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js czid.org collected 2026-09-25 18:40:03 UTC 2,860,802 bytes, 6 lines download raw bytes

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1,params:{cacheID:"f174e9e0fda6c823c5736180efe2073d",id:null,metadata:{},name:"SampleDetailsModeSampleMetadataFieldsQuery",operationKind:"query",text:"query SampleDetailsModeSampleMetadataFieldsQuery(\n  $snapshotLinkId: String\n  $input: queryInput_MetadataFields_input_Input!\n) {\n  MetadataFields(snapshotLinkId: $snapshotLinkId, input: $input) {\n    key\n    dataType\n    name\n    options\n    host_genome_ids\n    description\n    is_required\n    isBoolean\n    group\n  }\n}\n"}};i.hash="ce074b6ba509a8f02a4602d082a6c749";a.default=i},87718:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var l,r,o,i,u,d,c,p,m,h={argumentDefinitions:[],kind:"Fragment",metadata:null,name:"SampleDetailsModeSampleMetadataFragment",selections:[{alias:null,args:null,concreteType:"query_MetadataValues_additional_info",kind:"LinkedField",name:"additional_info",plural:!1,selections:[l={alias:null,args:null,kind:"ScalarField",name:"name",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"notes",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"host_genome_taxa_category",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"host_genome_name",storageKey:null},{alias:null,args:null,concreteType:"query_MetadataValues_additional_info_ercc_comparison_items",kind:"LinkedField",name:"ercc_comparison",plural:!0,selections:[{alias:null,args:null,kind:"ScalarField",name:"actual",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"expected",storageKey:null},l],storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"editable",storageKey:null},{alias:null,args:null,concreteType:"query_MetadataValues_additional_info_pipeline_run",kind:"LinkedField",name:"pipeline_run",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"error_message",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"guppy_basecaller_setting",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"host_subtracted",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"job_status",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"mapped_reads",storageKey:null},r={alias:null,args:null,kind:"ScalarField",name:"adjusted_remaining_reads",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"alert_sent",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"alignment_config_id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"assembled",storageKey:null},o={alias:null,args:null,kind:"ScalarField",name:"compression_ratio",storageKey:null},i={alias:null,args:null,kind:"ScalarField",name:"created_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"dag_vars",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"deleted_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"deprecated",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"executed_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"fraction_subsampled",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"fraction_subsampled_bases",storageKey:null},u={alias:null,args:null,kind:"ScalarField",name:"id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"known_user_error",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"max_input_fragments",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_branch",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_commit",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_execution_strategy",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_version",storageKey:null},d={alias:null,args:null,kind:"ScalarField",name:"qc_percent",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"results_finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"s3_output_prefix",storageKey:null},c={alias:null,args:null,kind:"ScalarField",name:"sample_id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"sfn_execution_arn",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"subsample",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"technology",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"time_to_finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"time_to_results_finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"total_bases",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"total_ercc_reads",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"total_reads",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"truncated",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"truncated_bases",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"unmapped_bases",storageKey:null},p={alias:null,args:null,kind:"ScalarField",name:"unmapped_reads",storageKey:null},m={alias:null,args:null,kind:"ScalarField",name:"updated_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"use_taxon_whitelist",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"wdl_version",storageKey:null},{alias:null,args:null,concreteType:"query_MetadataValues_additional_info_pipeline_run_version",kind:"LinkedField",name:"version",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"alignment_db",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline",storageKey:null}],storageKey:null}],storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"project_id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"project_name",storageKey:null},{alias:null,args:null,concreteType:"query_MetadataValues_additional_info_summary_stats",kind:"LinkedField",name:"summary_stats",plural:!1,selections:[r,o,{alias:null,args:null,kind:"ScalarField",name:"insert_size_mean",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"insert_size_standard_deviation",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"last_processed_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"percent_remaining",storageKey:null},d,{alias:null,args:null,kind:"ScalarField",name:"reads_after_bowtie2_ercc_filtered",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"reads_after_bowtie2_host_filtered",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"reads_after_czid_dedup",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"reads_after_fastp",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"reads_after_hisat2_host_filtered",storageKey:null},p],storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"upload_date",storageKey:null}],storageKey:null},{alias:null,args:null,concreteType:"query_MetadataValues_metadata_items",kind:"LinkedField",name:"metadata",plural:!0,selections:[{alias:null,args:null,kind:"ScalarField",name:"location_id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"raw_value",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"key",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"number_validated_value",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"metadata_field_id",storageKey:null},c,{alias:null,args:null,kind:"ScalarField",name:"string_validated_value",storageKey:null},m,u,{alias:null,args:null,kind:"ScalarField",name:"date_validated_value",storageKey:null},i,{alias:null,args:null,kind:"ScalarField",name:"base_type",storageKey:null}],storageKey:null}],type:"MetadataValues",abstractKey:null};h.hash="04fd5365aeef0f10041dbd0d51688521";a.default=h},61938:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var l,r,o,i,u,d,c,p,m,h,g,v,y,C,b,S,w,_={fragment:{argumentDefinitions:l=[{defaultValue:null,kind:"LocalArgument",name:"sampleId"},{defaultValue:null,kind:"LocalArgument",name:"snapshotLinkId"}],kind:"Fragment",metadata:null,name:"SampleDetailsModeSampleMetadataQuery",selections:[{alias:null,args:r=[{kind:"V

1ariable",name:"sampleId",variableName:"sampleId"},{kind:"Variable",name:"snapshotLinkId",variableName:"snapshotLinkId"}],concreteType:"SampleMetadata",kind:"LinkedField",name:"SampleMetadata",plural:!1,selections:[{args:null,kind:"FragmentSpread",name:"MetadataTabMetadataFragment"},{args:null,kind:"FragmentSpread",name:"NotesTabFragment"},{args:null,kind:"FragmentSpread",name:"MetadataSectionContentFragment"},{alias:null,args:null,concreteType:"query_SampleMetadata_additional_info",kind:"LinkedField",name:"additional_info",plural:!1,selections:[o={alias:null,args:null,kind:"ScalarField",name:"name",storageKey:null},{args:null,kind:"FragmentSpread",name:"PipelineTabFragment"},i={alias:null,args:null,kind:"ScalarField",name:"editable",storageKey:null},u={alias:null,args:null,kind:"ScalarField",name:"project_id",storageKey:null},d={alias:null,args:null,kind:"ScalarField",name:"project_name",storageKey:null},c={alias:null,args:null,kind:"ScalarField",name:"host_genome_taxa_category",storageKey:null},p={alias:null,args:null,kind:"ScalarField",name:"host_genome_name",storageKey:null},m={alias:null,args:null,kind:"ScalarField",name:"upload_date",storageKey:null}],storageKey:null}],storageKey:null}],type:"Query",abstractKey:null},kind:"Request",operation:{argumentDefinitions:l,kind:"Operation",name:"SampleDetailsModeSampleMetadataQuery",selections:[{alias:null,args:r,concreteType:"SampleMetadata",kind:"LinkedField",name:"SampleMetadata",plural:!1,selections:[{alias:null,args:null,concreteType:"query_SampleMetadata_additional_info",kind:"LinkedField",name:"additional_info",plural:!1,selections:[o,i,u,d,c,p,m,{alias:null,args:null,kind:"ScalarField",name:"notes",storageKey:null},{alias:null,args:null,concreteType:"query_SampleMetadata_additional_info_ercc_comparison_items",kind:"LinkedField",name:"ercc_comparison",plural:!0,selections:[{alias:null,args:null,kind:"ScalarField",name:"actual",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"expected",storageKey:null},o],storageKey:null},{alias:null,args:null,concreteType:"query_SampleMetadata_additional_info_pipeline_run",kind:"LinkedField",name:"pipeline_run",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"error_message",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"guppy_basecaller_setting",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"host_subtracted",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"job_status",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"mapped_reads",storageKey:null},h={alias:null,args:null,kind:"ScalarField",name:"adjusted_remaining_reads",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"alert_sent",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"alignment_config_id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"assembled",storageKey:null},g={alias:null,args:null,kind:"ScalarField",name:"compression_ratio",storageKey:null},v={alias:null,args:null,kind:"ScalarField",name:"created_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"dag_vars",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"deleted_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"deprecated",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"executed_at",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"fraction_subsampled",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"fraction_subsampled_bases",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"known_user_error",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"max_input_fragments",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_branch",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_commit",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_execution_strategy",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"pipeline_version",storageKey:null},y={alias:null,args:null,kind:"ScalarField",name:"qc_percent",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"results_finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"s3_output_prefix",storageKey:null},C={alias:null,args:null,kind:"ScalarField",name:"sample_id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"sfn_execution_arn",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"subsample",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"technology",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"time_to_finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"time_to_results_finalized",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"total_bases",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"total_ercc_reads",stor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a=_objectSpread(_objectSpread({},t.props.samplesAreNew?{new_sample_names:B("name",t.props.samples)}:{}),{},{project_id:t.props.project.id});(0,k.generateClientDownloadFromEndpoint)({endpoint:"/metadata/metadata_template_csv",params:a,fileName:"metadata_template.csv",fileType:"text/csv"})})),(0,C.default)((0,h.default)(t),"getRequiredLocationMetadataType",(function(){var a=t.state.projectMetadataFields;return(0,S.find)({dataType:"location",is_required:1},Object.values(a))})),(0,C.default)((0,h.default)(t),"renderTab",(function(){var a=t.props,l=a.onDirty,r=a.onShowCSVInstructions,o=a.project,u=a.samples,d=a.samplesAreNew,c=a.visible,p=a.withinModal,m=t.state,h=m.currentTab,g=m.hostGenomes,v=m.projectMetadataFields,y=m.sampleTypes;return h===i.MANUAL_INPUT?u&&v?w.default.createElement(D.default,{project:o,samples:u,samplesAreNew:d,onMetadataChange:t.onMetadataChangeManual,withinModal:p,projectMetadataFields:v,hostGenomes:g,sampleTypes:y}):w.default.createElement("div",{className:P.default.loadingMsg},"Loading..."):h===i.CSV_UPLOAD?w.default.createElement(w.default.Fragment,null,w.default.createElement("div",null,w.default.createElement("button",{className:(0,b.default)(P.default.link,"noStyleButton"),onClick:function onClick(){return r},onKeyDown:function onKeyDown(){return r}},"View CSV Upload Instructions")),w.default.createElement(L.default,{className:P.default.metadataCSVUpload,samples:u,onMetadataChange:t.onMetadataChangeCSV,project:o,samplesAreNew:d,visible:c,onDirty:l}),w.default.createElement("button",{className:(0,b.default)(P.default.link,"noStyleButton"),onClick:function onClick(){t.handleDownloadCSV()},onKeyDown:function onKeyDown(){t.handleDownloadCSV()}},"Download Metadata CSV 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t.tooltip?v.default.createElement(y.default,{trigger:a,content:t.tooltip,position:"top center",mouseEnterDelay:600}):a}},{key:"renderMenuItems",value:function renderMenuItems(){var t=this;return this.props.options.map((function(a){return{text:a.text,value:a.value,subtext:a.subtext,customNode:a.customNode?a.customNode:t.renderMenuItem(a)}}))}},{key:"render",value:function render(){var t=this.renderMenuItems(),a=this.props,l=a.className,r=a.initialSelectedValue,u=a.menuClassName,d=a.onChange,c=a.nullLabel,p=(0,i.default)(a,w);return v.default.createElement(b.default,(0,o.default)({},p,{className:l,menuClassName:u,options:t,value:r,onChange:d,nullLabel:c,usePortal:!0,withinModal:!0}))}}]),SubtextDropdown}(v.default.Component);a.default=_},64262:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var o=l(70131),i=l(28764),u=l(44480),d=r(l(96540)),c=l(33102),p=r(l(11074)),m=l(60487),h=l(59924),g=r(l(34621)),v=r(l(47499));a.default=function 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1a%2?ownKeys(Object(l),!0).forEach((function(a){(0,v.default)(t,a,l[a])})):Object.getOwnPropertyDescriptors?Object.defineProperties(t,Object.getOwnPropertyDescriptors(l)):ownKeys(Object(l)).forEach((function(a){Object.defineProperty(t,a,Object.getOwnPropertyDescriptor(l,a))}))}return t}function _createSuper(t){var a=function _isNativeReflectConstruct(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}();return function _createSuperInternal(){var l,r=(0,g.default)(t);if(a){var o=(0,g.default)(this).constructor;l=Reflect.construct(r,arguments,o)}else l=r.apply(this,arguments);return(0,h.default)(this,l)}}var P=[{text:"Coverage",value:"coverage"},{text:"Depth",value:"depth"},{text:"RPM (reads per million)",value:"rpm"},{text:"DPM (depth per million)",value:"dpm"},{text:"Mapped Reads",value:"total_reads"}],j=[{text:"Genes",value:"gene"},{text:"Alleles",value:"allele"}],B=[{text:"Logarithmic",value:"symlog"},{text:"Linear",value:"linear"}],V="sampleDetails",W="geneDetails";(a.default=function(t){(0,m.default)(AMRHeatmapView,t);var a,l=_createSuper(AMRHeatmapView);function AMRHeatmapView(t){var a;return(0,d.default)(this,AMRHeatmapView),a=l.call(this,t),(0,v.default)((0,p.default)(a),"updateOptions",(function(t){var l=a.state.selectedOptions,r=Object.assign({},l,t);a.setState({selectedOptions:r})})),(0,v.default)((0,p.default)(a),"onSampleLabelClick",(function(t){var l=a.state,r=l.sidebarVisible,o=l.sidebarMode,i=l.selectedSampleId;t?r&&o===V&&i===t?a.closeSidebar():a.setState({selectedSampleId:t,sidebarMode:V,sidebarVisible:!0}):a.closeSidebar()})),(0,v.default)((0,p.default)(a),"onGeneLabelClick",(function(t){var l=a.state,r=l.sidebarVisible,o=l.sidebarMode,i=l.selectedGene;!t||r&&o===W&&i===t?a.closeSidebar():a.setState({selectedGene:t,sidebarMode:W,sidebarVisible:!0})})),(0,v.default)((0,p.default)(a),"closeSidebar",(function(){a.setState({sidebarVisible:!1})})),(0,v.default)((0,p.default)(a),"onMetadataUpdate",(function(t,l){var r=a.state,o=r.selectedSampleId,i=r.samplesWithAMRCounts.map((function(a){return a.sampleId!==o||(a.metadata[t]=l),a})),u=a.extractSampleLabels(i);a.setState({samplesWithAMRCounts:i,sampleLabels:u})})),a.state={loading:!0,maxValues:null,rawSampleData:null,samplesWithAMRCounts:null,samplesMetadataTypes:null,selectedOptions:{metric:"coverage",viewLevel:"gene",scale:"symlog"},selectedSampleId:null,selectedGene:null,sidebarVisible:!1,sidebarMode:null},a}return(0,c.default)(AMRHeatmapView,[{key:"componentDidMount",value:function componentDidMount(){var t=this.props.sampleIds;this.requestSampleData(t)}},{key:"requestSampleData",value:(a=(0,u.default)(o.default.mark((function _callee(t){var a,l,r,u,d,c,p,m,h,g,v,y,C,b,_;return o.default.wrap((function _callee$(o){for(;;)switch(o.prev=o.next){case 0:return o.next=2,Promise.all([(0,S.getAMRCounts)(t),(0,w.getSampleMetadataFields)(t)]);case 2:a=o.sent,l=(0,i.default)(a,2),r=l[0],u=l[1],d=r.filter((function(t){return""===t.error})),c=d.map((function(t){return _objectSpread(_objectSpread({},t),{},{metadata:(0,T.processMetadata)({metadata:t.metadata,flatten:!0})})})),p=this.correctSampleAndGeneNames(c),m=this.findMaxValues(p),h=(0,T.processMetadataTypes)(u),g=this.extractSampleLabels(p),v=this.extractGeneAndAlleleLabels(p),y=(0,i.default)(v,2),C=y[0],b=y[1],_=this.mapAllelesToGenes(p),this.setState({rawSampleData:r,samplesWithAMRCounts:p,maxValues:m,samplesMetadataTypes:h,sampleLabels:g,geneLabels:C,alleleLabels:b,alleleToGeneMap:_,loading:!1});case 15:case"end":return o.stop()}}),_callee,this)}))),function requestSampleData(t){return a.apply(this,arguments)})},{key:"correctSampleAndGeneNames",value:function correctSampleAndGeneNames(t){var a=new Map;return t.forEach((function(t){if(a.has(t.sampleName)){var l=a.get(t.sampleName),r=t.sampleName;t.sampleName="".concat(t.sampleName," (").concat(l,")"),a.set(r,l+1)}else a.set(t.sampleName,1);t.amrCounts.forEach((function(t){var a=/[^_]+/.exec(t.gene)[0];t.gene=a}))})),t}}

1,{key:"assembleControlOptions",value:function assembleControlOptions(){return[{key:"viewLevel",options:j,label:"View Level"},{key:"metric",options:P,label:"Metric"},{key:"scale",options:B,label:"Scale"}]}},{key:"findMaxValues",value:function findMaxValues(t){return t.reduce((function(t,a){return a.amrCounts.forEach((function(a){t.depth=Math.max(t.depth,a.depth),t.coverage=Math.max(t.coverage,a.coverage),t.rpm=Math.max(t.rpm,a.rpm||0),t.dpm=Math.max(t.dpm,a.dpm||0),t.total_reads=Math.max(t.total_reads,a.total_reads||0)})),t}),{depth:0,coverage:0,rpm:0,dpm:0,total_reads:0})}},{key:"hasDataToDisplay",value:function hasDataToDisplay(t){return t.some((function(t){return t.amrCounts.length>0}))}},{key:"mapAllelesToGenes",value:function mapAllelesToGenes(t){var a={};return t.forEach((function(t){t.amrCounts.forEach((function(t){a[t.allele]=t.annotation_gene||t.gene}))})),a}},{key:"extractSampleLabels",value:function extractSampleLabels(t){return t.map((function(t){return{label:t.sampleName,id:t.sampleId,metadata:t.metadata}}))}},{key:"extractGeneAndAlleleLabels",value:function extractGeneAndAlleleLabels(t){var a={},l={};return t.forEach((function(t){t.amrCounts.forEach((function(t){null===t.annotation_gene||void 0===t.annotation_gene?a[t.gene]=!0:a[t.annotation_gene]=!0,l[t.allele]=!0}))})),[Object.keys(a).map((function(t){return{label:t}})),Object.keys(l).map((function(t){return{label:t}}))]}},{key:"computeHeatmapValuesForCSV",value:function computeHeatmapValuesForCSV(){var t=this.state.samplesWithAMRCounts,a=[];t.forEach((function(t){t.amrCounts.forEach((function(l){var r=["".concat(t.sampleName,",").concat(l.gene,",").concat(l.allele,",").concat(l.coverage,",").concat(l.depth,",").concat(l.rpm||"N/A",",").concat(l.dpm||"N/A",",").concat(l.total_reads||"N/A")];a.push(r)}))}));return[["sample_name,gene_name,allele_name,coverage,depth,rpm,dpm,mapped_reads"],a]}},{key:"getSidebarParams",value:function getSidebarParams(){var t=this.state,a=t.sidebarMode,l=t.selectedSampleId,r=t.selectedGene;switch(a){case V:return{sampleId:l,showReportLink:!0,onMetadataUpdate:this.onMetadataUpdate};case W:return{geneName:r}}}},{key:"getDownloadCSVLink",value:function getDownloadCSVLink(){var t=this.computeHeatmapValuesForCSV(),a=(0,i.default)(t,2),l=a[0],r=a[1];return C.default.createElement("a",{href:(0,R.createCSVObjectURL)(l,r),download:"idseq_amr_heatmap_values.csv",target:"_blank",rel:"noopener noreferrer",key:"Download_CSV_link"},"Download CSV")}},{key:"getDownloadOptions",value:function getDownloadOptions(){return[{text:this.getDownloadCSVLink(),value:"csv"}]}},{key:"renderHeader",value:function renderHeader(){var t=this.state.loading;return C.default.createElement(O.ViewHeader,{className:D.default.viewHeader},C.default.createElement(O.ViewHeader.Content,null,C.default.createElement(O.ViewHeader.Pretitle,{breadcrumbLink:"/home"},"Discovery View"),C.default.createElement(O.ViewHeader.Title,{label:"Antimicrobial Resistance Heatmap"})),!t&&C.default.createElement(O.ViewHeader.Controls,{className:D.default.controls},C.default.createElement(M.DownloadButtonDropdown,{className:D.default.controlElement,options:this.getDownloadOptions(),disabled:t,onClick:function onClick(){}})))}},{key:"renderControls",value:function renderControls(){var t=this.state,a=t.selectedOptions,l=t.loading,r=t.maxValues,o=r?r[a.metric]:0;return C.default.createElement(A.default,{controls:this.assembleControlOptions(),selectedOptions:a,onSelectedOptionsChange:this.updateOptions,isDataReady:!l,maxValueForLegend:o})}},{key:"renderDeprecationWarning",value:function renderDeprecationWarning(){return C.default.createElement(y.Callout,{className:D.default.deprecationWarning,intent:"info"},"This heatmap is created with data from a deprecated version of our Antimicrobial Resistance pipeline."," ",C.default.createElement(N.default,{href:k.AMR_DEPRECATED_HELP_LINK},"Learn more."))}},{key:"renderVisualization",value:function renderVisualization(){var t=this.state,a=t.loading,l=t.samplesWithAMRCounts,r=t.selectedOptions,o=t.samplesMetadataTypes,i=t.sampleLabels,u=t.geneLabels,d=t.alleleLabels,c=t.alleleToGeneMap;return a?C.default.createElement(x.default,{message:"Loading...",className:D.default.loadingIndicator}):this.hasDataToDisplay(l)?C.default.createElement("div",{className:"row visualization-content"},C.default.createElement(E.default,null,C.default.createElement(I.default,{samplesWithAMRCounts:l,selectedOptions:r,onSampleLabelClick:this.onSampleLabelClick,onGeneLabelClick:this.onGeneLabelClick,samplesMetadataTypes:o,sampleLabels:i,geneLabels:u,alleleLabels:d,alleleToGeneMap:c,metrics:P}))):C.default.createElement("p",{className:D.default.noDataMsg},"No Antimicrobial Resistance data for selected samples.")}}

1,{key:"renderSidebar",value:function renderSidebar(){var t=this.state,a=t.sidebarMode,l=t.sidebarVisible;return C.default.createElement(_.default,{visible:l,mode:a,onClose:this.closeSidebar,params:this.getSidebarParams()})}},{key:"render",value:function render(){var t=this;return C.default.createElement("div",{className:D.default.AMRHeatmapView},C.default.createElement(O.NarrowContainer,null,this.renderHeader()),C.default.createElement(b.StickyContainer,null,C.default.createElement(b.Sticky,null,(function(a){var l=a.style;return C.default.createElement("div",{style:l},C.default.createElement(O.NarrowContainer,null,t.renderControls()))})),C.default.createElement(O.NarrowContainer,null,this.renderDeprecationWarning()),this.renderVisualization()),this.renderSidebar())}}]),AMRHeatmapView}(C.default.Component)).contextType=L.UserContext},44548:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var 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l;return(0,o.default)(this,AMRHeatmapVis),l=a.call(this,t),(0,m.default)((0,u.default)(l),"colorFilter",(function(t,a,l,r,o){return t>0?l:o})),(0,m.default)((0,u.default)(l),"onNodeHover",(function(t){l.setState({nodeHoverInfo:l.getTooltipData(t),nodeHovered:!0,tooltipLocation:l.heatmap.getCursorLocation()})})),(0,m.default)((0,u.default)(l),"onNodeHoverOut",(function(){l.setState({nodeHoverInfo:null})})),(0,m.default)((0,u.default)(l),"onRowLabelClick",(function(t){var a=l.props,r=a.alleleToGeneMap,o=a.selectedOptions,i=a.onGeneLabelClick,u=t;o.viewLevel===_&&(u=r[t]),i(u)})),(0,m.default)((0,u.default)(l),"onMetadataLabelHover",(function(t){var a=l.heatmap.getColumnMetadataLegend(t.value);l.setState({columnMetadataLegend:a,metadataLabelHovered:!0,tooltipLocation:l.heatmap.getCursorLocation()})})),(0,m.default)((0,u.default)(l),"onMetadataNodeHover",(function(t,a){var r=l.heatmap.getColumnMetadataLegend(a.value),o=t.metadata[a.value]||"Unknown",i=(0,m.default)({},o,r[o]);l.setState({columnMetadataLegend:i,tooltipLocation:l.heatmap.getCursorLocation()})})),(0,m.default)((0,u.default)(l),"onMetadataLabelOut",(function(){l.setState({columnMetadataLegend:null})})),(0,m.default)((0,u.default)(l),"onMetadataAddButtonClick",(function(t){l.setState({addMetadataTrigger:t})})),(0,m.default)((0,u.default)(l),"onMetadataSelectionChange",(function(t){l.setState({selectedMetadata:t})})),l.state={nodeHoverInfo:null,tooltipLocation:null,columnMetadataLegend:null,addMetadataTrigger:null,nodeHovered:!1,metadataLabelHovered:!1,selectedMetadata:new Set(x)},l.heatmap=null,l}return(0,i.default)(AMRHeatmapVis,[{key:"componentDidMount",value:function componentDidMount(){this.updateHeatmap()}},{key:"componentDidUpdate",value:function componentDidUpdate(t,a){var 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t=a.props,l=t.allowedFeatures,r=t.domain,o=a.state,i=o.currentDisplay,u=o.currentTab,d=o.filteredProjectCount,c=o.filteredProjectDimensions,p=o.filteredSampleCountsByWorkflow,m=o.filteredSampleDimensions,h=o.filteredSampleStats,g=o.loadingDimensions,v=o.loadingStats,y=o.mapPreviewedLocationId,C=o.mapSidebarProjectCount,b=o.mapSidebarProjectDimensions,S=o.mapSidebarSampleCount,w=o.mapSidebarSampleDimensions,E=o.mapSidebarSampleStats,x=o.selectedSampleIdsByWorkflow,L=o.mapSidebarTab,O=o.plqcPreviewedSamples,N=o.projectDimensions,k=o.project,T=o.sampleDimensions,A=o.search,I=o.showStats,R=o.userDataCounts,D=a.props,P=D.snapshotShareId,j=D.snapshotProjectDescription,B=a.getFilterCount(),V=B||A?c:N,W=B||A?m:T,U=g||v,H=x[M.WorkflowType.SHORT_READ_MNGS],G=p[M.WorkflowType.SHORT_READ_MNGS];return 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1:V,projects:a.mapPreviewProjects,projectStats:{count:y?C:d},ref:function ref(t){return a.mapPreviewSidebar=t},sampleDimensions:y||O?w:W,samples:a.mapPreviewSamples,sampleStats:y||O?_objectSpread(_objectSpread({},E),{},{count:S}):_objectSpread(_objectSpread({},h),{},{count:G}),selectedSampleIds:H}):_.default.createElement(Z.DiscoverySidebar,{allowedFeatures:l,currentTab:u,noDataAvailable:Boolean(r===le.DISCOVERY_DOMAIN_MY_DATA&&R&&!R.projectCount),loading:U,onFilterClick:r!==le.DISCOVERY_DOMAIN_SNAPSHOT&&a.handleMetadataFilterClick,projectDimensions:V,projectStats:r===le.DISCOVERY_DOMAIN_SNAPSHOT?{count:G?1:null}:{count:d},sampleDimensions:W,sampleStats:_objectSpread(_objectSpread({},h),{},{count:h.count}),project:P?{editable:!1,description:j}:k,onProjectDescriptionSave:a.handleProjectDescriptionSave})))}));var r=a.props,i=r.domain,m=r.projectId,g=r.updateDiscoveryProjectId;a.urlParser=new A.default({filters:"object",projectId:"string",showFilters:"boolean",showStats:"boolean"});var v=a.urlParser.parse(location.search),y=(0,B.loadState)(sessionStorage,ae.KEY_DISCOVERY_VIEW_OPTIONS),L=(0,B.loadState)(localStorage,ae.KEY_DISCOVERY_VIEW_OPTIONS);g(m||v.projectId||null);var O=_objectSpread(_objectSpread(_objectSpread({},L),y),v);return a.state=_objectSpread(_objectSpread(_objectSpread({currentDisplay:"table",currentTab:m||i===le.DISCOVERY_DOMAIN_ALL_DATA?ae.TAB_SAMPLES:ae.TAB_PROJECTS,emptyStateModalOpen:a.isFirstTimeUser(),filteredProjectCount:null,filteredProjectDimensions:[],filteredSampleCountsByWorkflow:(0,C.default)((0,C.default)((0,C.default)((0,C.default)((0,C.default)({},M.WorkflowType.SHORT_READ_MNGS,null),M.WorkflowType.LONG_READ_MNGS,null),M.WorkflowType.AMR,null),M.WorkflowType.CONSENSUS_GENOME,null),M.WorkflowType.BENCHMARK,null),filteredSampleDimensions:[],filteredSampleStats:{},filteredVisualizationCount:null,filters:{},loadingDimensions:!0,loadingLocations:!0,loadingStats:!0,mapLevel:"country",mapLocationData:{},mapPreviewedLocationId:null,mapSidebarProjectCount:null,mapSidebarProjectDimensions:[],mapSidebarSampleCount:null,mapSidebarSampleDimensions:[],mapSidebarSampleStats:{},mapSidebarTab:"summary",project:null,projectDimensions:[],projectId:m,rawMapLocationData:{},sampleActiveColumnsByWorkflow:O.sampleActiveColumnsByWorkflow?void 0:P.DEFAULT_ACTIVE_COLUMNS_BY_WORKFLOW,sampleDimensions:[],search:null,selectableSampleIds:[],selectedSampleIdsByWorkflow:(0,C.default)((0,C.default)((0,C.default)((0,C.default)((0,C.default)({},M.WorkflowType.AMR,new Set),M.WorkflowType.CONSENSUS_GENOME,new Set),M.WorkflowType.SHORT_READ_MNGS,new Set),M.WorkflowType.LONG_READ_MNGS,new Set),M.WorkflowType.BENCHMARK,new Set),showFilters:!0,showStats:!0,userDataCounts:null,workflowCounts:void 0,workflow:M.WorkflowType.SHORT_READ_MNGS,workflowEntity:M.WORKFLOW_ENTITIES.SAMPLES},L),y),v),a.state=_objectSpread(_objectSpread({},a.state),{},{orderBy:y[a.getCurrentTabOrderByKey()],orderDirection:y[a.getCurrentTabOrderDirKey()]}),a.workflowEntity=M.WORKFLOWS[a.state.workflow].entity,a.dataLayer=new ne.DiscoveryDataLayer(i),a.samples=a.dataLayer.samples.createView({conditions:a.getConditionsWithSessionStorage(ae.TAB_SAMPLES,M.WorkflowType.SHORT_READ_MNGS),onViewChange:function onViewChange(){a.refreshSampleData(M.WorkflowType.SHORT_READ_MNGS)},shouldConvertIdToString:!0}),a.amrWorkflowRuns=a.dataLayer.amrWorkflowRuns.createView({conditions:a.getConditionsWithSessionStorage(ae.TAB_SAMPLES,M.WorkflowType.AMR),onViewChange:function onViewChange(){a.refreshWorkflowRunData(M.WorkflowType.AMR)},shouldConvertIdToString:!0}),a.benchmarkWorkflowRuns=a.dataLayer.benchmarkWorkflowRuns.createView({conditions:a.getConditionsWithSessionStorage(ae.TAB_SAMPLES,M.WorkflowType.BENCHMARK),onViewChange:function onViewChange(){a.refreshWorkflowRunData(M.WorkflowType.BENCHMARK)},shouldConvertIdToString:!0}),a.longReadMngsSamples=a.dataLayer.longReadMngsSamples.createView({conditions:a.getConditionsWithSessionStorage(ae.TAB_SAMPLES,M.WorkflowType.LONG_READ_MNGS),onViewChange:function onViewChange(){a.refreshSampleData(M.WorkflowType.LONG_READ_MNGS)},shouldConvertIdToString:!0}),a.projects=a.dataLayer.projects.createView({conditions:a.getConditionsWithSessionStorage(ae.TAB_PROJECTS),onViewChange:a.refreshProjectData,shouldConvertIdToString:!0}),a.visualizations=a.dataLayer.visualizations.createView({conditions:a.getConditionsWithSessionStorage(ae.TAB_VISUALIZATIONS),onViewChange:a.refreshVisualizationData,shouldConvertIdToString:!1}),a.setupWorkflowConfigs(),a.mapPreviewProjects=a.projects,a.mapPreviewSamples=a.samples,a.projectsView=null,a.samplesView=_.default.createRef(),a.mapPreviewSidebar=null,a.visualizationsView=null,a.props.fetchNextGenWorkflowRuns(a.getConditionsWithSessionStorage(ae.TAB_SAMPLES,M.WorkflowType.CONSENSUS_GENOME)),a.samples.loadPage(0),i!==le.DISCOVERY_DOMAIN_SNAPSHOT&&(a.projects.loadPage(0),a.visualizations.loadPage(0),a.amrWorkflowRuns.loadPage(0),a.longReadMngsSamples.loadPage(0)),a.updateBrowsingHistory("replace"),a}

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Run `relay-compiler` to update the generated files to receive the expected data."),c),z=a.DiscoveryViewFCFedWorkflowRunsAggregateQuery=(void 0!==p||(p=l(88697)).hash&&"caccf7f95c73f91dd9c9ba8d9f0e8239"!==p.hash&&console.error("The definition of 'DiscoveryViewFCFedWorkflowRunsAggregateQuery' appears to have changed. Run `relay-compiler` to update the generated files to receive the expected data."),p),q=a.DiscoveryViewFCFedWorkflowsTotalCountQuery=(void 0!==m||(m=l(68750)).hash&&"e447cbe8e119a4b0f564f01c18ec1c68"!==m.hash&&console.error("The definition of 'DiscoveryViewFCFedWorkflowsTotalCountQuery' appears to have changed. Run `relay-compiler` to update the generated files to receive the expected data."),m);function fetchProjectIds(t,a){return _fetchProjectIds.apply(this,arguments)}function _fetchProjectIds(){return(_fetchProjectIds=(0,b.default)(h.default.mark((function _callee7(t,a){var l;return h.default.wrap((function _callee7$(r){for(;;)switch(r.prev=r.next){case 0:return r.abrupt("return",(0,x.getProjects)({domain:t,filters:{visibility:null===(l=a.filters)||void 0===l?void 0:l.visibility},limit:0,offset:0,listAllIds:!0}).then((function(t){return t.all_projects_ids})));case 1:case"end":return r.stop()}}),_callee7)})))).apply(this,arguments)}function queryWorkflowRuns(t,a,l,r,o){return _queryWorkflowRuns.apply(this,arguments)}function _queryWorkflowRuns(){return(_queryWorkflowRuns=(0,b.default)(h.default.mark((function _callee8(t,a,l,r,o){var i,u,d,c,p,m,v,C,b,w,_,x,L,O,T,A,I,R,D,P,j,K,z,q,Z,Y,X,Q,J,$,ee,te,ae,ne,le,re,oe,ie,se;return h.default.wrap((function _callee8$(h){for(;;)switch(h.prev=h.next){case 0:return c=a.projectId,p=a.search,m=a.orderBy,v=a.orderDir,C=a.filters,b=a.nextGenFilters,null!=c&&void 0!==o?w={_in:o.includes(parseInt(c))?[parseInt(c)]:[]}:null!=c?w={_in:[parseInt(c)]}:void 0!==o&&(w={_in:o}),_={where:{workflowVersion:{workflow:{name:{_in:["consensus-genome"]}}},deprecatedById:{_is_null:!0},collectionId:w,startedAt:void 0!==(null==b?void 0:b.startedAtIso)?{_gte:b.startedAtIso}:void 0,entityInputs:{entityType:{_eq:"sequencing_read"},inputEntityId:{_is_null:!1}}},orderByArray:getWorkflowRunsOrderBys(m,v),todoRemove:{domain:l.domain,projectId:c,search:p,host:null==C?void 0:C.host,locationV2:null==C?void 0:C.locationV2,taxon:null==C?void 0:C.taxon,taxonLevels:null==C?void 0:C.taxaLevels,time:null==C?void 0:C.time,tissue:null==C?void 0:C.tissue,visibility:null==C?void 0:C.visibility,orderBy:m,orderDir:v,workflow:t}},L=(null==p?void 0:p.length)||(null==C||null===(i=C.locationV2)||void 0===i?void 0:i.length)||(null==C||null===(u=C.host)||void 0===u?void 0:u.length)||(null==C||null===(d=C.tissue)||void 0===d?void 0:d.length),(L||(null==b?void 0:b.taxonNames.length)||B(m))&&(x={where:{collectionId:w,sample:L?{name:null!=p&&p.length?{_iregex:p.trim().split(/\s+/).map((function(t){return"(?=.*".concat((0,S.escapeRegExp)(t),")")})).join("")+".*"}:void 0,collectionLocation:null!=C&&null!==(O=C.locationV2)&&void 0!==O&&O.length?{_in:C.locationV2}:void 0,hostOrganism:null!=C&&null!==(T=C.host)&&void 0!==T&&T.length?{name:{_in:C.host.map((function(t){return t.toString()}))}}:void 0,sampleType:null!=C&&null!==(A=C.tissue)&&void 0!==A&&A.length?{_in:C.tissue}:void 0}:void 0},orderByArray:B(m)?getSequencingReadsOrderBys(m,v):void 0,todoRemove:{domain:l.domain,projectId:c,search:p,host:null==C?void 0:C.host,locationV2:null==C?void 0:C.locationV2,taxons:null==C?void 0:C.taxon,taxaLevels:null==C?void 0:C.taxaLevels,time:null==C?void 0:C.time,tissue:null==C?void 0:C.tissue,visibility:null==C?void 0:C.visibility,orderBy:m,orderDir:v,workflow:t}}),V(m)&&(I={where:void 0!==w?{collectionId:w}:void 0,orderBy:getConsensusGenomesOrderBys(m,v),todoRemove:{domain:l.domain,projectId:c,search:p,host:null==C?void 0:C.host,locationV2:null==C?void 0:C.locationV2,taxons:null==C?void 0:C.taxon,taxaLevels:null==C?void 0:C.taxaLevels,time:null==C?void 0:C.time,tissue:null==C?void 0:C.tissue,visibility:null==C?void 0:C.visibility,orderBy:m,orderDir:v,workflow:t}}),R=(0,E.fetchQuery)(r,U,{input:_}).toPromise(),void 0!==x&&(D=null!=b&&b.taxonNames.length?Promise.all([(0,E.fetchQuery)(r,H,{input:_objectSpread(_objectSpread({},x),{},{where:_objectSpread(_objectSpread({},x.where),{},{taxon:{name:{_in:b.taxonNames}}})})}).toPromise(),R.then((function(t){return(0,E.fetchQuery)(r,H,{input:_objectSpread(_objectSpread({},x),{},{where:_objectSpread(_objectSpread({},x.where),{},{consensusGenomes:{producingRunId:{_in:t.fedWorkflowRuns.map((function(t){return t.id}))},taxon:{name:{_in:b.taxonNames}}}})})}).toPromise()}))]).then((function(t){var a=(0,y.default)(t,2),l=a[0],r=a[1];if(null==(null==l?void 0:l.fedSequencingReads)||null==(null==r?void 0:r.fedSequencingReads))throw new Error("Taxon filter request(s) failed: ".concat(JSON.stringify(l)," ").concat(JSON.stringify(r)));var o=new Set([].concat((0,g.default)(l.fedSequencingReads.filter(k.isNotNullish).map((function(t){return t.id}))),(0,g.default)(r.fedSequencingReads.filter(k.isNotNullish).map((function(t){return t.id})))));return{fedSequencingReads:(0,g.default)(o).map((function(t){return{id:t}}))}})):(0,E.fetchQuery)(r,H,{input:x}

