gramene-search 1.2.30 → 1.2.31

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 (8) hide show
  1. package/.parcel-cache/2b1c1cd7b577d2ca.txt +2 -2
  2. package/.parcel-cache/data.mdb +0 -0
  3. package/.parcel-cache/lock.mdb +0 -0
  4. package/dist/index.js +2 -2
  5. package/dist/index.js.map +1 -1
  6. package/package.json +1 -1
  7. package/src/components/results/details/Expression.js +1 -1
  8. package/src/components/results/details/location/dallianceBrowser.js +1 -2
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- 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bundles from './bundles';\nimport resultList from './components/resultList';\nimport resultSummary from './components/resultSummary';\nimport suggestions from './components/suggestions';\nimport {Status, Filters, Results, Views} from './components/geneSearchUI';\n\nexport { bundles, resultList, resultSummary, suggestions, Status, Filters, Results, Views };\n","import apiBundles from './api'\nimport filterBundle from './filters'\nimport viewsBundle from './views'\nimport docsBundle from './docs'\nimport genomesBundle from './genomes'\n\nexport default [...apiBundles, docsBundle, filterBundle, viewsBundle, genomesBundle];","import { createAsyncResourceBundle, createSelector } from 'redux-bundler'\nimport _ from 'lodash'\nimport binsClient from \"gramene-bins-client\";\nimport treesClient from \"gramene-trees-client\";\nimport {build} from \"gramene-taxonomy-with-genomes\";\n\nconst facets = [\n \"{!facet.limit='200' facet.mincount='1' key='taxon_id'}taxon_id\",\n \"{!facet.limit='100' facet.mincount='1' key='genetree'}gene_tree\",\n \"{!facet.limit='100' facet.mincount='1' key='pathways'}pathways__ancestors\",\n \"{!facet.limit='100' facet.mincount='1' key='domains'}domain_roots\",\n \"{!facet.limit='-1' facet.mincount='1' key='fixed_1000__bin'}fixed_1000__bin\"\n];\nconst genomesOfInterest = '(taxon_id:2769) OR (taxon_id:3055) OR (taxon_id:3218) OR (taxon_id:3702) OR (taxon_id:3847) OR (taxon_id:4555) OR (taxon_id:4558) OR (taxon_id:4577) OR (taxon_id:13333) OR (taxon_id:15368) OR (taxon_id:29760) OR (taxon_id:39947) OR (taxon_id:55577) OR (taxon_id:88036) OR (taxon_id:214687)';\n\nconst grameneSuggestions = createAsyncResourceBundle( {\n name: 'grameneSuggestions',\n actionBaseType: 'GRAMENE_SUGGESTIONS',\n persist: false,\n getPromise: ({store}) => {\n const t = store.selectSuggestionsQuery();\n const g = store.selectGrameneGenomes();\n return fetch(`${store.selectGrameneAPI()}/suggest?q={!boost b=relevance}name:${t}^3 id:${t}^5 synonym:${t}^2 text:${t}*^1`)\n .then(res => res.json())\n .then(suggestions => {\n if (Object.keys(g.active).length > 0) {\n suggestions.grouped.category.groups.forEach(group => {\n group.doclist.docs.forEach(sugg => {\n sugg.num_genes = 0;\n sugg.taxon_id.forEach((id,idx) => {\n if (g.active[id]) {\n sugg.num_genes += sugg.taxon_freq[idx]\n }\n })\n })\n })\n }\n return suggestions\n })\n }\n});\n\ngrameneSuggestions.reactGrameneSuggestions = createSelector(\n 'selectGrameneSuggestionsShouldUpdate',\n 'selectSuggestionsQuery',\n (shouldUpdate, queryString) => {\n if (shouldUpdate && queryString) {\n return { actionCreator: 'doFetchGrameneSuggestions' }\n }\n }\n);\n\ngrameneSuggestions.selectGrameneSuggestionsStatus = createSelector(\n 'selectGrameneSuggestionsShouldUpdate',\n 'selectGrameneSuggestionsIsLoading',\n 'selectGrameneSuggestionsRaw',\n 'selectSuggestionsQuery',\n (shouldUpdate, isLoading, suggestionsRaw, queryString) => {\n if (!queryString) return '';\n if (shouldUpdate) return 'update needed';\n if (isLoading) return 'loading';\n if (suggestionsRaw) return suggestionsRaw.data.grouped.category.matches + ' terms';\n return 'error';\n }\n);\n\ngrameneSuggestions.selectGrameneSuggestionsReady = createSelector(\n 'selectGrameneSuggestionsStatus',\n (status) => {\n const regex = RegExp('terms$');\n return regex.test(status);\n }\n);\n\ngrameneSuggestions.doFocusFirstGrameneSuggestion = arg => ({dispatch, getState}) => {\n console.log('inside doFocusFirstGrameneSuggestion');\n};\n\nconst grameneTaxonomy = createAsyncResourceBundle({\n name: 'grameneTaxonomy',\n actionBaseType: 'GRAMENE_TAXONOMY',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/taxonomy?subset=gramene&rows=-1`)\n .then(res => res.json())\n .then(taxNodes => {\n let taxonomy = _.keyBy(taxNodes, '_id');\n taxNodes.forEach(t => {\n t._id = +t._id; // ensure taxonomy id is a number\n if (t.hasOwnProperty(\"is_a\")) {\n t.is_a.forEach(p_id => {\n const p = taxonomy[p_id];\n if (!p.hasOwnProperty('children')) p.children = [];\n p.children.push(t._id)\n })\n }\n });\n return taxonomy\n })\n }\n});\ngrameneTaxonomy.reactGrameneTaxonomy = createSelector(\n 'selectGrameneTaxonomyShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneTaxonomy' }\n }\n }\n);\nconst grameneMaps = createAsyncResourceBundle({\n name: 'grameneMaps',\n actionBaseType: 'GRAMENE_MAPS',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${store.selectGrameneAPI()}/maps?rows=-1`)\n .then(res => res.json())\n .then(maps => _.keyBy(maps, 'taxon_id'))\n }\n});\ngrameneMaps.reactGrameneMaps = createSelector(\n 'selectGrameneMapsShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneMaps' }\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);\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 (shouldUpdate, status) => {\n if (shouldUpdate && status === 'search') {\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\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];\n","import {createSelector} from \"redux-bundler\";\nimport _ from 'lodash';\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 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(` ${node.operation} `)})`\n }\n else {\n // this node is a suggestion\n if (isQuery.test(node.fq_value))\n return `${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 ${MAX_IDLIST_LENGTH} genes`\n }\n let filters = ids.map((id,idx) => {\n return {\n category: 'Gene',\n name: id,\n fq_field: 'id',\n fq_value: id\n }\n });\n if (filters.length === 1) {\n actions.push({type: 'GRAMENE_FILTER_ADDED', payload: filters[0]})\n }\n else {\n let action = {type: 'GRAMENE_FILTER_SET_ADDED', payload: {operation: 'OR', filters:filters}};\n if (warning) {\n action.payload.warning = warning\n }\n actions.push(action)\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n};\n\ngrameneFilters.reactGrameneFilters = createSelector(\n 'selectQueryObject',\n 'selectGrameneFilters',\n 'selectActiveGenomes',\n 'selectUrlObject',\n (queryObject, filters, genomes, myUrl) => {\n if (filters.status === 'init') {\n if (queryObject.filters) {\n const newFilters = JSON.parse(queryObject.filters);\n let actions = [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_REPLACED', payload: newFilters}\n ];\n if (queryObject.genomes) {\n let active={};\n queryObject.genomes.split(',').forEach(t => {\n active[t]=true\n });\n actions.push({type: 'GRAMENE_GENOMES_UPDATED', payload: active});\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n }\n if (queryObject.hasOwnProperty('suggestion')) {\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: JSON.parse(queryObject.suggestion)}\n ]\n };\n }\n if (queryObject.hasOwnProperty('idList')) {\n return handleIdList(queryObject);\n }\n const url = new URL(myUrl.href);\n if (url.pathname === '/genes') {\n return {type: 'GRAMENE_FILTERS_CLEARED'}\n }\n }\n if (filters.status === 'finished') {\n const url = new URL(myUrl.href);\n url.search = `filters=${JSON.stringify(Object.assign({}, filters, {status: 'init'}))}&genomes=${genomes.join(',')}`;\n 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;","const grameneViews = {\n name: 'grameneViews',\n getReducer: () => {\n const initialState = {\n options: [\n // {\n // id: 'help',\n // name: 'Help / Demo',\n // show: 'off'\n // },\n {\n id: 'taxonomy',\n name: 'Taxonomic distribution',\n show: 'on'\n },\n {\n id: 'list',\n name: 'Gene list',\n show: 'on'\n }\n // {\n // id: 'pathways',\n // name: 'Pathways',\n // show: 'disabled'\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[payload].show = newState.options[payload].show === 'on' ? 