy[tid].name} - {n} {n === 1 ? 'study' : 'studies'}</Accordion.Header>\n <Accordion.Body><StudyList studies={props.expressionStudies[tid]}/></Accordion.Body>\n </Accordion.Item>\n })}\n </Accordion>\n </div>\n};\n\nexport default connect(\n 'selectConfiguration',\n 'selectGrameneSearch',\n 'selectGrameneTaxonomy',\n 'selectGrameneMaps',\n 'selectExpressionStudies',\n 'selectDesiredSamples', // current set of samples to fetch expression data for\n Expression\n);\n","import {connect} from \"redux-bundler-react\";\nimport React, { useEffect, useState } from 'react';\nimport {Table, Form, Button, Alert, Spinner, Container, Row, Col} from 'react-bootstrap';\nimport { firebaseApp } from \"../utils\";\nimport {getAuth, onAuthStateChanged} from \"firebase/auth\";\n\nconst auth = getAuth(firebaseApp);\n\nconst MAX_GENE_IDS = 1000; // Define the maximum number of gene IDs allowed\n\nconst GeneListDisplayComponent = props => {\n const [publicGeneLists, setPublicGeneLists] = useState([]);\n const [privateGeneLists, setPrivateGeneLists] = useState([]);\n const [error, setError] = useState(null);\n const [user, setUser] = useState({});\n onAuthStateChanged(auth, (user) => setUser(user));\n\n const fetchPrivateGeneLists = async () => {\n try {\n const token = await user.getIdToken();\n // Replace this with actual fetch from your backend or storage\n const response = await fetch(`${props.api}/gene_lists?site=${props.site}&isPublic=false`, {\n method: 'GET',\n headers: {\n \"Content-Type\": \"application/json\",\n \"Authorization\": `Bearer ${token}`\n }\n });\n const result = await response.json();\n\n if (response.ok) {\n setError(null);\n setPrivateGeneLists(result); // array of saved gene lists\n } else {\n setError('Error fetching gene lists.');\n }\n } catch (err) {\n setError('Failed to fetch private gene lists. Please try again later.');\n }\n };\n // Fetch saved gene lists from a backend or local storage\n const fetchPublicGeneLists = async () => {\n try {\n // Replace this with actual fetch from your backend or storage\n const response = await fetch(`${props.api}/gene_lists?site=${props.site}&isPublic=true`);\n const result = await response.json();\n\n if (response.ok) {\n setPublicGeneLists(result); // array of saved gene lists\n } else {\n setError('Error fetching gene lists.');\n }\n } catch (err) {\n setError('Failed to fetch gene lists. Please try again later.');\n }\n };\n\n // Fetch data when the component is mounted\n useEffect(() => {\n fetchPublicGeneLists();\n }, []);\n useEffect(() => {\n fetchPrivateGeneLists();\n }, [user]);\n\n return (\n <div className=\"gene-list-display-component\">\n <h4>Saved Gene Lists</h4>\n\n {error && (\n <Alert variant=\"danger\">\n {error}\n </Alert>\n )}\n\n {privateGeneLists.length > 0 && (\n <Table striped bordered hover className=\"mt-4\">\n <thead>\n <tr>\n <th>List Name</th>\n <th>Number of Genes</th>\n <th>Actions</th>\n </tr>\n </thead>\n <tbody>\n {privateGeneLists.map((list, index) => (\n <tr key={index}>\n <td>{list.label}</td>\n <td>{list.hash}</td>\n <td>\n <Button variant=\"info\" onClick={() => viewGeneList(list)}>\n View\n </Button>\n <Button variant=\"danger\" onClick={() => deleteGeneList(props.api, list._id)} className=\"ml-2\">\n Delete\n </Button>\n </td>\n </tr>\n ))}\n </tbody>\n </Table>\n )}\n\n {publicGeneLists.length > 0 ? (\n <Table striped bordered hover className=\"mt-4\">\n <thead>\n <tr>\n <th>List Name</th>\n <th>Number of Genes</th>\n <th>Actions</th>\n </tr>\n </thead>\n <tbody>\n {publicGeneLists.map((list, index) => (\n <tr key={index}>\n <td>{list.label}</td>\n <td>{list.hash}</td>\n <td>\n <Button variant=\"info\" onClick={() => viewGeneList(list)}>\n View\n </Button>\n <Button variant=\"danger\" onClick={() => deleteGeneList(props.api, list._id)} className=\"ml-2\">\n Delete\n </Button>\n </td>\n </tr>\n ))}\n </tbody>\n </Table>\n ) : (\n <Alert variant=\"warning\" className=\"mt-4\">\n No saved gene lists found.