1).toPromise()),void 0!==I&&(P=(0,E.fetchQuery)(r,G,{input:I}).toPromise()),h.next=12,R;case 12:if(j=h.sent,void 0===D){h.next=19;break}return h.next=16,D;case 16:h.t0=h.sent,h.next=20;break;case 19:h.t0=void 0;case 20:if(K=h.t0,void 0===P){h.next=27;break}return h.next=24,P;case 24:h.t1=h.sent,h.next=28;break;case 27:h.t1=void 0;case 28:if(z=h.t1,null!=(null==j?void 0:j.fedWorkflowRuns)){h.next=31;break}throw new Error("Missing data: ".concat(JSON.stringify(j)," ").concat(JSON.stringify(t)," ").concat(p," ").concat(m," ").concat(v," ").concat(JSON.stringify(C)," ").concat(JSON.stringify(l),"}"));case 31:if(void 0===D||null!=(null==K?void 0:K.fedSequencingReads)){h.next=33;break}throw new Error("Missing filtered sequencingReads data: ".concat(JSON.stringify(K)));case 33:if(void 0===P||null!=(null==z?void 0:z.fedConsensusGenomes)){h.next=35;break}throw new Error("Missing sorted consensusGenomes data: ".concat(JSON.stringify(z)));case 35:if(q=[],!B(m)){h.next=62;break}if(null!=(null==K?void 0:K.fedSequencingReads)){h.next=39;break}throw new Error("Impossible state: Sorting by SequencingRead but no SequencingRead response.");case 39:Z=new Map,Y=_createForOfIteratorHelper(j.fedWorkflowRuns.filter(k.isNotNullish)),h.prev=41,Y.s();case 43:if((X=Y.n()).done){h.next=51;break}if(J=X.value,null!=($=null===(Q=J.entityInputs.edges[0])||void 0===Q?void 0:Q.node.inputEntityId)){h.next=48;break}return h.abrupt("continue",49);case 48:Z.has($)?null===(ee=Z.get($))||void 0===ee||ee.push(J):Z.set($,[J]);case 49:h.next=43;break;case 51:h.next=56;break;case 53:h.prev=53,h.t2=h.catch(41),Y.e(h.t2);case 56:return h.prev=56,Y.f(),h.finish(56);case 59:q=K.fedSequencingReads.filter(k.isNotNullish).filter((function(t){return Z.has(t.id)})).flatMap((function(t){return Z.get(t.id)})),h.next=75;break;case 62:if(!V(m)){h.next=73;break}if(null!=(null==z?void 0:z.fedConsensusGenomes)){h.next=65;break}throw new Error("Impossible state: Sorting by ConsensusGenome but no ConsensusGenome response.");case 65:te=null!=(null==K?void 0:K.fedSequencingReads)?new Set(K.fedSequencingReads.filter(k.isNotNullish).map((function(t){return t.id}))):void 0,ae=new Map(j.fedWorkflowRuns.filter(k.isNotNullish).flatMap((function(t){var a,l=null===(a=t.entityInputs.edges[0])||void 0===a?void 0:a.node.inputEntityId;return null==l?[]:void 0===te||te.has(l)?[[t.id,t]]:[]}))),ne=z.fedConsensusGenomes.map((function(t){return null==t?void 0:t.producingRunId})).filter(k.isNotNullish).filter((function(t){return ae.has(t)})).flatMap((function(t){return ae.get(t)})),le=new Set(ne.map((function(t){return t.id}))),re=(0,g.default)(ae.values()).filter((function(t){return!le.has(t.id)})),q="ASC"===v?[].concat((0,g.default)(re),(0,g.default)(ne)):[].concat((0,g.default)(ne),(0,g.default)(re)),h.next=75;break;case 73:ie=void 0!==K?new Set(null===(oe=K.fedSequencingReads)||void 0===oe?void 0:oe.filter(k.isNotNullish).map((function(t){return t.id}))):void 0,q=j.fedWorkflowRuns.filter(k.isNotNullish).filter((function(t){var a,l=null===(a=t.entityInputs.edges[0])||void 0===a?void 0:a.node.inputEntityId;if(null==l)throw new Error("Couldn't find an entity input: ".concat(JSON.stringify(t)));return void 0===ie||ie.has(l)}));case 75:return se=q.map((function(t){var a,l,r,o,i,u,d,c,p=null===(a=t.entityInputs.edges[0])||void 0===a?void 0:a.node.inputEntityId;try{var m;d=JSON.parse(null!==(m=t.rawInputsJson)&&void 0!==m?m:"")}catch(t){}if("FAILED"===t.status&&null!=t.errorLabel)c=(0,N.sampleErrorInfo)({error:{label:t.errorLabel}}).pillStatus;else if(null!=t.status){var h;c=null!==(h=W[t.status])&&void 0!==h?h:t.status}return{id:t.id,createdAt:null!==(l=t.startedAt)&&void 0!==l?l:void 0,status:null===(r=c)||void 0===r?void 0:r.toLowerCase(),workflow:"consensus-genome",wdl_version:null!=(null===(o=t.workflowVersion)||void 0===o?void 0:o.version)?(0,M.formatSemanticVersion)(t.workflowVersion.version):void 0,creation_source:null!==(i=null===(u=d)||void 0===u?void 0:u.creation_source)&&void 0!==i?i:void 0,inputSequencingReadId:p,inputJson:d}})),"creation_source"===m&&se.sort((function(t,a){var l,r;return(null!==(l=t.creation_source)&&void 0!==l?l:"").localeCompare(null!==(r=a.creation_source)&&void 0!==r?r:"")*("ASC"===v?1:-1)})),h.abrupt("return",se);case 78:case"end":return h.stop()}}),_callee8,null,[[41,53,56,59]])})))).apply(this,arguments)}function getWorkflowRunsOrderBys(t,a){var l="ASC"===a?"asc_nulls_first":"desc_nulls_last";switch(t){case null:case void 0:case"createdAt":return[{startedAt:l}];case"wdl_version":return[{workflowVersion:{version:l}}];default:return}}function getSequencingReadsOrderBys(t,a){var l="ASC"===a?"asc_nulls_first":"desc_nulls_last";switch(t){case null:case void 0:return;case"technology":case"medakaModel":return[(0,C.default)({},t,l)];case"wetlabProtocol":return[{protocol:l}];case"sample":return[{sample:{name:l}}];case"host":return[{sample:{hostOrganism:{name:l}}}];

1default:return[{sample:{metadata:{fieldName:t,dir:l}}}]}}function getConsensusGenomesOrderBys(t,a){var l="ASC"===a?"asc_nulls_first":"desc_nulls_last";switch(t){case null:case void 0:return;case"referenceAccession":return[{accession:{accessionId:l}}];case"coverageDepth":case"gcPercent":case"refSnps":case"percentIdentity":case"nActg":case"percentGenomeCalled":case"nMissing":case"nAmbiguous":return[{metrics:(0,C.default)({},t,l)}];case"totalReadsCG":return[{metrics:{totalReads:l}}];case"referenceAccessionLength":return[{metrics:{referenceGenomeLength:l}}];default:(0,k.checkExhaustive)(t)}}function querySequencingReadObjects(t,a,l,r,o){return _querySequencingReadObjects.apply(this,arguments)}function _querySequencingReadObjects(){return(_querySequencingReadObjects=(0,b.default)(h.default.mark((function _callee9(t,a,l,r,o){var i,u,d,c,p,m;return h.default.wrap((function _callee9$(h){for(;;)switch(h.prev=h.next){case 0:return i=l.projectId,u=l.search,d=l.orderBy,c=l.orderDir,p=l.filters,h.next=3,(0,E.fetchQuery)(o,K,{input:{where:{id:{_in:t}},consensusGenomesInput:{where:{producingRunId:{_in:a}}},todoRemove:{domain:r.domain,projectId:null==i?void 0:i.toString(),search:u,host:null==p?void 0:p.host,locationV2:null==p?void 0:p.locationV2,taxons:null==p?void 0:p.taxon,taxaLevels:null==p?void 0:p.taxaLevels,time:null==p?void 0:p.time,tissue:null==p?void 0:p.tissue,visibility:null==p?void 0:p.visibility,orderBy:d,orderDir:c,workflow:T.WorkflowType.CONSENSUS_GENOME,workflowRunIds:a.map(Number).filter(Number.isInteger)}}}).toPromise();case 3:if(null!=(null==(m=h.sent)?void 0:m.fedSequencingReads)){h.next=6;break}throw new Error("Missing CG data: ".concat(u," ").concat(d," ").concat(c," ").concat(JSON.stringify(p)," ").concat(JSON.stringify(r),"}"));case 6:return h.abrupt("return",m.fedSequencingReads.filter(k.isNotNullish).flatMap((function(t){var a,l,r,o,i,u,d,c,p,m,h,g,v,y,C,b=t.sample;if(null==b)throw new Error("Sequencing read's sample was nullish: ".concat(JSON.stringify(t)));var S=[],w={sequencingReadId:t.id,sample:{id:null!==(a=null===(l=b.railsSampleId)||void 0===l?void 0:l.toString())&&void 0!==a?a:"",railsSampleId:null!==(r=b.railsSampleId)&&void 0!==r?r:void 0,name:b.name,project:null!==(o=null===(i=b.collection)||void 0===i?void 0:i.name)&&void 0!==o?o:void 0,publicAccess:null!==(u=null===(d=b.collection)||void 0===d?void 0:d.public)&&void 0!==u?u:void 0,uploadError:null!==(c=b.uploadError)&&void 0!==c?c:void 0,userId:null!==(p=b.ownerUserId)&&void 0!==p?p:void 0,user:null!==(m=b.ownerUserName)&&void 0!==m?m:void 0},host:null===(h=b.hostOrganism)||void 0===h?void 0:h.name,notes:null!==(g=b.notes)&&void 0!==g?g:void 0,medakaModel:null!==(v=t.medakaModel)&&void 0!==v?v:void 0,technology:t.technology,wetlabProtocol:null!=t.protocol?(0,D.formatWetlabProtocol)(t.protocol):void 0,collection_location_v2:null!==(y=b.collectionLocation)&&void 0!==y?y:void 0,nucleotide_type:t.nucleicAcid,sample_type:null!==(C=b.sampleType)&&void 0!==C?C:void 0,water_control:null!=b.waterControl?b.waterControl?"Yes":"No":void 0,referenceAccession:null!=t.taxon?{taxonName:t.taxon.name}:void 0},_=Object.fromEntries(b.metadatas.edges.filter(k.isNotNullish).map((function(t){return[t.node.fieldName,t.node.value]})));S.push(_objectSpread(_objectSpread({},w),_));var E,x=_createForOfIteratorHelper(t.consensusGenomes.edges);try{for(x.s();!(E=x.n()).done;){var L,O,N,T,A,I,M,R,P,j,B,V,W,U,H,G,K,z=E.value;if(null!=z){var q=z.node,Z=q.metrics;S.push(_objectSpread(_objectSpread(_objectSpread({},w),_),{},{consensusGenomeProducingRunId:null!==(L=q.producingRunId)&&void 0!==L?L:void 0,referenceAccession:{accessionName:null!==(O=null===(N=q.accession)||void 0===N?void 0:N.accessionName)&&void 0!==O?O:void 0,referenceAccessionId:null!==(T=null===(A=q.accession)||void 0===A?void 0:A.accessionId)&&void 0!==T?T:void 0,taxonName:null!==(I=null===(M=q.taxon)||void 0===M?void 0:M.name)&&void 0!==I?I:void 0},coverageDepth:null!==(R=null==Z?void 0:Z.coverageDepth)&&void 0!==R?R:void 0,totalReadsCG:null!==(P=null==Z?void 0:Z.totalReads)&&void 0!==P?P:void 0,gcPercent:null!==(j=null==Z?void 0:Z.gcPercent)&&void 0!==j?j:void 0,refSnps:null!==(B=null==Z?void 0:Z.refSnps)&&void 0!==B?B:void 0,percentIdentity:null!==(V=null==Z?void 0:Z.percentIdentity)&&void 0!==V?V:void 0,nActg:null!==(W=null==Z?void 0:Z.nActg)&&void 0!==W?W:void 0,percentGenomeCalled:null!==(U=null==Z?void 0:Z.percentGenomeCalled)&&void 0!==U?U:void 0,nMissing:null!==(H=null==Z?void 0:Z.nMissing)&&void 0!==H?H:void 0,nAmbiguous:null!==(G=null==Z?void 0:Z.nAmbiguous)&&void 0!==G?G:void 0,referenceAccessionLength:null!==(K=null==Z?void 0:Z.referenceGenomeLength)&&void 0!==K?K:void 0}))}}}catch(t){x.e(t)}finally{x.f()}return S})));case 7:case"end":return h.stop()}}),_callee9)})))).apply(this,arguments)}function queryWorkflowRunsAggregate(t,a,l,r,o,i){return _queryWorkflowRunsAggregate.apply(this,arguments)}function _queryWorkflowRunsAggregate(){return(_queryWorkflowRunsAggregate=(0,b.default)(h.default.mark((function _callee10(t,a,l,r,o,i){var u,d,c,p,m;return h.default.wrap((function _callee10$(h){for(;;)switch(h.prev=h.next){case 0:return u=a.projectId,d=a.search,c=a.filters,p={input:{where:{id:{_in:r},collectionId:{_in:t},workflowVersion:{workflow:{name:{_in:o}}},deprecatedById:{_is_null:!0}},todoRemove:{domain:l.domain,projectId:null==u?void 0:u.toString(),search:d,annotations:c.annotations,host:c.host,locationV2:c.locationV2,taxon:c.taxon,taxaLevels:c.taxaLevels,taxonThresholds:c.taxonThresholds,time:c.time,tissue:c.tissue,visibility:c.visibility}}},h.next=4,(0,E.fetchQuery)(i,z,p).toPromise();case 4:return m=h.sent,h.abrupt("return",Z(m));case 6:case"end":return h.stop()}}),_callee10)})))).apply(this,arguments)}var Z=function parseAggregateCounts(t){var a,l=null==t||null===(a=t.fedWorkflowRunsAggregate)||void 0===a?void 0:a.aggregate;if(!l)throw new Error("Missing project workflows aggregate data: ".concat(JSON.stringify(t)));var r={};

1return l.filter(k.isNotNullish).forEach((function(t){var a=t.count,l=t.groupBy,o=l.collectionId,i=l.workflowVersion.workflow.name;r[o]=_objectSpread(_objectSpread({},r[o]),{},(0,C.default)({},i,a))})),r};function queryWorkflowRunsTotalCount(t,a,l,r,o){return _queryWorkflowRunsTotalCount.apply(this,arguments)}function _queryWorkflowRunsTotalCount(){return(_queryWorkflowRunsTotalCount=(0,b.default)(h.default.mark((function _callee11(t,a,l,r,o){var i,u,d;return h.default.wrap((function _callee11$(c){for(;;)switch(c.prev=c.next){case 0:return null!=o?i={_in:[parseInt(o)]}:void 0!==r&&(i={_in:r}),u={input:{where:{collectionId:i,workflowVersion:{workflow:{name:{_in:a}}},deprecatedById:{_is_null:!0}},todoRemove:{domain:t.domain,projectId:o}}},c.next=4,(0,E.fetchQuery)(l,q,u).toPromise();case 4:return d=c.sent,c.abrupt("return",Y(d));case 6:case"end":return c.stop()}}),_callee11)})))).apply(this,arguments)}var Y=function parseTotalCounts(t){var a,l=null==t||null===(a=t.fedWorkflowRunsAggregateTotalCount)||void 0===a?void 0:a.aggregate;if(!l)throw new Error("Missing project workflows total count data: ".concat(JSON.stringify(t)));var r={};return l.filter(k.isNotNullish).forEach((function(t){var a=t.count,l=t.groupBy.workflowVersion.workflow.name;r[l]=a})),r};a.DiscoveryViewFC=function DiscoveryViewFC(t){var a=(0,w.useContext)(L.UserContext),l=a.admin,r=a.allowedFeatures,o=(0,w.useContext)(I.GlobalContext),i=(0,_.useRelayEnvironment)(),u=(0,w.useRef)(Promise.resolve([])),d=(0,w.useRef)(),c=(0,w.useRef)({}),p=(0,w.useState)(),m=(0,y.default)(p,2),g=m[0],C=m[1],S=(0,w.useState)([]),E=(0,y.default)(S,2),x=E[0],N=E[1],k=(0,w.useState)(void 0),M=(0,y.default)(k,2),P=M[0],j=M[1],B=function resetCg(){d.current=void 0,c.current={},C(void 0),N([])},V=function(){var a=(0,b.default)(h.default.mark((function _callee(a,l){var r,o;return h.default.wrap((function _callee$(d){for(;;)switch(d.prev=d.next){case 0:return B(),c.current=a,d.prev=2,r=l.then((function(l){return queryWorkflowRuns(T.WorkflowType.CONSENSUS_GENOME,a,t,i,l)})),u.current=r,d.next=7,r;case 7:if(o=d.sent,u.current===r){d.next=10;break}return d.abrupt("return");case 10:C(o.map((function(t){return t.id}))),U(0),d.next=17;break;case 14:d.prev=14,d.t0=d.catch(2),(0,O.logError)({message:"[DiscoveryViewError] fetchCgFilteredWorkflowRuns() failed",details:{error:d.t0}});case 17:case"end":return d.stop()}}),_callee,null,[[2,14]])})));return function fetchCgFilteredWorkflowRuns(t,l){return a.apply(this,arguments)}}(),W=function(){var a=(0,b.default)(h.default.mark((function _callee2(a,l){var r,o;return h.default.wrap((function _callee2$(d){for(;;)switch(d.prev=d.next){case 0:return d.next=2,u.current;case 2:return r=d.sent,d.next=5,queryWorkflowRunsAggregate(a,l,t,r.map((function(t){return t.id})),[T.WorkflowType.CONSENSUS_GENOME],i);case 5:o=d.sent,j((function(t){return _objectSpread(_objectSpread({},t),o)}));case 7:case"end":return 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1,params:{cacheID:"5450ae3241ae567cd6f176ce061ee835",id:null,metadata:{},name:"DiscoveryViewFCFedWorkflowsTotalCountQuery",operationKind:"query",text:"query DiscoveryViewFCFedWorkflowsTotalCountQuery(\n  $input: queryInput_fedWorkflowRunsAggregateTotalCount_input_Input\n) {\n  fedWorkflowRunsAggregateTotalCount(input: $input) {\n    aggregate {\n      count\n      groupBy {\n        workflowVersion {\n          workflow {\n            name\n          }\n        }\n      }\n    }\n  }\n}\n"}};o.hash="e447cbe8e119a4b0f564f01c18ec1c68";a.default=o},46716:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var l,r,o={fragment:{argumentDefinitions:l=[{defaultValue:null,kind:"LocalArgument",name:"input"}],kind:"Fragment",metadata:null,name:"DiscoveryViewFCSequencingReadIdsQuery",selections:r=[{alias:null,args:[{kind:"Variable",name:"input",variableName:"input"}],concreteType:"query_fedSequencingReads_items",kind:"LinkedField",name:"fedSequencingReads",plural:!0,selections:[{alias:null,args:null,kind:"ScalarField",name:"id",storageKey:null}],storageKey:null}],type:"Query",abstractKey:null},kind:"Request",operation:{argumentDefinitions:l,kind:"Operation",name:"DiscoveryViewFCSequencingReadIdsQuery",selections:r},params:{cacheID:"fd51764199c1fe5635fb0efa2a7eee79",id:null,metadata:{},name:"DiscoveryViewFCSequencingReadIdsQuery",operationKind:"query",text:"query DiscoveryViewFCSequencingReadIdsQuery(\n  $input: queryInput_fedSequencingReads_input_Input\n) {\n  fedSequencingReads(input: $input) {\n    id\n  }\n}\n"}};o.hash="132411c6c4e82b0d714a46551943fad6";a.default=o},97137:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var l,r,o,i,u={fragment:{argumentDefinitions:l=[{defaultValue:null,kind:"LocalArgument",name:"input"}],kind:"Fragment",metadata:null,name:"DiscoveryViewFCSequencingReadsQuery",selections:i=[{alias:null,args:[{kind:"Variable",name:"input",variableName:"input"}],concreteType:"query_fedSequencingReads_items",kind:"LinkedField",name:"fedSequencingReads",plural:!0,selections:[{alias:null,args:null,kind:"ScalarField",name:"id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"nucleicAcid",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"protocol",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"medakaModel",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"technology",storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_taxon",kind:"LinkedField",name:"taxon",plural:!1,selections:o=[r={alias:null,args:null,kind:"ScalarField",name:"name",storageKey:null}],storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_sample",kind:"LinkedField",name:"sample",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"railsSampleId",storageKey:null},r,{alias:null,args:null,kind:"ScalarField",name:"notes",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"collectionLocation",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"sampleType",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"waterControl",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"uploadError",storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_sample_hostOrganism",kind:"LinkedField",name:"hostOrganism",plural:!1,selections:o,storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_sample_collection",kind:"LinkedField",name:"collection",plural:!1,selections:[r,{alias:null,args:null,kind:"ScalarField",name:"public",storageKey:null}],storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"ownerUserId",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"ownerUserName",storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_sample_metadatas",kind:"LinkedField",name:"metadatas",plural:!1,selections:[{alias:null,args:null,concreteType:"query_fedSequencingReads_items_sample_metadatas_edges_items",kind:"LinkedField",name:"edges",plural:!0,selections:[{alias:null,args:null,concreteType:"query_fedSequencingReads_items_sample_metadatas_edges_items_node",kind:"LinkedField",name:"node",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"fieldName",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"value",storageKey:null}],storageKey:null}],storageKey:null}],storageKey:null}],storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_consensusGenomes",kind:"LinkedField",name:"consensusGenomes",plural:!1,selections:[{alias:null,args:null,concreteType:"query_fedSequencingReads_items_consensusGenomes_edges_items",kind:"LinkedField",name:"edges",plural:!0,selections:[{alias:null,args:null,concreteType:"query_fedSequencingReads_items_consensusGenomes_edges_items_node",kind:"LinkedField",name:"node",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"producingRunId",storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_consensusGenomes_edges_items_node_taxon",kind:"LinkedField",name:"taxon",plural:!1,selections:o,storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_consensusGenomes_edges_items_node_accession",kind:"LinkedField",name:"accession",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"accessionId",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"accessionName",storageKey:null}],storageKey:null},{alias:null,args:null,concreteType:"query_fedSequencingReads_items_consensusGenomes_edges_items_node_metrics",kind:"LinkedField",name:"metrics",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"coverageDepth",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"totalReads",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"gcPercent",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"refSnps",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"percentIdentity",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"nActg",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"percentGenomeCalled",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"nMissing",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"nAmbiguous",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"referenceGenomeLength",storageKey:null}],storageKey:null}],storageKey:null}],storageKey:null}],storageKey:null}],storageKey:null}],type:"Query",abstractKey:null},kind:"Request",operation:{argumentDefinitions:l,kind:"Operation",name:"DiscoveryViewFCSequencingReadsQuery",selections:i}

1,params:{cacheID:"0854606456916a206e74794250eff57d",id:null,metadata:{},name:"DiscoveryViewFCSequencingReadsQuery",operationKind:"query",text:"query DiscoveryViewFCSequencingReadsQuery(\n  $input: queryInput_fedSequencingReads_input_Input\n) {\n  fedSequencingReads(input: $input) {\n    id\n    nucleicAcid\n    protocol\n    medakaModel\n    technology\n    taxon {\n      name\n    }\n    sample {\n      railsSampleId\n      name\n      notes\n      collectionLocation\n      sampleType\n      waterControl\n      uploadError\n      hostOrganism {\n        name\n      }\n      collection {\n        name\n        public\n      }\n      ownerUserId\n      ownerUserName\n      metadatas {\n        edges {\n          node {\n            fieldName\n            value\n          }\n        }\n      }\n    }\n    consensusGenomes {\n      edges {\n        node {\n          producingRunId\n          taxon {\n            name\n          }\n          accession {\n            accessionId\n            accessionName\n          }\n          metrics {\n            coverageDepth\n            totalReads\n            gcPercent\n            refSnps\n            percentIdentity\n            nActg\n            percentGenomeCalled\n            nMissing\n            nAmbiguous\n            referenceGenomeLength\n          }\n        }\n      }\n    }\n  }\n}\n"}};u.hash="5d74d6f6ca976feb23f8398bfe79d269";a.default=u},69230:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var l,r,o={fragment:{argumentDefinitions:l=[{defaultValue:null,kind:"LocalArgument",name:"input"}],kind:"Fragment",metadata:null,name:"DiscoveryViewFCWorkflowsQuery",selections:r=[{alias:null,args:[{kind:"Variable",name:"input",variableName:"input"}],concreteType:"query_fedWorkflowRuns_items",kind:"LinkedField",name:"fedWorkflowRuns",plural:!0,selections:[{alias:null,args:null,kind:"ScalarField",name:"id",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"startedAt",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"status",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"errorLabel",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"rawInputsJson",storageKey:null},{alias:null,args:null,concreteType:"query_fedWorkflowRuns_items_workflowVersion",kind:"LinkedField",name:"workflowVersion",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"version",storageKey:null},{alias:null,args:null,concreteType:"query_fedWorkflowRuns_items_workflowVersion_workflow",kind:"LinkedField",name:"workflow",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"name",storageKey:null}],storageKey:null}],storageKey:null},{alias:null,args:null,concreteType:"query_fedWorkflowRuns_items_entityInputs",kind:"LinkedField",name:"entityInputs",plural:!1,selections:[{alias:null,args:null,concreteType:"query_fedWorkflowRuns_items_entityInputs_edges_items",kind:"LinkedField",name:"edges",plural:!0,selections:[{alias:null,args:null,concreteType:"query_fedWorkflowRuns_items_entityInputs_edges_items_node",kind:"LinkedField",name:"node",plural:!1,selections:[{alias:null,args:null,kind:"ScalarField",name:"inputEntityId",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"entityType",storageKey:null}],storageKey:null}],storageKey:null}],storageKey:null}],storageKey:null}],type:"Query",abstractKey:null},kind:"Request",operation:{argumentDefinitions:l,kind:"Operation",name:"DiscoveryViewFCWorkflowsQuery",selections:r},params:{cacheID:"1af3a794c6789bc8f2bb24e2fc23dd8f",id:null,metadata:{},name:"DiscoveryViewFCWorkflowsQuery",operationKind:"query",text:"query DiscoveryViewFCWorkflowsQuery(\n  $input: queryInput_fedWorkflowRuns_input_Input\n) {\n  fedWorkflowRuns(input: $input) {\n    id\n    startedAt\n    status\n    errorLabel\n    rawInputsJson\n    workflowVersion {\n      version\n      workflow {\n        name\n      }\n    }\n    entityInputs {\n      edges {\n        node {\n          inputEntityId\n          entityType\n        }\n      }\n    }\n  }\n}\n"}};o.hash="68e726f1671f65b2caeeba94e0b34abf";a.default=o},37135:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.BaseDiscoveryView=void 0;var o=r(l(17383)),i=r(l(34579)),u=r(l(12475)),d=r(l(29511)),c=r(l(28452)),p=r(l(63072)),m=r(l(43693)),h=r(l(32485)),g=r(l(96540)),v=r(l(45526)),y=r(l(72721)),C=r(l(56879));function _createSuper(t){var a=function _isNativeReflectConstruct(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return 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r={projectIds:l.context.discoveryProjectIds},o={};(0,v.isEqual)(l.state[x.KEY_TAXON_SELECTED],t)||(o[x.KEY_TAXON_SELECTED]=t,(0,C.trackEventFromClassComponent)(r,"DiscoveryFilters_".concat(x.KEY_TAXON_SELECTED.toLowerCase(),"_changed"),{selectedKey:t})),(0,v.isEqual)(l.state[x.KEY_TAXON_THRESHOLDS_SELECTED],a)||(o[x.KEY_TAXON_THRESHOLDS_SELECTED]=a,(0,C.trackEventFromClassComponent)(r,"DiscoveryFilters_".concat(x.KEY_TAXON_THRESHOLDS_SELECTED.toLowerCase(),"_changed"),{selectedKey:a})),l.setState(o,l.notifyFilterChangeHandler)})),(0,m.default)((0,u.default)(l),"handleRemoveTag",(function(t){var a=t.selectedKey,r=t.valueToRemove,o=void 0===r?"":r,i=null;

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l.handleRemoveThresholdFilterTag(t)}})})))})),(0,m.default)((0,u.default)(l),"renderAnnotationsFilter",(function(t){var a=t.disabled,r=t.workflow,o=l.state.annotationsSelected,i=y.default.createElement(h.Dropdown,{className:T.default.styledMinimal,label:y.default.createElement("div",{"data-testid":"annotation",className:(0,g.default)(T.default.filterLabel,a&&T.default.disabledFilterLabel)},"Annotation"),onChange:function onChange(t){t!==l.state[x.KEY_ANNOTATIONS_SELECTED]&&l.handleChange(x.KEY_ANNOTATIONS_SELECTED,t)},value:o||[],options:N.ANNOTATION_FILTER_OPTIONS,disabled:a,multiple:!0});return a?l.renderDisabledFilter(i,r):i})),(0,m.default)((0,u.default)(l),"renderTaxonThresholdFilter",(function(t){var a=t.disabled,r=t.disableThreshold,o=t.workflow,i=l.props.domain,u=l.state,d=u.taxonSelected,c=u.taxonThresholdsSelected,p=y.default.createElement(S.default,{disabled:a,thresholdFilterEnabled:!r,domain:i,onFilterApply:function onFilterApply(t,a){var r=null==a?void 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l={projectIds:this.context.discoveryProjectIds},r=[];r[t]=a,this.setState(r,this.notifyFilterChangeHandler),(0,C.trackEventFromClassComponent)(l,"DiscoveryFilters_".concat(t.toLowerCase(),"_changed"),{selectedKey:a})}},{key:"renderTags",value:function renderTags(t){var a=this,l="".concat(t,"Selected"),r=this.state[l],o=this.props[t];if(r){Array.isArray(r)||(r=[r]);var i=r.map((function(t){return t.text?t:(0,v.find)({value:t},o)||{text:t,value:t}})).map((function(t){return y.default.createElement(O.default,{className:T.default.filterTag,key:t.value,text:t.text,onClose:function onClose(){return a.handleRemoveTag({selectedKey:l,valueToRemove:t.value})}})}));return y.default.createElement("div",{className:T.default.tags},i)}}},{key:"render",value:function render(){var t=this.state,a=t.hostSelected,l=t.locationV2Selected,r=t.timeSelected,o=t.tissueSelected,i=t.visibilitySelected,u=this.props,d=u.className,c=u.currentTab,p=u.domain,m=u.host,h=u.locationV2,v=u.time,C=u.tissue,S=u.visibility,w=u.workflow,_=c===N.TAB_SAMPLES&&this.configForWorkflow[w].disableTaxonFilter,E=c===N.TAB_SAMPLES&&this.configForWorkflow[w].disableAnnotationFilter,x=c===N.TAB_SAMPLES&&this.configForWorkflow[w].disableTaxonThresholdFilter;return y.default.createElement("div",{className:(0,g.default)(T.default.filtersContainer,d)},p!==k.DISCOVERY_DOMAIN_SNAPSHOT&&y.default.createElement(y.default.Fragment,null,y.default.createElement("div",{className:T.default.filterHeader}," Taxon Filters 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Type"}),this.renderTags("tissue")))}}],[{key:"getDerivedStateFromProps",value:function getDerivedStateFromProps(t,a){var l=a;return(0,v.forEach)((function(r){a.prev&&t[r]===a.prev[r]||(l.prev=l.prev||{},l[r]=t[r],l.prev[r]=t[r])}),["hostSelected","locationSelected","locationV2Selected",x.KEY_ANNOTATIONS_SELECTED,x.KEY_TAXON_SELECTED,x.KEY_TAXON_THRESHOLDS_SELECTED,"timeSelected","tissueSelected","visibilitySelected"]),l}}]),DiscoveryFilters}(y.default.Component);(0,m.default)(A,"contextType",L.GlobalContext),A.defaultProps={host:[],location:[],locationV2:[],time:[],tissue:[],visibility:[]}},95934:(t,a,l)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),Object.defineProperty(a,"DiscoveryFilters",{enumerable:!0,get:function get(){return r.DiscoveryFilters}});var r=l(76179)},72027:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.DiscoveryHeader=void 0;var 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a=_createSuper(DiscoveryMapCC);function DiscoveryMapCC(t){var l;(0,i.default)(this,DiscoveryMapCC),l=a.call(this,t),(0,h.default)((0,d.default)(l),"updateViewport",(function(t){var a=l.props,r=a.zoomBoundaryCountry,o=a.zoomBoundaryState;if(l.setState({viewport:t}),l.onMapLevelChangeThrottled){var i=t.zoom<r?"country":t.zoom<o?"state":"city";l.onMapLevelChangeThrottled(i)}l.trackEventThrottled("DiscoveryMap_viewport_updated")})),(0,h.default)((0,d.default)(l),"handleMarkerClick",(function(t){var a=l.props.onMarkerClick;a&&a(t)})),(0,h.default)((0,d.default)(l),"handleMarkerMouseEnter",(function(t){var a=l.props.currentTab,r=(0,g.upperFirst)(a).slice(0,-1),o="".concat(t.pointCount," ").concat(r).concat(t.pointCount>1?"s":""),i=v.default.createElement(S.default,{lat:t.lat,lng:t.lng,title:o,body:t.name,onMouseEnter:l.handleTooltipMouseEnter,onMouseLeave:l.handleMarkerMouseLeave,onTitleClick:function onTitleClick(){return 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c="projects"===l?o:u;return{stats:{numSamples:DiscoverySidebar.formatNumber((d||{}).count),numProjects:DiscoverySidebar.formatNumber(i.count||d.projectCount||0),avgTotalReads:DiscoverySidebar.formatNumber((d||{}).avgTotalReads),avgAdjustedRemainingReads:DiscoverySidebar.formatNumber((d||{}).avgAdjustedRemainingReads)},metadata:{host:DiscoverySidebar.loadDimension(c,"host"),tissue:DiscoverySidebar.loadDimension(c,"tissue"),location:DiscoverySidebar.loadDimension(c,"location"),locationV2:DiscoverySidebar.loadDimension(c,"locationV2"),time:DiscoverySidebar.loadDimension(c,"time_bins")}}}},{key:"loadDimension",value:function loadDimension(t,a){return((0,h.find)({dimension:a},t)||{}).values||[]}},{key:"formatDate",value:function formatDate(t){return(0,g.default)(t).format("YYYY-MM-DD")}},{key:"formatNumber",value:function 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toggleEditing(){this.setState((function(t){return{editing:!t.editing}}))}},{key:"render",value:function render(){var t=this,a=this.state,l=a.description,r=a.showLess,o=a.errors,i=S.MAX_DESCRIPTION_LENGTH/2,u=!!l&&l.length>i;return y.default.createElement(b.default,{editable:this.props.project.editable,onEditToggle:this.toggleEditing,editing:this.state.editing,title:"Description",savePending:this.state.savePending,alwaysShowEditLink:this.props.project.editable,open:!0,toggleable:!0},this.state.editing?y.default.createElement("div",{className:_.default.descriptionContainer},y.default.createElement(w.default,{onChange:function onChange(a){return t.handleDescriptionChange(a)},onBlur:this.handleDescriptionSave,value:l,className:_.default.textarea,maxLength:S.MAX_DESCRIPTION_LENGTH}),y.default.createElement("div",{className:_.default.charCounter},S.MAX_DESCRIPTION_LENGTH-l.length,"/",S.MAX_DESCRIPTION_LENGTH," characters 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t=l.props,a=t.discoveryCurrentTab,r=t.projectStats,o=t.sampleStats,i="samples"===a?o.count:r.count;return[{label:b.default.createElement("span",{"data-testid":"summary-tablabel",className:O.default.tabLabel},"Summary"),value:"summary"},{label:b.default.createElement("div",null,b.default.createElement("span",{"data-testid":"sample-tablabel",className:O.default.tabLabel},(0,C.upperFirst)(a)),i>0&&b.default.createElement("span",{"data-testid":"sample-count",className:O.default.tabCounter},i)),value:a}]})),(0,g.default)((0,c.default)(l),"reset",(function(){l.samplesTable&&l.samplesTable.reset(),l.projectsTable&&l.projectsTable.reset()})),(0,g.default)((0,c.default)(l),"renderSamplesTab",(function(){var t=l.props,a=t.samples,r=t.selectedSampleIds,o=l.isSelectAllChecked();return b.default.createElement("div",{className:O.default.container},b.default.createElement("div",{className:O.default.table},b.default.createElement(x.default,{columns:l.sampleColumns,defaultRowHeight:60,headerClassName:O.default.tableHeader,initialActiveColumns:["sample"],loadingClassName:w.default.loading,onLoadRows:a.handleLoadObjectRows,onRowClick:l.handleSampleRowClick,onSelectAllRows:l.handleSelectAllRows,onSelectRow:l.handleSelectRow,protectedColumns:["sample"],ref:function ref(t){l.samplesTable=t},rowClassName:O.default.sampleRow,selectableColumnClassName:O.default.selectColumn,selectableKey:"id",selectAllChecked:o,selected:r})))})),(0,g.default)((0,c.default)(l),"renderSummaryTab",(function(){var t=l.props,a=t.allowedFeatures,r=t.discoveryCurrentTab,o=t.loading,i=t.onFilterClick,u=t.projectDimensions,d=t.projectStats,c=t.sampleDimensions,p=t.sampleStats;return 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[Int]\n  $selectedIdsStrings: [String]\n  $workflow: String!\n  $authenticityToken: String!\n) {\n  ValidateUserCanDeleteObjects(input: {selectedIds: $selectedIds, selectedIdsStrings: $selectedIdsStrings, workflow: $workflow, authenticityToken: $authenticityToken}) {\n    validIdsStrings\n    invalidSampleNames\n    error\n  }\n}\n"}};d.hash="8dd4e8c443c2011799269517634a8bba";a.default=d},11945:(t,a,l)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var r=l(82709);a.default=r.BulkDeleteModal},71225:(t,a,l)=>{"use strict";var r=l(24994),o=l(73738);Object.defineProperty(a,"__esModule",{value:!0}),a.BulkDeleteTrigger=void 0;var i=l(44480),u=function _interopRequireWildcard(t,a){if(!a&&t&&t.__esModule)return t;if(null===t||"object"!==o(t)&&"function"!=typeof t)return{default:t};var l=_getRequireWildcardCache(a);if(l&&l.has(t))return l.get(t);var r={},i=Object.defineProperty&&Object.getOwnPropertyDescriptor;for(var u in 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r=l(24994),o=l(73738);Object.defineProperty(a,"__esModule",{value:!0}),a.BulkDownloadModal=void 0;var i,u,d,c=r(l(54756)),p=r(l(43693)),m=r(l(29293)),h=r(l(85715)),g=l(44480),v=function _interopRequireWildcard(t,a){if(!a&&t&&t.__esModule)return t;if(null===t||"object"!==o(t)&&"function"!=typeof t)return{default:t};var l=_getRequireWildcardCache(a);if(l&&l.has(t))return l.get(t);var r={},i=Object.defineProperty&&Object.getOwnPropertyDescriptor;for(var u in t)if("default"!==u&&Object.prototype.hasOwnProperty.call(t,u)){var d=i?Object.getOwnPropertyDescriptor(t,u):null;d&&(d.get||d.set)?Object.defineProperty(r,u,d):r[u]=t[u]}r.default=t,l&&l.set(t,r);return r}(l(96540)),y=l(18312),C=l(69487),b=l(81672),S=l(38192),w=l(47116),_=l(85333),E=l(90),x=r(l(48652)),L=l(92843),O=l(20300),N=l(66462),k=l(21953),T=l(63112),A=r(l(22013)),I=l(5358),M=l(11671),R=l(44243),D=l(22081);function _getRequireWildcardCache(t){if("function"!=typeof WeakMap)return null;var a=new WeakMap,l=new WeakMap;return(_getRequireWildcardCache=function _getRequireWildcardCache(t){return t?l:a})(t)}function ownKeys(t,a){var l=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);a&&(r=r.filter((function(a){return Object.getOwnPropertyDescriptor(t,a).enumerable}))),l.push.apply(l,r)}return l}function _objectSpread(t){for(var a=1;a<arguments.length;a++){var l=null!=arguments[a]?arguments[a]:{};