'off' : 'on';\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 selectGrameneViews: state => state.grameneViews,\n};\n\nexport default grameneViews;","const grameneDocs = {\n name: 'grameneDocs',\n getReducer: () => {\n const initialState = {\n genes: {},\n trees: {},\n domains: {},\n pathways: {}\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\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_REQUESTED':\n // newState = Object.assign({}, state);\n // payload.forEach(id => {\n // if (!state.pathways.hasOwnProperty(id)) {\n // newState.pathways[id] = {};\n // }\n // });\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 }\n return state;\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=${id}`)\n .then(res => res.json())\n .then(res => {\n let trees = {};\n res.forEach(t => {\n function update_taxon_name(node) {\n if (maps.hasOwnProperty(node.taxon_id)) {\n node.taxon_name = maps[node.taxon_id].display_name\n }\n else if (node.taxon_id === 1100004558) {\n node.taxon_name = \"Sorghum bicolor\"\n }\n if (node.taxon_id === 45770001 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Zea mays\"\n }\n if (node.taxon_id === 297600009 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Vitis vinifera\"\n }\n if (node.hasOwnProperty('children')) {\n node.children.forEach(c => update_taxon_name(c))\n }\n }\n update_taxon_name(t);\n trees[t._id] = t;\n });\n dispatch({type: 'GRAMENE_TREE_RECEIVED', payload: trees})\n })\n }\n },\n doRequestGramenePathways: ids => ({dispatch, store}) => {\n const pathways = store.selectGramenePathways();\n let newIds = ids.filter(id => !pathways.hasOwnProperty(id));\n if (newIds) {\n dispatch({type: 'GRAMENE_PATHWAYS_REQUESTED', payload: newIds});\n fetch(`${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 selectGrameneGenes: state => state.grameneDocs.genes,\n selectGrameneTrees: state => state.grameneDocs.trees,\n selectGramenePathways: state => state.grameneDocs.pathways\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 default:\n return state;\n }\n }\n },\n doShowGrameneGenomes: () => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_GENOMES_TOGGLED'})\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 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 { Button, Badge, Alert } from 'react-bootstrap'\nimport './styles.css'\n\nfunction showMatches(text, x) {\n let re = new RegExp(`(${x})`, 'ig');\n let match = text.split(re);\n console.log('showMatches',text, x, match);\n return <span>\n {match.map((str, idx) => {\n if (idx % 2 === 1) {\n return <span key={idx} style={{fontWeight:'bolder'}}>{str}</span>\n }\n return <span key={idx}>{str}</span>\n })}\n </span>\n}\n\nconst Suggestions = props => {\n let suggestions = props.grameneSuggestions;\n if (suggestions && suggestions.grouped) {\n if (suggestions.grouped.category.matches === 0) {\n let sugg1 = {\n fq_field: 'text',\n fq_value: props.suggestionsQuery,\n name: `Genes containing \"${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={() => {props.doAcceptSuggestion(sugg1); props.doAcceptGrameneSuggestion(sugg1)}}>\n {`All genes that contain the word \"${props.suggestionsQuery}\"`}\n </Button>\n <Button id={'word'}\n size={'sm'}\n variant={'outline-secondary'}\n onClick={() => {props.doAcceptSuggestion(sugg2); props.doAcceptGrameneSuggestion(sugg2)}}>\n {`All genes that contain a word that starts with \"${props.suggestionsQuery}\"`}\n </Button>\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={() => {props.doAcceptSuggestion(sugg); props.doAcceptGrameneSuggestion(sugg)}}>\n {showMatches(sugg.display_name,props.suggestionsQuery)}{' '}\n <Badge variant=\"secondary\">{sugg.num_genes}</Badge>\n </Button>\n )}\n </div>\n })}\n </div>\n );\n }\n }\n else {\n return <div></div>\n }\n}\n\nexport default connect(\n 'selectGrameneSuggestions',\n 'selectSuggestionsQuery',\n 'doAcceptSuggestion',\n 'doAcceptGrameneSuggestion',\n Suggestions\n);\n","import React from 'react'\nimport { connect } from 'redux-bundler-react'\nimport { Alert, OverlayTrigger, Popover, Modal } from 'react-bootstrap'\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 TaxonomyModal from './TaxonomyModal'\nimport './styles.css';\n\nconst inventory = {\n help: HelpDemo,\n list: GeneList,\n taxonomy: TaxDist\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.Title as=\"h3\">Genomes Filter</Popover.Title>\n <Popover.Content>Searching {props.activeGenomeCount} genomes</Popover.Content>\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', backgroundColor:'dimgray', 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};\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={()=>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={()=>actions.deleteNode(node)}>delete</li>);\n menuItems.push(<li key={key++} onClick={()=>actions.markTargets(node,'move')}>move{node.isSource && ' select destination'}</li>);\n menuItems.push(<li key={key++} onClick={()=>actions.markTargets(node,'copy')}>copy{node.isSource && ' select destination'}</li>)\n }\n menuItems.push(<li key={key++} onClick={()=>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.Title as=\"h3\">Warning</Popover.Title>\n <Popover.Content>{node.warning}</Popover.Content>\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} |&nbsp;{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='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='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 '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.filter((v,idx) => {\n v.idx = idx;\n return v.show === 'on'\n });\n // if (props.grameneFilters.rightIdx === 1 || activeViews.length === 0) {\n // return <HelpDemo/>\n // }\n return props.grameneFilters.rightIdx > 1 ? (\n <div style={{padding:'10px'}}>\n {activeViews.map(v => {\n let p = Object.assign({}, props);\n p.key = v.idx;\n return (\n <div key={v.idx}>\n {/*<Alert variant=\"primary\" onClose={() => props.doToggleGrameneView(v.idx)} dismissible>*/}\n {/* {v.name}*/}\n {/*</Alert>*/}\n {React.createElement(inventory[v.id], p)}\n </div>\n )\n })}\n </div>\n ) : null;\n};\n\nconst Results = connect(\n 'selectGrameneFilters',\n 'selectGrameneViews',\n 'doToggleGrameneView',\n ResultsCmp\n);\n\nconst ViewsCmp = props => (\n <div className={'gramene-view-container'}>\n <b>Views</b>\n <ul className={'gramene-view'}>\n {props.grameneViews.options.map((view,idx) => (\n <li key={idx} className={`gramene-view-${view.show}`}\n onClick={(e) => {\n if (view.show !