\n </Alert>\n )}\n </div>\n );\n};\n\n// Example functions for viewing and deleting lists\nconst viewGeneList = (list) => {\n alert(`Viewing gene list: ${list.name}\\nGenes: ${list.genes.join(', ')}`);\n};\n\nconst deleteGeneList = async (api,listId) => {\n if (window.confirm('Are you sure you want to delete this gene list?')) {\n // Replace with the actual delete request\n try {\n await fetch(`${api}/gene_lists/${listId}`, {\n method: 'DELETE',\n });\n alert('Gene list deleted!');\n // Optionally refetch the updated list\n } catch (err) {\n alert('Failed to delete gene list.');\n }\n }\n};\n\n\nconst GeneListComponent = props => {\n const [geneList, setGeneList] = useState('');\n const [listHash, setListHash] = useState(null);\n const [validationError, setValidationError] = useState([]);\n const [listName, setListName] = useState('');\n const [listIsPublic, setListIsPublic] = useState(false);\n const [validatedList, setValidatedList] = useState([]);\n const [errorMessage, setErrorMessage] = useState('');\n const [loading, setLoading] = useState(false); // New loading state\n const [user, setUser] = useState({});\n onAuthStateChanged(auth, (user) => setUser(user));\n\n // Function to handle gene list input\n const handleGeneListChange = (event) => {\n setGeneList(event.target.value);\n };\n\n // Function to handle drag and drop of gene list\n const handleDrop = (event) => {\n event.preventDefault();\n const geneData = event.dataTransfer.getData('text');\n setGeneList(geneData);\n };\n\n // Function to handle drag over (needed for drop)\n const handleDragOver = (event) => {\n event.preventDefault();\n };\n\n // Function to submit gene list for validation\n const handleSubmit = async () => {\n const geneArray = geneList.split('\\n').filter(Boolean); // Convert the gene list into an array and filter out empty values\n\n if (geneArray.length > MAX_GENE_IDS) {\n setErrorMessage(`You have exceeded the maximum limit of ${MAX_GENE_IDS} gene IDs.`);\n return;\n }\n\n setErrorMessage(''); // Reset error message if validation passes\n setLoading(true); // Set loading state to true to show progress\n\n try {\n const response = await fetch(`${props.api}/gene_lists/validate`, {\n method: 'POST',\n headers: {\n 'Content-Type': 'application/json',\n },\n body: JSON.stringify(geneArray),\n });\n\n const result = await response.json();\n\n if (result.hash) {\n setListHash(result.hash);\n setValidatedList(result.ids);\n setValidationError(result.missing);\n } else {\n // Handle errors from validation\n alert('Error during validation.');\n }\n } catch (error) {\n alert('There was an error with the validation service.',error);\n } finally {\n setLoading(false); // Set loading to false when the request is complete\n }\n };\n\n // Function to save the validated gene list\n const handleSaveList = async () => {\n const queryParams = {\n label: listName,\n hash: listHash,\n site: props.site,\n isPublic: listIsPublic\n };\n const queryString = new URLSearchParams(queryParams).toString();\n\n const token = await user.getIdToken();\n try {\n const response = await fetch(`${props.api}/gene_lists?