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$workflow: String!\n  $authenticityToken: String!\n) {\n  BulkDownloadCGOverview(input: {workflowRunIdsStrings: $workflowRunIdsStrings, includeMetadata: $includeMetadata, downloadType: $downloadType, workflow: $workflow, authenticityToken: $authenticityToken}) {\n    cgOverviewRows\n  }\n}\n"}};c.hash="20951dadce7836e8207ee210b7b22a03";a.default=c},10579:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var 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1,'Background model cannot be named "',u,'", please enter a different name.')),b.default.createElement("div",{className:R.default.sectionHeader},b.default.createElement("div",{className:R.default.label},"Description"),b.default.createElement("span",{className:R.default.optional},"Optional")),b.default.createElement(A.default,{className:R.default.textArea,rows:a,onChange:l.handleDescriptionChange}),b.default.createElement("div",{className:R.default.sectionHeader},b.default.createElement("div",{className:R.default.label},"Applied Correction Method"),b.default.createElement(x.default,{trigger:b.default.createElement("span",null,b.default.createElement(v.Icon,{sdsIcon:"infoCircle",sdsSize:"s",sdsType:"interactive",className:(0,y.default)(R.default.infoIcon,R.default.extraSpacing)})),content:"Applied Correction Method is the method used when comparing a chosen set of samples against a background model.",link:"https://chanzuckerberg.zendesk.com/hc/en-us/articles/360050883054#h_01ECWXA46KAHRF7N61D7SE1M1F"})),b.default.createElement(k.default,{fluid:!0,className:R.default.dropdown,options:Object.values(p),initialSelectedValue:o,onChange:l.handleMethodChange}),l.renderSampleList(),h.length>1&&b.default.createElement(M.default,{className:R.default.notificationContainer,type:"warning",displayStyle:"flat"},b.default.createElement("span",{className:R.default.highlight},"The selected samples were run using different versions of our NCBI index: ",h.join(", "),"."," "),"We recommend using samples that were run against the same NCBI index date."),d.length>0&&l.renderInvalidSamplesWarning(),b.default.createElement("div",{className:R.default.buttons},b.default.createElement(O.default,{text:"Create",onClick:l.handleCreateBackground}),b.default.createElement(N.default,{text:"Cancel",onClick:l.closeModal})),b.default.createElement("div",{className:R.default.details},"A large number of samples may increase the processing time."))})),(0,g.default)((0,c.default)(l),"renderStatus",(function(){var t=l.state.backgroundCreationResponse;return b.default.createElement("div",null,"ok"===t.status?b.default.createElement(M.default,{className:R.default.notification,type:"success"},"Your Background Model is being created and will be visible on the report page once statistics have been computed."):b.default.createElement(M.default,{className:R.default.notification,type:"error"},t.message))})),l.state={appliedMethod:"",backgroundCreationResponse:null,backgroundDescription:null,backgroundName:"",invalidBackgroundName:null,invalidSampleNames:[],modalOpen:!1,validSampleIds:[]},l}return(0,d.default)(CollectionModal,[{key:"componentDidMount",value:function componentDidMount(){this.fetchBackgroundAvailability(),this.fetchSampleValidation()}},{key:"componentDidUpdate",value:function componentDidUpdate(t){t.selectedSampleIds!==this.props.selectedSampleIds&&(this.fetchBackgroundAvailability(),this.fetchSampleValidation())}},{key:"renderInvalidSamplesWarning",value:function renderInvalidSamplesWarning(){var t=this.state.invalidSampleNames,a=b.default.createElement("div",null,b.default.createElement("span",{className:R.default.highlight},t.length," sample",t.length>1?"s":""," won't be included in the background model"),", because they either failed or are still processing:"),l=t.map((function(t){return b.default.createElement("div",{key:t,className:R.default.messageLine},t)}));return b.default.createElement(I.default,{className:R.default.notificationContainer,content:l,displayStyle:"flat",header:a,open:!1,type:"warning"})}},{key:"render",value:function render(){var t=this.props.trigger,a=this.state.backgroundCreationResponse;return b.default.createElement("div",null,b.default.createElement("button",{className:"noStyleButton",onClick:this.openModal},t),this.state.modalOpen&&b.default.createElement(L.default,{open:!0,narrow:!0,className:R.default.collectionModal,onClose:this.closeModal},b.default.createElement("div",{className:R.default.title},"Create a Background Model"),b.default.createElement("div",{className:R.default.description},"A background is a group of samples. You can use a background as a

1statistical model to compare your samples to. When you select a background on a report or heatmap, the z-scores will indicate how much a sample deviates from the mean of that background."," ",b.default.createElement(_.default,{className:R.default.link,href:"https://chanzuckerberg.zendesk.com/hc/en-us/articles/360050883054-Background-Models"},"Learn More"),"."),this.renderForm(),a&&this.renderStatus()))}}]),CollectionModal}(b.default.Component);(0,g.default)(P,"contextType",E.GlobalContext),P.defaultProps={maxSamplesShown:10,numDescriptionRows:7};a.default=P},2627:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.SampleUploadErrors=a.SHORT_READ_MNGS_SAMPLE_TABLE_COLUMNS=a.SHARED_SAMPLE_TABLE_COLUMNS=a.PROHIBITED_BACKGROUND_MODEL_NAMES=a.LONG_READ_MNGS_SAMPLE_TABLE_COLUMNS=a.FINALIZED_SAMPLE_UPLOAD_ERRORS=a.BACKGROUND_CORRECTION_METHODS=void 0;var l,r="https://help.czid.org/hc/en-us/articles/";a.SHARED_SAMPLE_TABLE_COLUMNS={sample:{tooltip:"User-defined sample name."},createdAt:{tooltip:"Date on which the pipeline was run."},collection_location_v2:{tooltip:"User-defined location from which the sample was collected."},notes:{tooltip:"User-supplied notes."},nucleotide_type:{tooltip:"User-selected metadata field indicating the nucleotide type (RNA, DNA)."},pipelineVersion:{tooltip:"Version of the pipeline used for the last run of the sample."},readsLost:{tooltip:"Reads filtered during each step of the pipeline. The full length of the bar represents the Total Reads. Passed Filters represent the reads that passed quality control and filtering steps.",link:"https://chanzuckerberg.zendesk.com/hc/en-us/articles/360053758913-Sample-QC#Reads-Lost"},sample_type:{tooltip:"User-supplied metadata field indicating the sample type."},totalRuntime:{tooltip:"Total time required by the CZ ID pipeline to process .fastq files into\n    CZ ID reports."},water_control:{tooltip:"Whether a sample is water-only as a control."}},a.SHORT_READ_MNGS_SAMPLE_TABLE_COLUMNS={host:{tooltip:"User-selected organism from which the sample was collected. It dictates which genome is used for host subtraction.",link:r+"360035296613-Project-Page#metrics-meanings"},totalReads:{tooltip:"Total number of reads uploaded. For paired-end data, each R1 and R2 read counts as one read.",link:r+"360053758913-Sample-QC#Total-Reads",testid:"total-read-info-icon"},nonHostReads:{tooltip:"Reads remaining after QC filtering and removal of host and human reads. Values for pipeline v8.0 and up reflect reads remaining after subsampling.",link:r+"360034790554-Pipeline-Details#passed-filters"},qcPercent:{tooltip:"Percentage of reads remaining after QC filtering to remove low quality bases, short reads, and low complexity reads.",link:r+"360053758913-Sample-QC#Passed-QC",testid:"passed-qc-info-icon"},duplicateCompressionRatio:{tooltip:"Duplicate Compression Ratio is the ratio of the number of reads passing QC filtering and host/human read removal to the number of unique reads after duplicate removal.",link:r+"360053758913-Sample-QC#DCR-(duplicate-compression-ratio)",testid:"duplicate-compression-ratio-tooltip"},erccReads:{tooltip:"Total number of reads aligning to ERCC (External RNA Controls Consortium) sequences.",link:r+"360034790834-How-to-Interpret-ERCC-Quality"},meanInsertSize:{tooltip:"Average length of the nucleotide sequence that is inserted between sequencing adapters.",link:r+"360053758913-Sample-QC#Mean-Insert-Size",testid:"mean-insert-size-title"},subsampledFraction:{tooltip:"After QC filtering and host/human data removal, the remaining reads are subsampled to1M (single-end) or 2M (paired-e

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research you create with it. We donât own it and will never sell it. You do, however, give us limited rights to use it for the CZ ID service.")),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"Does CZ ID sell the data I upload?")},h.default.createElement("p",null,"No.")),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"How does CZ ID share the data I upload with other users?")},h.default.createElement(y.default,{listItems:[h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},"When you upload data to CZ ID, you control who the data is shared with. CZ ID relies on three key categories of data, and we want you to understand how each is treated."," ",h.default.createElement("b",null,"Upload Data")," refers to the original fastq sequence files you upload into CZ ID-- this data will only be available to you, the uploader, no matter who you add to the project."," ",h.default.createElement("b",null,"Sample Metadata")," includes details about the sample that researchers manually enter, such as when and where a sample was collected and its type (e.g. synovial fluid or cerebrospinal fluid). ",h.default.createElement("b",null,"Report Data")," includes the pathogen report CZ ID generates from the Upload Data, Sample Metadata, and other data derived from the Upload, such as phylogenetic trees."),h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},h.default.createElement("b",null,"Report Data")," and ",h.default.createElement("b",null,"Sample Metadata")," will be shared with anyone you share your project with."),h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},"You can decide to share your Report Data and associated Sample Metadata with all CZ ID users but that is completely up to you. You can choose to share your Report Data with a small group of CZ ID users, by adding them to a Project, or with all other CZ ID users by marking a Project as ",'"Public"',".")]})),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"Will CZ ID use my Upload Data to write research papers?")},h.default.createElement("p",null,"No, we will not.")),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"How is human genomic data handled and protected?")},h.default.createElement(y.default,{listItems:[h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},"You should not be able to find any human sequence data in CZ ID other than the original fastq files you yourself have uploaded. This is because we have a multi-step process in place to filter out and remove host sequence data in order to generate Reports. If you are able to find human sequence data elsewhere in CZ ID, please let us know at"," ",h.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),", and we will remove it. The fastq files you uploaded are only available to you, the uploader."),h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},"For the fastq files you yourself have uploaded, we understand this data is sensitive and we implement security measures designed to safeguard it. We seek to implement security best practices like encrypting data, hosting it on leading cloud providers with robust physical security, regular security assessments, data loss prevention systems, and working to ensure that only authorized staff have access to the data. If you need more information about our security practices please contact us at ",h.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),".")]}

1)),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"Can I use CZ ID for clinical diagnostic purposes?")},h.default.createElement("p",null,"No. CZ ID is for research use only. It is not for diagnostic, clinical or commercial use.")),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"What should I think about before uploading data to CZ ID?")},h.default.createElement("p",null,"You should make sure you have any permissions or consents necessary in order to upload and use the samples within CZ ID. Please check with your institution or organization if you have questions about meeting this responsibility.")),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",{className:C.default.multiLine},"What Metadata about the uploaded samples do you collect, and how do you make sure the metadata is non-identifiable?")},h.default.createElement(y.default,{listItems:[h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},"We require 4 metadata fields for uploaded samples. We believe these data are necessary to fully analyze the data. The 4 fields we require are:",h.default.createElement("div",{className:C.default.innerListItem},"1. Sample type (CSF, Stool, Serum, etc)"),h.default.createElement("div",{className:C.default.innerListItem},"2. Nucleotide type (RNA or DNA)"),h.default.createElement("div",{className:C.default.innerListItem},"3. Location (limited to state or country)"),h.default.createElement("div",{className:C.default.innerListItem},"4. Collection Date (limited to month and year)")),h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},"We limit the granularity of location and collection date to help maintain the anonymity of the uploaded data."),h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},"Other metadata can be uploaded to CZ ID but is not required and may be deleted at any point. We have put together a metadata ontology that you can find"," ",h.default.createElement(g.Link,{to:"/metadata/dictionary"},"here "),"that does not include any fields where Protected Health Information (PHI) can be derived.")]})),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",{className:C.default.multiLine},"Under what circumstances would CZ ID transfer rights to the data? Why, and what choices would I have?")},h.default.createElement("p",null,"If we can no longer keep operating CZ ID (which we hope wonât happen) or believe the community is better served by someone else operating it, we will transfer the project and all existing data in the tool so that the community can continue to be served. We will always let you know before something like this happens, and you will have the option to delete your account and any data youâve uploaded prior to such transfer.")),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"Where do I go for more questions?")},h.default.createElement("p",null,"Please contact"," ",h.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," if you have any security-related questions or concerns, and"," ",h.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," if you have any other questions about our privacy practices or legal documents.")),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"What is your address?")},h.default.createElement(y.default,{listItems:["Chan Zuckerberg Biohub, 499 Illinois Street, Fourth Floor San\n              Francisco, CA 94158","Chan Zuckerberg Initiative, LLC, 801 Jefferson Ave, Redwood City,\n              CA 94063"]})),h.default.createElement(v.Accordion,{className:C.default.question,header:h.default.createElement("h3",null,"Do you use Cookies in CZ ID?")},h.default.createElement("p",null,"Yes, we use cookies and similar technologies to help improve the website and provide a better experience while using the CZ ID service. We do not use cookies for advertising purposes."),h.default.createElement("p",null,"Cookies are small text files sent by your computer or device each time you visit our website. They are stored in your browserâs cache or mobile device and allow a website or a third party to recognize your browser. Some of the cookies we use are associated with your CZ ID account (including information about you, such as the email address you gave us) and other cookies are not."),h.default.createElement("p",null,"Cookies can be classified by their lifespan:"),h.default.createElement(y.default,{listItems:[h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},h.default.createElement("span",{className:C.default.listItemLabel},"Session cookies")," which are specific to a particular visit you make to CZ ID and hold certain information as you browse different pages so you donât have to re-enter information every time you change pages. Session cookies expire and delete themselves automatically in a short period of time like after you leave CZ ID or when you close your web browser."),h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},h.default.createElement("span",{className:C.default.listItemLabel},"Persistent cookies")," ","which remember certain information about your preferences for viewing CZ ID and allow us to recognize you each time you return. Persistent cookies are stored on your browser cache or mobile device until you choose to delete them, and otherwise delete themselves in a standard period of time.")]}),h.default.createElement("p",null,"A cookie can be classified by the domain to which it belongs, such as a first-party cookie (set by us) or a third party cookie:"),h.default.createElement(y.default,{listItems:[h.default.createElement(h.default.Fragment,{key:(0,m.nanoid)()},h.default.createElement("span",{className:C.default.listItemLabel},"Third party cookies")," ","which are a type of persistent cookie and are placed by someone other than us. These cookies may gather browsing activity across multiple websites and across multiple sessions. They are stored until you delete them or expire based on the time period set in each third party cookie.")]}),h.default.createElement("p",null,"We partner with third-party analytics providers (such as Google and Segment), which set cookies when you visit our website. These

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We will send you an email to reset your password."),u.default.createElement("div",{className:m.default.content},u.default.createElement("i",{className:"fa fa-envelope","aria-hidden":"true"}),u.default.createElement("label",{htmlFor:"user_password",className:m.default.emailLabel},"Email"),u.default.createElement("div",null,u.default.createElement(c.default,{className:m.default.inputField,onChange:r,placeholder:"Enter your registered email",type:"email"})))),u.default.createElement("button",{className:m.default.submit,onClick:function handleFormSubmit(){l&&((0,d.requestPasswordReset)(l),v(!0))}},"Send Email")))}},62348:(t,a,l)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var r=l(59036);a.default=r.ForgotPassword},89774:(t,a,l)=>{"use strict";var r=l(24994),o=l(73738);Object.defineProperty(a,"__esModule",{value:!0}),a.ImpactPage=void 0;var i=r(l(85715)),u=function _interopRequireWildcard(t,a){if(!a&&t&&t.__esModule)return t;if(null===t||"object"!==o(t)&&"function"!=typeof t)return{default:t};var l=_getRequireWildcardCache(a);if(l&&l.has(t))return l.get(t);var r={},i=Object.defineProperty&&Object.getOwnPropertyDescriptor;for(var u in t)if("default"!==u&&Object.prototype.hasOwnProperty.call(t,u)){var d=i?Object.getOwnPropertyDescriptor(t,u):null;d&&(d.get||d.set)?Object.defineProperty(r,u,d):r[u]=t[u]}r.default=t,l&&l.set(t,r);return r}(l(96540)),d=l(23594),c=l(36605),p=r(l(87145)),m=l(66196),h=l(61502),g=r(l(33615)),v=l(87509),y=l(49423);function _getRequireWildcardCache(t){if("function"!=typeof WeakMap)return null;var a=new WeakMap,l=new WeakMap;return(_getRequireWildcardCache=function _getRequireWildcardCache(t){return t?l:a})(t)}a.ImpactPage=function ImpactPage(){var t=(0,u.useState)(m.ImpactCountryData[0]),a=(0,i.default)(t,2),l=a[0],r=a[1];return u.default.createElement(u.default.Fragment,null,u.default.createElement(c.LandingHeader,{impactPage:!0}),u.default.createElement(g.default,null),u.default.createElement(v.ImpactIntro,{setSelectedCountry:function setSelectedCountry(t){return r(t)},selectedCountry:l}),u.default.createElement(h.ImpactCountryShowcase,{setSelectedCountry:function setSelectedCountry(t){return r(t)},selectedCountry:l}),u.default.createElement(y.ImpactVideoSection,null),u.default.createElement(p.default,null),u.default.createElement(d.Footer,null))}},87145:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var o=r(l(96540)),i=r(l(6493)),u=r(l(12503));a.default=function ImpactBottomCTA(){return o.default.createElement("div",{className:u.default.ctaContainer},o.default.createElement("div",{className:u.default.ctaText},o.default.createElement("h2",null,"The free, cloud-based metagenomics platform for researchers")),o.default.createElement("img",{width:"300",src:i.default,alt:""}))}},66196:(t,a,l)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.ImpactCountryData=void 0;var r="outline map of Kenya";a.ImpactCountryData=[{countryName:"Brazil",principalInvestigator:"Federico Costa, Fiocruz, Bahia",projectTitle:"Setting Up Infectious Disease Surveillance Systems in Brazil",institution:"Fiocruz, Bahia",summary:"Rapid urbanization in Salvador, a metropolitan municipality of nearly 3 million inhabitants in northeast Brazil, has produced a favorable environment for the emergence and spread of infectious diseases, including the recent Zika epidemic. This project will focus on collecting clinical samples from patients with suspected infections, mostly respiratory cases, at a local infectious disease reference hospital and an urban community to identify emerging pathogens.\n    ",cycle:1,mapPosition:{bottom:"32%",left:"32%"},nextCountryIndex:1,headshot:{src:l(44127),alt:"Federico Costa, Fiocruz"}},{countryName:"Brazil",principalInvestigator:"Ida Kolte, Fiocruz, Rio de Janeiro",projectTitle:"Discovering the Etiology Behind Severe Lung Infections Impacting Indigenous Peoples of Brazil",institution:"Fiocruz, Rio de Janeiro",summary:"From 2017-19, 8.5% of all deaths among Indigenous community members in Brazil did not have a registered cause â which is double the proportion observed in the non-Indigenous population. Many of Brazilâs Indigenous communities live in close proximity to wild and domestic animals and in precarious circumstances with food insecurity and limited access to sanitation. These challenges create an optimal environment for transmission of infectious diseases and for potential co-infections. Additionally, Indigenous patients rarely receive a laboratory-confirmed diagnosis, leading to increasing numbers of avoidable deaths. This project will leverage metagenomics and CZ ID to identify pathogens and co-infections and strengthen clinical diagnostic pathways.\n    ",cycle:2,mapPosition:{bottom:"32%",left:"33%"},headshot:{src:l(29071),alt:"Ida Kolte"},prevCountryIndex:0,nextCountryIndex:2},{countryName:"Bolivia",principalInvestigator:"Volga Ana IÃ±iguez Rojas, Universidad Mayor de San AndrÃ©s",projectTitle:"Surveillance of Emerging Zoonotic Diseases in Bolivia",institution:"Universidad Mayor de San AndrÃ©s",summary:"Bolivia is a diverse country that has faced emerging, re-emerging, and endemic zoonotic diseases due to a variety of environmental and socio-economic factors. The surveillance, identification, and monitoring of zoonotic pathogens in wildlife and domestic animals are central to the detection and early recognition of emerging diseases that can affect Bolivia and the global community. This project will leverage CZ ID to strengthen local and global disease surveillance, support existing research, and improve laboratory capacities for the detection and characterization of viruses with zoonotic potential.\n    ",cycle:2,mapPosition:{bottom:"28%",left:"27.5%"},mapImage:{src:l(62903),alt:"outline map of Bolivia"},headshot:{src:l(10478),alt:"Volga Ana IÃ±iguez Rojas"},prevCountryIndex:1,nextCountryIndex:3},{countryName:"Cambodia",principalInvestigator:"Jessica Manning, National Institute of Allergy and Infectious Diseases",projectTitle:"Understanding How Disease Spreads from Mosquitoes to Humans in Cambodia",institution:"National Institute of Allergy and Infectious Diseases",summary:"During Cambodiaâs worst dengue epidemic, this team documented the full range of pathogens carried by wild mosquitoes and in serum samples from febrile patients in the countryâs Kampong Speu province. This landscaping study revealed a complex and diverse set of pathogens in Cambodia. It also demonstrated how genetic changes in dengue virus can lead to large outbreaks. This team will c

1ontinue pathogen surveillance using CZ ID to develop a comprehensive landscape of endemic, zoonotic, and emerging pathogens to inform the countryâs public health response.\n    ",cycle:1,mapPosition:{bottom:"41.5%",left:"75.2%"},mapImage:{src:l(22425),alt:"outline map of Cambodia"},publications:[{src:"https://www.frontiersin.org/articles/10.3389/fepid.2022.926695/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Epidemiology&id=926695"},{src:"https://www.pnas.org/doi/10.1073/pnas.2115285119"}],headshot:{src:l(81516),alt:"Jessica Manning"},prevCountryIndex:2,nextCountryIndex:4},{countryName:"CÃ´te dâIvoire",principalInvestigator:"Kanny Diallo, Centre Suisse de Recherches Scientifiques en CÃ´te d'Ivoire",projectTitle:"Using Metagenomic Tools to Redefine the Etiology of Pediatric Meningitis in the African Meningitis Belt",institution:"Centre Suisse de Recherches Scientifiques en CÃ´te d'Ivoire",summary:"Meningitis is a severe infection of the brain and its protective layers â and the most severe forms are caused by bacteria. Every year, around 10.6 million cases and 288,000 deaths are reported globally, and more than half occur below the Sahara in a region called the African Meningitis Belt (AMB). Since national disease surveillance only focuses on the detection of four main meningitis pathogens by PCR (meningococcus, streptococcus, GBS and haemophilus influenzae), other causative pathogens are detected in less than 20% of cerebral spinal fluid samples. This study will use CZ ID to determine etiology and will build a collaboration between Swiss Centre for Scientifique Research, the National Meningitis Reference Laboratory in CÃ´te dâIvoire, the Centre for Vaccine Development in Mali, and the National Institute of Public Health in Guinea.\n    ",cycle:2,mapPosition:{bottom:"39%",left:"45%"},mapImage:{src:l(49029),alt:"outline map of CÃ´te dâIvoire"},headshot:{src:l(66084),alt:"Kanny Diallo"},prevCountryIndex:3,nextCountryIndex:5},{countryName:"The Gambia",principalInvestigator:"Thushan de Silva, Medical Research Council (UK)",projectTitle:"Identifying Resistant Pathogens in Young Children in The Gambia",institution:"Medical Research Council (UK)",summary:"Almost 3 million children under five die each year of neonatal infections in sub-Saharan Africa. A substantial proportion of these deaths is likely to be caused by pathogenic infections, including multi-drug resistant organisms. Defining the cause or etiology of neonatal infections is crucial for timely and effective treatment and for interventions that reduce transmission. This team will use CZ ID to determine etiology from clinical samples from hospitalized neonates in West Africa.",cycle:1,mapPosition:{bottom:"41.7%",left:"42.5%"},prevCountryIndex:4,nextCountryIndex:6},{countryName:"Guinea",principalInvestigator:"Karifa Kourouma, Centre National de Formation et de Recherche en SantÃ© Rurale de Maferinyah",projectTitle:"Embedding Metagenomics in Emerging Infectious Disease Surveillance in Guinea",institution:"Centre National de Formation et de Recherche en SantÃ© Rurale  de Maferinyah",summary:"Guinea is a recognized hotspot for viral hemorrhagic fevers (VHF). Following the largest Ebola outbreak recorded from 2014 to 2016, a nationwide disease monitoring system has been put in place. Although PCR is currently the gold standard for diagnosing VHF viruses, viral genetic diversity (for example, amongst Lassa virus lineages) and the accumulation of mutations can hinder test sensitivity and impact swift responses to future outbreaks. In addition, the current molecular blood-borne pathogen testing algorithm lacks testing for other relevant outbreak-prone viruses and bacterial pathogens with epidemic potential. This team will use metagenomic sequencing with CZ ID to overcome the challenges with  current methods and complement ongoing national VHF disease surveillance activities for the early detection of outbreaks.\n    ",cycle:2,mapPosition:{bottom:"41.5%",left:"44%"},headshot:{src:l(27383),alt:"Karifa Kourouma"}

1,prevCountryIndex:5,nextCountryIndex:7},{countryName:"India",principalInvestigator:"Rajpal Singh Kashyap, Dr. G.M. Taori Central India Institute of Medical Sciences",projectTitle:"Diagnostic Utility of mNGS Approach to Study Etiology of Meningoencephalitis from Central India",institution:"Dr. G.M. Taori Central India Institute of Medical Sciences",summary:"Central nervous system (CNS) diseases such meningoencephalitis (ME) are  associated with significant mortality and morbidity in tertiary neurointensive care settings in India. Etiological diagnosis of ME in such settings represents a formidable problem, as the number of causative organisms vastly outnumbers the available diagnostic tests on the market. This team will use CZ ID to study the etiology of undiagnosed ME infection in a tertiary health care setting.\n    ",cycle:2,mapPosition:{bottom:"45%",left:"67.6%"},mapImage:{src:l(67142),alt:"outline map of India"},headshot:{src:l(88007),alt:"Rajpal Singh Kashyap"},prevCountryIndex:6,nextCountryIndex:8},{countryName:"Kenya",principalInvestigator:"James Berkley, University of Oxford",projectTitle:"Identifying the Most Common, Illness-Causing Pathogens Among Malnourished Children in Kenya",institution:"University of Oxford",summary:"In many parts of the world, severely malnourished infants die after being discharged from a hospital due to infectious diseases. However, the causative pathogen remains unidentified in the vast majority of cases due to the limited sensitivity of current diagnostic methods. This project will leverage CZ ID to perform metagenomic analyses of samples from patients to identify causative pathogens.\n    ",cycle:1,mapPosition:{bottom:"33.5%",left:"56%"},mapImage:{src:l(17960),alt:r},prevCountryIndex:7,nextCountryIndex:9},{countryName:"Kenya",principalInvestigator:"Victor Tunje Jeza, Technical University of Mombasa",projectTitle:"Characterization of Febrile Illness Causing Pathogens Among Children in the Coast and Western Regions of Kenya",institution:"Technical University of Mombasa",summary:"Febrile illnesses, which are common among children in the coastal and western regions of Kenya, are caused by diverse microbial pathogens. Patients who do not test positive for malaria are almost always treated with broad spectrum antibiotics â without regard to increasing development of drug resistance. Previous studies have shown that up to 50% of cases of febrile illnesses are a result of malaria, chikungunya, and/or dengue, but the rest remain unknown. This project will leverage CZ ID to identify the etiology, or cause, of febrile illness not associated with malaria, chikungunya and dengue through ongoing surveillance.\n    ",cycle:2,mapPosition:{bottom:"36.5%",left:"56.5%"},mapImage:{src:l(33499),alt:r},headshot:{src:l(72985),alt:"Victor Tunje Jeza"},prevCountryIndex:8,nextCountryIndex:10},{countryName:"Kenya",principalInvestigator:"Solomon Langat, Kenya Medical Research Institute",projectTitle:"Designing a Metagenomics Enrichment Method and Characterization of Viral Pathogens in Arbovirus and Viral Haemorrhagic Fever-Suspect Samples from Kenya",institution:"Kenya Medical Research Institute",summary:"Over the last decade, the global community has seen a resurgence of known viruses, as well as the emergence of novel viruses. Kenya, in particular, has experienced numerous outbreaks caused by arboviruses and other viral infectious pathogens. This study will develop a targeted viral enrichment protocol for metagenomic sequencing of known and novel arbovirus and viral hemorrhagic fever pathogens. Researchers will apply this method with CZ ID to screen and characterize pathogenic viruses in samples from routine disease surveillance and new outbreaks.\n    ",cycle:2,mapPosition:{bottom:"35.5%",left:"55.2%"},mapImage:{src:l(33499),alt:r},headshot:{src:l(89794),alt:"Solomon Langat"},prevCountryIndex:9,nextCountryIndex:11},{countryName:"Madagascar",principalInvestigator:"Cara Brook, University of Chicago and Pasteur Institute of Madagascar",projectTitle:"Examining Fruit Bats as a Potential Host for Emerging Infectious Diseases in Madagascar",institution:"University of Chicago and Pasteur Institute of Madagascar",summary:"Like many bats worldwide, fruit bats in Madagascar act as reservoirs for viruses of high zoonotic potential, including close relatives of Ebola and SARS-CoV. Identifying novel bat viruses that transmit to humans via traditional diagnostic methods requires the development of targeted assays and is laborious and inefficient. This project will use CZ ID to analyze archived, human clinical samples from febrile patients for possible infection with novel, emerging bat pathogens.\n    ",cycle:1,mapPosition:{bottom:"25%",left:"59%"},publications:[{src:"https://pubmed.ncbi.nlm.nih.gov/35223729/"},{src:"https://journals.asm.org/doi/10.1128/jvi.00921-22"}