== 'disabled') {\n props.doToggleGrameneView(idx)\n }\n }}\n >{view.name}</li>\n ))}\n </ul>\n {/*<div>*/}\n {/* &nbsp;Key:*/}\n {/* <ul className={'gramene-view'}>*/}\n {/* <li className='gramene-view-on'>On</li>*/}\n {/* <li className='gramene-view-off'>Off</li>*/}\n {/* <li className='gramene-view-disabled'>Disabled</li>*/}\n {/* </ul>*/}\n {/*</div>*/}\n &nbsp;\n </div>\n);\n\nconst Views = connect(\n 'selectGrameneViews',\n 'doToggleGrameneView',\n ViewsCmp\n);\n\nexport {Status, Filters, Results, Views};","import React from 'react'\nimport ReactGA from 'react-ga'\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 Xrefs from \"./details/Xrefs\"\nimport {GrFormPrevious, GrFormNextLink, GrFormNext, GrHpe} from 'react-icons/gr'\nimport { Badge } 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 location: Location,\n expression: Expression,\n homology: Homology,\n pathways: Pathways,\n xrefs: Xrefs\n};\n\nfunction renderTairSummary(searchResult) {\n const summary = searchResult.summary;\n if(summary && searchResult.taxon_id === 3702) {\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}\n\nconst ClosestOrtholog = ({gene}) =>\n{\n let name, desc, species;\n\n 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 }\n\n else 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 }\n\n return (\n <div className=\"closest-ortholog\">\n <h4>\n <span className=\"gene-id\">{name}</span>\n <small className=\"species-name\"> {species}</small>\n </h4>\n <p>{desc}</p>\n </div>\n );\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\nclass Gene extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n details: [\n {\n id: 'location',\n label: 'Location',\n available: false\n },\n {\n id: 'expression',\n label: 'Expression',\n available: false\n },\n {\n id: 'homology',\n label: 'Homology',\n available: false\n },\n {\n id: 'pathways',\n label: 'Pathways',\n available: false\n },\n // {\n // id: 'pubs',\n // label: 'Publications',\n // available: false\n // },\n {\n id: 'xrefs',\n label: 'Xrefs',\n available: false\n }\n ],\n expandedDetail: props.expandedDetail\n };\n let hasData = {};\n props.searchResult.capabilities.forEach(c => hasData[c]=true);\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 return d.available ? 'closed' : 'disabled';\n }\n setExpanded(d) {\n if (d.available) {\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 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].name;\n }\n if (gene.closest_rep_taxon_id) {\n gene.closest_rep_species_name = this.props.taxLut[gene.closest_rep_taxon_id].name;\n }\n return renderTairSummary(gene) || renderClosestOrtholog(gene);\n }\n render() {\n const ensemblURL = this.props.ensemblURL;\n const searchResult = this.props.searchResult;\n const taxName = this.props.taxName;\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 <h3 className=\"gene-title\">\n <span className=\"gene-name\">{searchResult.name}</span>\n {searchResult.id !== searchResult.name && <small className=\"gene-id\">{' '}{searchResult.id}</small>}\n <ReactGA.OutboundLink\n eventLabel={searchResult.system_name}\n to={`${ensemblURL}/${searchResult.system_name}/Info/Index`}\n className=\"external-link\"\n >\n <small className=\"gene-species\">{taxName}</small>\n </ReactGA.OutboundLink>\n </h3>\n {searchResult.synonyms && <small className=\"gene-synonyms\">{searchResult.synonyms.join(', ')}</small>}\n {numWordsInDescription > 1 && <p className=\"gene-description\">{searchResult.description}</p>}\n </div>\n {this.renderMetadata()}\n </div>\n <div className=\"gene-detail-tabs\">\n {this.state.details.map((d,idx) => (\n <div key={idx}\n className={`col-md-1 text-center gene-detail-tab-${this.getDetailStatus(d)}`}\n onClick={()=>this.setExpanded(d)}\n >{d.label}</div>\n ))}\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 ensemblURL={props.configuration.ensemblURL}\n ensemblRest={props.configuration.ensemblRest}\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 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 'doRequestGrameneGene',\n 'doRequestOrthologs',\n 'doRequestResultsPage',\n GeneList);\n","import React from 'react'\nimport {connect} from \"redux-bundler-react\";\n\nconst PREFIX = (global.location ? global.location.origin + global.location.pathname + '/' : '');\n\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n const url = `${PREFIX}static/atlasWidget.html?${gene.taxon_id === 112509 ? gene.synonyms[0] : gene._id}`;\n const height = '500px';\n return (\n <iframe src={url} frameBorder=\"0\" width=\"100%\" height={height}>\n <p>browser doesn't support iframes</p>\n </iframe>\n );\n};\n\nexport default connect(Detail);\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 {Spinner} from \"react-bootstrap\";\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/msa.less';\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/tree.less';\n\nfunction 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\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 ${this.gene.name}`\n }))\n }\n orthologList() {\n return this.orthoParaList('ortholog');\n }\n\n paralogList() {\n return this.orthoParaList('within_species_paralog');\n }\n\n orthoParaList(type) {\n var homology, thisGeneId;\n homology = _.get(this.gene, 'homology.homologous_genes');\n thisGeneId = this.gene._id;\n\n if (homology) {\n var homologs = _(homology)\n .pickBy(function filterCategories(thing, name) {\n return name.indexOf(type) === 0;\n })\n .values()\n .flatten()\n .value();\n\n if (!_.isEmpty(homologs)) {\n homologs.push(thisGeneId);\n return homologs; // only return something if we have something. We're testing for truthiness later.\n }\n }\n }\n explorations() {\n let x = [{\n name: 'Homologs',\n category: 'Gene Tree',\n count: this.tree.geneCount,\n handleClick: this.filterAllHomologs.bind(this)\n }];\n if (this.orthologs) {\n x.push({\n name: 'Orthologs',\n category: 'Gene Tree',\n count: this.orthologs.length,\n handleClick: this.filterOrthologs.bind(this)\n });\n }\n if (this.paralogs) {\n x.push({\n name: 'Paralogs',\n category: 'Gene Tree',\n count: this.paralogs.length,\n handleClick: this.filterParalogs.bind(this)\n });\n }\n return x;\n }\n links() {\n let links = [\n {\n name: 'Ensembl Gene Tree view',\n url: `${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 if (!this.props.geneDocs.hasOwnProperty(this.props.searchResult.id)) {\n return <Spinner/>\n }\n this.gene = this.props.geneDocs[this.props.searchResult.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 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 </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 '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-ga\";\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\"}} variant='dark'>{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 <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 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: `${this.props.ensemblURL}/${gene.system_name}/Gene/Summary?g=${gene._id}`},\n {name: 'PhytoMine', url: `https://phytozome.jgi.doe.gov/phytomine/keywordSearchResults.do?searchTerm=${jgiify(gene._id)}&searchSubmit=Search`},\n ];\n if (gene.taxon_id === 3702)\n links.push({name: 'Thalemine', url: `https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=${gene._id}&searchSubmit=search`});\n if (gene.taxon_id === 4577)\n links.push({name: 'MaizeGDB', url: `http://www.maizegdb.org/gene_center/gene/${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()}&nbsp;{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// 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 = (global.location ? global.location.origin + global.location.pathname + '/' : '')\n + '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.ensemblRest,\n species: g.system_name,\n tier_type: 'sequence'\n },\n {\n name: 'Genes',\n uri: this.props.