${queryString}`, {\n method: 'POST',\n headers: {\n \"Content-Type\": \"application/json\",\n \"Authorization\": `Bearer ${token}`\n }\n });\n if (!response.ok) {\n throw new Error('Failed to save list');\n }\n const result = await response.json();\n console.log(result);\n\n } catch (error) {\n console.error(\"There was an problem with fetch\", error)\n }\n };\n\n return (\n <div className=\"gene-list-component\">\n <h4>Gene List Validator</h4>\n\n <Form>\n {/ Input for Gene List /}\n <Form.Group controlId=\"geneList\">\n <Form.Label>Paste or drop your gene list here:</Form.Label>\n <Form.Control\n as=\"textarea\"\n rows={10}\n value={geneList}\n onChange={handleGeneListChange}\n placeholder={`Paste or drop your gene list here (Maximum: ${MAX_GENE_IDS} IDs)`}\n onDrop={handleDrop}\n onDragOver={handleDragOver}\n />\n </Form.Group>\n\n {/ Display error if gene list exceeds limit /}\n {errorMessage && (\n <Alert variant=\"danger\">\n {errorMessage}\n </Alert>\n )}\n\n {/ Button to submit for validation /}\n <Button variant=\"primary\" onClick={handleSubmit}>\n Validate Gene List\n </Button>\n </Form>\n\n {/ Display validation in progress /}\n {loading && (\n <div className=\"validation-summary mt-4\">\n <h3>Validation in Progress...</h3>\n <Spinner animation=\"border\" role=\"status\">\n <span className=\"sr-only\">Validating...</span>\n </Spinner>\n </div>\n )}\n\n\n {/ Display validation summary /}\n {!loading && listHash && (\n <div className=\"validation-summary mt-4\">\n <h3>Validation Summary</h3>\n <Alert variant=\"info\">\n <p>hash: <code>{listHash}</code></p>\n <p>Items Validated: {validatedList.length}</p>\n <p>Items Not Validated: {validationError.length}</p>\n </Alert>\n <ul>\n {validationError.map((errorItem, index) => (\n <li key={index}>{errorItem}</li>\n ))}\n </ul>\n </div>\n )}\n\n {/ Input for saving validated gene list */}\n {!loading && validatedList.length > 0 && (\n <div className=\"save-list mt-4\">\n <Form.Group controlId=\"listName\">\n <Form.Label>Save Validated Gene List</Form.Label>\n <Form.Control\n type=\"text\"\n value={listName}\n onChange={(e) => setListName(e.target.value)}\n placeholder=\"Enter list name\"\n />\n <Form.Check\n type='switch'\n id='listIsPublic'\n label='Public'\n onChange={(e) => setListIsPublic(!listIsPublic)}\n />\n </Form.Group>\n {user ?\n <Button variant=\"success\" onClick={handleSaveList}>\n Save Gene List\n </Button>\n : <Button variant=\"dark\" disabled>Login Required</Button> }\n </div>\n )}\n </div>\n );\n};\n\nconst UserGeneListsComponent = props => {\n return (\n <Container fluid>\n <Row>\n <Col><GeneListComponent api={props.configuration.grameneData} site={props.configuration.id}/></Col>\n <Col><GeneListDisplayComponent api={props.configuration.grameneData} site={props.configuration.id}/></Col>\n </Row>\n </Container>\n )\n}\n\nexport default connect(\n 'selectConfiguration',\n UserGeneListsComponent\n);\n","import React, { useState } from 'react'\nimport { Button, Modal } from 'react-bootstrap'\nimport { connect } from \"redux-bundler-react\";\nimport { firebaseApp } from \"./utils\";\nimport { getAuth, onAuthStateChanged, signOut, GoogleAuthProvider, signInWithPopup } from \"firebase/auth\";\n\nconst auth = getAuth(firebaseApp);\n\nconst provider = new GoogleAuthProvider();\n\nconst Auth = props => {\n const [user, setUser] = useState({});\n onAuthStateChanged(auth, (user) => setUser(user));\n\n function handleLogin() {\n signInWithPopup(auth, provider)\n .then((result) => {\n setUser(result.user)\n }).catch((err) => {\n console.log(err)\n });\n }\n function handleLogout() {\n signOut(auth)\n .then(() => {\n setUser(null);\n }).catch((err) => {\n console.log(err)\n });\n }\n return (\n <div className={props.configuration.id === 'sorghum' ? 'sorghumbase-auth-container': 'gramene-auth-container'}>\n <b>Account</b>\n <div>\n {user\n ? <Button size=\"sm\" variant=\"success\" onClick={handleLogout}>{user.displayName}</Button>\n : <Button size=\"sm\" variant=\"success\" onClick={handleLogin}>Login</Button>\n }\n </div>\n </div>\n )\n}\n\nexport default connect(\n 'selectConfiguration',\n Auth\n)\n"],"names":[],"version":3,"file":"index.js.map"}