1],headshot:{src:l(13144),alt:"Cara Brook"},mapImage:{src:l(14224),alt:"outline map of Madagascar"},prevCountryIndex:10,nextCountryIndex:12},{countryName:"Malawi",principalInvestigator:"Tisungane Mvalo, Lilongwe Medical Relief Fund Trust",projectTitle:"Improving the Diagnosis of Sepsis in Infants in Malawi",institution:"Lilongwe Medical Relief Fund Trust",summary:"Antibiotic treatment has become the standard practice for all young infants that have a suspected bacterial infection â despite the fact that causative pathogen was only identified in half of suspected cases. In this project, the team is sequencing samples from two critical populations â infants under three months of age with suspected blood infections and mothers enrolled in an existing study in an urban hospital - to determine etiology and improve diagnostic methods to detect infections.",cycle:1,mapPosition:{bottom:"26%",left:"56%"},mapImage:{src:l(56067),alt:"outline map of Malawi"},publications:[{src:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783117/"}],prevCountryIndex:11,nextCountryIndex:13},{countryName:"Malaysia",principalInvestigator:"Yoke-Fun Chan, University of Malaya",projectTitle:"Accelerating the Diagnosis of Neuroinfections in Malaysia",institution:"University of Malaya",summary:"Neuroinfection occurs when bacteria, viruses, fungi, or parasites attack the brain and/or spinal cord, which can lead to long-term disability and death. The causes of 60-80% of neuroinfection cases remain unknown, especially as commercial diagnostic tests often do not detect diseases seen in developing countries, including mosquito-borne viruses like dengue and chikungunya viruses, infections of animal origin such as Leptospira, and newly emerging or re-emerging pathogens like Zika virus. This project will use metagenomic sequencing with CZ ID to identify and characterize a broad range of existing and emerging infectious diseases in a tropical setting.",cycle:2,mapPosition:{bottom:"37%",left:"74.5%"},mapImage:{src:l(34015),alt:"outline map of Malaysia"},headshot:{src:l(34814),alt:"Yoke-Fun Chan"},prevCountryIndex:12,nextCountryIndex:14},{countryName:"Nepal",principalInvestigator:"Rajeev Shrestha, Dhulikhel Hospital, Kathmandu University Hospital",projectTitle:"Identifying the Cause of an Encephalitis outbreak in Nepal",institution:"Dhulikhel Hospital, Kathmandu University Hospital",summary:"Acute encephalitis syndrome (AES) affects over 100,000 individuals in low- and middle-income countries annually, causing substantial morbidity and mortality. This complex disease can be caused by over 100 different pathogens, including viruses and parasites â making accurate diagnosis difficult and hindering prevention and treatment efforts. To better characterize the pathogens causing AES, this project will focus on using CZ ID to analyze cerebral spinal fluid samples collected from fatal acute encephalitis cases, with the goal of validating and refining their diagnostic methods.",cycle:1,mapPosition:{bottom:"51%",left:"69.5%"},mapImage:{src:l(31702),alt:"outline map of Nepal"},headshot:{src:l(21911),alt:"Rajeev Shrestha"},prevCountryIndex:13,nextCountryIndex:15},{countryName:"Pakistan",principalInvestigator:"Muhammad Imran Nisar, Aga Khan University",projectTitle:"Identifying Bacterial Causes of Neonatal Deaths and Potential Antibiotic Resistance in Pakistan",institution:"Aga Khan University",summary:"In Pakistan, almost one-third of neonatal deaths are thought to be caused by an infectious disease. Despite using elaborate detection methods, cause or etiology is only determined in 28% of suspected infectious cases. This project will establish a hypothesis-free, metagenomics approach using CZ ID software to analyze sequences from blood and nasopharyngeal specimens of  newborns and infants with suspected infections in Karachi, Pakistan.",cycle:1,mapPosition:{bottom:"52%",left:"66%"},headshot:{src:l(83649),alt:"Muhammad Imran Nisar"},prevCountryIndex:14,nextCountryIndex:16},{countryName:"Senegal",principalInvestigator:"Aida Sadikh Badiane, Universite Cheikh Anta Diop de Dakar",projectTitle:"Metagenomics-Driven Discovery of Pathogens Causing Nosocomial Infection in Senegal",institution:"Universite Cheikh Anta Diop de Dakar",summary:"Nosocomial infections cause substantial morbidity and mortality in Senegal but arenât well-understood. Testing is often done through classical diagnostic methods, such as microscopy and culture, which are often unable to detect pathogens â  resulting in an underestimation of the frequency of cases. This team will use CZ ID to identify and characterize microorganisms responsible for nosocomial infections and suitable specimens to improve diagnosis and treatment.",cycle:2,mapPosition:{bottom:"46.7%",left:"42.5%"},mapImage:{src:l(43010),alt:"outline map of Senegal"},headshot:{src:l(12339),alt:"Aida Sadikh Badiane"},prevCountryIndex:15,nextCountryIndex:17},{countryName:"South Africa",principalInvestigator:"Shabir Madhi, University of the Witwatersrand, Wits Health Consortium",projectTitle:"Identifying the Underlying Cause of Stillbirths and Neonatal Deaths in South Africa",institution:"University of the Witwatersrand, Wits Health Consortium",summary:"Globally, there are around 2.5 million neonatal deaths and 2.6 million stillbirths annually â the vast majority occurring in low- to middle-income countries. Conventional methods have shown that infectious pathogens cause far more of these deaths than previously thought, and that many cases may be linked to multi-drug resistant organisms, hospital-acquired infections. This project will apply CZ ID to archived blood samples from stillbirths and analyze the results to identify novel, unculturable, or untargeted pathogens that were not identified using  more traditional microbiological methods.",cycle:1,mapPosition:{bottom:"18%",left:"53%"},mapImage:{src:l(80338),alt:"outline map of South Africa"},headshot:{src:l(18874),alt:"Shabir Madhi"},prevCountryIndex:16,nextCountryIndex:18},{countryName:"Thailand",principalInvestigator:"Elizabeth Batty, University of Oxford",projectTitle:"Determining the Causes of Febrile Illness in South and Southeast  Asia",institution:"University of Oxford",summary:"Febrile illness contributes substantially to morbidity and mortality within South and Southeast Asia. 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Run `relay-compiler` to update the generated files to receive the expected data."),i);a.AnchorMenu=function AnchorMenu(t){var a=t.pathogenData,l=t.setCurrentSectionIndex,r=(0,c.useFragment)(y,a),o=(0,d.useState)(null),i=(0,u.default)(o,2),C=i[0],b=i[1],S=(0,d.useMemo)((function(){return(0,p.categorizeItems)(r.pathogens)}),[r.pathogens]),w=(0,d.useCallback)((function(t){var a=t.filter((function(t){return null==t?void 0:t.isIntersecting}));if(a.length>0){var r=Object.keys(S).findIndex((function(t){var l;return(0,v.getSectionId)(t)===(null===(l=a[0])||void 0===l||null===(l=l.target)||void 0===l?void 0:l.id)}));l(r)}}),[l,S]);return(0,d.useEffect)((function(){var t=new IntersectionObserver(w,{root:null,rootMargin:"-20% 0% -65% 0%"});b(t)}),[w]),d.default.createElement("div",{className:h.default.sections},Object.keys(S).map((function(t){return d.default.createElement(g.Section,{id:(0,v.getSectionId)(t),key:"section-".concat((0,v.getSectionId)(t)),name:t,observer:C},d.default.createElement(m.Pathogens,{pathogensByHeader:S[t]}))})))}},90966:(t,a)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var l={argumentDefinitions:[],kind:"Fragment",metadata:null,name:"AnchorMenuFragment",selections:[{alias:null,args:null,concreteType:"Pathogen",kind:"LinkedField",name:"pathogens",plural:!0,selections:[{alias:null,args:null,kind:"ScalarField",name:"category",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"name",storageKey:null},{alias:null,args:null,kind:"ScalarField",name:"taxId",storageKey:null}],storageKey:null}],type:"PathogenList",abstractKey:null,hash:"f0bc3416b8eba1148aa2f9119707a15a"};a.default=l},46023:(t,a,l)=>{"use strict";var r=l(24994),o=l(73738);Object.defineProperty(a,"__esModule",{value:!0}),a.Section=void 0;var i=function _interopRequireWildcard(t,a){if(!a&&t&&t.__esModule)return t;if(null===t||"object"!==o(t)&&"function"!=typeof t)return{default:t};var l=_getRequireWildcardCache(a);if(l&&l.has(t))return l.get(t);var r={},i=Object.defineProperty&&Object.getOwnPropertyDescriptor;for(var u in t)if("default"!==u&&Object.prototype.hasOwnProperty.call(t,u)){var d=i?Object.getOwnPropertyDescriptor(t,u):null;d&&(d.get||d.set)?Object.defineProperty(r,u,d):r[u]=t[u]}r.default=t,l&&l.set(t,r);return r}(l(96540)),u=r(l(84093));function _getRequireWildcardCache(t){if("function"!=typeof WeakMap)return null;var a=new WeakMap,l=new WeakMap;return(_getRequireWildcardCache=function _getRequireWildcardCache(t){return t?l:a})(t)}a.Section=function Section(t){var a=t.children,l=t.id,r=t.name,o=t.observer,d=(0,i.useRef)(null);return(0,i.useEffect)((function(){var t=d.current;return t&&o&&o.observe(t),function(){t&&o&&o.unobserve(t)}}),[o,d]),i.default.createElement("div",{className:u.default.section,id:l,ref:d},i.default.createElement("h2",null,r),a)}},32310:(t,a,l)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),Object.defineProperty(a,"Section",{enumerable:!0,get:function get(){return r.Section}});var r=l(46023)},15091:(t,a,l)=>{"use strict";var r=l(24994),o=l(73738);Object.defineProperty(a,"__esModule",{value:!0}),a.getSectionId=a.SectionNavigationFragment=a.SectionNavigation=void 0;var i,u=function _interopRequireWildcard(t,a){if(!a&&t&&t.__esModule)return t;if(null===t||"object"!==o(t)&&"function"!=typeof t)return{default:t};var l=_getRequireWildcardCache(a);if(l&&l.has(t))return l.get(t);var r={},i=Object.defineProperty&&Object.getOwnPropertyDescriptor;for(var u in t)if("default"!==u&&Object.prototype.hasOwnProperty.call(t,u)){var d=i?Object.getOwnPropertyDescriptor(t,u):null;d&&(d.get||d.set)?Object.defineProperty(r,u,d):r[u]=t[u]}r.default=t,l&&l.set(t,r);return r}(l(96540)),d=l(18312),c=l(46348),p=l(85353),m=r(l(30142));function _getRequireWildcardCache(t){if("function"!=typeof WeakMap)return null;var a=new WeakMap,l=new WeakMap;return(_getRequireWildcardCache=function _getRequireWildcardCache(t){return t?l:a})(t)}var h=a.getSectionId=function getSectionId(t){return t.replace(/\s+/g,"-").toLowerCase()},g=a.SectionNavigationFragment=(void 0!==i||(i=l(27920)).hash&&"47b49e2df54c147fdb127d4b0a3417ba"!==i.hash&&console.error("The definition of 'SectionNavigationFragment' appears to have changed. 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It serves to highlight organisms with known pathogenicity in humans, but may not be fully comprehensive. Thus, researchers should reference the literature for rare causes of disease. Additionally, some of these organisms are known pathobionts - commensals within particular body sites (ie Candida aureus may be found in the lung without causing an infection), and should be interpreted with respect to the literature."),o.default.createElement("p",null,"Reach out to"," ",o.default.createElement("a",{href:i.CONTACT_US_LINK,target:"_blank",rel:"noopener noreferrer"},"our Help Center")," ","to help us make the list better, or if there is any questions or comments. 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a=l.state,r=a.projectList,o=a.projectId,i=a.projectPipelineRunsLoaded,u=a.projectPipelineRunIds,d=a.projectPipelineRunsSelectAllChecked,c=a.selectedProjectPipelineRuns,p=a.otherPipelineRunsLoaded,m=a.otherPipelineRunIds,h=a.otherPipelineRunsSelectAllChecked,g=a.selectedOtherPipelineRuns,v={projectIds:l.context.discoveryProjectIds};return{listTrees:b.default.createElement(V.default.Page,{key:"page_1",className:"wizard__page-1",skipDefaultButtons:!0,title:"Phylogenetic Trees",small:!0},b.default.createElement("div",{className:"wizard__page-1__subtitle"},l.state.taxonName),b.default.createElement("div",{className:"wizard__page-1__table"},l.state.phyloTreesLoaded&&b.default.createElement(U.default,{headers:l.phyloTreeHeaders,columns:["name","user","last_update","view"],data:l.state.phyloTrees})),b.default.createElement("div",{className:"wizard__page-1__action"},b.default.createElement(V.default.Action,{action:"continue",onAfterAction:function 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taxon",onLoad:l.loadProjectSearchContext,onContinue:l.canContinueWithTaxonAndProject},b.default.createElement("div",{className:"wizard__page-2__subtitle"}),b.default.createElement("div",{className:"wizard__page-2__searchbar"},b.default.createElement("div",{className:K.default.searchTitle},"Project"),b.default.createElement("div",null,l.state.projectsLoaded?b.default.createElement(O.default,{onChange:l.handleSelectProject,projects:r,showSelectedItemSubtext:!1,value:o}):b.default.createElement(P.IconLoading,null))),b.default.createElement("div",{className:"wizard__page-2__searchbar"},b.default.createElement("div",{className:K.default.searchTitle},"Taxon"),b.default.createElement("div",null,b.default.createElement(R.SubtextDropdown,{fluid:!0,initialSelectedValue:l.state.taxonId,onChange:l.handleSelectTaxon,onFilterChange:l.handleTaxonInputChange,options:l.state.taxonList,placeholder:"Select taxon",search:!0}))),b.default.createElement("div",null,l.state.showErrorTaxonAndProject?"Please select a project and organism":null)),selectNameAndProjectSamples:b.default.createElement(V.default.Page,{key:"wizard__page_3",title:"Name phylogenetic tree and select samples from project '".concat(l.state.projectName,"'"),onLoad:l.loadPipelineRunIds,onContinueAsync:l.canContinueWithTreeName},b.default.createElement("div",{className:"wizard__page-3__subtitle"},l.state.taxonName),b.default.createElement("div",{className:"wizard__page-3__form"},b.default.createElement("div",null,b.default.createElement("div",{className:"wizard__page-3__form__label-name"},"Name"),b.default.createElement(W.default,{className:!l.state.showErrorName||l.state.treeNameValid||(0,C.isEmpty)(l.state.treeName)?"":"error",placeholder:"Tree Name",onChange:l.handleNameChange,defaultValue:l.state.treeName}))),b.default.createElement("div",{className:"wizard__page-3__table"},i&&u.size>0?b.default.createElement(A.default,{headerLabelClassName:K.default.columnHeaderLabel,columns:H.COLUMNS.slice(1),onLoadRows:l.handleLoadProjectPipelineRunRows,onSelectAllRows:l.handleSelectAllProjectPipelineRuns,onSelectRow:l.handleSelectProjectPipelineRunsRow,rowRenderer:l.rowRenderer,selectAllChecked:d,selected:c,selectRowDataGetter:function selectRowDataGetter(t){var a=t.rowData;return 0!==(0,C.get)("num_contigs",a)?(0,C.get)("pipeline_run_id",a):null},selectableKey:"pipeline_run_id",ref:function ref(t){return l.infiniteTable=t},defaultRowHeight:75}):i&&0===u.size?b.default.createElement("div",null,"No samples containing ",l.state.taxonName," available"):b.default.createElement(P.IconLoading,null)),b.default.createElement("div",{className:"wizard__page-3__notifications"},l.renderNotifications())),addIdseqSamples:b.default.createElement(V.default.Page,{key:"wizard__page_4",title:"Add additional samples from CZ ID that contain ".concat(l.state.taxonName,"?")},b.default.createElement("div",{className:"wizard__page-4__subtitle"}),b.default.createElement("div",{className:"wizard__page-4__searchbar"},b.default.createElement("div",{className:"wizard__page-4__searchbar__container"},b.default.createElement(W.default,{placeholder:"Search",onChange:l.handleFilterChange})),b.default.createElement("div",{className:"wizard__page-4__searchbar__container"},l.state.selectedProjectPipelineRuns.size," Project Samples"),b.default.createElement("div",{className:"wizard__page-4__searchbar__container"},l.state.selectedOtherPipelineRuns.size," CZ ID Samples"),b.default.createElement("div",{className:"wizard__page-4__searchbar__container"},l.getTotalPageRendering())),b.default.createElement("div",{className:"wizard__page-4__table"},p&&m.size>0?b.default.createElement(A.default,{headerLabelClassName:K.default.columnHeaderLabel,columns:H.COLUMNS,onLoadRows:l.handleLoadOtherPipelineRunRows,onSelectAllRows:l.handleSelectAllOtherPipelineRuns,onSelectRow:l.handleSelectOtherPipelineRunsRow,rowRenderer:l.rowRenderer,selectAllChecked:h,selected:g,selectRowDataGetter:function selectRowDataGetter(t){var a=t.rowData;return 0!==(0,C.get)("num_contigs",a)?(0,C.get)("pipeline_run_id",a):null},selectableKey:"pipeline_run_id",ref:function ref(t){return l.infiniteTable=t},defaultRowHeight:75}):p&&0===m.size?b.default.createElement("div",null,"No samples containing ",l.state.taxonName," available"):b.default.createElement(P.IconLoading,null)),b.default.createElement("div",{className:"wizard__page-4__notifications"},l.renderNotifications()))}[t]})),(0,g.default)((0,c.default)(l),"getPages",(function(){var t=[];return l.state.skipListTrees||t.push(l.page("listTrees")),l.skipSelectProjectAndTaxon||t.push(l.page("selectTaxonAndProject")),t.push(l.page("selectNameAndProjectSamples"),l.page("addIdseqSamples")),t})),l.state={defaultPage:0,skipListTrees:!1,phyloTreesLoaded:!1,phyloTrees:[],projectPipelineRunsLoaded:!1,projectPipelineRunIds:new Set,selectableProjectPipelineRuns:new Set,selectedProjectPipelineRuns:new Set,projectPipelineRunsSelectAllChecked:!1,projectCoverageBreadths:null,otherPipelineRunsLoaded:!1,otherPipelineRunIds:new Set,selectedOtherPipelineRuns:new Set,otherPipelineRunsSelectAllChecked:!1,otherCoverageBreadths:null,otherSamplesFilter:"",taxonList:[],projectsLoaded:!1,projectList:[],taxonId:l.props.taxonId,taxonName:l.props.taxonName,projectId:l.props.projectId,projectName:l.props.projectName,showErrorTaxonAndProject:!1,showErrorName:!1,showErrorSamples:!1,showLowCoverageWarning:!1,treeName:"",taxonQuery:null},l.phyloTreeHeaders={name:"Phylogenetic Tree",user:"Creator",last_update:"Last Updated",view:"View"},l.skipSelectProjectAndTaxon=l.props.projectId&&l.props.taxonId,l.inputTimeout=null,l.inputDelay=200,l.isTreeNameValidDebounced=(0,C.debounce)(l.inputDelay,l.isTreeNameValid),l.handleTaxonSearchActionDebounced=(0,C.debounce)(l.inputDelay,l.handleTaxonSearchAction),l.wizard=b.default.createRef(),l.infiniteTable=null,l}

1return(0,d.default)(PhyloTreeCreationModal,[{key:"componentDidMount",value:function componentDidMount(){this.loadPhylotrees()}},{key:"isNumberOfSamplesValid",value:function isNumberOfSamplesValid(){var t=this.state.selectedProjectPipelineRuns.size+this.state.selectedOtherPipelineRuns.size;return G.default.isNumberOfSamplesValid(t)}},{key:"getTotalPageRendering",value:function getTotalPageRendering(){var t=this.state.selectedProjectPipelineRuns.size+this.state.selectedOtherPipelineRuns.size;return"".concat(t," Total Samples")}},{key:"renderNotifications",value:function renderNotifications(){var t,a=this.state,l=a.treeName,r=a.treeNameValid,o=a.showErrorSamples,i=a.showErrorName,u=a.selectedProjectPipelineRuns,d=a.selectedOtherPipelineRuns,c=a.projectCoverageBreadths,p=a.otherCoverageBreadths,m=this.props.minCoverageBreadth,h=!1,g=_createForOfIteratorHelper(u);try{for(g.s();!(t=g.n()).done;){var v=t.value;if(!(0,C.isEmpty)(c)&&c[v])if(100*c[v]<m){h=!0;break}}}catch(t){g.e(t)}finally{g.f()}if(!h){var y,S=_createForOfIteratorHelper(d);try{for(S.s();!(y=S.n()).done;){var w=y.value;if(!(0,C.isEmpty)(p)&&p[w])if(100*p[w]<m){h=!0;break}}}catch(t){S.e(t)}finally{S.f()}}return i&&!r&&l?b.default.createElement(j.default,{type:"error",displayStyle:"flat"},"The current tree name is taken. Please choose a different name."):o&&!this.isNumberOfSamplesValid()?b.default.createElement(j.default,{type:"error",displayStyle:"flat"},"Phylogenetic Tree creation must have between"," ",G.default.MIN_SAMPLES," and ",G.default.MAX_SAMPLES," ","samples."):h?b.default.createElement(j.default,{type:"warning",displayStyle:"flat"},"Some of the samples you have selected have low coverage breadth, under"," ",m,"%. This may reduce the quality of the output results."," ",b.default.createElement(N.default,{coloredBackground:!0,href:k.PHYLO_TREE_LINK},"Learn more")):null}},{key:"render",value:function render(){var t=this.props.onClose,a=this.state,l=a.defaultPage,r=a.phyloTreesLoaded,o=a.skipListTrees,i={projectIds:this.context.discoveryProjectIds};return b.default.createElement(B.default,{open:!0,tall:!0,onClose:t,xlCloseIcon:!0},r?b.default.createElement(V.default,{className:"phylo-tree-creation-wizard",skipPageInfoNPages:o?0:1,onComplete:(0,x.withAnalyticsFromClassComponent)(i,this.handleComplete,x.ANALYTICS_EVENT_NAMES.PHYLO_TREE_CREATION_MODAL_CREATE_TREE_BUTTON_CLICKED),defaultPage:l,labels:{finish:"Create Tree"},wizardType:"PhyloTreeCreationWizard",ref:this.wizard},this.getPages()):b.default.createElement(P.IconLoading,null))}}]),PhyloTreeCreationModal}(b.default.Component);(0,g.default)(z,"contextType",I.GlobalContext),z.defaultProps={minCoverageBreadth:25};a.default=z},42170:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var o=r(l(94634)),i=r(l(91847)),u=r(l(17383)),d=r(l(34579)),c=r(l(12475)),p=r(l(29511)),m=r(l(28452)),h=r(l(63072)),g=r(l(43693)),v=r(l(96540)),y=r(l(19151)),C=r(l(66410)),b=r(l(92522)),S=["showPhyloTreeNgOptions","tree","treeContainer"];function _createSuper(t){var a=function _isNativeReflectConstruct(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}();return function _createSuperInternal(){var l,r=(0,h.default)(t);if(a){var o=(0,h.default)(this).constructor;l=Reflect.construct(r,arguments,o)}else l=r.apply(this,arguments);return(0,m.default)(this,l)}}var w="phylotree.clustermap_svg",_="phylotree.clustermap_png",E="phylotree.ska_distances",x=function(t){(0,p.default)(PhyloTreeDownloadButton,t);var a=_createSuper(PhyloTreeDownloadButton);function PhyloTreeDownloadButton(t){var l;return(0,u.default)(this,PhyloTreeDownloadButton),l=a.call(this,t),(0,g.default)((0,c.default)(l),"getPhyloTreeOptions",(function(){var t=l.props.tree,a=l.dataOptions.filter((function(a){return!!t[a.value]}));return a=a.concat(l.treeOptions.filter((function(t){return!l.phyloTreeNgOptions.includes(t.value)})))})),(0,g.default)((0,c.default)(l),"getPhyloTreeNgItems",(function(){var t=l.treeOptions.concat(l.matrixImageOptions).map((function(t){return v.default.createElement(C.default.Item,{key:t.value,onClick:function onClick(){return l.download(t.value)},text:t.text})}));return t.push(v.default.createElement(C.default.Divider,{key:"divider_one"})),t=t.concat(l.skaOptions.map((function(t){return v.default.createElement(C.default.Item,{key:t.value,onClick:function onClick(){return l.download(t.value)},text:t.text})})))})),(0,g.default)((0,c.default)(l),"getMatrixItems",(function(){var t=l.matrixImageOptions.map((function(t){return v.default.createElement(C.default.Item,{key:t.value,onClick:function onClick(){return l.download(t.value)},text:t.text})}));return t.push(v.default.createElement(C.default.Divider,{key:"divider_one"})),t=t.concat(l.skaOptions.map((function(t){if(l.matrixOnlyOptions.includes(t.value))return v.default.createElement(C.default.Item,{key:t.value,onClick:function onClick(){return l.download(t.value)},text:t.text})})))})),l.dataOptions=[{text:"VCF",value:"vcf"},{text:"SNP annotations",value:"snp_annotations"}],l.treeOptions=[{text:"Tree File (.nwk)",value:"phylotree.phylotree_newick"},{text:"Tree Image (.svg)",value:"svg"},{text:"Tree Image (.png)",value:"png"}],l.matrixImageOptions=[{text:"Matrix Image (.svg)",value:w},{text:"Matrix Image (.png)",value:_}],l.skaOptions=[{text:"SKA Distances (.tsv)",value:E},{text:"SKA Variants (.aln)",value:"phylotree.variants"}],l.phyloTreeNgOptions=["phylotree.phylotree_newick",w,_,E,"phylotree.variants"],l.matrixOnlyOptions=[w,_,E],l.download=l.download.bind((0,c.default)(l)),l.svgSaver=new y.default,l}return(0,d.default)(PhyloTreeDownloadButton,[{key:"download",value:function download(t){var a=this.props,l=a.tree,r=a.treeContainer;this.dataOptions.map((function(t){return t.value})).includes(t)?location.href="/phylo_trees/".concat(l.id,"/download?output=").concat(t):this.phyloTreeNgOptions.includes(t)?location.href="/phylo_tree_ngs/".concat(l.id,"/download?output=").concat(t):"svg"===t?this.svgSaver.asSvg(r,"phylo_tree.svg"):"png"===t?this.svgSaver.asPng(r,"phylo_tree.png"):console.error("Bad download option: ".concat(t))}},{key:"render",value:function render(){var t=this.props,a=t.showPhyloTreeNgOptions,l=t.tree,r=(t.tree

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1)),C.default.createElement("div",{className:"phylo-tree-vis__tooltip-container",ref:function ref(a){t.warningTooltipContainer=a}},this.state.showWarningTooltip&&C.default.createElement(S.default,{content:"Coverage breadth is less than 25%. This is low and may affect analysis quality. Learn more in our Help Center.",open:!0,trigger:C.default.createElement("div",null)})))}}]),PhyloTreeVis}(C.default.Component);a.default=k},14107:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.SAMPLE_METRIC_FIELDS=a.SAMPLE_METADATA_FIELDS=a.SAMPLE_FIELDS=void 0;var o=r(l(96540)),i=r(l(93300)),u=l(93527);a.SAMPLE_FIELDS=[{name:"name",label:"Name"},{name:"project_name",label:"Project"},{name:"created_at",label:"Upload Date",parser:function DateParser(t){return o.default.createElement(i.default,{fromNow:!0,date:t})}}],a.SAMPLE_METADATA_FIELDS=["collection_location_v2","collection_date","sample_type","nucleotide_type"],a.SAMPLE_METRIC_FIELDS=[{default:"See coverage viz",name:"coverage_breadth",label:"Coverage Breadth",parser:u.formatPercent}]},88922:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var o=r(l(54756)),i=r(l(91847)),u=r(l(85715)),d=r(l(29293)),c=r(l(41132)),p=r(l(17383)),m=r(l(34579)),h=r(l(12475)),g=r(l(29511)),v=r(l(28452)),y=r(l(63072)),C=r(l(43693)),b=r(l(32485)),S=l(2296),w=l(44480),_=r(l(96540)),E=l(15572),x=l(52519),L=r(l(99191)),O=r(l(31207)),N=r(l(22988)),k=l(63112),T=l(142),A=r(l(96101)),I=r(l(1447)),M=r(l(87931)),R=l(45640),D=["id"];function ownKeys(t,a){var l=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);a&&(r=r.filter((function(a){return Object.getOwnPropertyDescriptor(t,a).enumerable}))),l.push.apply(l,r)}return l}function _objectSpread(t){for(var a=1;a<arguments.length;a++){var l=null!=arguments[a]?arguments[a]:{};a%2?ownKeys(Object(l),!0).forEach((function(a){(0,C.default)(t,a,l[a])})):Object.getOwnPropertyDescriptors?Object.defineProperties(t,Object.getOwnPropertyDescriptors(l)):ownKeys(Object(l)).forEac

1h((function(a){Object.defineProperty(t,a,Object.getOwnPropertyDescriptor(l,a))}))}return t}function _createSuper(t){var a=function _isNativeReflectConstruct(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}();return function _createSuperInternal(){var l,r=(0,y.default)(t);if(a){var o=(0,y.default)(this).constructor;l=Reflect.construct(r,arguments,o)}else l=r.apply(this,arguments);return(0,v.default)(this,l)}}var P=-1,j=-2,B=function(t){(0,g.default)(PipelineViz,t);var a,l=_createSuper(PipelineViz);function PipelineViz(t){var a;(0,p.default)(this,PipelineViz),a=l.call(this,t),(0,C.default)((0,h.default)(a),"handleNodeBlur",(function(){var t=a.lastMouseMoveInfo,l=t.graphIndex,r=t.nodeId,o=t.alteredGraphs;if(null!=r){var i=a.getNodeStatusOptions(a.getStepDataAtIndices({stageIndex:l,stepIndex:r}).status);a.graphs[l].updateNodes([r],i),o.forEach((function(t){var l=a.graphs[t],r=l.getEdges((function(t){return t.id.match(/-colored$/g)}));l.updateEdges(r,{hidden:!0})})),o.clear(),a.setState({hovered:!1,interStageArrows:["","",""]})}})),(0,C.default)((0,h.default)(a),"closeSidebar",(function(){a.graphs.forEach((function(t){return t.unselectAll()})),a.setState({sidebarVisible:!1})})),(0,C.default)((0,h.default)(a),"handleWindowResize",(function(){a.graphs.forEach((function(t,l){a.state.stagesOpened[l]&&t.minimizeSizeGivenScale(1)}))})),(0,C.default)((0,h.default)(a),"handleZoom",(function(t){var l=a.props.zoomSpeed;return function(){a.panZoomContainer&&a.panZoomContainer.current&&(t?a.panZoomContainer.current.zoomIn(l):a.panZoomContainer.current.zoomOut(l))}}));var r=t.showExperimental,o=t.pipelineTechnology;return a.stageNames="ONT"===o?["ONT mNGS Pipeline"]:["Host Filtering","Alignment","Post Processing"].concat((0,c.default)(r?["Experimental"]:[])),a.graphs=[],a.graphContainers=[],a.lastMouseMoveInfo={graphIndex:null,nodeId:null,x:0,y:0,alteredGraphs:new Set},a.panZoomContainer=_.default.createRef(),a.state={stagesOpened:a.stageNames.map((function(t,l){return l<a.props.graphData.stages.length})),interStageArrows:["","",""],sidebarVisible:!1,sidebarParams:{},hovered:!1,graphData:t.graphData},a}return(0,m.default)(PipelineViz,[{key:"componentDidMount",value:function componentDidMount(){var t=this,a=this.props.updateInterval;this.drawGraphs(),window.addEventListener("resize",this.handleWindowResize),this.pipelineIsFinished()||(this.updateLoop=setInterval((function(){return t.updateGraphs()}),a))}},{key:"componentWillUnmount",value:function componentWillUnmount(){window.removeEventListener("resize",this.handleWindowResize),clearInterval(this.updateLoop)}},{key:"updateGraphs",value:(a=(0,d.default)(o.default.mark((function _callee(){var t,a,l,r,d,c,p,m=this;return o.default.wrap((function _callee$(o){for(;;)switch(o.prev=o.next){case 0:return t=this.props,a=t.sample,l=t.pipelineRun,r=this.state.graphData,d=r,o.next=5,(0,x.getGraph)(a.id,l.version.pipeline);case 5:c=o.sent,this.setState({graphData:c},(function(){return m.pipelineIsFinished()&&clearInterval(m.updateLoop)})),(p=(0,S.diff)(d,c)).stages&&Object.entries(p.stages).forEach((function(t){var a=(0,u.default)(t,2),l=a[0],r=a[1],o=parseInt(l);if(o<m.graphs.length){var d=m.graphs[o],c=r.steps;Object.entries(c).forEach((function(t){var a=(0,u.default)(t,2),l=a[0],r=a[1],o=parseInt(l),i=r.status;d.updateNodes([o],_objectSpread({group:i},m.getNodeStatusOptions(i)))}))}else{for(var p=function _loop(){var t=m.graphs[h];m.generateEdgeData(h).forEach((function(a){var l=a.id,r=(0,i.default)(a,D);t.updateEdges([l],r)}))},h=0;h<o;h++)p();m.drawStageGraph(o)}}));case 9:case"end":return o.stop()}}),_callee,this)}))),function updateGraphs(){return a.apply(this,arguments)})},{key:"pipelineIsFinished",value:function pipelineIsFinished(){var t=this.state.graphData.status;return["finished","userErrored","pipelineErrored"].includes(t)}},{key:"getStepDataAtIndices",value:function getStepDataAtIndices(t){var a=t.stageIndex,l=t.stepIndex;return this.state.graphData.stages[a].steps[l]}},{key:"getEdgeInfoFor",value:function getEdgeInfoFor(t,a,l){var r=this.state.graphData.edges,o=this.getStepDataAtIndices({stageIndex:t,stepIndex:a});switch(l){case"input":return o.inputEdges.map((function(t){return r[t]}));case"output":return o.outputEdges.map((function(t){return r[t]}));default:return o.inputEdges.concat(o.outputEdges).map((function(t){return r[t]}))}}},{key:"getNodeIdAtCoords",value:function getNodeIdAtCoords(t,a,l){var r=(0,R.inverseTransformDOMCoordinates)(this.panZoomContainer.current.dragContainer.current,a,l),o=r.x,i=r.y;return t.getNodeAt(o,i)}},{key:"handleStageClick",value:function handleStageClick(t,a){var l=this,r=this.props,o=r.sample,i=r.pipelineRun,u=this.graphs[t],d=this.getNodeIdAtCoords(u,a.pointer.DOM.x,a.pointer.DOM.y);if(null!=d){this.graphs.forEach((function(a,l){return l!==t&&a.unselectAll()})),u.selectNodes([d]);var c=this.getEdgeInfoFor(t,d,"input").map((function(t){return{fromStepName:t.from?l.getStepDataAtIndices(t.from).name:"",files:t.files.map((function(t){return{fileName:t.displayName,url:t.url}}))}})),p=new Set,m=this.getEdgeInfoFor(t,d,"output").map((function(t){return t.files.reduce((function(t,a){var l=JSON.stringify(a);return p.has(l)||(p.add(l),t.push({fileName:a.displayName,url:a.url})),t}),[])})).flat(),h=this.getStepDataAtIndices({stageIndex:t,stepIndex:d});

1this.setState({sidebarVisible:!0,sidebarParams:{stepName:h.name,description:h.description,inputFiles:c,outputFiles:m,status:h.status,startTime:h.startTime,endTime:h.endTime,resources:h.resources,sample:o,pipelineRun:i}})}}},{key:"shouldUpdateMoveMouse",value:function shouldUpdateMoveMouse(t,a){var l=this.props.minMouseMoveUpdateDistance;return Math.sqrt(Math.pow(t-this.lastMouseMoveInfo.x,2)+Math.pow(a-this.lastMouseMoveInfo.y,2))>=l}},{key:"handleMouseMove",value:function handleMouseMove(t,a){var l=this.graphs[t];if(this.shouldUpdateMoveMouse(a.clientX,a.clientY)){var r=a.target.getBoundingClientRect(),o=this.getNodeIdAtCoords(l,a.clientX-r.left,a.clientY-r.top);t===this.lastMouseMoveInfo.graphIndex&&o===this.lastMouseMoveInfo.nodeId||this.handleNodeBlur(),Object.assign(this.lastMouseMoveInfo,{graphIndex:t,nodeId:o,x:a.clientX,y:a.clientY}),null!=o&&this.handleNodeHover(t,o)}}},{key:"handleNodeHover",value:function handleNodeHover(t,a){var l=this,r=this.props,o=r.inputEdgeColor,i=r.outputEdgeColor,u=this.graphs[t],d=(0,c.default)(this.state.interStageArrows),p=this.getNodeStatusOptions(this.getStepDataAtIndices({stageIndex:t,stepIndex:a}).status,!0);u.updateNodes([a],p),this.lastMouseMoveInfo.alteredGraphs.add(t);var m={color:{color:o,hover:o,inherit:!1},width:2,hidden:!1},h=this.getEdgeInfoFor(t,a,"input").reduce((function(r,o){if(o.isIntraStage)r.push("".concat(o.from.stepIndex,"-").concat(a,"-colored"));else{if(o.from){var i=l.graphs[o.from.stageIndex],u="".concat(o.from.stepIndex,"-").concat(j,"-colored");i.updateEdges([u],m);for(var c=o.from.stageIndex;c<t;c++)d[c]="from";l.lastMouseMoveInfo.alteredGraphs.add(o.from.stageIndex)}r.push("".concat(P,"-").concat(a,"-colored"))}return r}),[]);u.updateEdges(h,m);var g={color:{color:i,hover:i,inherit:!1},width:2,hidden:!1},v=this.getEdgeInfoFor(t,a,"output").reduce((function(r,o){if(o.to)if(o.isIntraStage)r.push("".concat(a,"-").concat(o.to.stepIndex,"-colored"));else{var i=l.graphs[o.to.stageIndex],u="".concat(P,"-").concat(o.to.stepIndex,"-colored");i.updateEdges([u],g);for(var c=t;c<o.to.stageIndex;c++)d[c]="to";l.lastMouseMoveInfo.alteredGraphs.add(o.to.stageIndex),r.push("".concat(a,"-").concat(j,"-colored"))}return r}),[]);u.updateEdges(v,g),this.setState({hovered:!0,interStageArrows:d})}},{key:"toggleStage",value:function toggleStage(t){var a=!(arguments.length>1&&void 0!==arguments[1])||arguments[1],l=(0,c.default)(this.state.stagesOpened);l[t]=!l[t],this.setState({stagesOpened:l}),a&&history.replaceState(l,null,this.urlWithStagesOpenedState(l))}},{key:"getStatusGroupFor",value:function getStatusGroupFor(t,a){return this.getStepDataAtIndices({stageIndex:t,stepIndex:a}).status}},{key:"generateNodeData",value:function generateNodeData(t,a){var l=this.state.graphData.stages[t].steps.map((function(t,a){return{id:a,label:t.name,group:t.status}}));return l.push({id:P,group:"startEndNodes"}),l.push({id:j,group:"startEndNodes"}),this.addPositionToNodes(l,a),l}},{key:"getNodeStatusOptions",value:function getNodeStatusOptions(t){var a=arguments.length>1&&void 0!==arguments[1]&&arguments[1],l=this.props["".concat(t,"NodeColor")];if(!l)return{};var r=a&&l.hovered?l.hovered:l.default,o=l.textColor,i=l.shadowColor;return _objectSpread(_objectSpread({color:{background:r,border:r,highlight:{background:r,border:r}}},o?{font:{color:o}}:{font:{color:M.default.defaultNodeText}}),i?{shadow:{color:i,x:0,y:2,size:8}}:{})}},{key:"addPositionToNodes",value:function addPositionToNodes(t,a){var l=(0,w.groupBy)("from",a),r=(0,w.groupBy)("to",a);this.addXCoordinatesToNodes(t,l),this.addYCoordinatesToNodes(t,l,r)}},{key:"addXCoordinatesToNodes",value:function addXCoordinatesToNodes(t,a){var l=this.props.xLayoutInterval,r={};t.forEach((function(t){r[t.id]=0}));for(var o=[P],i=function _loop2(){var t=o.shift();if(t>j){var 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1(),function renderSummaryTable(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("table",{className:m.default.privacySummaryTable},i.default.createElement("tbody",null,i.default.createElement("tr",{className:m.default.topRow},i.default.createElement("td",null,"Type of Data"),i.default.createElement("td",null,"What is it?"),i.default.createElement("td",null,"Whatâs it used for?"),i.default.createElement("td",null,"How is it shared?"),i.default.createElement("td",null,"Your Choices")),i.default.createElement("tr",{className:m.default.sectionRow},i.default.createElement("td",{colSpan:5},i.default.createElement("b",null,"Data you upload to or create using CZ ID"))),i.default.createElement("tr",{className:m.default.contentRow},i.default.createElement("td",null,i.default.createElement("b",null,"Raw Sample Data")),i.default.createElement("td",null,"Genetic sequence files (ex: FASTA/FASTQ) uploaded by Users."),i.default.createElement("td",null,"Upon upload, Raw Sample Data is processed through our data pipeline and all host (ex: human, mosquito) genetic information is filtered out in order to generate Reports. We always filter out all human genetic information, regardless of host. We use the remaining data, with Sample Metadata, to create Reports and Visualizations showing the microorganisms in your sample. These Reports and Visualizations can be shared with other CZ ID users."),i.default.createElement("td",null,"Raw Sample Data is not shared with any other CZ ID user, nor is it ever accessed by anyone working on CZ ID unless specifically requested by a User, such as to debug an issue. This data is disclosed to our service providers (ex: AWS) in order to operate and secure the service."),i.default.createElement("td",{rowSpan:4},"Users can request deletion of Raw Sample Data or their CZ ID account data by contacting us at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," and we will fulfill the request within the timelines set forth under applicable privacy laws. You can learn more about your choices in the Section titled, âChoices About Your Data.â")),i.default.createElement("tr",{className:m.default.contentRow},i.default.createElement("td",null,i.default.createElement("b",null,"Sample Metadata")),i.default.createElement("td",null,"Data about Samples annotated by Users (ex: sequencer used, sample collection date)."),i.default.createElement("td",null,"See above."),i.default.createElement("td",null,i.default.createElement("div",null,i.default.createElement("p",null,"Report Data and Visualizations that Users create can include Sample Metadata. CZ ID Users may choose to share that Report Data and/or Visualizations (including Sample Metadata) with other CZ ID Users."),i.default.createElement("br",null),i.default.createElement("p",null,"This data is also shared with technical partners (Chan Zuckerberg Initiative, LLC - CZI LLC) and service providers (ex: AWS) that help operate, improve, and secure CZ ID. CZI LLC and service providers are limited by this Privacy Policy and will not use any data shared with them for any purpose beyond operating, improving, and securing CZ ID."),i.default.createElement("br",null),i.default.createElement("p",null,"We will never sell your data or share it with anyone that does.")))),i.default.createElement("tr",{className:m.default.contentRow},i.default.createElement("td",null,i.default.createElement("b",null,"Report Data")),i.default.createElement("td",null,"Data about non-host microorganisms that may be contained in the uploaded sample (includes Sample Metadata)."),i.default.createElement("td",null,"See above."),i.default.createElement("td",null,"See above.")),i.default.createElement("tr",{className:m.default.contentRow},i.default.createElement("td",null,i.default.createElement("b",null,"Visualizations")),i.default.createElement("td",null,"Analyses created by Users based on Report Data (ex: heatmaps and phylogenetic trees). Can include Sample Metadata."),i.default.createElement("td",null,"See above."),i.default.createElement("td",null,"See above.")),i.default.createElement("tr",{className:m.default.sectionRow},i.default.createElement("td",{colSpan:5},i.default.createElement("b",null,"Data CZ ID collects"))),i.default.createElement("tr",{className:m.default.contentRow},i.default.createElement("td",null,i.default.createElement("b",null,"User Data")),i.default.createElement("td",null,"Data about researchers with CZ ID accounts such as name, email, institution, basic information about how they are using CZ ID (ex: search queries), and information provided through surveys, during an in-person event, or for user support (ex: resolving support requests)."),i.default.createElement("td",null,"We use this data only to operate, secure, and improve the CZ ID services."),i.default.createElement("td",null,i.default.createElement("div",null,i.default.createElement("p",null,"Basic CZ ID account information such as name and institution may be visible to other CZ ID Users (ex: with collaborators on a shared project)."),i.default.createElement("br",null),i.default.createElement("p",null,"This data is also shared with technical partners (CZI LLC) and service providers (ex: AWS) that help operate, improve, and secure CZ ID."),i.default.createElement("br",null),i.default.createElement("p",null,"CZI LLC and service providers are limited by this Privacy Policy and will not use any data shared with them for any purpose beyond operating, improving, and securing CZ ID."),i.default.createElement("br",null),i.default.createElement("p",null,"We will never sell your data or share it with anyone that does."))),i.default.createElement("td",{rowSpan:2}