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// };","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\";\nimport {TreeMenu} from \"react-tree-menu\";\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.children) {\n path.push(0);\n parent = node;\n node = node.children[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 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 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().convert(nodes);\n\n this.setState({hierarchy: [nested], selectedNode: undefined});\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 nodes.forEach(function(n) {\n nodeRef = nodeRef.children[n];\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 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 from 'react'\nimport ReactGA from 'react-ga'\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 members, vals, db;\n db = this.props.displayName;\n\n members = this.props.members;\n\n vals = _(members)\n .map(function (m) {\n return m.val;\n })\n .flatten(true)\n .sort()\n .uniq(true) // TODO figure out why there are duplicates.\n .map(function (item, idx) {\n var url = members[0].url(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 <ReactGA.OutboundLink\n eventLabel={db}\n to={url}\n target=\"_blank\"\n >\n {item}{external}\n </ReactGA.OutboundLink>\n </li>\n )\n })\n .value();\n\n vals = this.possiblyTruncateList(vals);\n\n return (\n <tr>\n <td className=\"xref-name-col\">{this.props.displayName}</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 .keyBy('db')\n .pickBy(function(val, name) {\n return dbxrefs.isKnown(name);\n })\n .map(function(val, name) {\n var xref = dbxrefs.fetch(name);\n return {url: xref.url, label: xref.label, val: val.ids};\n })\n .groupBy('label')\n .map(function(members, displayName) {\n return (\n <Xref key={displayName} displayName={displayName} members={members} />\n )\n })\n .value();\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 { 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 <button type=\"button\" className=\"btn btn-primary btn-sm\" onClick={this.toggleEmpties.bind(this)}>{this.state.collapseEmpties ? 'Expand' : 'Collapse'} empty branches</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&nbsp;|<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, CardDeck} 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 <CardDeck 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 </CardDeck>\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'\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 = true;\n })\n }\n else {\n this.state.genomes.forEach(g => {\n g.selected = props.grameneGenomes.active[g.taxon_id];\n })\n }\n }\n getSelectedGenomes() {\n let selected = {};\n let notAll = false;\n this.state.genomes.forEach(g => {\n if (g.selected) {\n selected[g.taxon_id] = true;\n }\n else {\n notAll = true;\n }\n });\n return notAll ? selected : {};\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 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"],"names":["apiBundles","docsBundle","filterBundle","viewsBundle","genomesBundle","facets","genomesOfInterest","grameneSuggestions","name","actionBaseType","persist","getPromise","store","t","selectSuggestionsQuery","g","selectGrameneGenomes","fetch","selectGrameneAPI","then","res","json","suggestions","Object","keys","active","length","grouped","category","groups","forEach","group","doclist","docs","sugg","num_genes","taxon_id","id","idx","taxon_freq","reactGrameneSuggestions","shouldUpdate","queryString","actionCreator","selectGrameneSuggestionsStatus","isLoading","suggestionsRaw","data","matches","selectGrameneSuggestionsReady","status","regex","RegExp","test","doFocusFirstGrameneSuggestion","arg","dispatch","getState","console","log","grameneTaxonomy","taxNodes","taxonomy","_","keyBy","_id","hasOwnProperty","is_a","p_id","p","children","push","reactGrameneTaxonomy","grameneMaps","maps","reactGrameneMaps","grameneSearch","offset","selectGrameneSearchOffset","rows","selectGrameneSearchRows","taxa","fq","join","selectGrameneFiltersQueryString","response","d","can_show","capabilities","c","reactGrameneSearch","formatFacetCountsForViz","a","count","displayName","sorted","counts","i","fc","sort","b","grameneTaxDist","getReducer","initialState","state","type","payload","selectGrameneTaxDist","forIn","map","tid","display_name","binnedResults","facet_counts","facet_fields","fixed_1000__bin","speciesTree","treesClient","tree","values","binMapper","binsClient","bins","taxDist","setBinType","setResults","grameneOrthologs","newState","assign","doRequestOrthologs","geneId","orthologs","selectGrameneOrthologs","API","taxonId","selectTargetTaxonId","newOrthologs","MAX_IDLIST_LENGTH","findNodeWithLeftIdx","node","leftIdx","result","child","rightIdx","parentIdx","markSubtree","source","invert","marked","reindexTree","grameneFilters","operation","negate","showMarked","showMenu","moveCopyMode","searchOffset","pick","filter","filters","warning","nextIdx","f","parent","target","targetCopy","fq_field","fq_value","sourceCopy","mode","moveCopySource","doNegateGrameneFilter","actions","doDeleteGrameneFilter","doChangeGrameneFilterOperation","doMoveOrCopyGrameneFilter","toUpperCase","doCopyGrameneFilter","doMarkGrameneFilterTargets","doUnmarkGrameneFilterTargets","doAcceptGrameneSuggestion","suggestion","doAddGrameneRangeQuery","terms","doToggleGrameneFilterMenu","doRequestResultsPage","page","doReplaceGrameneFilters","doClearGrameneFilters","selectGrameneFilters","selectGrameneFiltersStatus","hasSpaces","isQuery","idWithColon","getQuery","replace","handleIdList","queryObject","ids","uniq","idList","split","slice","action","reactGrameneFilters","genomes","myUrl","newFilters","JSON","parse","url","URL","href","pathname","search","stringify","grameneViews","options","show","doToggleGrameneView","selectGrameneViews","grameneDocs","genes","trees","domains","pathways","doRequestGrameneGene","selectGrameneGenes","doRequestGrameneTree","selectGrameneTrees","selectGrameneMaps","update_taxon_name","taxon_name","doRequestGramenePathways","selectGramenePathways","newIds","grameneGenomes","doShowGrameneGenomes","doUpdateGrameneGenomes","selectActiveGenomes","selectActiveGenomeCount","Gene","gene","Genes","results","doChangeQuantity","numFound","moreButton","e","fewerButton","docsToShow","doc","Pathway","pathway","Pathways","Domain","domain","Domains","Taxon","taxon","Species","ResultList","grameneGenes","grameneDomains","gramenePathways","searchUI","searchUpdated","Gramene","getStatus","cat","isChecked","toggle","tally","ResultSummary","doToggleCategory","showMatches","text","x","re","match","str","fontWeight","Suggestions","props","sugg1","suggestionsQuery","sugg2","margin","maxWidth","doAcceptSuggestion","groupValue","jdx","inventory","help","HelpDemo","list","GeneList","TaxDist","StatusCmp","content","grameneFiltersStatus","popover","activeGenomeCount","cursor","padding","backgroundColor","color","fontSize","Status","handleClick","window","event","cancelBubble","stopPropagation","selectTarget","unmarkTargets","Filter","classes","menu","key","menuItems","changeOperation","deleteNode","markTargets","isSource","toggleMenu","FiltersCmp","Filters","ResultsCmp","activeViews","v","React","createElement","Results","ViewsCmp","view","Views","external","location","Location","expression","Expression","homology","Homology","xrefs","Xrefs","renderTairSummary","searchResult","summary","trimSummary","start","substr","rest","ClosestOrtholog","desc","species","model_rep_id","model_rep_name","model_rep_description","model_rep_species_name","closest_rep_id","closest_rep_name","closest_rep_description","closest_rep_species_name","renderClosestOrtholog","shouldShowClosestOrtholog","details","label","available","expandedDetail","hasData","setState","geneDocs","requestGene","model_rep_taxon_id","taxLut","closest_rep_taxon_id","ensemblURL","taxName","numWordsInDescription","description","system_name","synonyms","renderMetadata","getDetailStatu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ndles/docs.js","src/bundles/genomes.js","src/components/resultList.js","src/components/resultSummary.js","src/components/suggestions.js","src/components/geneSearchUI.js","src/components/results/GeneList.js","src/components/results/details/Expression.js","src/components/results/details/Homology.js","src/components/results/details/generic.js","src/components/results/details/Location.js","src/components/results/details/location/browser.js","src/components/results/details/location/dallianceBrowser.js","src/components/results/details/Pathways.js","src/components/results/details/Xrefs.js","src/components/results/TaxDist.js","src/components/results/selection.js","src/components/results/HelpDemo.js","src/components/TaxonomyModal.js"],"sourcesContent":["import