1,"Users can request deletion of their CZ ID account data by contacting us at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," and we will fulfill the request within the timelines set forth under applicable privacy laws. You can learn more about your choices in the Section titled, âChoices About Your Data.â")),i.default.createElement("tr",{className:m.default.contentRow},i.default.createElement("td",null,i.default.createElement("b",null,"Device and Analytics Data")),i.default.createElement("td",null,"Device Data (ex: browser type, operating system, and IP address) and Analytics Information (ex: links within CZ ID you click on and how often you log into CZ ID) includes basic information about how Users and Visitors are interacting with CZ ID and a general location (i.e. country) of where they are accessing the Services."),i.default.createElement("td",null,"See above."),i.default.createElement("td",null,"See above.")),i.default.createElement("tr",{className:m.default.contentRow},i.default.createElement("td",null,i.default.createElement("b",null,"Visitor Data")),i.default.createElement("td",null,"Data about visitors (non-Users) to CZ ID pages, such as czid.org and includes basic analytics information (ex: links clicked)."),i.default.createElement("td",null,"See above."),i.default.createElement("td",null,"See above."),i.default.createElement("td",null,"This data is not personally identifiable.")))))}(),function renderAboutCZID(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h3",null,"About CZ ID"),i.default.createElement("p",null,"CZ ID is an online platform designed to enable the research community to research pathogens in metagenomic sequencing and to help further the study of infectious diseases. To do this, CZ ID processes genetic data in order to identify pathogens contained within."),i.default.createElement("p",null,"Hereâs how CZ ID works: Users submit Upload Data (as described below). This data may contain human and non-human genetic sequences (âRaw Sample Dataâ; as further defined below), as well as information about those sequences, such as the date the sample was collected and the host species it was collected from (âSample Metadataâ as further defined below). For example, a researcher might upload genetic information from mosquitoes, which are often a source of infectious disease, or from humans, who can be infected by such diseases. CZ ID then processes this Upload Data in order to identify pathogens found within the genetic sequence (e.g., the mosquito may be carrying the chikungunya virus)."),i.default.createElement("p",null,"We hope that this sharing of pathogen data will help to create a global dashboard that helps researchers better understand pathogens."),i.default.createElement("p",null,"CZ ID also collects information about Users in order to offer and improve the Service. Other than basic information required to create an account (e.g. email address, name), the User determines what information they want to upload onto CZ ID. Please note: CZ ID is not designed for or directed toward children under the age of sixteen and we do not have actual knowledge that we have sold or shared the personal information of users under 16 years of age. If we become aware that we have the information of such children collected through CZ ID, we will promptly delete it."),i.default.createElement("h2",null,"Data CZ ID Collects"),i.default.createElement("p",null,"We will never share your personal information for behavioral advertising purposes nor will we ever sell your personal information. We do collect, use, and retain your data as follows:"))}(),function renderUploadDataPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"1."),"Upload Data."),i.default.createElement("p",null,"âUpload Dataâ is data that Users upload to CZ ID (other than the information Users provide during registration to create an account). As explained below, Upload Data consists of genetic sequence information (human or non-human) and metadata about those genetic sequences (such as time and location of sample collection)."),i.default.createElement("p",null,"As described

1in our Terms, Users are required to obtain and maintain all necessary consents, permissions, and authorizations required by applicable laws prior to uploading, sharing, and exporting Upload Data with the Services."),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"What Is Upload Data?")),i.default.createElement("p",null,"Upload Data includes Sample Data and Sample Metadata."),i.default.createElement(c.default,{listItems:[i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},i.default.createElement("span",{className:m.default.listItemLabel},"Raw Sample Data:"),"âRaw Sample Dataâ is full genetic sequence data uploaded by Users (i.e. FASTA or FASTQ files). Genetic sequence data contains genetic information about pathogens in the sample and of the host from which the sample was taken. The host could be a human or non-human (e.g., mosquito). Host genetic information is filtered out in order to generate Reports, so Report Data should not contain any human sequence data."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},i.default.createElement("span",{className:m.default.listItemLabel},"Sample Metadata:"),"âSample Metadataâ includes information related to the Raw Sample Data, such as the host type (e.g., human or mosquito), upload date, and tissue type and free-text research notes entered by Users. This data should not include personally-identifying information regarding the individual to whom the Raw Sample Data relates.")]}),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"Sensitive Personal Information")),i.default.createElement("p",null,"Raw Sample Data a User uploads from a human host is sensitive personal information (genetic sequence data) and we collect this information to operate and provide the requested service to you."),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"How We Use Upload Data")),i.default.createElement("p",null,"Upload Data is used for the following business purposes:"),i.default.createElement(c.default,{listItems:["To create Report Data (described below), including new reports for\n        Users when we update our Data Pipeline.","To improve the way CZ ID creates Report Data, including improving\n        our Data Pipeline.","To debug in the event you reach out to us with a specific issue related to your Upload Data. "]}),i.default.createElement("p",null,"We will never sell your data or share it with anyone that does nor will we share your personal information for behavioral advertising purposes."),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"How We Share Upload Data")),i.default.createElement("p",null,"Raw Sample Data is ",i.default.createElement("b",null,"never")," disclosed to any other CZ ID User other than the User that uploaded the Sample, but it is disclosed to service providers in order to provide the Services, such as AWS for data storage. Even staff working on CZ ID cannot access this information except as specifically instructed by a User, such as to debug an issue."),i.default.createElement("p",null,"In order to advance CZ ID's goal of creating a global pathogen dashboard for researchers, Users will have the option (at their discretion) to share Report Data and Sample Metadata with all CZ ID Users. Users can also choose to share their Report Data and Sample Metadata by creating Projects (groups of Reports) and sharing those Projects with other CZ ID Users."),i.default.createElement("p",null,"If you have questions about how this to share your Report Data and Sample Metadata, then please reach out to"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),"."),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"Whatâs our legal basis to use and disclose Upload Data?")),i.default.createElement("p",null,"To the extent that the European Unionâs General Data Protection Regulation (âGDPRâ) applies, we rely on the following legal bases to use and disclose personal data within Upload Data:"),i.default.createElement(c.default,{listItems:["The explicit consent of the individual whose data is contained in Raw Sample Data, where such consent has been obtained by the User in accordance with the GDPR; and","The public interest and our and our Usersâ legitimate interest in investigating and stopping the spread of infectious diseases and promoting global health. The use and sharing of personal data within Upload Data furthers the public interest in the area of public health, particularly by helping to protect against serious cross-border threats to health. The processing of personal data within Upload Data is also necessary for scientific research purposes."]}))}(),function renderReportDataPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"2."),"Report Data."),i.default.createElement("p",null,"Report Data is information CZ ID produced from Upload Data. We generate Report Data by processing Upload Data through our Data Pipeline. The âData Pipelineâ cleans (e.g., by removing duplicate nucleotides) and analyzes (e.g., by matching Raw Sample Data nucleotide sequences with known pathogen sequences) the Upload Data. Report Data may include, for example, data about the pathogen sequences identified in the Raw Sample Data and the frequency of such identification (âPathogen Dataâ) or raw numeric counts of non-personally identifying gene expression profiles that were found in the Raw Sample Data (âGene Countsâ)."),i.default.createElement("p",null,"Once Raw Sample Data has been put through the Data Pipeline, the Report Data that is produced no longer includes any human genetic sequence data, and is not personal data, and does not, on its own, permit association with any specific individual. If you are able to find human sequence data in any Reports in CZ ID, please let us know at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," and we will address it."),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"Who can see Report Data?")),i.default.createElement("p",null,"As mentioned above in Section 1 (How We Disclose Upload Data), Users can choose to share their Report Data by creating Projects (groups of Reports) and share those Projects with other CZ ID Users or Users can decide to share it more broadly with all CZ ID Users by marking a Project as âPublic.â This ",i.default.createElement("b",null,"does not")," include Raw Sample Data - those genetic sequence files are available only to the User that uploaded the Sample."),i.default.createElement("p",null,"Users also have the option to share their Report Data with certain third party tools, like"," ",i.default.createElement(d.default,{href:p.NEXTCLADE_APP_LINK},"Nextclade"),". You control whether to use this integration or not. If you do, we will c

1ollect basic information about your use of that integration, such as how often you use it."))}(),function renderVisitorAndUserDataPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"3."),"Visitor and User Data."),i.default.createElement("p",null,"Visitor and User Data is the information we collect from you and your use of CZ ID."),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"What We Collect")),i.default.createElement(c.default,{listItems:[i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},i.default.createElement("span",{className:m.default.listItemLabel},"Visitor Data."),"This is information collected from visitors to our website, whether or not they are Users (âVisitor Dataâ)."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},i.default.createElement("span",{className:m.default.listItemLabel},"User Data."),"User Data is any information we collect from a User about that User such as identifiers and professional or employment-related information (âUser Dataâ). It may include information necessary to create or access your account such as your name, username, email address, and login credentials. This could also include information we collect if you decide to respond to a voluntary survey or join us for an in-person event."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},i.default.createElement("span",{className:m.default.listItemLabel},"Device and Analytics Data."),"When Visitors and Users visit or use our Service, we may automatically collect Device Data or Analytics Information which includes internet or other electronic network activity and geolocation data. âDevice Dataâ includes information about your browser type and operating system, IP address and/or device ID, including basic analytics from your device or browser. âAnalytics Informationâ relates to any of your requests, queries, or use of the Services, such as the amount of time spent viewing particular web pages. We use service providers for this service. Learn more in our"," ",i.default.createElement("a",{href:"/faqs"},"FAQ"),"."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},i.default.createElement("span",{className:m.default.listItemLabel},"Cookies, Web Beacons, and other Technologies."),"A cookie is a small file that may be stored on your computer or other device. Web beacons and similar technologies are small bits of code embedded in web pages or an email, for example, that communicate with third parties. We use these technologies to recognize your device and browser and do things such as keep you logged in or to understand usage patterns by Users and Visitors to our Services. We do not use cookies to service third party ads. For more information about our use of cookies, please see our"," ",i.default.createElement("a",{href:"/faqs"},"FAQ"),".")]}),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"How We Use That Data")),i.default.createElement("p",null,"Visitor Data and User Data (including any personal data in the Visitor Data and User Data) will be used for the following business purposes:"),i.default.createElement(c.default,{listItems:["To identify you, create a profile for Users, and verify Userâs\n          identity so you can log in to and use CZ ID.","To provide you with notices about your account and updates about\n          CZ ID.","To respond to your inquiries and requests.","To learn about what Users find valuable with CZ ID, to analyze how Users are using CZ ID, and to learn the general location (i.e., country) of where Users are accessing the Service so we can optimize and improve it.","To protect the security and integrity of CZ ID."]}),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"What is our legal basis for using personal data in Visitor Data and User Data?")),i.default.createElement("p",null,"To the extent that the GDPR applies, we rely on the following legal bases to use and disclose personal data in Visitor and User Data:"),i.default.createElement(c.default,{listItems:["We (along with CZIF and CZI LLC) have a legitimate interest in using personal\n        data within Visitor Data and User Data in the ways described

1in this\n        Privacy Policy to operate, secure, and improve CZ ID. This allows us to\n        improve the service that we provide to Users which, in turn, supports\n        research regarding the study of infectious disease with the potential to\n              benefit global public health.","We rely on consent as a legal basis when processing data through the use of cookies when required under applicable law."]}))}(),function renderHowLongWeRetainData(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"4."),"How Long We Retain Data and Data Deletion."),i.default.createElement("p",null,"We retain your personal data as long as is reasonably necessary:"),i.default.createElement(c.default,{listItems:["Raw Sample Data, Sample Metadata, and Report Data is retained until Users delete it from CZ ID. Users may submit deletion requests by emailing [email protected] and we will delete the requested Raw Sample Data and corresponding Report Data (including Sample Metadata) within the timelines set forth under applicable privacy laws.","User Data is retained until Users close their CZ ID account as such data is required to manage the service. Users may submit a request for account closure by emailing [email protected]. We will delete your data within 60 days following the close of your account."]}),i.default.createElement("p",null,"Please note that we do not control, and so cannot delete, personal data that Users have copied outside of CZ ID."))}(),function renderVendorAndThirdPartyPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"5."),"Vendors and Service Providers."),i.default.createElement("p",null,"CZ Biohub and CZIF collaborate closely in order to build, design, and operate CZ ID so that it can be as useful as possible to researchers and the public health community. CZI LLC is our primary technology partner, focusing on CZ ID infrastructure, security, and compliance. The three parties are all data controllers for data within CZ ID and will use data only as described in this Privacy Policy."),i.default.createElement("p",null,"We also disclose Upload Data, Report Data, Visitor Data, and User Data with service providers, including service providers to CZI LLC, such as database providers like Amazon Web Services, customer support providers like Zendesk, and survey providers. We may also share Visitor and User data with analytics vendors that assist us to improve and optimize CZ ID. To learn more about our vendors we use, please see our"," ",i.default.createElement("a",{href:"/faqs"},"FAQ")," or contact us at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),"."),i.default.createElement("p",null,"If we can no longer keep operating CZ ID or believe that its purpose is better served by having another entity operating it, we will transfer CZ ID and all data existing therein (Upload Data, Report Data, Visitor Data, and User Data) so that the Users can continue to be served. We will always let you know before this happens, and you will have the option to delete your account and any data youâve uploaded prior to any such transfer. Should this occur, the entity to which we transfer your data will be obliged to use it in a manner that is consistent with this Privacy Policy and the Terms."),i.default.createElement("p",null,"We may disclose Upload Data, Report Data, Visitor Data, and/or User Data if we believe in good faith that such disclosure is necessary (a) in connection with any legal investigation; (b) to comply with relevant laws or to respond to subpoenas or warrants served on us; (c) to protect or defend our rights or property or those of Users; and/or (d) to investigate or assist in preventing any violation or potential violation of the law, this Privacy Policy, or our Terms."))}(),function renderInformationProtectionPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"6."),"How We Protect the Information."),i.default.createElement("p",null,"We use industry standard security measures to ensure the confidentiality, integrity and availability of data uploaded into CZ ID. This includes practices like encrypting connections to CZ ID using TLS, hosting CZ ID on leading cloud providers with robust physical security, and ensuring that access to any personal data within CZ ID by staff working on the tool is strictly limited. And as mentioned above, Raw Sample Data is ",i.default.createElement("b",null,"not shared")," with anyone other than the User that uploaded the Sample or the service providers necessary to operate the service. Even staff working on CZ ID cannot access this information except as specifically instructed by a User, such as to debug an issue."),i.default.createElement("p",null,"Security takes ongoing work and we will c

1ontinue to monitor and adjust our security measures as CZ ID develops. For more information you can take a look at the"," ",i.default.createElement("a",{href:"https://czid.org/security_white_paper"},"CZ ID Security White Paper")," ","which provides details regarding our infrastructure, application, and physical security, as well as our security governance and policies. Please notify us immediately at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," if you suspect your account has been compromised or are aware of any other security issues relating to CZ ID."))}(),function renderUserDataChoicesPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"7."),"Choices About Your Data."),i.default.createElement("p",null,"If you are a User, you have the following choices and rights:"),i.default.createElement(c.default,{listItems:["Users are able to request the deletion of User Data that constitutes their personal data or Raw Sample Data that they submitted to CZ ID.","Users are able to access and download Report Data relating to Upload Data they submitted within CZ ID.",i.default.createElement(i.default.Fragment,null,"Users may also object to the processing of User Data in certain circumstances by emailing"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),". In such cases, we will stop processing that data unless we have legitimate grounds to continue processing it -- for example, it is needed for legal reasons."),i.default.createElement(i.default.Fragment,null,"Users can also contact us by emailing"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," should they wish to access, restrict the processing of, or rectify their User Data.")]}),i.default.createElement("p",null,"If a User has submitted Upload Data containing your personal data, please see below:"),i.default.createElement(c.default,{listItems:["We require Users who submit Upload Data to ensure they have all necessary consents, permissions, and authorizations to do so. We are unable to relate Upload Data to i

1dentifiable individuals and so cannot directly process requests from persons whose personal sequencing data may be contained in Upload Data. As a result, CZ ID is able to receive access, restriction, rectification, objection, or deletion requests only from Users.","If you believe your information has been uploaded to CZ ID, you should contact the researcher or User that uploaded this information to (i) request access to the information, (ii) object to the processing of the information, or (iii) seek deletion, restriction, or rectification of the information. Similarly, if you previously provided consent to a researcher or User, you may have the right to withdraw that consent. You should contact the researcher or User to make such a withdrawal or otherwise exercise your rights."]}),i.default.createElement("p",null,"Please contact us at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," if you would like to exercise the privacy choices discussed above or if you have any questions. We may ask for additional information that allows us to reasonably verify that you are the person about whom we collected personal information. If you would like an authorized agent to make a request for you, have that agent email"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," with information that is sufficient for us to verify that the authorized agent is acting on your behalf. If you would like to appeal a decision with respect to a request to exercise any of these rights, please email us at",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," and explain the basis for your appeal. If your data is subject to the EU data protection law (e.g., GDPR) and you wish to raise a concern about our use of your information (and without prejudice to any other rights you may have), you have the right to do so with your local supervisory authority or by emailing us at ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),"."))}(),function renderDoNotTrackSignals(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"8."),"Do Not Track Signals."),i.default.createElement("p",null,"We donât share personal data with third parties for their direct marketing purposes or behavioral advertising and never will, nor do we support any Do Not Track signals since thereâs currently no standard for how online services respond to those signals. As standards develop, we may establish policies for responding to DNT signals that we would describe in this Privacy Policy. You can learn more about DNT"," ",i.default.createElement("a",{href:"https://allaboutdnt.com/"}," here"),"."))}(),function renderDataTransferPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"9."),"Data Transfers."),i.default.createElement("p",null,"CZ ID is a global service. By using CZ ID, Users authorize us to transfer and store the uploaded data outside of your home country, including to the United States, for the purposes described in this Privacy Policy."),i.default.createElement("p",null,"If you want to use CZ ID, you must first agree to our"," ",i.default.createElement("a",{href:"/terms"},"Terms"),", which set out the contract between CZ ID and our Users. We operate in countries worldwide (including in the United States) and use technical infrastructure in the United States to deliver the Services to you. In accordance with the contract between us and our Users, we need to transfer personal data to the United States and to other jurisdictions as necessary to provide the Services. Such transfers are necessary for important reasons of public interest, namely global health and providing information which can be used by researchers to better understand the spread of infectious diseases. Please note that the privacy protections and the rights of authorities to access your information in these countries may not be the same as in your home country."))}(),function renderAdditionalInformationForCalifornia(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"10."),"Additional Information For California Residents"),i.default.createElement("p",null,"The California Consumer Privacy Act (âCCPAâ) requires certain businesses to give California residents a number of rights regarding their personal information. We are offering these rights to you, including the right to have your personal information deleted (sub

1ject to certain exceptions), the right to change or correct your personal information, the right to limit the use or disclosure of your sensitive personal information (if applicable), the right to access your personal information, the right to opt-out of the âsellingâ or âsharingâ of personal information (if applicable), and the right not to be discriminated against for exercising these rights."),i.default.createElement("p",null,"These rights, and how to exercise them, are described in more detail in the Section titled âChoices About Your Dataâ of this Policy Policy. In addition to these rights, we give you a right to request the following information about your personal information that we have collected in the past 12 months:"),i.default.createElement("p",null,i.default.createElement("strong",null,"The Right to Know.")," This right allows you to request the following information about the personal information that weâve collected about you in the past 12 months:"),i.default.createElement("p",null,i.default.createElement("strong",null,"Information about Data Collection")),i.default.createElement(c.default,{listItems:["The categories of personal information that have been collected.","The categories of sources from which we have collected personal information.","The business purpose for which we have collected personal information."]}),i.default.createElement("p",null,i.default.createElement("strong",null,"Information about Data Disclosure")),i.default.createElement(c.default,{listItems:["The categories of personal information, if any, that have been sold, shared, or disclosed for a business purpose to third parties.",'"The categories of third parties to whom personal information was sold (if applicable), shared, or disclosed for a business purpose. Note: CZ ID does not share your personal information for behavioral advertising purposes nor will we ever sell your personal information.']}),i.default.createElement("p",null,"We have described in fuller detail in this Privacy Policy the personal information that we collect, how we use, and disclose it, but provide the following additional disclosure:"),i.default.createElement("p",null,i.default.createElement("strong",null,"Information about Data Collection")),i.default.createElement(c.default,{listItems:[i.default.createElement(i.default.Fragment,null,i.default.createElement("strong",null,"Information we collect.")," ","We have collected the following categories of personal information from consumers within the past 12 months: (1) identifiers; (2) professional or employment-related information, (3) internet or other electronic network activity within CZ ID; (4) geolocation data; (5) User uploaded genetic data; (6) inferences drawn from your internet or other electronic network activity within CZ ID; and (7) information provided within survey responses."),i.default.createElement(i.default.Fragment,null,i.default.createElement("strong",null,"Sources of information.")," ","We obtain i

1dentifiers, professional or employment-related information, information provided within survey responses, and the genetic data Users upload directly from you. We obtain the other categories of personal information from the sources described in the Section 3 above."),i.default.createElement(i.default.Fragment,null,i.default.createElement("strong",null,"Purposes of collection.")," ","We collect personal information for one or more of the business purposes as described in Sections 1 through 3 above.")]}),i.default.createElement("p",null,i.default.createElement("strong",null,"Information about Data Disclosure")),i.default.createElement(c.default,{listItems:[i.default.createElement(i.default.Fragment,null,i.default.createElement("strong",null,"Information we disclose.")," ","We have disclosed the following categories of personal information in order to provide the Service within the past 12 months: (1) identifiers; (2) professional or employment-related information, (3) internet or other electronic network activity within CZ ID; (4) geolocation data; (5) User uploaded genetic data; (6) inferences drawn from your internet or other electronic network activity within CZ ID; and (7) information provided within survey responses."),i.default.createElement(i.default.Fragment,null,i.default.createElement("strong",null,"Third parties to whom we disclose.")," ","The categories of third parties to whom we have disclosed this personal information are described in the Section titled âVendors and service providersâ in this Privacy Policy."),i.default.createElement(i.default.Fragment,null,i.default.createElement("strong",null,"Purposes of disclosure.")," ","We disclose the personal information we collect about you for one or more of the business purposes as described in Sections 1 through 3 above."),i.default.createElement(i.default.Fragment,null,i.default.createElement("strong",null,"Sensitive data.")," ","We do collect sensitive personal information as described in Section 1 above and only disclose it for the purpose of providing the requested service to you.")]}))}(),function renderAdditionalInformationForVirginia(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"11."),"Additional Information for Residents of Virginia, Colorado, Connecticut, and Utah."),i.default.createElement("p",null,"Virginia, Colorado, Connecticut, and Utah also have adopted privacy laws that give consumers certain rights, including the right to confirm whether controllers are processing the consumerâs personal data, the right to access that data, the right to obtain a copy of that data, the right to correct inaccuracies in that data, and the right to delete that data. As discussed above in the Section titled âChoices About Your Data,â we provide these rights to all consumers, regardless of where they reside."),i.default.createElement("p",null,"Additionally, these four states have adopted rights to opt-out of: (1) targeted advertising; (2) the sale of personal data; and (3) profiling in furtherance of decisions that produce legal or similarly significant effects concerning the consumer. We do not sell your data, use it for targeted advertising, or to profile you in furtherance of decisions that produce legal or similarly significant effects."))}(),function renderExternalLinks(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"12."),"External Links."),i.default.createElement("p",null,"We may link to another companyâs website (e.g., Nextclade as mentioned above), which may have different policies than us. We arenât responsible for their policies or content so we recommend you read their policies if you decide to use their service."," "))}(),function renderContactInfo(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"13."),"How to Contact Us."),i.default.createElement("p",null,"If you have any questions, comments, or concerns with this Privacy Policy, you may contact our Data Protection Officer (DPO) by email at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," or by physical mail at the addresses below."),i.default.createElement("p",null,"To comply with article 27 of the GDPR and the UK-GDPR, we have appointed a representative who can accept communications in relation to personal data processing activities falling within the scope of the GDPR or the UK-GDPR. If you wish to contact them, their details are as follows:"),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"European GDPR Representative:"),i.default.createElement("p",null,"Bird & Bird GDPR Representative Services S

1RL",i.default.createElement("br",null),"Avenue Louise 235",i.default.createElement("br",null),"1050 Bruxelles",i.default.createElement("br",null),"Belgium",i.default.createElement("br",null),i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"))),i.default.createElement("p",null,i.default.createElement("div",{className:m.default.underlineHeader},"UK Data Protection Representative:"),i.default.createElement("p",null,"Bird & Bird GDPR Representative Services UK",i.default.createElement("br",null),"12 New Fetter Lane",i.default.createElement("br",null),"London EC4A 1JP",i.default.createElement("br",null),"United Kingdom",i.default.createElement("br",null),i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"))))}(),function renderChangesToPrivacyPolicy(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:m.default.number},"14."),"Changes to This Privacy Policy."),i.default.createElement("p",{className:m.default.last},'This Privacy Policy was last updated on the "Last Updated" date. We may\n        update this Privacy Policy from time to time and will provide you with\n        notice of any material updates before they become effective.'),i.default.createElement("div",{style:{height:"50px"}}))}())}},58018:(t,a,l)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var r=l(58478);a.default=r.PrivacyNotice},97498:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.PrivacyNoticeForUserResearch=void 0;var o=r(l(96540)),i=l(20887),u=r(l(73965)),d=r(l(10096));a.PrivacyNoticeForUserResearch=function PrivacyNoticeForUserResearch(){return o.default.createElement(i.NarrowContainer,{className:d.default.privacyNoticeForUserResearch,size:"small"},function renderIntro(){return o.default.createElement(o.default.Fragment,null,o.default.createElement("div",{className:d.default.title},o.default.createElement("h1",null,"Privacy Notice for User Research"),o.default.createElement("h4",{className:d.default.subtitle},"Last Updated: September 9, 2021. ")),o.default.createElement("p",null,"This Privacy Notice describes the data that CZI, LLC and CZIF (collectively, âChan Zuckerberg Initiativeâ or âCZIâ) collects from individuals participating in research with the Chan Zuckerberg Initiative. For more information about CZ ID specific privacy practices, please see our ",o.default.createElement("a",{href:"/privacy"},"Privacy Notice"),"."))}(),function renderAboutSurveys(){return o.default.createElement(o.default.Fragment,null,o.default.createElement("h2",null,"User Research Surveys"),o.default.createElement("p",null,"The Chan Zuckerberg Initiative (âCZI,â which includes the Chan Zuckerberg Initiative Foundation (a 501(c)(3) non-profit and the Chan Zuckerberg Initiative, LLC) is conducting a survey to improve the CZ ID experience."),o.default.createElement("p",null,"By responding to this survey, you consent to participate in this research as well as have your responses be shared in a de-identified and/or aggregated manner. The only individuals who will have access to identifiable responses are the researchers and designers at CZI working on a project or program relating to your survey. Raw data will be stored via an encrypted, password-protected server."),o.default.createElement("p",null,"For more information about how weâll manage your data, please see the User Data section. If you have any general questions about CZIâs data use policies for User Research, or to exercise your personal data rights, please email"," ",o.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),"."))}(),function renderUserDataSection(){return o.default.createElement(o.default.Fragment,null,o.default.createElement("h2",null,"User Data"),o.default.createElement("h3",{className:d.default.first},"How we collect data"),o.default.createElement("p",null,"When you choose to participate in User Research, we collect information about you on behalf of CZI Science. We will gather informed consent through an opt-in approach from each individual prior to their participation in a research study."),o.default.createElement("p",{className:d.default.list},"Examples of studies include:"),o.default.createElement(u.default,{listItems:["Remote or in person interviews","Group sessions","Diary studies","Surveys"]}),o.default.createElement("p",{className:d.default.list},"Examples of the data we could collect include:"),o.default.createElement(u.default,{listItems:["Name","Email","User ID","Role","Institution","Usage on our platform","Screenshots or photos of home-made solutions created to various challenges (e.g., databases, questions guides or cheat sheets)","Details on scientific experiments or te

1ch tools"]}),o.default.createElement("h3",null,"How we use your data"),o.default.createElement("p",{className:d.default.list},"We use only your user data, outlined above, to answer a question or understand an experience, workflow, or problem. This may help us better understand user experience and improve our programs and services. Outputs from this could include:"),o.default.createElement(u.default,{listItems:["Publications","Articles","Videos","Reports","Audio clips","Create aggregated journey maps or systems diagrams"]}),o.default.createElement("p",null,"Any outputs from this research will not identify your responses by name, data will be presented in a de-identified and aggregated manner."),o.default.createElement("p",null,o.default.createElement("div",{className:d.default.italics},"Note: Any output resulting from this research does not include data you uploaded or created in CZ ID, such as raw sample data, sample metadata, or report data.")),o.default.createElement("h3",null,"How we share your data"),o.default.createElement("p",null,"We will link your identity to your response and will retain your identifiable information for 3 years. Consequently, de-identified and/or anonymized data will be retained for longer. The only individuals who will have access to identifiable responses are the researchers and designers at CZI working on a project or program relating to your research. Raw data will be stored via an encrypted, password-protected server."),o.default.createElement("p",null,"We donât sell your data. We may share certain data you may voluntarily provide to comply with government reporting requirements. We may share learnings and findings to contribute to the broader knowledge base on this topic, but any reports or presentations resulting from this research would be de-identified and anonymized and would not be shared in any manner that identifies you by name. 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a.apply(this,arguments)}}()),(0,C.default)((0,h.default)(t),"handleTaxonChange",(function(a){(0,_.isEqual)(a,t.state.selectedTaxon)||(t.props.onDirty(),t.setState({selectedTaxon:a}))})),(0,C.default)((0,h.default)(t),"handleWetlabProtocolChange",(function(a){t.props.onDirty(),t.setState({selectedWetlabProtocol:a}),t.props.trackEvent("UploadSampleStep_".concat(a,"-protocol_selected"))})),(0,C.default)((0,h.default)(t),"handleGuppyBasecallerSettingChange",(function(a){t.props.onDirty(),t.setState({selectedGuppyBasecallerSetting:a})})),(0,C.default)((0,h.default)(t),"handleMedakaModelChange",(function(a){t.props.onDirty(),t.setState({selectedMedakaModel:a})})),(0,C.default)((0,h.default)(t),"handleClearLabsChange",(function(a){t.props.onDirty(),t.setState({usedClearLabs:a,selectedWetlabProtocol:a?P.DEFAULT_NANOPORE_WETLAB_OPTION:t.state.selectedWetlabProtocol,selectedMedakaModel:a?P.DEFAULT_MEDAKA_MODEL_OPTION:t.state.selectedMedakaModel})})),(0,C.default)((0,h.default)(t),"getSelectedSampleIdsKey",(function(t){return"".concat(t,"SelectedSampleIds")})),(0,C.default)((0,h.default)(t),"getSamplesKey",(function(t){return"".concat(t,"Samples")})),(0,C.default)((0,h.default)(t),"getSelectedSampleIds",(function(a){return t.state[t.getSelectedSampleIdsKey(a)]})),(0,C.default)((0,h.default)(t),"getSelectedSamples",(function(a){var l=t.getSelectedSampleIds(a),r=t.getSamplesKey(a);return(0,_.filter)((function(t){return l.has(t[P.SELECT_ID_KEY])}),t.state[r])})),(0,C.default)((0,h.default)(t),"getSampleDataForUploadTable",(function(a){if(a===P.BASESPACE_UPLOAD)return(0,B.groupSamplesByLane)({samples:t.state.basespaceSamples,sampleType:P.BASESPACE_UPLOAD});if(a===P.REMOTE_UPLOAD||a===P.LOCAL_UPLOAD){var l=t.getSamplesKey(a),r=t.state[l];if(a===P.LOCAL_UPLOAD){var o=[],i=(0,B.groupSamplesByLane)({samples:r,sampleType:P.LOCAL_UPLOAD}),u=function _loop(){var a=i[d].files,l={},r={},u={};a.forEach((function(a){var o=a.files;for(var i in o){l[i]=a.finishedValidating;var d=t.validateCorrectFormat(a);r[i]=a.isValid&&d;var c=d?a.error:z.MISMATCH_FORMAT_ERROR;u[i]=c||""}})),o.push((0,C.default)((0,C.default)((0,C.default)((0,C.default)({file_names_R1:i[d].filesR1.map((function(t){return t.name})),file_names_R2:i[d].filesR2.map((function(t){return t.name})),name:(0,B.removeLaneFromName)(a[0].name)},P.SELECT_ID_KEY,a.map((function(t){return t[P.SELECT_ID_KEY]})).join(",")),"finishedValidating",l),"isValid",r),"error",u))};for(var d in i)u();return o}return r.map((function(t){var a=(0,_.map)((function(t){return t.name||t.source}),t.input_files_attributes).sort();return _objectSpread(_objectSpread({},(0,_.pick)(["name",P.SELECT_ID_KEY],t)),{},{file_names_R1:[a[0]],file_names_R2:[a[1]]})}))}})),(0,C.default)((0,h.default)(t),"addSelectIdToSamples",(function(t){return(0,_.map)((function(t){return(0,_.set)(P.SELECT_ID_KEY,(0,_.uniqueId)(),t)}),t)})),(0,C.default)((0,h.default)(t),"mergeSamples",(function(t,a){var l=(0,_.keyBy)("name",t),r=(0,_.keyBy)("name",a),o=(0,_.mergeWith)((function(t,a){if(a&&t)return(0,_.flow)((0,_.set)("input_files_attributes",(0,_.uniqBy)("source",(0,_.concat)(t.input_files_attributes,a.input_files_attributes))),(0,_.set)("files",_objectSpread(_objectSpread({},t.files),a.files)))(a)}),r,l);return(0,_.values)(o)})),(0,C.default)((0,h.default)(t),"validateSampleNames",function(){var a=(0,c.default)(o.default.mark((function _callee7(a){var l,r,i,u,d;return o.default.wrap((function _callee7$(o){for(;;)switch(o.prev=o.next){case 0:if(l=a.samples,r=a.project,(i=r||t.state.selectedProject)&&!((0,_.size)(l)<=0)){o.next=4;break}return o.abrupt("return",{samples:l});case 4:return o.next=6,(0,L.validateSampleNames)((0,_.get)("id",i),(0,_.map)("name",l));case 6:return u=o.sent,d=(0,_.zipObject)((0,_.map)("name",l),u),o.abrupt("return",{samples:l.map((function(t){return _objectSpread(_objectSpread({},t),{},{name:d[t.name]})}))});case 9:case"end":return o.stop()}}),_callee7)})));return function(t){return a.apply(this,arguments)}}()),(0,C.default)((0,h.default)(t),"validateAddedSamples",function(){var a=(0,c.default)(o.default.mark((function _callee8(

1a,l){var r,i,u,c,p,m,h;return o.default.wrap((function _callee8$(o){for(;;)switch(o.prev=o.next){case 0:if(l===P.LOCAL_UPLOAD){o.next=2;break}return o.abrupt("return",t.validateSampleNames({samples:a}));case 2:if(!((0,_.size)(a)<=0)){o.next=4;break}return o.abrupt("return",{samples:a,removedLocalFiles:[]});case 4:return r=(0,_.flatten)((0,_.map)((function(t){return(0,_.keys)(t.files)}),a)),o.next=7,Promise.all([t.validateSampleNames({samples:a}),(0,L.validateSampleFiles)(r)]);case 7:return i=o.sent,u=(0,d.default)(i,2),c=u[0].samples,p=u[1],m=(0,_.zipObject)(r,p),c=(c=c.map((function(t){return(0,_.set)("files",(0,_.pickBy)((function(t,a){return m[a]}),t.files),t)}))).map((function(t){return(0,_.set)("input_files_attributes",(0,_.filter)((function(t){return m[t.source]}),t.input_files_attributes),t)})),h=(0,_.filter)((function(t){return(0,_.size)(t.files)>0}),c),o.abrupt("return",{samples:h,removedLocalFiles:(0,_.keys)((0,_.pickBy)((function(t){return!t}),m))});case 16:case"end":return o.stop()}}),_callee8)})));return function(t,l){return a.apply(this,arguments)}}()),(0,C.default)((0,h.default)(t),"handleSampleSelect",(function(a,l,r){t.props.onDirty();var o=t.getSamplesKey(r),i=t.state[o];if(r===P.LOCAL_UPLOAD){var u=i.find((function(t){return t[P.SELECT_ID_KEY]===a}));if(!u||!1===u.isValid||!t.validateCorrectFormat(u))return}var d=t.getSelectedSampleIdsKey(r),c=t.state[d];l?c.add(a):c.delete(a),t.setState((0,C.default)({},d,c))})),(0,C.default)((0,h.default)(t),"handleInvalidSample",(function(a,l,r){t.props.onDirty();var o=t.getSelectedSampleIdsKey(r),i=t.state[o];l?i.add(a):i.delete(a),t.setState((0,C.default)({},o,i))})),(0,C.default)((0,h.default)(t),"handleAllSamplesSelect",(function(a,l){t.props.onDirty();var r=t.getSelectedSampleIdsKey(l),o=t.getSamplesKey(l),i=t.state[o];l===P.LOCAL_UPLOAD&&(i=i.filter((function(a){return a.isValid&&t.validateCorrectFormat(a)}))),t.setState((0,C.default)({},r,a?new Set((0,_.map)(P.SELECT_ID_KEY,i)):new Set))})),(0,C.default)((0,h.default)(t),"handleSamplesAdd",function(){var a=(0,c.default)(o.default.mark((function _callee9(a,l){var r,i,u,d,c,p,m,h,g,v;return o.default.wrap((function _callee9$(o){for(;;)switch(o.prev=o.next){case 0:return t.props.onDirty(),r=t.getSamplesKey(l),i=t.getSelectedSampleIdsKey(l),t.setState(_objectSpread({validatingSamples:!0},l===P.LOCAL_UPLOAD?{removedLocalFiles:[]}:{})),u=t.addSelectIdToSamples(a),o.next=7,t.validateAddedSamples(u,l);case 7:d=o.sent,c=d.samples,p=d.removedLocalFiles,m=t.mergeSamples(t.state[r],c),h=(0,_.map)(P.SELECT_ID_KEY,m),g=(0,_.intersection)((0,_.map)(P.SELECT_ID_KEY,c),h),v=new Set((0,_.union)(Array.from(t.state[i]),g)),t.setState(_objectSpread(_objectSpread((0,C.default)((0,C.default)({validatingSamples:!1},r,m),i,v),l===P.LOCAL_UPLOAD?{removedLocalFiles:p}:{}),{},{files:t.state.files.concat(c)})),t.props.trackEvent("UploadSampleStep_sample_changed",_objectSpread(_objectSpread({newSamples:c.length,totalSamples:m.length,sampleType:l},l===P.LOCAL_UPLOAD?{removedLocalFiles:p.length}:{}),t.getLocalAnalyticsContext()));case 16:case"end":return o.stop()}}),_callee9)})));return function(t,l){return a.apply(this,arguments)}}()),(0,C.default)((0,h.default)(t),"handleSamplesRemove",(function(a,l){t.props.onDirty();var r=t.getSamplesKey(l),o=t.getSelectedSampleIdsKey(l),i=(0,_.reject)((function(t){return(0,_.includes)(t[P.SELECT_ID_KEY],a)}),t.state[r]),u=new Set((0,_.difference)(Array.from(t.getSelectedSampleIds(l)),a)),d=(0,C.default)((0,C.default)({},r,i),o,u);t.setState(d)})),(0,C.default)((0,h.default)(t),"handleContinue",(0,c.default)(o.default.mark((function _callee10(){var a,l,r,i,u,d,c,p,m,h,g,v,y,C,b,S,w,E,x;return o.default.wrap((function _callee10$(o){for(;;)switch(o.prev=o.next){case 0:if(a=t.props.onUploadSamples,l=t.state,r=l.bedFile,i=l.currentTab,u=l.refSeqAccession,d=l.refSeqFile,c=l.selectedTaxon,p=l.selectedTechnology,m=l.selectedMedakaModel,h=l.selectedGuppyBasecallerSetting,g=l.selectedProject,v=l.selectedWorkflows,y=l.selectedWetlabProtocol,C=l.usedClearLabs,i!==P.BASESPACE_UPLOAD){o.next=6;break}t.requestBasespaceReadProjectPermissions(),o.next=17;break;case 6:if(b=t.getSelectedSamples(i),i!==P.LOCAL_UPLOAD){o.next=15;break}return S=(0,B.groupSamplesByLane)({samples:b,sampleType:P.LOCAL_UPLOAD}),b=(0,_.map)((function(t){return t.concatenated}),S),o.next=12,t.validateSampleNames({samples:b});case 12:w=o.sent,E=w.samples,b=E;case 15:x=(null==c?void 0:c.name)===P.UNKNOWN_TAXON_OPTION.name,a({samples:b,project:g,technology:p,uploadType:i,workflows:v,guppyBasecallerSetting:h,bedFile:r,refSeqAccession:u,refSeqFile:d,refSeqTaxon:x?null:c,wetlabProtocol:y,clearlabs:C,medakaModel:m});case 17:case"end":return o.stop()}}),_callee10)})))),(0,C.default)((0,h.default)(t),"handleValidatedFilesChange",(function(a){t.setState({localSamples:a})})),(0,C.default)((0,h.default)(t),"handleContinueButtonTooltip",(function(){var a=t.state,l=a.currentTab,r=a.localSamples,o=a.refSeqFile,i=a.selectedGuppyBasecallerSetting,u=a.selectedProject,d=a.selectedTaxon,c=a.selectedTechnology,p=a.selectedWetlabProtocol,m=a.selectedWorkflows;return l!==P.LOCAL_UPLOAD||r.every((function(t){return t.finishedValidating}))?u?m&&c!==P.NO_TECHNOLOGY_SELECTED?t.isWorkflowSelected(P.UPLOAD_WORKFLOWS.MNGS.value)&&c===P.SEQUENCING_TECHNOLOGY_OPTIONS.NANOPORE&&!i?"Please select a basecaller to continue":t.isWorkflowSelected(P.UPLOAD_WORKFLOWS.COVID_CONSENSUS_GENOME.value)&&!p?"Please select a wetlab protocol to continue":t.isWorkflowSelected(P.UPLOAD_WORKFLOWS.VIRAL_CONSENSUS_GENOME.value)&&!d?"Please select a taxon to continue":t.isWorkflowSelected(P.UPLOAD_WORKFLOWS.VIRAL_CONSENSUS_GENOME.value)&&!o?"Please upload a reference sequence to continue":t.isWorkflowSelected(P.UPLOAD_WORKFLOWS.VIRAL_CONSENSUS_GENOME.value)&&!t.isRefSeqFileNameValid()?z.REF_SE

1Q_FILE_NAME_ERROR_MESSAGE:t.isWorkflowSelected(P.UPLOAD_WORKFLOWS.COVID_CONSENSUS_GENOME.value)&&!t.isBedFileNameValid()?"Bed file name can only contain letters, numbers, dashes, parenthesis and underscores":(0,_.size)(t.getSelectedSamples(l))<1?"Please select a sample to continue":(0,_.size)(t.getSelectedSamples(l))>500?"CZ ID supports a max of 500 samples per upload. 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1,"Friendly Message"),"To ensure every user can use our pipeline smoothly, kindly limit your upload to a max of 200 samples per month so we can share the compute equally. If you need to upload more samples than the limit, please reach out to us at"," ",x.default.createElement(R.default,{href:"mailto:[email protected]"},"[email protected]"),". 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1case 6:return r=i.sent,o=r.validIds,u=r.invalidSampleNames,this.setState({sampleIds:o,invalidSampleNames:u},(function(){return u.length>0&&E.showNotification(oe.NOTIFICATION_TYPES.invalidSamples)})),i.prev=10,i.next=13,Promise.all([this.fetchHeatmapData(o),this.fetchMetadataFieldsBySampleIds(o)]);case 13:h=i.sent,g=(0,p.default)(h,2),c=g[0],m=g[1],i.next=23;break;case 19:return i.prev=19,i.t0=i.catch(10),this.handleLoadingFailure(i.t0),i.abrupt("return");case 23:v=(0,L.compact)((0,L.map)((0,L.property)("pipeline_version"),c)),(y=new Set((0,L.map)((function(t){return"".concat(t.split(".")[0],".x")}),v))).size>1&&this.showNotification(oe.NOTIFICATION_TYPES.multiplePipelineVersions,(0,d.default)(y)),C=(0,L.uniq)((0,L.compact)((0,L.map)((0,L.property)("alignment_config_name"),c))),b=[],l&&(b=(null===(S=(0,L.find)({value:l},t))||void 0===S?void 0:S.alignmentConfigNames)||[]),w=(0,L.pullAll)(C,b),C.length>1?this.showNotification(oe.NOTIFICATION_TYPES.multipleIndexVersions,C):w.length>0&&this.showNotification(oe.NOTIFICATION_TYPES.backgroundDifferentIndexVersion,{}),_={},(0,L.isEmpty)(c)||(_=this.extractData(c)),null!==m&&(_.metadataTypes=m),_.loadingFailed=!1,this.updateHistoryState(),this.setState(_,this.filterTaxaES);case 37:case"end":return i.stop()}}),_callee5,this,[[10,19]])}))),function fetchViewData(){return r.apply(this,arguments)})},{key:"extractData",value:function extractData(t){for(var a=this,l=[],r=new Map,o={},i=[],u=[],c=[],m={},h={},g=[],v=this.state.pathogenFlags,y=!0,C=function _loop(C){var b=t[C];if(l.push(b.sample_id),y=b.ercc_count>0&&(0,K.isPipelineFeatureAvailable)(K.MASS_NORMALIZED_FEATURE,b.pipeline_version)&&y,r.has(b.name)){var S=r.get(b.name),w=b.name;b.name="".concat(b.name," (").concat(S,")"),r.set(w,S+1)}else r.set(b.name,1);if(o[b.sample_id]={id:b.sample_id,name:b.name,index:C,host_genome_name:b.host_genome_name,metadata:(0,ae.processMetadata)({metadata:b.metadata,flatten:!0}),taxa:[],duplicate:!1},b.taxons)for(var _=function _loop2(){var l,r=b.taxons[E];r.tax_id in m?(l=m[r.tax_id].index,m[r.tax_id].sampleCount+=1):(l=i.length,i.push(r.tax_id),r.tax_level===oe.TAXON_LEVEL_OPTIONS.species?u.push(r.tax_id):c.push(r.tax_id),m[r.tax_id]={id:r.tax_id,index:l,name:r.name,category:r.category_name,parentId:r.tax_id===r.species_taxid&&r.genus_taxid,phage:!!r.is_phage,genusName:r.genus_name,taxLevel:r.tax_level,sampleCount:1},m[r.name]=m[r.tax_id]),o[b.sample_id].taxa.push(r.tax_id),a.props.metrics.forEach((function(t){var a=t.value.split("."),o=(0,p.default)(a,2),i=o[0],u=o[1];h[t.value]=h[t.value]||[],h[t.value][l]=h[t.value][l]||[],h[t.value][l][C]=r[i][u]}));var y=t.length;g[l]=g[l]||Array(y);var S,w=(0,L.get)([b.sample_id,r.tax_id],v);w&&(g[l][C]=g[l][C]||[],(S=g[l][C]).push.apply(S,(0,d.default)(w)))},E=0;E<b.taxons.length;E++)_()},b=0;b<t.length;b++)C(b);return{sampleIds:l,sampleDetails:o,allTaxonIds:i,allSpeciesIds:u,allGeneraIds:c,allTaxonDetails:m,allData:h,allPathogenFlagData:g,taxonFilterState:{},enableMassNormalizedBackgrounds:y}}},{key:"fetchBackgroundData",value:function fetchBackgroundData(){return(0,k.getTaxaDetails)({sampleIds:this.state.sampleIds,taxonIds:Array.from(this.state.allTaxonIds),removedTaxonIds:[],background:this.state.selectedOptions.background,updateBackgroun

1dOnly:!0,heatmapTs:this.props.heatmapTs,presets:this.state.selectedOptions.presets})}},{key:"fetchBackground",value:(l=(0,c.default)(i.default.mark((function _callee6(){var t,a;return i.default.wrap((function _callee6$(l){for(;;)switch(l.prev=l.next){case 0:return this.setState({loading:!0}),l.prev=1,l.next=4,this.fetchBackgroundData();case 4:t=l.sent,l.next=11;break;case 7:return l.prev=7,l.t0=l.catch(1),this.handleLoadingFailure(l.t0),l.abrupt("return");case 11:(a=this.extractBackgroundMetrics(t)).loadingFailed=!1,this.updateHistoryState(),this.setState(a,this.filterTaxaES);case 15:case"end":return l.stop()}}),_callee6,this,[[1,7]])}))),function fetchBackground(){return l.apply(this,arguments)})},{key:"extractBackgroundMetrics",value:function extractBackgroundMetrics(t){for(var a=this.state,l=a.sampleDetails,r=a.allTaxonDetails,o=a.allData,i=function _loop3(){var a=t[u],i=l[a.sample_id].index;if(a.taxons)for(var d=function _loop4(){var t=a.taxons[c],l=r[t.tax_id].index;oe.BACKGROUND_METRICS.forEach((function(a){var r=a.value.split("."),u=(0,p.default)(r,2),d=u[0],c=u[1];o[a.value]=o[a.value]||[],o[a.value][l]=o[a.value][l]||[],o[a.value][l][i]=t[d][c]}))},c=0;c<a.taxons.length;c++)d()},u=0;u<t.length;u++)i();return{allData:o}}},{key:"filterTaxa",value:function filterTaxa(){var t,a=this,l=this.getTaxonThresholdFilterState(),r=l.taxonFilterState,o=l.taxonPassesThresholdFilters,i=this.state,u=i.allTaxonIds,d=i.notifiedFilteredOutTaxonIds,c=i.addedTaxonIds,p=this.state.newestTaxonId,m=this.state.allTaxonDetails,h=new Set;u.forEach((function(t){var l=m[t];!h.has(t)&&a.taxonPassesSelectedFilters(l)&&o[l.index]?h.add(l.id):c.has(l.id)&&!d.has(l.id)&&(a.showNotification(oe.NOTIFICATION_TYPES.taxaFilteredOut,l),d.add(l.id),p=null)})),t=this.state.allData,h=Array.from(h),this.updateHistoryState(),this.setState({taxonFilterState:r,taxonIds:h,loading:!1,data:t,notifiedFilteredOutTaxonIds:d,newestTaxonId:p})}},{key:"filterTaxaES",value:function filterTaxaES(){var t,a=this,l=this.state,r=l.sampleDetails,o=l.allData,i=l.allPathogenFlagData,u=l.allTaxonDetails,c=l.addedTaxonIds,p=this.props.metrics,m=this.getTaxonThresholdFilterState().taxonFilterState,h={},g=[],v=new Set,y=Object.values(r).map((function(t){return t.taxa})),C=new Set((0,L.flatten)(y)),b=_createForOfIteratorHelper([].concat((0,d.default)(C),(0,d.default)(c)));try{var S=function _loop5(){var l=t.value;if(!v.has(l)&&!a.removedTaxonIds.has(l)){v.add(l);var r=u[l];p.forEach((function(t){h[t.value]=h[t.value]||[],h[t.value].push(o[t.value][r.index])})),g.push(i[r.index])}};for(b.s();!(t=b.n()).done;)S()}catch(t){b.e(t)}finally{b.f()}this.updateHistoryState(),this.setState({taxonFilterState:m,taxonIds:Array.from(v),loading:!1,data:h,pathogenFlagData:g})}},{key:"getTaxonThresholdFilterState",value:function getTaxonThresholdFilterState(){var t=this,a=this.state,l=a.sampleDetails,r=a.allTaxonDetails,o=a.allData,i=a.taxonFilterState,u={};return Object.values(l).forEach((function(a){Object.values(r).forEach((function(l){i[l.index]=i[l.index]||{},i[l.index][a.index]=t.taxonThresholdFiltersCheck(a.index,l,o),u[l.index]=u[l.index]||i[l.index][a.index]}))})),{taxonFilterState:i,taxonPassesThresholdFilters:u}}},{key:"taxonThresholdFiltersCheck",value:function taxonThresholdFiltersCheck(t,a,l){var r,o=_createForOfIteratorHelper(this.state.selectedOptions.thresholdFilters);try{for(o.s();!(r=o.n()).done;){var i=r.value,u=i.metric.split("_").join(".");if(Object.keys(l).includes(u)){var d=l[u][a.index][t];if(!d)return!1;if(">="===i.operator){if(d<parseFloat(i.value))return!1}else if("<="===i.operator&&d>parseFloat(i.value))return!1}}}catch(t){o.e(t)}finally{o.f()}return!0}},{key:"taxonPassesSelectedFilters",value:function taxonPassesSelectedFilters(t){var a=this.state.selectedOptions,l=a.readSpecificity,r=a.categories,o=a.subcategories,i=a.species,u=o.Viruses&&o.Viruses.includes("Phage");if(i&&1!==t.taxLevel||!i&&2!==t.taxLevel)return!1;if(l&&t.id<0)return!1;if(r.length){if(!u&&t.phage)return!1;if(!(V.default.caseInsensitiveIncludes(r,t.category)||u&&t.phage))return!1}else if(u&&!t.phage)return!1;return!0}},{key:"fetchNewTaxa",value:function fetchNewTaxa(t){return(0,k.getTaxaDetails)({sampleIds:this.state.sampleIds,taxonIds:t,removedTaxonIds:[],background:this.state.selectedOptions.background,updateBackgroun

1dOnly:!1,heatmapTs:this.props.heatmapTs})}},{key:"updateTaxa",value:(a=(0,c.default)(i.default.mark((function _callee7(t){var a,l,r,o,u,d,c,m,h,g,v,y=this;return i.default.wrap((function _callee7$(i){for(;;)switch(i.prev=i.next){case 0:return this.setState({loading:!0}),i.next=3,this.fetchNewTaxa(t);case 3:a=i.sent,l=this.extractData(a),r=this.state,o=r.allData,u=r.allPathogenFlagData,d=r.allGeneraIds,c=r.allSpeciesIds,m=r.allTaxonIds,h=r.allTaxonDetails,g=r.sampleDetails,v=l.allData,d.concat(l.allGeneraIds),c.concat(l.allSpeciesIds),l.allTaxonIds.forEach((function(t){var a=l.allTaxonDetails[t],r=a.index,i=m.length;a.index=i,m.push(t),h[a.id]=a,h[a.name]=a,Object.entries(g).map((function(t){var a=(0,p.default)(t,2),d=a[0],c=a[1];c.taxa.concat(l.sampleDetails[d].taxa);var m=c.index,h=l.sampleDetails[d].index;y.props.metrics.forEach((function(t){o[t.value][i]=o[t.value][i]||[],o[t.value][i][m]=v[t.value][r][h]})),u[i]=u[i]||[],u[i][m]=l.allPathogenFlagData[r][h]}))})),this.setState({allData:o,allPathogenFlagData:u,allGeneraIds:d,allSpeciesIds:c,allTaxonIds:m,allTaxonDetails:h,sampleDetails:g},this.filterTaxaES);case 11:case"end":return i.stop()}}),_callee7,this)}))),function updateTaxa(t){return a.apply(this,arguments)})}

1,{key:"updateBackground",value:function updateBackground(){this.fetchBackground()}},{key:"renderLoading",value:function renderLoading(){var t=this.state.sampleIds;if(!t)return null;var a=t.length;return N.default.createElement("p",{className:ie.default.loadingIndicator},N.default.createElement("i",{className:"fa fa-spinner fa-pulse fa-fw"}),"Loading for ",a," samples. Please expect to wait a few minutes.")}},{key:"renderHeatmap",value:function renderHeatmap(){var t,a=this,l=this.state,r=l.loadingFailed,o=l.selectedOptions.background,i=new Set(this.state.taxonIds,this.state.addedTaxonIds);if(i=new Set((0,d.default)(i).filter((function(t){return!a.removedTaxonIds.has(t)}))),r)return N.default.createElement(P.SampleMessage,{icon:N.default.createElement(ee.IconAlert,{className:ie.default.iconAlert,type:"error"}),link:U.CONTACT_US_LINK,linkText:"Contact us for help.",message:"Oh no! Something went wrong. Please try again or contact us for help.",status:"error",type:"error"});if(this.state.loading||!this.state.data||!(this.state.data[this.state.selectedOptions.metric]||[]).length||!this.state.metadataTypes||!this.state.taxonIds.length)return N.default.createElement("div",{className:ie.default.noDataMsg},"No data to render");var u=this.state.selectedOptions.dataScaleIdx;return N.default.createElement(D.default,null,N.default.createElement(X.default,{data:this.state.data,defaultMetadata:this.state.selectedMetadata,metadataTypes:this.state.metadataTypes,metadataSortField:this.metadataSortField,metadataSortAsc:this.metadataSortAsc,metric:this.state.selectedOptions.metric,onMetadataSortChange:this.handleMetadataSortChange,onMetadataChange:this.handleMetadataChange,onPinSample:this.handlePinnedSampleChange,onPinSampleApply:this.handlePinnedSampleChangeApply,onPinSampleCancel:this.handlePinnedSampleChangeCancel,onUnpinSample:this.handleUnpinSample,pendingPinnedSampleIds:Array.from(this.state.pendingPinnedSampleIds),pinnedSampleIds:Array.from(this.state.pinnedSampleIds),onAddTaxon:this.handleAddedTaxonChange,newTaxon:this.state.newestTaxonId,onRemoveTaxon:this.handleRemoveTaxon,onSampleLabelClick:this.handleSampleLabelClick,onTaxonLabelClick:this.handleTaxonLabelClick,options:this.getControlOptions(),loading:this.state.loading,ref:function ref(t){a.heatmapVis=t},sampleIds:this.state.sampleIds,sampleDetails:this.state.sampleDetails,scale:oe.SCALE_OPTIONS[u][1],selectedTaxa:this.state.addedTaxonIds,selectedOptions:this.state.selectedOptions,taxLevel:oe.TAXON_LEVEL_SELECTED[this.state.selectedOptions.species],tempSelectedOptions:(0,Z.getTempSelectedOptions)({selectedOptions:this.state.selectedOptions,source:Z.HEATMAP_SOURCE_TEMP_PERSISTED_OPTIONS}),allTaxonIds:this.state.selectedOptions.species?this.state.allSpeciesIds:this.state.allGeneraIds,taxonIds:Array.from(i),taxonCategories:this.state.selectedOptions.categories,taxonDetails:this.state.allTaxonDetails,taxonFilterState:this.state.taxonFilterState,sampleSortType:this.state.selectedOptions.sampleSortType,fullScreen:this.state.hideFilters,taxaSortType:this.state.selectedOptions.taxaSortType,appliedFilters:this.getAppliedFilters(),backgroundName:o?null===(t=(0,L.find)({value:o},this.props.backgrounds))||void 0===t?void 0:t.name:oe.NONE_BACKGROUND.name}))}},{key:"renderInvalidSamplesWarning",value:function renderInvalidSamplesWarning(t){var a=this.state.invalidSampleNames,l=N.default.createElement("div",null,N.default.createElement("span",{className:ie.default.highlight},a.length," sample",a.length>1?"s":""," won't be included in the heatmap"),", because they either failed or are still processing:"),r=N.default.createElement("span",null,a.map((function(t,a){return N.default.createElement("div",{key:a,className:ie.default.messageLine},t)})));return N.default.createElement(te.default,{header:l,content:r,open:!1,type:"warning",displayStyle:"elevated",onClose:t})}},{key:"renderFilteredOutWarning",value:function renderFilteredOutWarning(t,a){return N.default.createElement(w.Notification,{intent:"warning",onClose:t,slideDirection:"right"},N.default.createElement("div",null,N.default.createElement("span",{className:ie.default.highlight},a.name," is filtered out by your current filter settings.")," ","Remove some filters to

1see it appear."))}},{key:"renderFilteredMultiplePipelineVersionsWarning",value:function renderFilteredMultiplePipelineVersionsWarning(t,a){return N.default.createElement(w.Notification,{intent:"warning",onClose:t,slideDirection:"right"},N.default.createElement("div",null,N.default.createElement("span",{className:ie.default.highlight},"The selected samples come from multiple major pipeline versions:"," ",a.join(", "),".")," ","A major change in the pipeline may produce results that are not comparable across all metrics. We recommend re-running samples on the latest major pipeline version."))}},{key:"renderCustomBackgroundWarning",value:function renderCustomBackgroundWarning(t){return N.default.createElement(w.Notification,{intent:"warning",onClose:t,slideDirection:"right"},N.default.createElement("div",null,"We're busy generating your heatmap with a new background model. It may take a couple of minutes to load."))}},{key:"showNotification",value:function showNotification(t,a){var l=this;switch(t){case oe.NOTIFICATION_TYPES.invalidSamples:(0,z.showToast)((function(t){var a=t.closeToast;return l.renderInvalidSamplesWarning(a)}),{autoClose:12e3});break;case oe.NOTIFICATION_TYPES.taxaFilteredOut:(0,z.showToast)((function(t){var r=t.closeToast;return l.renderFilteredOutWarning(r,a)}),{autoClose:12e3});break;case oe.NOTIFICATION_TYPES.multiplePipelineVersions:(0,z.showToast)((function(t){var r=t.closeToast;return l.renderFilteredMultiplePipelineVersionsWarning(r,a)}),{autoClose:12e3});break;case oe.NOTIFICATION_TYPES.multipleIndexVersions:(0,z.showToast)((function(t){var l=t.closeToast;return N.default.createElement(w.Notification,{intent:"warning",onClose:l,slideDirection:"right"},N.default.createElement("div",null,N.default.createElement("span",{className:ie.default.highlight},"The selected samples were run on different versions of our NCBI index: ",a.join(", "),".")," ","Changes across indices may produce results that are not comparable. We recommend choosing samples and a background model with the same NCBI index date."))}),{autoClose:12e3});break;case oe.NOTIFICATION_TYPES.backgroundDifferentIndexVersion:(0,z.showToast)((function(t){var a=t.closeToast;return N.default.createElement(w.Notification,{intent:"warning",onClose:a,slideDirection:"right"},N.default.createElement("div",null,"The background model you selected contains sample(s) run against a different version of our NCBI index than sample(s) in this heatmap."))}),{autoClose:12e3});break;case oe.NOTIFICATION_TYPES.customBackground:(0,z.showToast)((function(t){var a=t.closeToast;return l.renderCustomBackgroundWarning(a)}),{autoClose:12e3})}}},{key:"render",value:function render(){var t=this,a=this.state,l=a.addedTaxonIds,r=a.downloadModalOpen,o=a.hideFilters,i=a.loading,u=a.sampleIds,c=a.selectedOptions,p=a.sidebarMode,m=a.sidebarVisible,h=a.taxonIds,g=[].concat((0,d.default)(h),(0,d.default)(l)),v=new Set((0,d.default)(g).filter((function(a){return!t.removedTaxonIds.has(a)})));return N.default.createElement("div",{className:ie.default.heatmap},N.default.createElement(re.SamplesHeatmapHeader,{sampleIds:u,heatmapId:this.props.savedParamValues&&this.props.savedParamValues.id,loading:i,heatmapName:this.props.name,presets:this.state.selectedOptions.presets,onDownloadClick:this.handleDownloadModalOpen,onNewPresetsClick:this.handleHeatmapCreationModalOpen,onShareClick:this.handleShareClick,onSaveClick:this.handleSaveClick,onFilterToggleClick:this.toggleDisplayFilters,filterPanelOpen:!this.state.hideFilters,data:this.state.data,selectedOptions:c,options:this.getControlOptions()}),N.default.createElement("div",{className:"visualization-content"},N.default.createElement("div",{className:ie.default.filtersAndHeatmapContainer},N.default.createElement("div",{className:(0,_.cx)(ie.default.filterPanelContainer,o&&ie.default.hideFilterPanel)},N.default.createElement(B.default,{hideFilters:o,content:N.default.createElement(le.default,{options:this.getControlOptions(),selectedOptions:c,onSelectedOptionsChange:this.handleSelectedOptionsChange,loading:i,data:this.state.data,filteredTaxaCount:v.size,totalTaxaCount:c.species?this.state.allSpeciesIds.length:this.state.allGeneraIds.length,prefilterConstants:this.props.prefilterConstants,enableMassNormalizedBackgroun

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componentWillUnmount(){C.default.select(this.wheelRef.current).on("wheel",null,!0),document.removeEventListener("keydown",this.handleKeyDown,!1),document.removeEventListener("keyup",this.handleKeyUp,!1)}},{key:"componentDidUpdate",value:function componentDidUpdate(t){this.props.scale!==this.scale&&(this.scale=this.props.scale,this.heatmap.updateScale(this.props.scale)),this.props.sampleDetails!==t.sampleDetails&&this.heatmap.updateData({columnLabels:this.extractSampleLabels()}),this.props.data!==t.data&&(this.heatmap.updateData({values:this.props.data[this.props.metric],rowLabels:this.extractTaxonLabels()}),this.scrollToRow()),(0,b.isEqual)(this.props.taxonIds,t.taxonIds)||this.heatmap.updateData({values:this.props.data[this.props.metric],rowLabels:this.extractTaxonLabels()}),(0,b.isEqual)(this.props.pinnedSampleIds,t.pinnedSampleIds)||this.heatmap.updateData({columnLabels:this.extractSampleLabels()}),(0,b.isEqual)(this.props.appliedFilters,t.appliedFilters)||this.heatmap.updatePrintCaption(this.generateHeatmapCaptions()),this.props.sampleSortType!==t.sampleSortType&&this.heatmap.updateSortColumns("alpha"===this.props.sampleSortType),this.props.taxaSortType!==t.taxaSortType&&this.heatmap.updateSortRows("genus"===this.props.taxaSortType)}},{key:"extractSampleLabels",value:function extractSampleLabels(){var t=this,a=arguments.length>0&&void 0!==arguments[0]?arguments[0]:"truncated";return this.props.sampleIds.map((function(l){var r=t.props.sampleDetails[l],o=r.name,i=r.metadata,u=r.duplicate,d=(0,V.getTruncatedLabel)(o);return{label:"full"===a?o:d,metadata:i,printLabel:o,id:l,duplicateLabel:u,pinned:t.props.pinnedSampleIds.includes(l),filterStateColumn:r.index}}))}},{key:"extractTaxonLabels",value:function extractTaxonLabels(){var t=this;return this.props.taxonIds.map((function(a){var l=t.props.taxonDetail

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a=this,l=this.props,r=l.data,o=l.taxonFilterState,i=l.sampleIds,u=l.taxonIds,d=i[t.columnIndex],c=u[t.rowIndex],p=this.props.sampleDetails[d],m=this.props.taxonDetails[c],h=this.metrics.some((function(a){return!!r[a.key][t.rowIndex][t.columnIndex]})),g=o[m.index][p.index],v=null;h&&(v=this.metrics.map((function(l){var r=a.props.data[l.key][t.rowIndex][t.columnIndex],o=null!==r?parseFloat(r.toFixed(4)):"-";return[l.label,l.key===a.props.metric?S.default.createElement("b",null,o):o]})));var y=null;h?g||(y="This taxon does not satisfy the threshold filters."):y="This taxon was not found in the sample.",y&&(y=S.default.createElement("div",{className:W.default.warning},S.default.createElement(P.IconAlertSmall,{className:W.default.warningIcon,type:"warning"}),S.default.createElement("div",{className:W.default.warningText},y)));var C=[{name:"Info",data:[["Sample",p.name],["Taxon",m.name],["Category",m.category]],disabled:!g}];return h&&C.push({name:"Values",data:v,disabled:!g}),{subtitle:y,data:C,nodeHasData:h}}},{key:"getAvailableTaxa",value:function getAvailableTaxa(){var t=this.props,a=t.allTaxonIds,l=t.taxonDetails;return a.map((function(t){return{value:t,label:l[t].name,count:l[t].sampleCount}}))}},{key:"scrollToRow",value:function scrollToRow(){var t;this.props.newTaxon&&this.heatmap.scrollToRow(null===(t=this.props.taxonDetails[this.props.newTaxon])||void 0===t?void 0:t.name)}},{key:"getSelectedMetadata",value:function getSelectedMetadata(){var t=this;return Array.from(this.state.selectedMetadata).filter((function(a){return!!t.metadataTypes[a]})).map((function(a){return{value:a,label:t.metadataTypes[a].name}})).sort((function sortByLabel(t,a){return t.label>a.label?1:-1}))}},{key:"getAvailableMetadataOptions",value:function getAvailableMetadataOptions(){return this.props.metadataTypes.filter((function(t){return t.key&&t.name})).map((function(t){return{value:t.key,label:t.name}}))}},{key:"handleZoom",value:function handleZoom(t){var a=Math.min(3,Math.max(.2,this.heatmap.options.zoom+t));this.heatmap.updateZoom(a)}},{key:"render",value:function render(){var t=this,a=this.state,l=a.addTaxonTrigger,r=a.tooltipLocation,o=a.nodeHoverInfo,i=a.columnMetadataLegend,u=a.rowGroupLegend,d=a.addMetadataTrigger,c=a.selectedMetadata,p=a.pinSampleTrigger,m=a.pinIconHovered,h=this.props.sampleIds.map((function(a){return{id:a,name:t.props.sampleDetails[a].name,pinned:t.props.pinnedSampleIds.includes(a)}}));return h=(0,b.orderBy)(["pinned","name"],["desc","asc"],h),S.default.createElement(S.default.Fragment,null,S.default.createElement("div",{className:W.default.samplesHeatmapVis,ref:this.wheelRef},S.default.createElement("div",{className:W.default.rightSideOverlay}),S.default.createElement(k.default,{onPlusClick:function onPlusClick(){return t.handleZoom(.25)},onMinusClick:function onMinusClick(){return 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We have summarized key updates below:"),u.default.createElement("h2",null,"CZ ID Terms of Use"),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We updated our timelines for addressing Usersâ data privacy requests and our Contact Information.")]}),u.default.createElement("h2",null,"CZ ID Privacy Policy"),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,null,"To give you more control over your data, we have removed the automatic sharing of your Report Data and Sample Metadata after the 1-year anniversary of the Raw Sample Data being uploaded to CZ ID. Users will still have the option to share their Report Data and Sample Metadata with other Users at their discretion."),u.default.createElement(u.default.Fragment,null,"We clarified our legal basis (consent) for collecting data through the use of cookies when GDPR applies."," "),u.default.createElement(u.default.Fragment,null,"We added a section about Do Not Track signals."),u.default.createElement(u.default.Fragment,null,"We clarified that we use IP addresses to infer the approximate location (i.e., country) of our Users so that we can comply with applicable laws and to better understand the geographic distribution of our Users."," "),u.default.createElement(u.default.Fragment,null,"We updated the timelines for addressing a Userâs data privacy requests."),u.default.createElement(u.default.Fragment,null,"We added additional information for California residents. We also added additional information for Virginia, Colorado, Connecticut, and Utah to keep up with changes in privacy law."," ")]}),u.default.createElement("p",{className:(0,o.default)(p.default.large,p.default.last)},"For questions about these changes, please contact us at"," ",u.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),"."))}(),function termsUpdateForDecember2021(){return u.default.createElement(u.default.Fragment,null,u.default.createElement("div",{className:p.default.title},u.default.createElement("h1",null,"IDseq Terms and Privacy Notice Update for December 2021")),u.default.createElement("p",{className:(0,o.default)(p.default.large,p.default.last)},"Effective December 7, 2021, we are changing our product name to Chan Zuckerberg ID. As a result, we have updated our"," ",u.default.createElement("a",{href:"/terms"},"Terms of Use")," and"," ",u.default.createElement("a",{href:"/privacy"},"Privacy Policy")," to reflect this name change. No additional changes were made to our terms in this update."))}(),function termsUpdateForApril2021(){return u.default.createElement(u.default.Fragment,null,u.default.createElement("div",{className:p.default.title},u.default.createElement("h1",null,"IDseq Terms and Privacy Notice Update for April 2021")),u.default.createElement("p",{className:p.default.large},"We periodically update our ",u.default.createElement("a",{href:"/terms"},"Terms of Use")," and"," ",u.default.createElement("a",{href:"/privacy"},"Privacy Policy")," to help ensure that we are providing useful transparency regarding how we collect, use and protect their data and so our Users understand their responsibilities and rights when they use IDseq."),u.default.createElement("p",{className:p.default.large},"We are planning to update our Terms of Use and Privacy Policy for the IDseq service to be effective on April 1, 2021, and have also summarized key updates below:"),u.default.createElement("h2",null,"IDseq Terms of Use"),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},u.default.createElement("i",null,"Disputes between IDseq and you will now be resolved through final and binding arbitration.")," ","This is a more efficient and cost effective (we will bear most costs) way of resolving disputes related to IDseq. Our Terms of Use describes in detail how this works, and how you can opt out."),"To help make the document easier to understand, weâve provided a summary\n           at the top of our Terms of Use of key things to know."]}),u.default.createElement("h2",null,"IDseq Privacy Policy"),u.default.createElement(c.default,{listItems:["To help make the document easier to understand, weâve created a Summary Table at\n          the top of our Privacy Policy that explains the key aspects of our data practices in a concise way.",u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},u.default.createElement("i",null,"Chan Zuckerberg Initiative Foundation.")," IDseq, as of April 1, 2021, will be provided by the Chan Zuckerberg Biohub in close collaboration with the Chan Zuckerberg Initiative Foundation. This is part of the Chan Zuckerberg Initiativeâs shifting of its Scie

1nce employees, projects, and activities to live within the existing CZI Foundation, a 501(c)(3) nonprofit entity. We want to assure you that this does not change our commitment to delivering a high-quality experience for you within IDseq. This is a largely back-end organizational change that will take effect on April 1, 2021, and will have minimal impacts on CZIâs work with grantees and partners, or on the CZI Science team day-to-day."),u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},u.default.createElement("i",null,"Nextclade.")," Users now can choose to share certain Report Data with third party tools, like Nextclade. This integration is purely optional and you choose to use it or not. As a reminder, we will never share raw sample data youâve uploaded -- only you can access that data.")]}),u.default.createElement("p",{className:(0,o.default)(p.default.large,p.default.last)},"For questions about these changes, please contact us at"," ",u.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),"."))}(),function termsUpdateForJune2019(){return u.default.createElement(u.default.Fragment,null,u.default.createElement("div",{className:p.default.title},u.default.createElement("h1",null,"IDseq Terms and Privacy Notice Update for June 2019")),u.default.createElement("p",{className:p.default.large},"Control over your data is important to the success of IDseq. We periodically update our Terms of Use and Data Privacy Notice to help ensure that our Users understand their responsibilities and rights when they use IDseq, as well as how we collect, use and protect their data."),u.default.createElement("p",{className:p.default.large},"We are planning to update our Terms of Use and Data Privacy Notice for the IDseq service to be effective on June 24, 2019. We encourage our Users to read the revised ",u.default.createElement("a",{href:"/terms"},"Terms")," and"," ",u.default.createElement("a",{href:"/privacy"},"Privacy Notice"),". We have also provided more information about our updates through a new ",u.default.createElement("a",{href:"/faqs"},"FAQ page"),"."),u.default.createElement("h2",null,"IDseq Terms of Use"),u.default.createElement("p",{className:p.default.large},"This summary is intended to help you better understand the most recent changes to the IDseq Terms of Use and how they may impact you. To be clear, many important matters are not changing, including your responsibility to get appropriate permissions to upload and share data through IDseq and our promise not to sell your data."," ",u.default.createElement("b",null,"You own your data - using IDseq doesnât change that.")),u.default.createElement("p",{className:p.default.large},"We also encourage you to read the full revised"," ",u.default.createElement("a",{href:"/terms"},"Terms"),"."),u.default.createElement("h3",null,"Introduction Section."),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We clarified that the purpose of IDseq is for research purposes only and"," ",u.default.createElement("u",null,"is not intended to be used to make decisions regarding health care of persons.")),"We provided more information about how IDseq works, including how\n        and when your data will be shared with other Users of IDseq. As\n        before, we seek to filter out human data from the data that is\n        uploaded by our Users.","We added more clarity by providing new and more nuanced definitions\n        of the types of data that IDseq processes. We have retired the broad\n        definition of âResearch Dataâ and replaced it with several more\n        specific terms, such as âUpload Dataâ (data you upload), âSample\n        Data,â (part of Upload Data that includes full genetic sequence\n        data), âSample Metadataâ (part of Upload Data that provides context\n        for the Sample Data) and âReport Dataâ (the report about the\n        pathogen produced by the IDseq service)."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"1.")," Upload and Report Data."),u.default.createElement(c.default,{listItems:["We added more details about how you can have your data removed\n        and/or deleted from IDseq.",u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We added more clarity about when âReport Dataâ becomes visible to other Users of IDseq. Report Data and Sample Metadata will be available to all other IDseq Users for their use"," ",u.default.createElement("b",null,"after 1 year of it being uploaded unless you take action to remove it"),". Making this Report Data available to others is important IDseq's success as a research tool to advance the study of infectious diseases."),"We added that the representations and warranties you make about the\n        data you upload, extend not just to us, but also the service\n        providers that we use.","We emphasized that your obligation to get appropriate permissions to\n        upload data to IDseq should include a review of the ethical\n        standards that apply to you.","We clarified our requirement that Users do not attempt to âidentifyâ\n        the person to whom any particular set of data may apply.","We made it clearer that we do not want you to upload any regulated\n        health information into IDseq."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"2.")," Authorization To Use IDseq."),u.default.createElement(c.default,{listItems:["We made it clearer that Users should not share their accounts with\n        others and that everyone who wishes to access and use IDseq should\n        have their own account, including your research associates."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"3.")," Restrictions On Use."),u.default.createElement(c.default,{listItems:["In the unlikely event we need to terminate your access to IDseq, we\n        added that we will try to provide you notice through the contact\n        information that you have provided to us."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"4.")," Registration And Contact Information."),u.default.createElement(c.default,{listItems:["We added that we can notify you regarding updates to our Terms of\n        Use and Privacy Notice through the contact information that we have\n        for you."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"5.")," Changes to IDseq or the Terms."),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We clarified that when we provide notice of changes to our Terms of Use, that we will attempt to provide notice ",u.default.createElement("b",null,"before")," the changes are effective."),"We provided clearer information about how you can close your account\n        in the event you do not find our changed terms acceptable, or if you\n        choose to no longer use IDseq."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"6.")," Intellectual Property and Security."),u.default.createElement(c.default,{listItems:["We added clearer and simpler language to de