bundles from './bundles';\nimport resultList from './components/resultList';\nimport resultSummary from './components/resultSummary';\nimport suggestions from './components/suggestions';\nimport {Status, Filters, Results, Views} from './components/geneSearchUI';\n\nexport { bundles, resultList, resultSummary, suggestions, Status, Filters, Results, Views };\n","import apiBundles from './api'\nimport filterBundle from './filters'\nimport viewsBundle from './views'\nimport docsBundle from './docs'\nimport genomesBundle from './genomes'\n\nexport default [...apiBundles, docsBundle, filterBundle, viewsBundle, genomesBundle];","import { createAsyncResourceBundle, createSelector } from 'redux-bundler'\nimport _ from 'lodash'\nimport binsClient from \"gramene-bins-client\";\nimport treesClient from \"gramene-trees-client\";\nimport {build} from \"gramene-taxonomy-with-genomes\";\n\nconst facets = [\n \"{!facet.limit='200' facet.mincount='1' key='taxon_id'}taxon_id\",\n \"{!facet.limit='100' facet.mincount='1' key='genetree'}gene_tree\",\n \"{!facet.limit='100' facet.mincount='1' key='pathways'}pathways__ancestors\",\n \"{!facet.limit='100' facet.mincount='1' key='domains'}domain_roots\",\n \"{!facet.limit='-1' facet.mincount='1' key='fixed_1000__bin'}fixed_1000__bin\"\n];\nconst genomesOfInterest = '(taxon_id:2769) OR (taxon_id:3055) OR (taxon_id:3218) OR (taxon_id:3702) OR (taxon_id:3847) OR (taxon_id:4555) OR (taxon_id:4558) OR (taxon_id:4577) OR (taxon_id:13333) OR (taxon_id:15368) OR (taxon_id:29760) OR (taxon_id:39947) OR (taxon_id:55577) OR (taxon_id:88036) OR (taxon_id:214687)';\n\nconst grameneSuggestions = createAsyncResourceBundle( {\n name: 'grameneSuggestions',\n actionBaseType: 'GRAMENE_SUGGESTIONS',\n persist: false,\n getPromise: ({store}) => {\n const t = store.selectSuggestionsQuery();\n const g = store.selectGrameneGenomes();\n return fetch(`${store.selectGrameneAPI()}/suggest?q={!boost b=relevance}name:${t}^3 id:${t}^5 synonym:${t}^2 text:${t}*^1`)\n .then(res => res.json())\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]) {\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) return suggestionsRaw.data.grouped.category.matches + ' terms';\n return 'error';\n }\n);\n\ngrameneSuggestions.selectGrameneSuggestionsReady = createSelector(\n 'selectGrameneSuggestionsStatus',\n (status) => {\n const regex = RegExp('terms$');\n return regex.test(status);\n }\n);\n\ngrameneSuggestions.doFocusFirstGrameneSuggestion = arg => ({dispatch, getState}) => {\n console.log('inside doFocusFirstGrameneSuggestion');\n};\n\nconst grameneTaxonomy = createAsyncResourceBundle({\n name: 'grameneTaxonomy',\n actionBaseType: 'GRAMENE_TAXONOMY',\n persist: true,\n getPromise: ({store}) => {\n return fetch(`${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 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(`${store.selectGrameneAPI()}/maps?rows=-1`)\n .then(res => res.json())\n .then(maps => _.keyBy(maps, 'taxon_id'))\n }\n});\ngrameneMaps.reactGrameneMaps = createSelector(\n 'selectGrameneMapsShouldUpdate',\n (shouldUpdate) => {\n if (shouldUpdate) {\n return { actionCreator: 'doFetchGrameneMaps' }\n }\n }\n);\n\nconst grameneSearch = createAsyncResourceBundle({\n name: 'grameneSearch',\n actionBaseType: 'GRAMENE_SEARCH',\n persist: false,\n getPromise: ({store}) => {\n const offset = store.selectGrameneSearchOffset();\n const rows = store.selectGrameneSearchRows();\n const g = store.selectGrameneGenomes();\n const taxa = Object.keys(g.active);\n let fq='';\n if (taxa.length) {\n console.log('search add a fq for ',taxa);\n fq = `&fq=taxon_id:(${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 (shouldUpdate, status) => {\n if (shouldUpdate && status === 'search') {\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:${taxonId}&fl=id`)\n .then(res => res.json())\n .then(res => {\n let newOrthologs = {};\n newOrthologs[geneId] = res.response.docs.map(d => d.id);\n dispatch({type: 'GRAMENE_ORTHOLOGS_RECEIVED', payload: newOrthologs})\n })\n }\n },\n selectGrameneOrthologs: state => state.grameneOrthologs\n};\n\n\n// function selectFacetIDs(store, field) {\n// const path = `grameneGenes.data.facet_counts.facet_fields.${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];\n","import {createSelector} from \"redux-bundler\";\nimport _ from 'lodash';\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 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(` ${node.operation} `)})`\n }\n else {\n // this node is a suggestion\n if (isQuery.test(node.fq_value))\n return `${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 ${MAX_IDLIST_LENGTH} genes`\n }\n let filters = ids.map((id,idx) => {\n return {\n category: 'Gene',\n name: id,\n fq_field: 'id',\n fq_value: id\n }\n });\n if (filters.length === 1) {\n actions.push({type: 'GRAMENE_FILTER_ADDED', payload: filters[0]})\n }\n else {\n let action = {type: 'GRAMENE_FILTER_SET_ADDED', payload: {operation: 'OR', filters:filters}};\n if (warning) {\n action.payload.warning = warning\n }\n actions.push(action)\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n};\n\ngrameneFilters.reactGrameneFilters = createSelector(\n 'selectQueryObject',\n 'selectGrameneFilters',\n 'selectActiveGenomes',\n 'selectUrlObject',\n (queryObject, filters, genomes, myUrl) => {\n if (filters.status === 'init') {\n if (queryObject.filters) {\n const newFilters = JSON.parse(queryObject.filters);\n let actions = [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTERS_REPLACED', payload: newFilters}\n ];\n if (queryObject.genomes) {\n let active={};\n queryObject.genomes.split(',').forEach(t => {\n active[t]=true\n });\n actions.push({type: 'GRAMENE_GENOMES_UPDATED', payload: active});\n }\n return { type: 'BATCH_ACTIONS', actions: actions };\n }\n if (queryObject.hasOwnProperty('suggestion')) {\n return {\n type: 'BATCH_ACTIONS', actions: [\n {type: 'GRAMENE_SEARCH_CLEARED'},\n {type: 'GRAMENE_FILTER_ADDED', payload: JSON.parse(queryObject.suggestion)}\n ]\n };\n }\n if (queryObject.hasOwnProperty('idList')) {\n return handleIdList(queryObject);\n }\n const url = new URL(myUrl.href);\n if (url.pathname === '/genes') {\n return {type: 'GRAMENE_FILTERS_CLEARED'}\n }\n }\n if (filters.status === 'finished') {\n const url = new URL(myUrl.href);\n url.search = `filters=${JSON.stringify(Object.assign({}, filters, {status: 'init'}))}&genomes=${genomes.join(',')}`;\n 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;","const grameneViews = {\n name: 'grameneViews',\n getReducer: () => {\n const initialState = {\n options: [\n // {\n // id: 'help',\n // name: 'Help / Demo',\n // show: 'off'\n // },\n {\n id: 'taxonomy',\n name: 'Taxonomic distribution',\n show: 'on'\n },\n {\n id: 'list',\n name: 'Gene list',\n show: 'on'\n }\n // {\n // id: 'pathways',\n // name: 'Pathways',\n // show: 'disabled'\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[payload].show = newState.options[payload].show === 'on' ? 