1scribe intellectual\n        property rights ownership related to IDseq. Neither we nor any other\n        Users get any ownership rights or the intellectual property rights\n        you own simply because you used IDseq. At the same time, your use of\n        IDseq does not give you ownership of any intellectual property\n        rights you didnât already own.","If you decide to provide feedback to us about IDseq, we clarified\n        that we are free to use it, but are not obligated to use your\n        feedback."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"7.")," Disclaimers and 8. Limitation of Liability."),u.default.createElement(c.default,{listItems:["We added that the disclaimers and limitation of liability also\n        applies to our service providers.","We clarified that local law may give you additional rights and that\n        our limitation of liability may not apply to you."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"8.")," Choice of Law and Arbitration."),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We removed the mandatory arbitration requirements. In the unlikely event of a dispute between us, itâs still possible for us to mutually agree that arbitration is the most effective way to settle our dispute, but under the revised terms, you will no longer be obligated to ",u.default.createElement("b",null,"only")," seek remedies in arbitration -- you can now have any dispute resolved through court.")]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"9.")," Miscellaneous."),u.default.createElement(c.default,{listItems:["We removed language about export compliance because it was\n        duplicative of the already existing obligation to comply with law.","We added more information about how to contact us through a new FAQ."]}),u.default.createElement("h2",null,"IDseq Data Privacy Notice"),u.default.createElement("p",{className:p.default.large},"This summary is intended to help you better understand the most recent changes to the ",u.default.createElement("a",{href:"/privacy"},"IDseq Data Privacy Notice")," and how they may impact you."),u.default.createElement("h3",null,"Introduction Section."),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We clarified that the purpose of IDseq is for research purposes only and"," ",u.default.createElement("u",null,"is not intended to be used to make decisions regarding health care of persons.")),u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We provided more information about how IDseq works,"," ",u.default.createElement("u",null,"including how and when data will be shared with other Users of IDseq"),". 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Report Data."),u.default.createElement(c.default,{listItems:["We added more details about how you can exercise your right to have\n        your data removed and/or deleted from IDseq.","We added more clarity about your choices with regard to your data,\n        including by using the âProject Featureâ where you can choose who to\n        share your data with.",u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We provided more clarity about when âSample Metadataâ and âReport Dataâ will automatically become visible to other Users of IDseq. All Users of IDseq will be able to access and use this data"," ",u.default.createElement("b",null,"after 1 year of it being uploaded unless you take action to remove it"),". Making this Report Data available to others is important IDseq's success as a research tool to advance the study of infectious diseases."),"We added that the representations and warranties you make about the\n        data you upload, extend not just to us, but also the service\n        providers that we use.","We added that the representations and warranties you make about the\n        data you upload, extend not just to us, but also the service\n        providers that we use.","We clarified that your obligation to get appropriate permissions to\n        upload data to IDseq, should include review of the ethical standards\n        that apply to you.","We clarified our requirement that Users do not attempt to âidentifyâ\n        the person to whom any particular set of data may apply.","We made it clearer that we do not want you to upload any regulated\n        health information into IDseq."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"3.")," Visitor and User Data."),u.default.createElement(c.default,{listItems:["We clarified that the term âUser Dataâ means information collected\n        from a User.","We provided more information about our use of cookies, beacons and\n        similar technologies through our new FAQ.","We added that we do not use cookies and similar technologies to\n        serve ads for third parties.","We clarified that we analyze how Visitors use our services, and not\n        just Users.","We provided additional details about why we believe that we have a\n        valid legal basis to use data provided to IDseq and that we have\n        legitimate interest in using personal data to enable our operation\n        of IDseq."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"4.")," Vendors and Other Third Parties."),u.default.createElement(c.default,{listItems:["We provided more information about the Chan Zuckerberg Initiative\n        which acts as a technology partner in developing and operating IDseq\n        and who is a âjoint-controllerâ of personal data for EU legal\n        purposes.","We provided more information about third party services provided\n        access to personal data in connection with the development and\n        operation of IDseq, including providing more information in our FAQ.",u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"In the unlikely event we stop providing the IDseq service, we added that we will let you know ",u.default.createElement("b",null,"before")," we allow another entity to take over its development and operation and that we will require that the third party be bound by the Data Privacy Notice and Terms of Use.")]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"6.")," How Long We Retain Data and Data Retention and 7. Choices About Your Data."),u.default.createElement(c.default,{listItems:["We clarified that we retain personal data only as long as reasonably\n        necessary.","We provided more information about how to delete your data and how\n        to exercise your rights about your personal data, including requests\n        to access, delete, or restrict our use of their personal data.","We added a notice that those in the EU have the right to contact\n        their local data protection authority."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"8.")," Data Transfers."),u.default.createElement(c.default,{listItems:["We provided more information about why transferring data uploaded to\n          IDseq to the US is necessary to help researchers to better\n          understand infectious diseases."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"9.")," How to Contact Us."),u.default.createElement(c.default,{listItems:["We put our contact information into a separate FAQ."]}),u.default.createElement("h3",null,u.default.createElement("span",{className:p.default.number},"10.")," Changes to the Privacy Notice."),u.default.createElement(c.default,{listItems:[u.default.createElement(u.default.Fragment,{key:(0,i.nanoid)()},"We added that we will provide you notice of any material changes to the Privacy Notice ",u.default.createElement("b",null,"before")," they become effective.")]}))}())}},19442:(t,a,l)=>{"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var r=l(80152);a.default=r.TermsChanges},9049:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.TermsOfUse=function TermsOfUse(){return i.default.createElement(u.NarrowContainer,{className:c.default.termsOfUse,size:"small"},function renderIntro(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("div",{className:c.default.title},i.default.createElement("h1",null,"Chan Zuckerberg ID (formerly IDseq) Terms of Use"),i.default.createElement("h4",{className:c.default.subtitle},"Last Updated: January 1, 2023."," ",i.default.createElement("a",{href:"/terms_changes"}

1,"See Recent Changes"))),i.default.createElement("p",{className:c.default.last},i.default.createElement("b",null,"PLEASE BE ADVISED THAT THIS AGREEMENT CONTAINS AN ARBITRATION PROVISION IN SECTION 9 BELOW THAT AFFECTS YOUR RIGHTS UNDER THIS AGREEMENT.")," ","EXCEPT FOR CERTAIN TYPES OF DISPUTES MENTIONED IN THAT PROVISION, YOU AND CZ BIOHUB (AND ITS PARTNERS AND AFFILIATES, INCLUDING WITHOUT LIMITATION CZI, LLC AND CZIF) AGREE THAT (1) DISPUTES BETWEEN US WILL BE RESOLVED BY INDIVIDUAL BINDING ARBITRATION, AND (2) YOU AND CZ BIOHUB (AND ITS PARTNERS AND AFFILIATES, INCLUDING WITHOUT LIMITATION CZI, LLC AND CZIF) WAIVE ANY RIGHT TO PARTICIPATE IN A CLASS-ACTION LAWSUIT, CLASS-WIDE ARBITRATION, OR ANY OTHER REPRESENTATIVE ACTION."),i.default.createElement("p",null,"Please read these Terms of Use (âTermsâ) before using Chan Zuckerberg ID (âServicesâ or âCZ IDâ). These Terms are entered into between the Chan Zuckerberg Biohub, Inc. (âCZ Biohubâ, â weâ, âusâ or âourâ) and you (âUserâ or â youâ) and govern your use of CZ ID. CZ ID is comprised of our research portal, any associated online services or platforms that link to or refer to these Terms, and any databases or data accessible through the portal, associated services or platforms. CZ ID is designed to enable the research community to investigate pathogens using metagenomic sequencing data and to help further the study of infectious diseases."),i.default.createElement("p",null,"Please carefully read these terms and indicate your acceptance by registering for CZ ID. If you do not agree to these Terms, do not register for an account or use CZ ID. For more information about our privacy practices, please see our ",i.default.createElement("a",{href:"/privacy"},"Privacy Notice"),"."))}

1(),function renderSummaryOfKeyThingsToKnow(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h3",null,"Summary of Key Things to Know (see ",i.default.createElement("a",{href:"/faqs"},"FAQ")," for more)"),i.default.createElement(d.default,{listItems:[i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"CZ ID does not provide medical advice. The output from CZ ID does not constitute and should not be relied upon to provide medical advice, diagnosis or treatment. It is intended for research, educational, or informational purposes only."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"You must ensure that all personally-identifying information and Protected Health Information is fully removed from Sample Metadata before it is uploaded to CZ ID."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"You are responsible for obtaining the permissions necessary to collect and submit the Upload Data. You represent that you have obtained, and will maintain, all consents, permissions, and authorizations needed to collect, share, use, and export Upload Data within CZ ID, and for CZ ID to use and share the information as described in its ",i.default.createElement("a",{href:"/privacy"},"Privacy Notice"),"."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"You may not attempt to re-identify Upload Data. By using CZ ID, you agree that you will not attempt to re-identify any Upload Data with a person, and you will not disclose any Upload Data of other Users downloaded from the Database except for the limited purposes described in these Terms."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"CZ ID does not own any research outputs you create with your Report Data, such as consensus genomes and phylogenetic trees for pathogens of interest. This is your data and you control it.")]}))}(),function renderAboutCZID(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h3",null,"About CZ ID"),i.default.createElement("p",null,"Hereâs how CZ ID works: Users submit Upload Data (as described below). This data may contain human and non-human genetic sequences (âSample Dataâ as further defined below), as well as information about those sequences, such as the date the sample was collected and the species it was collected from (âSample Metadataâ as further defined below). For example, a researcher might upload genetic information from mosquitoes, which are often a source of infectious disease, or from humans, who can be infected by such diseases. CZ ID then processes this Upload Data in order to identify pathogens found within the genetic sequence (e.g., the mosquito may be carrying the chikungunya virus)."),i.default.createElement("p",null,"âUpload Dataâ is data that Users upload to CZ ID (other than the information Users provide during registration to create an account). Upload Data consists of genetic sequence information (human or non-human) and metadata about those genetic sequences (such as time and location of sample collection). Upload Data includes Sample Data and Sample Metadata."),i.default.createElement("p",null,"âSample Dataâ is full genetic sequence data uploaded by Users. Genetic sequence data contains genetic information about pathogens in the sample and of the host from which the sample was taken. The host could be a human or non-human (e.g., mosquito). You should not be able to find any human sequence data in CZ ID other than those embedded in samples you yourself have uploaded. This is because we filter out and discard host sequence data in order to generate Reports."),i.default.createElement("p",null,"âSample Metadataâ includes information related to the Sample Data, such as the host type (e.g., human or mosquito), upload date, and tissue type and free-text research notes entered by Users. This data"," ",i.default.createElement("u",null,"should not")," include personally-identifying information regarding the individual to whom the Sample Data relates."),i.default.createElement("p",null,"âReport Dataâ is information CZ ID produced from Upload Data. We generate Report Data by processing Upload Data through our Data Pipeline. CZ IDâs âData Pipelineâ cleans (e.g., by removing duplicate nucleotides) and analyzes (e.g., by matching Sample Data nucleotide sequences with known pathogen sequences) the Upload Data. Report Data may include, for example, data about the pathogen sequences identified in the Sample Data and the frequency of such identification (âPathogen Dataâ) or raw numeric counts of non-personally identifying gene expression profiles that were found in the Sample Data (âGene Countsâ)."),i.default.createElement("p",null,"âDatabaseâ refers to both the data and database(s) of CZ ID."))}(),function renderUploadAndReportDataTerms(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"1."),"Upload and Report Data."),i.default.createElement(d.default,{listItems:[i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"1.1 Use of Your Upload Data. We need limited rights to your Upload Data solely in order to offer CZ ID for you and other Users. 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1on of your Upload Data from CZ ID by emailing"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," and including a description of your Upload Data that you wish to have removed. We will delete the requested Upload Data within the timelines set forth under applicable privacy laws. Please note, that our removal of your Upload Data from CZ ID will not impact any use of Upload Data by others you may have chosen to share it with prior to the effective date of removal and we are not able to require others Users to stop using Upload Data they accessed or downloaded prior to removal. More information about Upload Data can be found in our"," ",i.default.createElement("a",{href:"/privacy"},"Privacy Notice"),"."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"1.2 Use and Visibility of Your Report Data. You understand that your Report Data is data generated by CZ ID, does not contain personally-identifying information (i.e. personal data) and may be shared with other CZ ID Users in order to further CZ IDâs mission and advance the study of infectious diseases."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"1.3 You represent and warrant to us and our service partners that (A) your provision of the Upload Data to CZ ID complies with all applicable laws, rules, and regulations, including the Nagoya Protocol and relevant export laws (âApplicable Lawâ) and industry guidelines and ethical standards that apply to you (e.g. CIOMS or GA4GH) (âApplicable Standardsâ), and you will otherwise comply with all Applicable Law in connection with CZ ID; (B) you have all consents, permissions, and authorizations necessary and sufficient to upload, share, use, and export the Upload Data to us for the purposes described in these Terms and in our"," ",i.default.createElement("a",{href:"/privacy"},"Privacy Notice")," and to grant the rights and permissions herein; and (C) the Upload Data -- and our use of the Upload Data in accordance with these Terms and our"," ",i.default.createElement("a",{href:"/privacy"},"Privacy Notice")," -- does not and will not violate Applicable Law or infringe or violate any third party rights."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"1.4 TO THE EXTENT UPLOAD DATA IS OBTAINED FROM A HUMAN, YOU AGREE NOT TO PROVIDE UPLOAD DATA IN A FORM THAT CAN IDENTIFY (DIRECTLY OR INDIRECTLY TAKING INTO ACCOUNT ALL THE MEANS REASONABLY LIKELY TO BE USED) THE PERSON TO WHOM THE DATA RELATES OR THAT CONSTITUTES OR WOULD CONSTITUTE âPROTECTED HEALTH INFORMATIONâ OR REGULATED HEALTH INFORMATION UNDER APPLICABLE LAWS, SUCH AS THE U.S. HEALTH INSURANCE PORTABILITY AND ACCOUNTABILITY ACT (âHIPAAâ). For example, the Upload Data shall not include any personal identifiers, including without limitation name, address, dates, telephone numbers, e-mail addresses, or medical health records."),i.default.createElement(i.default.Fragment,{key:(0,o.nanoid)()},"1.5 To the extent that any Upload Data is obtained from a human data subject, you also specifically represent and warrant to us and our service partners that (A) you have provided any required notice to, and obtained any necessary informed consent of, any such person for the collection, use, and provision to CZ ID of the Upload Data; and (B) your provision of the Upload Data to CZ ID is covered under all such notices and consents, as well as Applicable Standards and Applicable Law. Please note that we filter out and discard human sequence data as part of generating Report Data because we donât need this data for CZ ID. See ",i.default.createElement("a",{href:"/faqs"},"here")," for more details.")]}))}(),function renderAuthorizationToUseCZID(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"2."),"Authorization To Use CZ ID."),i.default.createElement(d.default,{listItems:["2.1 Subject to and conditioned on your compliance with these Terms, we grant you permission to access and use CZ ID in accordance with Applicable Law, solely for your own internal academic or internal scientific research purposes. You may not permit any third party to access or use or âshareâ your Account. All persons wishing to access the Service must create their own separate account and agree to these Terms.","2.2 CZ ID may not be used to provide medical or other services to any third party (for instance, to inform or provide disease diagnoses). CZ ID is not intended to diagnose, treat, cure, or prevent any disease and is not a substitute for medical advice.","2.3 You shall not disclose or distribute the Database, in whole or in part, or any works derived from the Database to any third party for any purpose, except for the following:","You may disclose the documents that you download from the Database using CZ IDâs intended functionality to your employees and agents who are registered Users of the Service and who are engaged in conducting your research (âResearch Associatesâ) for the sole purpose of carrying out your internal research. Your Research Associates must also agree to use CZ ID and Database in accordance with these Terms.","You may share research f

1indings derived from use of CZ ID to others, including with the public, so long as these findings include no personally-identifying information and you comply with Applicable Law and these Terms.","You may disclose the Database to the minimum extent necessary to comply with Applicable Law or court order, so long as you promptly notify us prior to making such disclosure (to the extent Applicable Law and court order permit you to so notify us)."]}))}(),function renderLimitationsOnUse(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"3."),"Limitations On Use."),i.default.createElement(d.default,{listItems:["3.1 You shall not re-identify or attempt to re-identify any Database records or content for any purpose other than responding to a request from the individual whom the record within your Upload Data is about, including without limitation to make employment decisions or to make eligibility, coverage, underwriting, premium-setting or other decisions with respect to insurance.","3.2 You shall not otherwise access or use, or attempt to access or use, CZ ID to take any action that could harm us, CZ ID or its Users, or any third party, or use CZ ID in any manner that violates Applicable Law or infringes or otherwise violates third party rights.","3.3 You represent and warrant that you are a natural person of legal age who is competent and able to enter into and carry out these Terms, and, if you are using CZ ID on behalf of any entity, that you are authorized to enter into these Terms on such entityâs behalf and that such entity agrees to be responsible to us if you or that entity violates these Terms.","3.4 We may restrict or terminate your access to CZ ID at any time, including for breach of these Terms. In such case we will attempt to provide you notice through the contact information we have for you."]}))}(),function renderRegistrationAndContactInfo(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"4."),"Registration And Contact Information."),i.default.createElement(d.default,{listItems:["4.1 To access CZ ID you will need to be a registered âUser.â At registration, you will be asked to provide certain information (âAccount Informationâ) to create an individual user account (an âAccountâ). You agree that you will not create more than one Account, or create an Account for anyone other than yourself. You may not share your Account credentials.",i.default.createElement(i.default.Fragment,null,"4.2 You agree to keep your Account Information accurate and up-to-date. You agree that we may send to the e-mail address you provide us or otherwise electronically deliver notices or communications regarding CZ ID, including notices of updates to these terms and the ",i.default.createElement("a",{href:"/privacy"},"Privacy Notice"),".")]}

1))}(),function renderChangesToCZIDOrTerms(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"5."),"Changes To CZ ID Or These Terms."),i.default.createElement(d.default,{listItems:["5.1 Changes to CZ ID. We may, from time to time, withdraw, suspend, change or update CZ ID (including the Database) or its features without notice, subject to Applicable Law. Neither we, nor our service providers, will be liable if all or any part of CZ ID is unavailable or changes at any time.","5.2 Changes to these Terms. We may update these Terms from time to time and will notify you of material changes to the Terms, prior to their becoming effective. If you do not agree to the updated Terms, your remedy will be to close your Account prior to the effective date of those changes.",i.default.createElement(i.default.Fragment,null,"5.3 Closing Your Account. You can close your Account at any time. Just contact us at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),".")]}))}(),function renderIntellectualPropertyAndSecurityTerms(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"6."),"Intellectual Property And Security."),i.default.createElement(d.default,{listItems:["6.1 Intellectual Property Rights. Just because you upload data to CZ ID, you are not giving us any ownership of your intellectual property rights (see Section 1.1 above). Subject to these Terms, we grant you a limited right to access CZ ID, and we reserve all other of our intellectual property rights in CZ ID. Using CZ ID does not give you any ownership in CZ ID, our services or the content or information made available through CZ ID that is not already yours. Trademarks and logos used in connection with CZ ID are the trademarks of their respective owners. Our logos and other trademarks, service marks, graphics, and logos used for our services are trademarks or registered trademarks of ours and these Terms do not grant you any rights to use them.",i.default.createElement(i.default.Fragment,null,"6.2 Feedback. Weâd love your feedback about how to improve CZ ID at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),". That said, by giving us feedback, you agree that we can use and share it for any purpose without compensation to you. You agree that we are not required to use your feedback."),i.default.createElement(i.default.Fragment,null,"6.3 Security. You will establish, implement, and maintain appropriate physical, technical and organizational measures that are designed to: (a) protect the security and integrity of any network or system used to access CZ ID, including any Database records; and (b) guard against the accidental or unauthorized access, use, alteration or disclosure of CZ ID through your Account. Please notify us immediately at"," ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]")," if you suspect your Account has been compromised or are aware of any other security issues relating to CZ ID.")]}))}(),function renderDisclaimerTerms(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"7."),"Disclaimers."),i.default.createElement(d.default,{listItems:[i.default.createElement(i.default.Fragment,null,"7.1 In order to further infectious disease research, we rely upon Users to upload data to the Database. We and our service providers do not review or correct any data uploaded into CZ ID. If you would like to report any issue with CZ ID or the Database please contact us at ",i.default.createElement("a",{href:"mailto:[email protected]"},"[email protected]"),". CZ ID is not intended as a storage service, so please back up your Upload Data using a secure service of your choice."),"7.2 TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW:","7.2.1 YOUR ACCESS AND USE CZ ID AT YOUR SOLE RISK AND AGREE THAT WE AND OUR SERVICE PROVIDERS WILL NOT BE RESPONSIBLE FOR ANY ACTIONS YOU TAKE BASED ON CZ ID OR FOR ANY INACCURATE DATA OR OUTPUTS OF CZ ID (INCLUDING MISIDENTIFICATION OF -- OR THE FAILURE TO IDENTIFY -- DISEASE SEQUENCES).","7.2.2 CZ ID IS PROVIDED âAS ISâ WITH ALL FAULTS, AND WE AND OUR SERVICE PROVIDERS HEREBY DISCLAIM ALL REPRESENTATIONS AND WARRANTIES, EXPRESS, STATUTORY, OR IMPLIED (INCLUDING, WITHOUT LIMITATION, IMPLIED WARRANTIES OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND ALL WARRANTIES ARISING FROM THE COURSE OF DEALING, USAGE, OR TRADE PRACTICE) WITH RESPECT TO CZ ID. CZ ID IS NOT INTENDED TO BE USED AND SHOULD NOT BE USED AS A MEDICAL DEVICE OR FOR PURPOSES OF MEDICAL DIAGNOSIS OR TREATMENT.","7.2.3 FOR CLARITY AND WITHOUT LIMITING THE FOREGOING, WE AND OUR SERVICE PROVIDERS DO NOT MAKE ANY GUARANTEES (I) REGARD

1ING THE ACCURACY, COMPLETENESS, TIMELINESS, SECURITY, AVAILABILITY OR INTEGRITY OF CZ ID, (II) THAT CZ ID WILL BE UNINTERRUPTED OR OPERATE IN COMBINATION WITH ANY SOFTWARE, SERVICE, SYSTEM OR OTHER DATA, OR (III) THAT CZ ID WILL MEET ANY REQUIREMENTS OF ANY PERSON OR ENTITY, OR ANY REGULATORY APPROVALS OR REQUIREMENTS. WITHOUT LIMITATION, YOU ACKNOWLEDGE THAT CZ ID IS NOT A BUSINESS ASSOCIATE FOR PURPOSES OF HIPAA."]}))}(),function renderLawTerms(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"8."),"Indemnification, Limitation Of Liability, And Choice Of Law."),i.default.createElement(d.default,{listItems:["8.1 To the maximum extent permitted by Applicable Law, you agree to indemnify and hold harmless CZ Biohub, its affiliates (including without limitation the Chan Zuckerberg Initiative Foundation (CZIF), the Chan Zuckerberg Initiative, LLC (CZI LLC), and their successors, assigns, officers, directors, employees, and agents (collectively, the âCZ Biohub Protected Partiesâ) from and against any and all liabilities, costs, damages, charges, losses, penalties, judgments, settlements, and expenses (including reasonable attorneyâs fees) (âLossesâ) arising out of or related to any suit, demand, action, proceeding, or other claim by a third party (âClaimsâ) arising out of or relating to: (a) your actual or alleged failure to comply with Applicable Law or these Terms, (b) your Upload Data, or (c) your actual or alleged violation of any third party rights.","8.2 LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE CZ BIOHUB PROTECTED PARTIES WILL NOT BE LIABLE FOR ANY INDIRECT, INCIDENTAL, SPECIAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES OF ANY KIND (INCLUDING LOST PROFITS, LOST DATA, BUSINESS INTERRUPTION, OR LOSS OF GOODWILL) IRRESPECTIVE OF WHETHER SUCH DAMAGES ARISE FROM CLAIMS BROUGHT IN CONTRACT, TORT, NEGLIGENCE, WARRANTY, STRICT LIABILITY, OR ANY OTHER THEORY AT LAW OR IN EQUITY, AND EVEN IF ANY CZ BIOHUB PROTECTED PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. WITHOUT LIMITING THE FOREGOING, TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL THE CZ BIOHUB PROTECTED PARTIESâ AGGREGATE LIABILITY ARISING OUT OF OR RELATING TO THESE TERMS OR CZ ID EXCEED USD $100. THE EXCLUSIONS AND LIMITATIONS SET FORTH IN THIS SECTION 8 DO NOT APPLY TO LOSSES ARISING FROM A CZ BIOHUB PROTECTED PARTYâS GROSS NEGLIGENCE OR WILLFUL MISCONDUCT. IF ANY LIMITATION IN THIS SECTION 8 IS UNENFORCEABLE IN ANY INSTANCE, THEN SUCH LIMITATION WILL APPLY TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW.","SOME LAWS DO NOT ALLOW THE LIMITATION OR EXCLUSION OF LIABILITY, SO THESE LIMITS MAY NOT APPLY TO YOU.","Choice of Law / Jurisdiction / Venue. These Terms, and all matters arising out of or relating to these Terms, whether sounding in contract, tort, or statute, will be governed by, and construed in accordance with, the laws of the State of California and/or applicable federal law (including the Federal Arbitration Act), without regard to conflict of law provisions. Subject to and without waiver of the arbitration provisions below, and unless prohibited by the laws of your country, you agree that any judicial proceedings (other than small claims actions as discussed above) will be brought in and you hereby consent to the exclusive jurisdiction and venue in the state courts in the City and County of San Mateo, California, or federal court for the Northern District of California. For countries where this is not permissible, this wonât deprive you of any protection you have under the law of the country where you live, or access to the courts in that country."]}))}(),function renderArbitrationTerms(){return i.default.createElement(i.default.Fragment,null,i.default.createElement("h2",null,i.default.createElement("span",{className:c.default.number},"9.")," ARBITRATION AGREEMENT AND CLASS ACTION WAIVER."),i.default.createElement("p",null,"THIS SECTION CONSTITUTES AN ARBITRATION AGREEMENT (â",i.default.createElement("b",null,"Arbitration Agreement"),"â); IT REQUIRES YOU AND CZ BIOHUB AND ITS AFFILIATES, INCLUDING WITHOUT LIMITATION THE CHAN ZUCKERBERG INITIATIVE FOUNDATION AND CHAN ZUCKERBERG INITIATIVE, LLC (COLLECTIVELY, THE â",i.default.createElement("b",null,"CZ Parties"),"â) TO AGREE TO RESOLVE ALL DISPUTES BETWEEN US THROUGH BINDING INDIVIDUAL ARBITRATION, SO PLEASE READ IT CAREFULLY."),i.default.createElement(d.default,{ordered:!0,listItems:[i.default.createElement(i.default.Fragment,null,i.default.createElement("b",null,"Applicability.")," You and the CZ Parties agree that all Disputes, including Enforceability Disputes, will be resolved exclusively in binding arbitration on an individual basis, except that you and the CZ Parties are not required to arbitrate IP Disputes. 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1)).attr("x",(function(a){return h+r(a.x0)+l*t.getBarWidth(r,a)})).attr("width",(function(a){return t.getBarWidth(r,a)})).attr("y",(function(t){return i(t.length)})).attr("height",(function(t){return i(u)-i(t.length)})).style("opacity",d).on("mousemove",t.onBarMouseMove).on("mouseover",(function(a,r){t.onBarMouseOver(a,l,r)})).on("mouseleave",(function(a,r){return t.onBarMouseOut(l,r)})).on("mousedown",(function(a,r){return t.onBarMouseDown(l,r)})).on("mouseup",(function(a,r){return t.onBarMouseUp(l,r)})).on("click",(function(a,r){t.onBarClick(l,r),g.event.stopPropagation()})),o[l].forEach((function(a,o){var i=t.getBarWidth(r,a);t.barWidth=t.getBarWidth(r,a);var u=r(a.x0)+l*i+i/2;c[u]=[l,o],m.push(u)})),t.options.showStatistics){var v=(0,p.mean)(t.data[l]),y=(0,p.deviation)(t.data[l]),b=t.svg.append("g");b.append("line").attr("stroke",a[l]).attr("x1",r(v)).attr("x2",r(v)).attr("y1",t.margins.top).attr("y2",t.size.height-t.margins.bottom);var S=(0,p.max)([r(v-y),t.margins.left]),w=(0,p.min)([r(v+y),t.size.width-t.margins.right])-S;b.append("rect").attr("fill",a[l]).attr("fill-opacity",.2).attr("x",S).attr("width",w).attr("y",t.margins.top).attr("height",t.size.height-t.margins.top-t.margins.bottom).lower()}if(t.options.refValues&&t.options.refValues.length){var _,E=t.svg.append("g").attr("class","refs"),x=_createForOfIteratorHelper(t.options.refValues);try{for(x.s();!(_=x.n()).done;){var L=_.value,O=r(L.values[l]);E.append("line").attr("stroke",a[l]).style("stroke-dasharray","4, 4").attr("x1",O).attr("x2",O).attr("y1",t.margins.top).attr("y2",t.size.height-t.margins.bottom),E.append("text").attr("x",-t.margins.top).attr("y",O-4).attr("transform","rotate(-90)").attr(C.TEXT_ANCHOR,"end").attr(C.FONT_WEIGHT,"bold").attr("font-size",10).style("fill",a[l]).text(L.name)}}catch(t){x.e(t)}finally{x.f()}}},y=0;y<o.length;y++)v(y);if(this.barCentersToIndices=c,this.sortedBarCenters=m.sort((function(t,a){return t-a})),this.options.hoverBuffer>0&&this.svg.append("rect").attr("class",S.default.hoverRect).attr("transform","translate(".concat(this.margins.left,", ").concat(this.margins.top,")")).attr("width",this.size.width-this.margins.right-this.margins.left).attr("height",this.size.height-this.margins.top-this.margins.bottom).on("mousemove",this.onMouseMove).on("mouseleave",this.onMouseLeave),this.options.seriesNames){var b=this.svg.append("g").attr("class","histogram__legend").attr("font-family","sans-serif").attr("font-size",10).attr(C.TEXT_ANCHOR,"end").attr(C.TEXT_ANCHOR,"end").selectAll("g").data(this.options.seriesNames).enter().append("g").attr("transform",(function(t,a){return"translate(-20,".concat(20*(a+1),")")}));b.append("rect").attr("x",this.size.width-5).attr("width",14).attr("height",14).attr("fill",(function(t,l){return a[l]})),b.append("text").attr("x",this.size.width-10).attr("y",this.margins.top).attr("dy",-11).attr("alignment-baseline","middle").text((function(t){return t}))}}}}]),Histogram}()},22988:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var o=r(l(43693)),i=r(l(91847)),u=r(l(17383)),d=r(l(34579)),c=l(83416),p=["onClick","onNodeHover","onNodeBlur"];function ownKeys(t,a){var l=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);a&&(r=r.filter((function(a){return Object.getOwnPropertyDescriptor(t,a).enumerable}))),l.push.apply(l,r)}return l}function _objectSpread(t){for(var a=1;a<arguments.length;a++){var l=null!=arguments[a]?arguments[a]:{};a%2?ownKeys(Object(l),!0).forEach((function(a){(0,o.default)(t,a,l[a])})):Object.getOwnPropertyDescriptors?Object.defineProperties(t,Object.getOwnPropertyDescriptors(l)):ownKeys(Object(l)).forEac

1h((function(a){Object.defineProperty(t,a,Object.getOwnPropertyDescriptor(l,a))}))}return t}a.default=function(){function NetworkGraph(t,a,l,r){(0,u.default)(this,NetworkGraph);var o=r.onClick,d=r.onNodeHover,m=r.onNodeBlur,h=(0,i.default)(r,p);this.data={nodes:new c.DataSet(a),edges:new c.DataSet(l)},this.graph=new c.Network(t,this.data,h),this.graph.on("click",o),this.graph.on("hoverNode",d),this.graph.on("blurNode",m)}return(0,d.default)(NetworkGraph,[{key:"moveNodeToPosition",value:function moveNodeToPosition(t,a,l){var r=this.graph.DOMtoCanvas({x:a,y:l});this.graph.moveNode(t,r.x,r.y)}},{key:"getNodePosition",value:function getNodePosition(t){var a=this.graph.getPositions([t])[t];return this.graph.canvasToDOM(a)}},{key:"getEdges",value:function getEdges(t){return this.data.edges.getIds({filter:t})}},{key:"updateEdges",value:function updateEdges(t,a){var l=this;t.forEach((function(t){l.data.edges.update(_objectSpread({id:t},a))}))}},{key:"updateNodes",value:function updateNodes(t,a){var l=this;t.forEach((function(t){l.data.nodes.update(_objectSpread({id:t},a))}))}},{key:"getNodeAt",value:function getNodeAt(t,a){return this.graph.getNodeAt({x:t,y:a})}},{key:"getEdgeAt",value:function getEdgeAt(t,a){return this.graph.getEdgeAt({x:t,y:a})}},{key:"minimizeSizeGivenScale",value:function minimizeSizeGivenScale(t){var a=this;this.graph.moveTo({scale:t});var l=Number.MAX_VALUE,r=Number.MIN_VALUE,o=Number.MAX_VALUE,i=Number.MIN_VALUE;this.data.nodes.getIds().forEach((function(t){var u=a.graph.getBoundingBox(t);l=Math.min(l,u.left),r=Math.max(r,u.right),o=Math.min(o,u.top),i=Math.max(i,u.bottom)}));var u=this.graph.canvasToDOM({x:l,y:o}),d=u.x,c=u.y,p=this.graph.canvasToDOM({x:r,y:i}),m=p.x,h=p.y;this.graph.setSize(m-d+"px",h-c),this.graph.moveTo({scale:1,position:{x:0,y:0}})}},{key:"afterDrawingOnce",value:function afterDrawingOnce(t){this.graph.once("afterDrawing",t)}},{key:"unselectAll",value:function unselectAll(){this.graph.unselectAll()}},{key:"selectNodes",value:function selectNodes(t){this.graph.selectNodes(t)}}]),NetworkGraph}()},42053:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.TidyTree=void 0;var o=r(l(41132)),i=r(l(17383)),u=r(l(34579)),d=l(28520),c=l(36647),p=l(46048),m=l(92913);a.TidyTree=function(){function TidyTree(t,a,l){(0,i.default)(this,TidyTree),this.container=(0,p.select)(t),this.svg=null,this.pathContainer=null,this.nodeContainer=null,this.options=Object.assign({addOverlays:!0,attribute:"aggregatescore",leafNodeHeight:35,minWidth:960,minHeight:300,transitionDuration:500,onNodeHover:null,onCreatedTree:null,tooltipContainer:null,collapseThreshold:.4,useCommonName:!1,minNonCollapsableChildren:2,smallerFont:8,largerFont:12,onCollapsedStateChange:function onCollapsedStateChange(){},collapsed:new Set,svgBackgroundColor:"white"},l||{}),this.margins={top:20,right:200,left:40,bottom:20},this.range=[0,1],this.setTree(a)}return(0,u.default)(TidyTree,[{key:"initialize",value:function initialize(){this.svg=this.container.append("svg").attr("class","tidy-tree").attr("width",this.options.width).attr("height",this.options.height).attr("style","background-color: ".concat(this.options.svgBackgroundColor)),this.pathContainer=this.svg.append("g").attr(m.TRANSFORM,"".concat(m.TRANSLATE,"(").concat(this.margins.left,",").concat(this.margins.top,")")),this.nodeContainer=this.svg.append("g").attr(m.TRANSFORM,"".concat(m.TRANSLATE,"(").concat(this.margins.left,",").concat(this.margins.top,")")),this.tooltipContainer=(0,p.select)(this.options.tooltipContainer)}},{key:"setOptions",value:function setOptions(t){Object.assign(this.options,t),(t.attribute||t.collapseThreshold)&&this.sortAndScaleTree(),this.update()}},{key:"setTree",value:function setTree(t){var a=(0,d.stratify)().id((function(t){return t.id})).parentId((function(t){return t.parentId}));this.root=a(t),this.options.onCreatedTree&&this.options.onCreatedTree(this.root),this.sortAndScaleTree(),this.update()}},{key:"resetTree",value:function resetTree(){this.root.eachBefore((function(t){(t.children||t.collapsedChildren||t.hiddenChildren)&&(t.children=(t.children||[]).concat(t.collapsedChildren||[]).concat(t.hiddenChildren||[]),t.children=t.children.filter((function(t){return!t.isAggregated})),t.collapsedChildren=null,t.hiddenChildren=null),t.isAggregated=!1}))}},{key:"sortAndScaleTree",value:function sortAndScaleTree(){var t=this;this.resetTree(),this.root.sort((function(a,l){return l.data.values[t.options.attribute]-a.data.values[t.options.attribute]})),this.range=[Math.min.apply(Math,(0,o.default)(this.root.leaves().map((function(a){return a.data.values[t.options.attribute]})))),this.root.data.values[this.options.attribute]];var a=(0,c.scaleLinear)().domain(this.range).range([0,1]);this.root.eachAfter((function(l){t.options.collapsed.has(l.id)||!l.data.highlight&&a(l.data.values[t.options.attribute])<t.options.collapseThreshold?(l.collapsedChildren=l.children,l.children=null):l.children&&(l.collapsedChildren=l.children.filter((function(l){return!l.data.highlight&&a(l.data.values[t.options.attribute])<t.options.collapseThreshold})),l.collapsedChildren.length<=t.options.minNonCollapsableChildren?l.collapsedChildren=null:(l.children=l.children.filter((function(l){return l.data.highlight||a(l.data.values[t.options.attribute])>