'off' : 'on';\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 selectGrameneViews: state => state.grameneViews,\n};\n\nexport default grameneViews;","const grameneDocs = {\n name: 'grameneDocs',\n getReducer: () => {\n const initialState = {\n genes: {},\n trees: {},\n domains: {},\n pathways: {}\n };\n return (state = initialState, {type, payload}) => {\n let newState;\n switch (type) {\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_REQUESTED':\n // newState = Object.assign({}, state);\n // payload.forEach(id => {\n // if (!state.pathways.hasOwnProperty(id)) {\n // newState.pathways[id] = {};\n // }\n // });\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 }\n return state;\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=${id}`)\n .then(res => res.json())\n .then(res => {\n let trees = {};\n res.forEach(t => {\n function update_taxon_name(node) {\n if (maps.hasOwnProperty(node.taxon_id)) {\n node.taxon_name = maps[node.taxon_id].display_name\n }\n else if (node.taxon_id === 1100004558) {\n node.taxon_name = \"Sorghum bicolor\"\n }\n if (node.taxon_id === 45770001 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Zea mays\"\n }\n if (node.taxon_id === 297600009 && node.hasOwnProperty('children')) {\n node.taxon_name = \"Vitis vinifera\"\n }\n if (node.hasOwnProperty('children')) {\n node.children.forEach(c => update_taxon_name(c))\n }\n }\n update_taxon_name(t);\n trees[t._id] = t;\n });\n dispatch({type: 'GRAMENE_TREE_RECEIVED', payload: trees})\n })\n }\n },\n doRequestGramenePathways: ids => ({dispatch, store}) => {\n const pathways = store.selectGramenePathways();\n let newIds = ids.filter(id => !pathways.hasOwnProperty(id));\n if (newIds) {\n dispatch({type: 'GRAMENE_PATHWAYS_REQUESTED', payload: newIds});\n fetch(`${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 selectGrameneGenes: state => state.grameneDocs.genes,\n selectGrameneTrees: state => state.grameneDocs.trees,\n selectGramenePathways: state => state.grameneDocs.pathways\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 default:\n return state;\n }\n }\n },\n doShowGrameneGenomes: () => ({dispatch, getState}) => {\n dispatch({type: 'GRAMENE_GENOMES_TOGGLED'})\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 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 { Button, Badge, Alert } from 'react-bootstrap'\nimport './styles.css'\n\nfunction showMatches(text, x) {\n let re = new RegExp(`(${x})`, 'ig');\n let match = text.split(re);\n console.log('showMatches',text, x, match);\n return <span>\n {match.map((str, idx) => {\n if (idx % 2 === 1) {\n return <span key={idx} style={{fontWeight:'bolder'}}>{str}</span>\n }\n return <span key={idx}>{str}</span>\n })}\n </span>\n}\n\nconst Suggestions = props => {\n let suggestions = props.grameneSuggestions;\n if (suggestions && suggestions.grouped) {\n if (suggestions.grouped.category.matches === 0) {\n let sugg1 = {\n fq_field: 'text',\n fq_value: props.suggestionsQuery,\n name: `Genes containing \"${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={() => {props.doAcceptSuggestion(sugg1); props.doAcceptGrameneSuggestion(sugg1)}}>\n {`All genes that contain the word \"${props.suggestionsQuery}\"`}\n </Button>\n <Button id={'word'}\n size={'sm'}\n variant={'outline-secondary'}\n onClick={() => {props.doAcceptSuggestion(sugg2); props.doAcceptGrameneSuggestion(sugg2)}}>\n {`All genes that contain a word that starts with \"${props.suggestionsQuery}\"`}\n </Button>\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={() => {props.doAcceptSuggestion(sugg); props.doAcceptGrameneSuggestion(sugg)}}>\n {showMatches(sugg.display_name,props.suggestionsQuery)}{' '}\n <Badge variant=\"secondary\">{sugg.num_genes}</Badge>\n </Button>\n )}\n </div>\n })}\n </div>\n );\n }\n }\n else {\n return <div></div>\n }\n}\n\nexport default connect(\n 'selectGrameneSuggestions',\n 'selectSuggestionsQuery',\n 'doAcceptSuggestion',\n 'doAcceptGrameneSuggestion',\n Suggestions\n);\n","import React from 'react'\nimport { connect } from 'redux-bundler-react'\nimport { Alert, OverlayTrigger, Popover, Modal } from 'react-bootstrap'\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 TaxonomyModal from './TaxonomyModal'\nimport './styles.css';\n\nconst inventory = {\n help: HelpDemo,\n list: GeneList,\n taxonomy: TaxDist\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.Title as=\"h3\">Genomes Filter</Popover.Title>\n <Popover.Content>Searching {props.activeGenomeCount} genomes</Popover.Content>\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', backgroundColor:'dimgray', 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};\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={()=>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={()=>actions.deleteNode(node)}>delete</li>);\n menuItems.push(<li key={key++} onClick={()=>actions.markTargets(node,'move')}>move{node.isSource && ' select destination'}</li>);\n menuItems.push(<li key={key++} onClick={()=>actions.markTargets(node,'copy')}>copy{node.isSource && ' select destination'}</li>)\n }\n menuItems.push(<li key={key++} onClick={()=>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.Title as=\"h3\">Warning</Popover.Title>\n <Popover.Content>{node.warning}</Popover.Content>\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} |&nbsp;{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='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='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 '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.filter((v,idx) => {\n v.idx = idx;\n return v.show === 'on'\n });\n // if (props.grameneFilters.rightIdx === 1 || activeViews.length === 0) {\n // return <HelpDemo/>\n // }\n return props.grameneFilters.rightIdx > 1 ? (\n <div style={{padding:'10px'}}>\n {activeViews.map(v => {\n let p = Object.assign({}, props);\n p.key = v.idx;\n return (\n <div key={v.idx}>\n {/*<Alert variant=\"primary\" onClose={() => props.doToggleGrameneView(v.idx)} dismissible>*/}\n {/* {v.name}*/}\n {/*</Alert>*/}\n {React.createElement(inventory[v.id], p)}\n </div>\n )\n })}\n </div>\n ) : null;\n};\n\nconst Results = connect(\n 'selectGrameneFilters',\n 'selectGrameneViews',\n 'doToggleGrameneView',\n ResultsCmp\n);\n\nconst ViewsCmp = props => (\n <div className={'gramene-view-container'}>\n <b>Views</b>\n <ul className={'gramene-view'}>\n {props.grameneViews.options.map((view,idx) => (\n <li key={idx} className={`gramene-view-${view.show}`}\n onClick={(e) => {\n if (view.show !== 'disabled') {\n props.doToggleGrameneView(idx)\n }\n }}\n >{view.name}</li>\n ))}\n </ul>\n {/*<div>*/}\n {/* &nbsp;Key:*/}\n {/* <ul className={'gramene-view'}>*/}\n {/* <li className='gramene-view-on'>On</li>*/}\n {/* <li className='gramene-view-off'>Off</li>*/}\n {/* <li className='gramene-view-disabled'>Disabled</li>*/}\n {/* </ul>*/}\n {/*</div>*/}\n &nbsp;\n </div>\n);\n\nconst Views = connect(\n 'selectGrameneViews',\n 'doToggleGrameneView',\n ViewsCmp\n);\n\nexport {Status, Filters, Results, Views};","import React from 'react'\nimport ReactGA from 'react-ga'\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 Xrefs from \"./details/Xrefs\"\nimport {GrFormPrevious, GrFormNextLink, GrFormNext, GrHpe} from 'react-icons/gr'\nimport { Badge } 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 location: Location,\n expression: Expression,\n homology: Homology,\n pathways: Pathways,\n xrefs: Xrefs\n};\n\nfunction renderTairSummary(searchResult) {\n const summary = searchResult.summary;\n if(summary && searchResult.taxon_id === 3702) {\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}\n\nconst ClosestOrtholog = ({gene}) =>\n{\n let name, desc, species;\n\n 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 }\n\n else 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 }\n\n return (\n <div className=\"closest-ortholog\">\n <h4>\n <span className=\"gene-id\">{name}</span>\n <small className=\"species-name\"> {species}</small>\n </h4>\n <p>{desc}</p>\n </div>\n );\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\nclass Gene extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n details: [\n {\n id: 'location',\n label: 'Location',\n available: false\n },\n {\n id: 'expression',\n label: 'Expression',\n available: false\n },\n {\n id: 'homology',\n label: 'Homology',\n available: false\n },\n {\n id: 'pathways',\n label: 'Pathways',\n available: false\n },\n // {\n // id: 'pubs',\n // label: 'Publications',\n // available: false\n // },\n {\n id: 'xrefs',\n label: 'Xrefs',\n available: false\n }\n ],\n expandedDetail: props.expandedDetail\n };\n let hasData = {};\n props.searchResult.capabilities.forEach(c => hasData[c]=true);\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 return d.available ? 'closed' : 'disabled';\n }\n setExpanded(d) {\n if (d.available) {\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 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].name;\n }\n if (gene.closest_rep_taxon_id) {\n gene.closest_rep_species_name = this.props.taxLut[gene.closest_rep_taxon_id].name;\n }\n return renderTairSummary(gene) || renderClosestOrtholog(gene);\n }\n render() {\n const ensemblURL = this.props.ensemblURL;\n const searchResult = this.props.searchResult;\n const taxName = this.props.taxName;\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 <h3 className=\"gene-title\">\n <span className=\"gene-name\">{searchResult.name}</span>\n {searchResult.id !== searchResult.name && <small className=\"gene-id\">{' '}{searchResult.id}</small>}\n <ReactGA.OutboundLink\n eventLabel={searchResult.system_name}\n to={`${ensemblURL}/${searchResult.system_name}/Info/Index`}\n className=\"external-link\"\n >\n <small className=\"gene-species\">{taxName}</small>\n </ReactGA.OutboundLink>\n </h3>\n {searchResult.synonyms && <small className=\"gene-synonyms\">{searchResult.synonyms.join(', ')}</small>}\n {numWordsInDescription > 1 && <p className=\"gene-description\">{searchResult.description}</p>}\n </div>\n {this.renderMetadata()}\n </div>\n <div className=\"gene-detail-tabs\">\n {this.state.details.map((d,idx) => (\n <div key={idx}\n className={`col-md-1 text-center gene-detail-tab-${this.getDetailStatus(d)}`}\n onClick={()=>this.setExpanded(d)}\n >{d.label}</div>\n ))}\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 ensemblURL={props.configuration.ensemblURL}\n ensemblRest={props.configuration.ensemblRest}\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 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 'doRequestGrameneGene',\n 'doRequestOrthologs',\n 'doRequestResultsPage',\n GeneList);\n","import React from 'react'\nimport {connect} from \"redux-bundler-react\";\n\nconst PREFIX = (global.location ? global.location.origin + global.location.pathname + '/' : '');\n\nconst Detail = props => {\n const gene = props.geneDocs[props.searchResult.id];\n const url = `/static/atlasWidget.html?${gene.taxon_id === 112509 ? gene.synonyms[0] : gene._id}`;\n const height = '500px';\n return (\n <iframe src={url} frameBorder=\"0\" width=\"100%\" height={height}>\n <p>browser doesn't support iframes</p>\n </iframe>\n );\n};\n\nexport default connect(Detail);\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 {Spinner} from \"react-bootstrap\";\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/msa.less';\nimport '../../../../node_modules/gramene-genetree-vis/src/styles/tree.less';\n\nfunction 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\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 ${this.gene.name}`\n }))\n }\n orthologList() {\n return this.orthoParaList('ortholog');\n }\n\n paralogList() {\n return this.orthoParaList('within_species_paralog');\n }\n\n orthoParaList(type) {\n var homology, thisGeneId;\n homology = _.get(this.gene, 'homology.homologous_genes');\n thisGeneId = this.gene._id;\n\n if (homology) {\n var homologs = _(homology)\n .pickBy(function filterCategories(thing, name) {\n return name.indexOf(type) === 0;\n })\n .values()\n .flatten()\n .value();\n\n if (!_.isEmpty(homologs)) {\n homologs.push(thisGeneId);\n return homologs; // only return something if we have something. We're testing for truthiness later.\n }\n }\n }\n explorations() {\n let x = [{\n name: 'Homologs',\n category: 'Gene Tree',\n count: this.tree.geneCount,\n handleClick: this.filterAllHomologs.bind(this)\n }];\n if (this.orthologs) {\n x.push({\n name: 'Orthologs',\n category: 'Gene Tree',\n count: this.orthologs.length,\n handleClick: this.filterOrthologs.bind(this)\n });\n }\n if (this.paralogs) {\n x.push({\n name: 'Paralogs',\n category: 'Gene Tree',\n count: this.paralogs.length,\n handleClick: this.filterParalogs.bind(this)\n });\n }\n return x;\n }\n links() {\n let links = [\n {\n name: 'Ensembl Gene Tree view',\n url: `${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 if (!this.props.geneDocs.hasOwnProperty(this.props.searchResult.id)) {\n return <Spinner/>\n }\n this.gene = this.props.geneDocs[this.props.searchResult.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 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 </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 '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-ga\";\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\"}} variant='dark'>{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 <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 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: `${this.props.ensemblURL}/${gene.system_name}/Gene/Summary?g=${gene._id}`},\n {name: 'PhytoMine', url: `https://phytozome.jgi.doe.gov/phytomine/keywordSearchResults.do?searchTerm=${jgiify(gene._id)}&searchSubmit=Search`},\n ];\n if (gene.taxon_id === 3702)\n links.push({name: 'Thalemine', url: `https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=${gene._id}&searchSubmit=search`});\n if (gene.taxon_id === 4577)\n links.push({name: 'MaizeGDB', url: `http://www.maizegdb.org/gene_center/gene/${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()}&nbsp;{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// 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.ensemblRest,\n species: g.system_name,\n tier_type: 'sequence'\n },\n {\n name: 'Genes',\n uri: this.props.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// };","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\";\nimport {TreeMenu} from \"react-tree-menu\";\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.children) {\n path.push(0);\n parent = node;\n node = node.children[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 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 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().convert(nodes);\n\n this.setState({hierarchy: [nested], selectedNode: undefined});\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 nodes.forEach(function(n) {\n nodeRef = nodeRef.children[n];\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 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 from 'react'\nimport ReactGA from 'react-ga'\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 members, vals, db;\n db = this.props.displayName;\n\n members = this.props.members;\n\n vals = _(members)\n .map(function (m) {\n return m.val;\n })\n .flatten(true)\n .sort()\n .uniq(true) // TODO figure out why there are duplicates.\n .map(function (item, idx) {\n var url = members[0].url(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 <ReactGA.OutboundLink\n eventLabel={db}\n to={url}\n target=\"_blank\"\n >\n {item}{external}\n </ReactGA.OutboundLink>\n </li>\n )\n })\n .value();\n\n vals = this.possiblyTruncateList(vals);\n\n return (\n <tr>\n <td className=\"xref-name-col\">{this.props.displayName}</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 .keyBy('db')\n .pickBy(function(val, name) {\n return dbxrefs.isKnown(name);\n })\n .map(function(val, name) {\n var xref = dbxrefs.fetch(name);\n return {url: xref.url, label: xref.label, val: val.ids};\n })\n .groupBy('label')\n .map(function(members, displayName) {\n return (\n <Xref key={displayName} displayName={displayName} members={members} />\n )\n })\n .value();\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 { 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 <button type=\"button\" className=\"btn btn-primary btn-sm\" onClick={this.toggleEmpties.bind(this)}>{this.state.collapseEmpties ? 'Expand' : 'Collapse'} empty branches</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&nbsp;|<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, CardDeck} 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 <CardDeck 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 </CardDeck>\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'\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 = true;\n })\n }\n else {\n this.state.genomes.forEach(g => {\n g.selected = props.grameneGenomes.active[g.taxon_id];\n })\n }\n }\n getSelectedGenomes() {\n let selected = {};\n let notAll = false;\n this.state.genomes.forEach(g => {\n if (g.selected) {\n selected[g.taxon_id] = true;\n }\n else {\n notAll = true;\n }\n });\n return notAll ? selected : {};\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 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"],"names":["apiBundles","docsBundle","filterBundle","viewsBundle","genomesBundle","facets","genomesOfInterest","grameneSuggestions","name","actionBaseType","persist","getPromise","store","t","selectSuggestionsQuery","g","selectGrameneGenomes","fetch","selectGrameneAPI","then","res","json","suggestions","Object","keys","active","length","grouped","category","groups","forEach","group","doclist","docs","sugg","num_genes","taxon_id","id","idx","taxon_freq","reactGrameneSuggestions","shouldUpdate","queryString","actionCreator","selectGrameneSuggestionsStatus","isLoading","suggestionsRaw","data","matches","selectGrameneSuggestionsReady","status","regex","RegExp","test","doFocusFirstGrameneSuggestion","arg","dispatch","getState","console","log","grameneTaxonomy","taxNodes","taxonomy","_","keyBy","_id","hasOwnProperty","is_a","p_id","p","children","push","reactGrameneTaxonomy","grameneMaps","maps","reactGrameneMaps","grameneSearch","offset","selectGrameneSearchOffset","rows","selectGrameneSearchRows","taxa","fq","join","selectGrameneFiltersQueryString","response","d","can_show","capabilities","c","reactGrameneSearch","formatFacetCountsForViz","a","count","displayName","sorted","counts","i","fc","sort","b","grameneTaxDist","getReducer","initialState","state","type","payload","selectGrameneTaxDist","forIn","map","tid","display_name","binnedResults","facet_counts","facet_fields","fixed_1000__bin","speciesTree","treesClient","tree","values","binMapper","binsClient","bins","taxDist","setBinType","setResults","grameneOrthologs","newState","assign","doRequestOrthologs","geneId","orthologs","selectGrameneOrthologs","API","taxonId","selectTargetTaxonId","newOrthologs","MAX_IDLIST_LENGTH","findNodeWithLeftIdx","node","leftIdx","result","child","rightIdx","parentIdx","markSubtree","source","invert","marked","reindexTree","grameneFilters","operation","negate","showMarked","showMenu","moveCopyMode","searchOffset","pick","filter","filters","warning","nextIdx","f","parent","target","targetCopy","fq_field","fq_value","sourceCopy","mode","moveCopySource","doNegateGrameneFilter","actions","doDeleteGrameneFilter","doChangeGrameneFilterOperation","doMoveOrCopyGrameneFilter","toUpperCase","doCopyGrameneFilter","doMarkGrameneFilterTargets","doUnmarkGrameneFilterTargets","doAcceptGrameneSuggestion","suggestion","doAddGrameneRangeQuery","terms","doToggleGrameneFilterMenu","doRequestResultsPage","page","doReplaceGrameneFilters","doClearGrameneFilters","selectGrameneFilters","selectGrameneFiltersStatus","hasSpaces","isQuery","idWithColon","getQuery","replace","handleIdList","queryObject","ids","uniq","idList","split","slice","action","reactGrameneFilters","genomes","myUrl","newFilters","JSON","parse","url","URL","href","pathname","search","stringify","grameneViews","options","show","doToggleGrameneView","selectGrameneViews","grameneDocs","genes","trees","domains","pathways","doRequestGrameneGene","selectGrameneGenes","doRequestGrameneTree","selectGrameneTrees","selectGrameneMaps","update_taxon_name","taxon_name","doRequestGramenePathways","selectGramenePathways","newIds","grameneGenomes","doShowGrameneGenomes","doUpdateGrameneGenomes","selectActiveGenomes","selectActiveGenomeCount","Gene","gene","Genes","results","doChangeQuantity","numFound","moreButton","e","fewerButton","docsToShow","doc","Pathway","pathway","Pathways","Domain","domain","Domains","Taxon","taxon","Species","ResultList","grameneGenes","grameneDomains","gramenePathways","searchUI","searchUpdated","Gramene","getStatus","cat","isChecked","toggle","tally","ResultSummary","doToggleCategory","showMatches","text","x","re","match","str","fontWeight","Suggestions","props","sugg1","suggestionsQuery","sugg2","margin","maxWidth","doAcceptSuggestion","groupValue","jdx","inventory","help","HelpDemo","list","GeneList","TaxDist","StatusCmp","content","grameneFiltersStatus","popover","activeGenomeCount","cursor","padding","backgroundColor","color","fontSize","Status","handleClick","window","event","cancelBubble","stopPropagation","selectTarget","unmarkTargets","Filter","classes","menu","key","menuItems","changeOperation","deleteNode","markTargets","isSource","toggleMenu","FiltersCmp","Filters","ResultsCmp","activeViews","v","React","createElement","Results","ViewsCmp","view","Views","external","location","Location","expression","Expression","homology","Homology","xrefs","Xrefs","renderTairSummary","searchResult","summary","trimSummary","start","substr","rest","ClosestOrtholog","desc","species","model_rep_id","model_rep_name","model_rep_description","model_rep_species_name","closest_rep_id","closest_rep_name","closest_rep_description","closest_rep_species_name","renderClosestOrtholog","shouldShowClosestOrtholog","details","label","available","expandedDetail","hasData","setState","geneDocs","requestGene","model_rep_taxon_id","taxLut","closest_rep_taxon_id","ensemblURL","taxName","numWordsInDescription","description","system_name","synonyms","renderMetadata","getDetailStatu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