1=t.options.collapseThreshold})),l.children.length||(l.children=null),t.hasVisibleChildren(l)&&t.hasHiddenChildren(l)&&l.children.push({id:"other-".concat(l.id),depth:l.depth+1,height:0,parent:l,isAggregated:!0,data:{commonName:"(".concat(l.collapsedChildren.length,")"),highlight:l.collapsedChildren.some((function(t){return t.data.highlight})),scientificName:"(".concat(l.collapsedChildren.length,")"),lineageRank:l.collapsedChildren[0].data.lineageRank,values:l.collapsedChildren[0].data.values}})))}))}},{key:"toggleCollapseNode",value:function toggleCollapseNode(t){var a=this,l=t;if(this.hasAllChildrenCollapsed(t)||this.hasAllChildrenVisible(t)){var r=t.children;t.children=t.collapsedChildren,t.collapsedChildren=r,t.collapsedChildren||(t.collapsedChildren=t.hiddenChildren,t.hiddenChildren=null)}else if(this.hasHiddenChildren(t))t.hiddenChildren=t.collapsedChildren,t.collapsedChildren=t.children,t.children=null;else if(t.isAggregated){var o=t.parent;o.children.pop(),o.children=o.children.concat(o.collapsedChildren),o.collapsedChildren=null,l=o}l.children&&l.children.forEach((function(t){a.expandCollapsedWithFewChildrenOrNoName(t)})),this.update(Object.assign(t,{x0:t.x,y0:t.y})),this.options.onCollapsedStateChange&&this.options.onCollapsedStateChange(t)}},{key:"expandCollapsedWithFewChildrenOrNoName",value:function expandCollapsedWithFewChildrenOrNoName(t){var a=this;t&&t.collapsedChildren&&(t.collapsedChildren.length<=this.options.minNonCollapsableChildren||!(t.data||{}).name)&&(t.children=(t.children||[]).concat(t.collapsedChildren),t.collapsedChildren=null,t.children.forEach((function(t){a.expandCollapsedWithFewChildrenOrNoName(t)})))}},{key:"curvedPath",value:function curvedPath(t,a){return"M ".concat(t.y," ").concat(t.x,"\n            C ").concat((t.y+a.y)/2," ").concat(t.x,",\n            ").concat((t.y+a.y)/2," ").concat(a.x,",\n            ").concat(a.y," ").concat(a.x)}},{key:"getNodeBoxRefSvg",value:function getNodeBoxRefSvg(t,a){var l=a.getBBox(),r=t.y+this.margins.left;return{x:t.x+this.margins.top,y:r,width:l.width,height:l.height}}},{key:"hasAllChildrenCollapsed",value:function hasAllChildrenCollapsed(t){return!(t.children||!t.collapsedChildren)}},{key:"hasAllChildrenVisible",value:function hasAllChildrenVisible(t){return!(!t.children||t.collapsedChildren)}},{key:"hasChildren",value:function hasChildren(t){return!(!t.children&&!t.collapsedChildren)}},{key:"hasHiddenChildren",value:function hasHiddenChildren(t){return!!t.collapsedChildren}},{key:"hasVisibleChildren",value:function hasVisibleChildren(t){return!!t.children}},{key:"wrap",value:function wrap(t,a){var l=this;t.each((function(t,r,o){var i,u=(0,p.select)(o[r]),d=u.text().split(/\s+/),c=[],m=1,h=parseFloat(u.style("font-size")),g=1.2*h,v=u.attr("x"),y=u.text(null).append("tspan").attr("x",v);if(1===d.length)y.text(d[0]);else for(;i=d.pop();)c.unshift(i),y.text(c.join(" ")),y.node().getComputedTextLength()>a&&(c.shift(),y.text(c.join(" ")),c=[i],y=u.append("tspan").attr("x",v).attr("dy","".concat(-g,"px")).text(i),m++);l.hasVisibleChildren(t)||u.attr("dy","".concat((h+(m-1)*g-3)/2,"px"))}))}},{key:"update",value:function update(t){var a=this;if(this.svg||this.initialize(),this.options.attribute){var l=this.options.minWidth,r=Math.max(this.options.minHeight,this.options.leafNodeHeight*this.root.leaves().length);this.root.x0=r/2,this.root.y0=0,this.svg.transition().duration(this.options.transitionDuration).attr("width",l+this.margins.left+this.margins.right).attr("height",r+this.margins.top+this.margins.bottom),(0,d.tree)().size([r,l])(this.root),t=t||this.root;var o=(0,c.scaleLinear)().domain(this.range).range([4,20]),i=(0,c.scaleLinear)().domain(this.range).range([1,20]),u=(0,c.scaleLinear)().domain(this.range).range([this.options.smallerFont,this.options.largerFont]),h=this.pathContainer.selectAll(".link").data(this.root.links(),(function(t){return t.target.id}));h.enter().append("path").attr("class",(function(t){return"link ".concat(t.target.data.highlight?"highlighted":"")})).attr("d",(function(){var l={x:t.x0,y:t.y0};return a.curvedPath(l,l)})).merge(h).lower().transition().duration(this.options.transitionDuration).attr("class",(function(t){return"link ".concat(t.target.data.highlight?"highlighted":"")}

1)).attr("d",(function(t){return a.curvedPath(t.source,t.target)})).attr("stroke-width",(function(t){return i(t.target.data.values[a.options.attribute])})),h.exit().transition().duration(this.options.transitionDuration).attr("d",this.curvedPath(t,t)).remove();var g=this.nodeContainer.selectAll("g.node").data(this.root.descendants(),(function(t){return t.id})),v=g.enter().append("g").attr("class","node").attr(m.TRANSFORM,(function(){var l=t&&t.x0||a.root.x0,r=t&&t.y0||a.root.y0;return"translate(".concat(r,",").concat(l,")")})),y=v.append("g").attr("class","clickable").attr("testid","clickable");y.append("circle").attr("r",0),y.filter((function(t){return a.hasChildren(t)||t.isAggregated})).append("path").attr("class","cross").attr("d","M0,0");var C=v.append("text").style(m.FILL_OPACITY,0).on("click",this.options.onNodeLabelClick);this.tooltipContainer&&v.on("mouseenter",(function(t){a.options.onNodeHover&&a.options.onNodeHover(t),a.tooltipContainer.classed("visible",!0)})).on("mousemove",(function(){a.tooltipContainer.style("left",p.event.pageX+20+"px").style("top",p.event.pageY+20+"px")})).on("mouseleave",(function(){a.tooltipContainer.classed("visible",!1)}));var b=g.merge(v);b.transition().duration(this.options.transitionDuration).attr("class",(function(t){return"node "+"node-".concat(t.id)+(a.hasChildren(t)?" node__internal":" node__leaf")+(a.hasAllChildrenCollapsed(t)||t.isAggregated?"--collapsed":"")})).attr(m.TRANSFORM,(function(t){return"".concat(m.TRANSLATE,"(").concat(t.y,",").concat(t.x,")")}));var S=C.merge(g.select("text"));S.text((function(t){return(a.options.useCommonName?t.data.commonName:null)||t.data.scientificName})).style("text-anchor",(function(t){return 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1:250,right:150},w=48,_=250,E=20,x=16;a.default=function(){function Dendogram(t,a,l){var r=this;(0,o.default)(this,Dendogram),(0,u.default)(this,"getColorGroupAttrValForNode",(function(t){var a=r.options.colorGroupAttribute,l=r.options.colorGroupAbsentName,o=(0,h.get)(a,t.data)||l;return(0,h.isObject)(o)?o.name:o})),(0,u.default)(this,"updateOptions",(function(t){r.options=Object.assign(r.options,t),r.viz&&r.viz.selectAll("*").remove(),r.updateColors(),r.update()})),this.svg=null,this.viz=null,this.container=t,this.tree=null,this.root=null,this.legend=null,this.options=Object.assign({curvedEdges:!1,defaultColor:"#cccccc",absentColor:"#000000",colorGroupAttribute:null,colorGroupLegendTitle:null,colorGroupAbsentName:null,iconPath:"/assets/icons",legendX:x,legendY:E,onWarningExit:null,onWarningHover:null,onNodeTextClick:null,onNodeClick:null,onNodeHover:null,tooltipContainer:null,scaleLabel:null,svgBackgroundColor:"white",warningTooltipContainer:null},l||{}),this.minTreeSize={width:600,height:500},this.margins=S,this.nodeSize={width:1,height:25},this._highlighted=new Set,this._clickTimeout=null,this.setTree(a),this.initialize()}return(0,i.default)(Dendogram,[{key:"initialize",value:function initialize(){this.svg=(0,p.select)(this.container).append("svg").attr("width",this.minTreeSize.width+this.margins.left+this.margins.right).attr("height",this.minTreeSize.height+this.margins.top+this.margins.bottom).attr("style","background-color: ".concat(this.options.svgBackgroundColor)),this.viz=this.svg.append("g").attr("class","viz").attr("transform","translate(".concat(this.margins.left,", ").concat(this.margins.top,")")),this.tooltipContainer=(0,p.select)(this.options.tooltipContainer),this.warningTooltipContainer=(0,p.select)(this.options.warningTooltipContainer)}},{key:"adjustHeight",value:function adjustHeight(t){this.svg.attr("height",Math.max(t,this.minTreeSize.height)+this.margins.top+this.margins.bottom)}},{key:"setTree",value:function setTree(t){this.viz&&this.viz.selectAll("*").remove(),this._clickTimeout&&(this._clickTimeout.stop(),this._clickTimeout=null),this._highlighted.clear(),this.tree=t,this.root=t?(0,c.hierarchy)(this.tree.root):null,this.updateColors()}},{key:"computeDistanceToRoot",value:function computeDistanceToRoot(t){var a=arguments.length>1&&void 0!==arguments[1]?arguments[1]:0,l=0;if(t.distanceToRoot=(t.data.distance||0)+a,void 0!==t.children)for(var r=0;r<t.children.length;r++)l=Math.max(this.computeDistanceToRoot(t.children[r],t.distanceToRoot),l);return Math.max(l,t.distanceToRoot)}},{key:"detachFromParent",value:function detachFromParent(t){var a=(t.parent.children||[]).indexOf(t);t.parent.children.splice(a,1),delete t.parent}},{key:"rerootOriginalTree",value:function rerootOriginalTree(t){this.tree.rerootTree(t.data.id),this.root=(0,c.hierarchy)(this.tree.root),this.update()}},{key:"markAsHighlight",value:function markAsHighlight(t){this._highlighted.has(t.data.id)?this._highlighted.delete(t.data.id):this._highlighted.add(t.data.id),this.update()}},{key:"updateHighlights",value:function updateHighlights(){var t=this;

1this.root.descendants().forEach((function(t){t.data.highlight=!1})),this.root.leaves().forEach((function(a){t._highlighted.has(a.data.id)&&a.ancestors().forEach((function(t){t.data.highlight=!0}))}))}},{key:"updateColors",value:function updateColors(){var t=this;if(this.options.colorGroupAttribute){var a=this.options.colorGroupAbsentName,l=new Set;this.root.leaves().forEach((function(a){a.data&&l.add(t.getColorGroupAttrValForNode(a))}));var r=Array.from(l);if(this.skipColoring=!1,1===r.length&&r[0]===a)return this.skipColoring=!0,this.allColorAttributeValues=["Uncolored",a],void(this.colors=[this.options.defaultColor,this.options.defaultColor]);r=["Uncolored"].concat(r),this.allColorAttributeValues=r,this.colors=(new g.CategoricalColormap).getNScale(r.length),this.colors=[this.options.defaultColor].concat(this.colors);var o=r.indexOf(a);o>-1&&this.colors.splice(o,0,this.options.absentColor);!function colorNode(a){if(!a.data)return 0;var l=0;if(a.children&&0!==a.children.length){var o,i=new Set,u=_createForOfIteratorHelper(a.children);try{for(u.s();!(o=u.n()).done;){var d=o.value;i.add(colorNode(d))}}catch(t){u.e(t)}finally{u.f()}1===i.size&&(l=i.values().next().value)}else l=r.indexOf(t.getColorGroupAttrValForNode(a));return a.data.colorIndex=l,l}(this.root)}}},{key:"updateLegend",value:function updateLegend(){if(this.options.colorGroupAttribute){var t=this.allColorAttributeValues;this.legend=this.svg.select(".legend"),this.legend.empty()&&(this.legend=this.svg.append("g").attr("class","legend")),this.legend.selectAll("*").remove();var a=this.options.legendX,l=this.options.legendY,r=(this.options.colorGroupLegendTitle||"Legend")+":";this.legend.append("text").attr("class","legend-title").attr("x",a).attr("y",l).text(r),a+=5,l+=25;for(var o=1;o<t.length;o++,l+=30){var i=this.colors[o];this.legend.append("circle").attr("r",5).attr("transform","translate(".concat(a,", ").concat(l,")")).style("fill",i),this.legend.append("text").attr("x",a+15).attr("y",l+5).text(t[o])}var u=this.legend.node().getBBox();this.legend.append("rect").attr("class","legend-background").attr("x",u.x-10).attr("y",u.y-10).attr("width",u.width+20).attr("height",u.height+20).lower()}}},{key:"clickHandler",value:function clickHandler(t,a){var l=this,r=arguments.length>2&&void 0!==arguments[2]?arguments[2]:250;this._clickTimeout?(this._clickTimeout.stop(),this._clickTimeout=null,"function"==typeof a&&a()):this._clickTimeout=(0,m.timeout)((function(){l._clickTimeout=null,t()}),r)}},{key:"formatBase10",value:function formatBase10(t,a){return a>=-1&&a<=1?1*Number.parseFloat(t*Math.pow(10,a)).toFixed(2):"".concat(t,"E").concat(a)}},{key:"adjustXPositions",value:function adjustXPositions(){var t=this.root.x,a=this.root.x;this.root.each((function(l){l.x<t&&(t=l.x),l.x>a&&(a=l.x)}));var l=a-t,r=l<this.minTreeSize.height?this.minTreeSize.height:l;this.root.each((function(a){a.x=(a.x-t)*r/l})),this.adjustHeight(r)}},{key:"adjustYPositions",value:function adjustYPositions(t){var a=this;this.root.each((function(l){l.y=a.minTreeSize.width*l.distanceToRoot/t}))}},{key:"createScale",value:function createScale(t,a,l,r){var o=this;function drawScale(t,a,l){return"M".concat(a," ").concat(t," L").concat(l," ").concat(t)}var i=100*r/l,u=Math.floor(Math.log10(i)),d=100*Math.pow(10,u)/i,c=Math.round(100/d);c&&(d*=c);var p=function createTicks(t,a,l,r){for(var o=[{id:0,y:t,multiplier:0}],i=0;i<=a/l;i++)o.push({id:i+1,y:t+i*l,multiplier:i%2?void 0:i*r/2});return o}(0,l,d/2,c),m=this.svg.select(".scale");m.empty()?((m=this.svg.append("g").attr("transform","translate(".concat(a,",").concat(t,")")).attr("class","scale")).append("path").attr("class","scale-line").attr("d",(function(){return drawScale(10,0,l)})),m.append("text").attr("class",y.default.scaleLabel).attr("x",-2).attr("y",-30).text(this.options.scaleLabel)):m.select("path").transition().duration(500).attr("d",(function(){return drawScale(10,0,l)}));var h=m.selectAll(".scale-tick").data(p,(function(t){return t.id})),g=h.enter().append("g").attr("class","scale-tick").attr("transform",(function(t){return"translate(".concat(t.y,",0)")}));g.append("path").attr("d",function drawTick(t,a,l){return"M".concat(l," ").concat(t," L").concat(l," ").concat(a)}(0,10,0)),g.append("text").attr("dy",-3).style("text-anchor","middle").text((function(t){return void 0===t.multiplier?"":o.formatBase10(t.multiplier,u)})),h.transition().duration(500).attr("transform",(function(t){return"translate(".concat(t.y,",0)")})),h.exit().transition(500).style("opacity",0).remove()}}

1,{key:"update",value:function update(){var t=this;if(this.root){this.viz||this.initialize(),(0,c.cluster)().size([this.minTreeSize.height,this.minTreeSize.width]).nodeSize([this.nodeSize.height,this.nodeSize.width])(this.root);var a=this.computeDistanceToRoot(this.root);this.updateHighlights(),this.updateLegend(),this.adjustXPositions(),this.adjustYPositions(a),this.createScale(w,_,this.minTreeSize.width,a);var l=this.viz.selectAll(".link").data(this.root.descendants().slice(1),(function linkId(t){if(t.parent){var a=[t.data.id,t.parent.data.id];return a.sort(),"".concat(a[0],"-").concat(a[1])}return null}));l.exit().transition(500).style("opacity",0).remove(),l.enter().append("path").attr("class","link").attr("d",this.options.curvedEdges?curveEdge:rectEdge),l.classed("highlight",(function(t){return t.data.highlight&&t.parent.data.highlight})),l.transition().duration(500).attr("d",this.options.curvedEdges?curveEdge:rectEdge),this.viz.selectAll(".link.highlight").raise(),this.viz.selectAll(".link").style("stroke-width",1),this.root.each((function(t){t.y+=t.children?1:2}));var r=this.viz.selectAll(".node").data(this.root.descendants(),(function nodeId(t){return t.data.id}));r.exit().transition(500).style("opacity",0).remove(),r.raise(),r.transition().duration(500).attr("transform",(function(t){return"translate("+t.y+","+t.x+")"})),r.classed("highlight",(function(t){return t.data.highlight})),r.select("text").transition().duration(500).attr("stroke",(function(t){return this.colors[t.data.colorIndex]})).attr("x",(function(t){return 0===t.depth?-(this.getBBox().width+15):t.children?-8:15}));var o=r.enter().append("g").attr("class",(function(t){return"node"+(t.children?" node-internal":" node-leaf")})).attr("transform",(function(t){return"translate(".concat(t.y,",").concat(t.x,")")}));this.tooltipContainer.empty()||o.on("mouseenter",(function(a){a.children||(t.options.onNodeHover&&t.options.onNodeHover(a),t.tooltipContainer.classed("visible",!0))})).on("mousemove",(function(a){a.children||t.tooltipContainer.style("left",p.event.pageX+20+"px").style("top",p.event.pageY+20+"px")})).on("mouseleave",(function(){r.children||t.tooltipContainer.classed("visible",!1)})),o.append("circle").attr("r",(function(t){return t.children?1:2})).on("click",(function(a){t.clickHandler((function(){return t.markAsHighlight(a)}),(function(){return t.rerootOriginalTree(a)}))})),o.append("text").attr("dy",(function(t){return t.children?-2:5})).attr("x",(function(t){return t.children?-8:15})).text((function(t){return t.children?"":t.data.name.split("__")[0]})).on("click",(function(a){return t.options.onNodeTextClick&&t.options.onNodeTextClick(a)}));var i=this.svg.append("defs");if((0,v.default)(i,"warning-medium",C),(0,v.default)(i,"warning-dark",b),o.append("svg:image").attr("xlink:href","".concat(this.options.iconPath,"/IconAlertSmall.svg")).attr("class",y.default.warningIcon).attr("y",-7).attr("x",(function(t){return d.default.select(this.previousSibling).node().getBBox().width+(t.children?-8:15)+4})).attr("display",(function(t){return t.data.coverage_breadth&&t.data.coverage_breadth<.25?"default":"none"})).on("mouseenter",(function(a){a.children||(t.options.onWarningIconHover&&t.options.onWarningIconHover(),t.warningTooltipContainer.style("left",p.event.pageX+"px").style("top",p.event.pageY-10+"px"),t.warningTooltipContainer.classed("visible",!0))})).on("mouseleave",(function(){r.children||(t.options.onWarningIconExit&&t.options.onWarningIconExit(),t.warningTooltipContainer.classed("visible",!1))})),this.options.colorGroupAttribute&&!this.skipColoring){var u=this.colors;this.viz.selectAll(".node").style("fill",(function(t){return u[t.data.colorIndex]})),this.viz.selectAll(".link").style("stroke",(function(t){return u[t.data.colorIndex]}))}else this.viz.selectAll(".node").style("fill",this.options.defaultColor);this.legend&&this.legend.raise()}function curveEdge(t){return"M"+t.y+","+t.x+"C"+(t.y+t.parent.y)/2+","+t.x+" "+(t.y+t.parent.y)/2+","+t.parent.x+" "+t.parent.y+","+t.parent.x}function rectEdge(t){return"M".concat(t.y," ").concat(t.x," L").concat(t.parent.y," ").concat(t.x," L").concat(t.parent.y," ").concat(t.parent.x)}}}]),Dendogram}()},82083:(t,a,l)=>{"use strict";var r=l(24994);Object.defineProperty(a,"__esModule",{value:!0}),a.default=void 0;var o=r(l(41132)),i=r(l(85715)),u=r(l(17383)),d=r(l(34579)),c=r(l(43693)),p=r(l(32485)),m=r(l(85781)),h=r(l(24143)),g=l(36647),v=l(84814),y=l(2543),C=l(44480),b=r(l(19151)),S=r(l(47903)),w=l(25922),_=l(58974),E=r(l(95021)),x=r(l(3004)),L=r(l(1929));function ownKeys(t,a){var l=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);a&&(r=r.filter((function(a){return Object.getOwnPropertyDescriptor(t,a).enumerable}))),l.push.apply(l,r)}return l}function _objectSpread(t){for(var a=1;a<arguments.length;a++){var l=null!=arguments[a]?arguments[a]:{};

1a%2?ownKeys(Object(l),!0).forEach((function(a){(0,c.default)(t,a,l[a])})):Object.getOwnPropertyDescriptors?Object.defineProperties(t,Object.getOwnPropertyDescriptors(l)):ownKeys(Object(l)).forEach((function(a){Object.defineProperty(t,a,Object.getOwnPropertyDescriptor(l,a))}))}return t}var O=L.default.primaryLight,N="text-anchor",k="xlink:href";h.default.selection.prototype.lower=function(){return this.each((function(){var t=this.parentNode.firstChild;t&&this.parentNode.insertBefore(this,t)}))};a.default=function(){function Heatmap(t,a,l){var r=this;if((0,u.default)(this,Heatmap),(0,c.default)(this,"unpinColumn",(function(t){r.options.onUnpinColumn&&r.options.onUnpinColumn(t.id)})),(0,c.default)(this,"showPrintCaption",(function(){var t=r.options.printCaption?r.options.printCaption.length*(r.options.captionLineHeight+1):0;r.svg.attr("height",(r.height+t)*r.options.zoom),r.renderCaption()})),(0,c.default)(this,"hidePrintCaption",(function(){r.svg.attr("height",r.height*r.options.zoom),r.gCaption.selectAll(".".concat(L.default.caption)).remove()})),(0,c.default)(this,"expandColumnLabels",(function(){r.updateData({columnLabels:r.columnLabels.map((function(t){return _objectSpread(_objectSpread({},t),{},{label:t.printLabel})}))})})),(0,c.default)(this,"removeRow",(function(t){r.clearOverlays(),r.options.onRemoveRow&&r.options.onRemoveRow(t.label),delete t.pos,t.hidden=!0,r.processData("filter")})),(0,c.default)(this,"handleRowLabelMouseEnter",(function(t){if(r.updateLabelHighlights(r.gRowLabels.selectAll(".".concat(L.default.rowLabel)),r.rowLabels),r.highlightRowOrColumn(t),!r.rowClustering){r.gRowLabels.selectAll(".".concat(L.default.rowLabel)).classed(L.default.rowLabelHover,(function(a){return a.sortKey&&a.sortKey===t.sortKey}));var a=r.gRowLabels.selectAll(".".concat(L.default.rowLabel,".").concat(L.default.rowLabelHover))[0][0];a&&r.options.onRowGroupEnter&&r.options.onRowGroupEnter(t,a.getBoundingClientRect(),r.gColumnMetadata.node().getBoundingClientRect().bottom)}})),(0,c.default)(this,"handleRowLabelMouseLeave",(function(t){r.updateLabelHighlights(r.gRowLabels.selectAll(".".concat(L.default.rowLabel)),r.rowLabels),r.highlightRowOrColumn(null),r.rowClustering||(r.gRowLabels.selectAll(".".concat(L.default.rowLabel)).classed(L.default.rowLabelHover,!1),r.options.onRowGroupLeave&&r.options.onRowGroupLeave(t))})),(0,c.default)(this,"handleColumnLabelMouseEnter",(function(t){r.updateLabelHighlights(r.gColumnLabels.selectAll(".".concat(L.default.columnLabel)),r.columnLabels),r.highlightRowOrColumn(t)})),(0,c.default)(this,"handleColumnLabelMouseLeave",(function(){r.updateLabelHighlights(r.gColumnLabels.selectAll(".".concat(L.default.columnLabel)),r.columnLabels),r.highlightRowOrColumn(null)})),(0,c.default)(this,"handleCellMouseOver",(function(t){r.gCellHover.attr("visibility","visible").attr("x",r.columnLabels[t.columnIndex].pos*r.cell.width).attr("y",r.rowLabels[t.rowIndex].pos*r.cell.height),r.rowLabels[t.rowIndex].highlighted=!0,r.columnLabels[t.columnIndex].highlighted=!0,r.updateLabelHighlights(r.gRowLabels.selectAll(".".concat(L.default.rowLabel)),r.rowLabels),r.updateLabelHighlights(r.gColumnLabels.selectAll(".".concat(L.default.columnLabel)),r.columnLabels),r.options.onNodeHover&&r.options.onNodeHover(t)})),(0,c.default)(this,"handleCellMouseLeave",(function(t){r.gCellHover.attr("visibility","hidden"),r.rowLabels[t.rowIndex].highlighted=!1,r.columnLabels[t.columnIndex].highlighted=!1,r.updateLabelHighlights(r.gRowLabels.selectAll(".".concat(L.default.rowLabel)),r.rowLabels),r.updateLabelHighlights(r.gColumnLabels.selectAll(".".concat(L.default.columnLabel)),r.columnLabels),r.options.onNodeHoverOut&&r.options.onNodeHoverOut(t)})),(0,c.default)(this,"handleCellClick",(function(t){r.options.onCellClick&&r.options.onCellClick(t,h.default.event)})),this.mouseDown=!1,this.svg=null,this.g=null,this.container=h.default.select(t),this.data=a,this.svgSaver=new b.default,this.options=Object.assign({numberOfLevels:10,scale:"linear",fontSize:"9pt",textRotation:-65,marginTop:30,marginLeft:20,marginBottom:20,marginRight:20,marginAddLink:25,marginAddLinkImg:20,metadataSortIconSize:16,minCellWidth:26,minCellHeight:26,minWidth:1240,maxWidth:1600,zoom:null,minHeight:500,clustering:!0,shouldSortColumns:!1,shouldSortRows:!1,defaultClusterStep:6,maxRowClusterWidth:100,maxColumnClusterHeight:100,spacing:10,metadataAddLinkHeight:14,transitionDuration:200,nullValue:0,columnMetadata:[],enableColumnMetadata:!1,metadataColorScale:new _.CategoricalColormap,iconPath:"/assets/icons",svgBackgroun

1dColor:"white",scaleMin:null,scaleMax:null,customColorCallback:null,colors:null,colorNoValue:"#eaeaea",printCaption:[],captionLineHeight:18},l),!this.options.colors){var o=(0,g.scaleSequential)(v.interpolateYlOrRd);this.options.colors=this.range(this.options.numberOfLevels).map((function(t){return o(t/(r.options.numberOfLevels-1))}))}this.rowClusterWidth=this.options.maxRowClusterWidth,this.columnClusterHeight=this.options.maxRowClusterWidth,this.scaleType=this.getScaleType(),this.addMetadataTrigger=null,this.columnMetadataSortField=this.options.initialColumnMetadataSortField,this.columnMetadataSortAsc=this.options.initialColumnMetadataSortAsc,this.addRowTrigger=null,this.overlays=[],this.overlaysDebounce=!1,this.previousNullHover=null,this.bgGrid=null,this.bgPattern=null,this.gCellHover=null}return(0,d.default)(Heatmap,[{key:"getScaleType",value:function getScaleType(){return"symlog"===this.options.scale?E.default:h.default.scale.linear}},{key:"start",value:function start(){this.processData()}},{key:"processData",value:function processData(t){switch(t||(t="setupContainers"),t){case"setupContainers":this.setupContainers();case"parse":this.parseData();case"filter":this.filterData();case"processMetadata":this.processMetadata();case"cluster":this.cluster();case"placeContainers":this.placeContainers();case"update":this.update()}}},{key:"updateZoom",value:function updateZoom(t){this.options.zoom=t,this.svg.attr("width",this.width*this.options.zoom).attr("height",this.height*this.options.zoom)}},{key:"updateScale",value:function updateScale(t){this.options.scale=t,this.scaleType=this.getScaleType(),this.processData("cluster")}},{key:"updateSortColumns",value:function updateSortColumns(t){this.options.shouldSortColumns=t,this.processData("cluster")}},{key:"updateSortRows",value:function updateSortRows(t){this.options.shouldSortRows=t,this.processData("cluster")}},{key:"updateColumnMetadata",value:function updateColumnMetadata(t){this.options.columnMetadata=t,this.processData("processMetadata")}},{key:"updateData",value:function updateData(t){this.data=Object.assign(this.data,t),this.processData("parse")}},{key:"updatePrintCaption",value:function updatePrintCaption(t){this.options.printCaption=t}},{key:"parseData",value:function parseData(){var t=this;this.rowLabels=this.data.rowLabels.map((function(t,a){return Object.assign({pos:a,shaded:!1},t)})),this.columnLabels=this.data.columnLabels.map((function(t,a){return Object.assign({pos:a,shaded:!1},t)})),this.rowLabelsWidth=0,this.columnLabelsHeight=0;for(var a=function labelWidth(a){return(0,S.default)(a,{size:t.options.fontSize})},l=0;l<this.rowLabels.length;l++){var r=this.rowLabels[l].label;this.rowLabelsWidth=Math.max(this.rowLabelsWidth,a(r))}for(var o=0;o<this.options.columnMetadata.length;o++){var i=this.options.columnMetadata[o].label+this.options.metadataSortIconSize;this.rowLabelsWidth=Math.max(this.rowLabelsWidth,a(i))}for(var u=0;u<this.columnLabels.length;u++){var d=this.columnLabels[u].label;this.columnLabelsHeight=Math.max(this.columnLabelsHeight,a(d))}this.columnLabelsHeight*=Math.abs(Math.cos((90+this.options.textRotation)*(Math.PI/180))),this.rowLabelsWidth+=this.options.spacing+2*this.options.spacing,this.columnLabelsHeight+=this.options.spacing,this.limits={min:Math.min(h.default.min(this.data.values,(function(t){return h.default.min(t)})),this.options.nullValue),max:Math.max(h.default.max(this.data.values,(function(t){return h.default.max(t)})),this.options.nullValue)},this.scaleLimits={min:this.options.scaleMin||0===this.options.scaleMin?this.options.scaleMin:this.limits.min,max:this.options.scaleMax||0===this.options.scaleMax?this.options.scaleMax:this.limits.max},this.cells=[];for(var c=0;c<this.rowLabels.length;c++){var p=this.data.taxonFilterState;this.rowLabels[c].rowIndex=c;for(var m=this.rowLabels[c].filterStateRow,g=0;g<this.columnLabels.length;g++){this.columnLabels[g].columnIndex=g;var v=this.columnLabels[g].filterStateColumn,y=!(void 0!==p&&void 0!==m&&void 0!==v)||p[m][v];this.cells.push({id:"".concat(c,",").concat(g),rowIndex:c,columnIndex:g,value:this.data.values[c][g],meetsUserFilters:y})}}}},{key:"filterData",value:function filterData(){var t=this;this.filteredCells=this.cells.filter((function(a){return!t.rowLabels[a.rowIndex].hidden&&null!=a.value})),this.filteredRowLabels=(0,y.orderBy)(this.rowLabels.filter((function(t){return!t.hidden})),(function(t){return t.sortKey||t.label}))}},{key:"setupContainers",value:function setupContainers(){this.svg=this.container.append("svg").attr("class",L.default.heatmap).attr("id","visualization").attr("xmlns","http://www.w3.org/2000/svg"),this.svg.attr("style","background-color: ".concat(this.options.svgBackgroun

1dColor));var t=this.svg.append("defs");this.defs=t,(0,x.default)(t,"blue",O),this.g=this.svg.append("g"),this.gCells=this.g.append("g"),this.gRowDendogram=this.g.append("g").attr("class",(0,p.default)(L.default.dendogram,L.default.rowDendogram)),this.gColumnDendogram=this.g.append("g").attr("class",(0,p.default)(L.default.dendogram,"columnDendogram")),this.rowLabelsBackground=this.g.append("rect").attr("class","rowLabelBackground").style("fill","white"),this.gRowLabels=this.g.append("g").attr("class",L.default.rowLabels),this.columnLabelsBackground=this.g.append("rect").attr("class","columnLabelBackground").style("fill","white"),this.gColumnLabels=this.g.append("g").attr("class",L.default.columnLabels),this.metadataLabelsBackground=this.g.append("rect").attr("class","metadataLabelsBackground").style("fill","white"),this.addRowBackground=this.g.append("rect").attr("class","addRowBackground").style("fill","white"),this.gColumnMetadata=this.g.append("g").attr("class",L.default.columnMetadata),this.gAddRow=this.g.append("g").attr("class",L.default.columnMetadata),this.gPinColumn=this.g.append("g").attr("class",L.default.columnMetadata),this.gCaption=this.g.append("g").attr("class",L.default.captionContainer)}},{key:"placeContainers",value:function placeContainers(){var t=this;this.rowClusterWidth=Math.min(this.getDepth(this.rowClustering)*this.options.defaultClusterStep+this.options.spacing,this.options.maxRowClusterWidth),this.columnClusterHeight=Math.min(this.getDepth(this.columnClustering)*this.options.defaultClusterStep+this.options.spacing,this.options.maxColumnClusterHeight),this.cell={width:Math.max((this.options.minWidth-this.rowLabelsWidth-this.rowClusterWidth)/this.columnLabels.length,this.options.minCellWidth),height:Math.max((this.options.minHeight-this.columnLabelsHeight-this.columnClusterHeight)/this.rowLabels.length,this.options.minCellHeight)};var a=this.cell.width*this.columnLabels.length,l=this.options.clustering?this.rowClusterWidth:0,r=this.columnLabelsHeight;this.totalMetadataHeight=this.options.columnMetadata.length*this.options.minCellHeight+this.options.metadataAddLinkHeight;var o=this.cell.height*this.filteredRowLabels.length,i=this.options.clustering?this.columnClusterHeight+2*this.options.spacing:0;this.totalRowAddLinkHeight=this.options.onAddRowClick?2*this.options.metadataAddLinkHeight:this.options.metadataAddLinkHeight,this.width=this.options.marginLeft+this.rowLabelsWidth+a+l+this.options.marginRight,this.height=this.options.marginTop+this.columnLabelsHeight+this.totalMetadataHeight+this.totalRowAddLinkHeight+o+i+this.options.marginBottom+this.options.spacing,this.svg.attr("viewBox","0 0 ".concat(this.width," ").concat(this.height)),this.options.zoom=this.getZoomFactor(),this.svg.attr("width",this.width*this.options.zoom).attr("height",this.height*this.options.zoom),this.g.attr("transform","translate(".concat(this.options.marginLeft,",").concat(this.options.marginTop,")")),this.rowLabelsBackground.attr("width",this.rowLabelsWidth+this.options.marginLeft).attr("height",o+i),this.placeRowLabelContainers(0),this.columnLabelsBackground.attr("width",this.rowLabelsWidth+a+l+this.options.marginRight).attr("height",r+this.totalMetadataHeight+this.options.marginTop),this.metadataLabelsBackground.attr("width",this.rowLabelsWidth+this.options.marginLeft).attr("height",r+this.options.marginTop),this.scrollToRowInProgess?this.scrollToRowInProgess=!1:(this.placeColumnLabelAndMetadataContainers(this.columnLabelsHeight),this.placePinColumnLinkContainer(this.columnLabelsHeight),this.addRowBackground.attr("width",this.rowLabelsWidth+a+l+this.options.marginRight).attr("height",this.totalRowAddLinkHeight+this.options.metadataAddLinkHeight),this.placeAddRowLinkContainer(this.columnLabelsHeight)),this.gCells.attr("transform","translate(".concat(this.rowLabelsWidth,",\n        ").concat(r+this.totalMetadataHeight+this.totalRowAddLinkHeight,")")),this.gRowDendogram.attr("transform","translate(\n        ".concat(this.rowLabelsWidth+a,",\n        ").concat(r+this.totalMetadataHeight+this.totalRowAddLinkHeight,"\n      )")),this.gColumnDendogram.attr("transform","translate(\n        ".concat(this.rowLabelsWidth,",\n        ").concat(r+this.totalMetadataHeight+this.totalRowAddLinkHeight+o,"\n      )")),this.gCaption.attr("transform","translate(".concat(this.rowLabelsWidth,",\n        ").concat(r+this.totalMetadataHeight+this.totalRowAddLinkHeight+o+i+this.options.spacing,"\n      )")),h.default.select("body").on("keydown",(function(){"Space"===h.default.event.code&&(t.svg.style("cursor","move"),t.spacePressed=!0)})).on("keyup",(function(){"Space"===h.default.event.code&&(t.svg.style("cursor","auto"),t.spacePressed=!1)})),this.svg.on("mousedown",(function(){t.mouseDown=!0,t.spacePressed&&(t.mouseX=h.default.event.clientX,t.mouseY=h.default.event.clientY,h.default.event.preventDefault())})).on("mousemove",this.drag.bind(this)).on("mouseup",(function(){t.mouseDown=!1})),this.g.on("wheel.zoom",this.scroll.bind(this))}},{key:"drag",value:function drag(){this.mouseDown&&this.spacePressed&&(this.pan(h.default.event.clientX-this.mouseX,h.default.event.clientY-this.mouseY),this.mouseX=h.default.event.clientX,this.mouseY=h.default.event.clientY)}},{key:"scroll",value:function scroll(t){t?this.pan(-t.deltaX,-t.deltaY):this.pan(-h.default.event.deltaX,-h.default.event.deltaY),h.default.event.preventDefault(),h.default.event.stopPropagation()}},{key:"scrollToRow",value:function scrollToRow(t){var a=this,l=this.rowLabels.filter((function(a){return a.label===t}))[0];if(l){var r=l.rowIndex,o=this.container[0][0].offsetHeight,i=this.totalMetadataHeight+this.totalRowAddLinkHeight,u=o/4-(this.cellYPosition(l)+i);this.scrollToRowInProgess=!0,this.pan(0,u,!0),this.rowLabels[r].highlighted=!0,this.highlightRowOrColumn(this.rowLabels[r]),this.updateLabelHighlights(this.gRowLabels.selectAll(".".concat(L.default.rowLabel)),this.rowLabels),this.rowLabels[r].highlighted=!1,setTimeout((function(){a.highlightRowOrColumn(null),a.rowLabels[r].highlighted=!1,a.updateLabelHighlights(a.gRowLabels.selectAll(".".concat(L.default.rowLabel)),a.rowLabels)}),2750)}}},{key:"pan",value:function pan(t,a){var l=arguments.length>2&&void 0!==arguments[2]&&arguments[2],r=this.container[0][0].offsetWidth,o=this.container[0][0].offsetHeight,i=(r-Number(this.svg.attr("width")))/this.options.zoom,u=(o-Number(this.svg.attr("height")))/this.options.zoom,d=h.default.transform(this.g.attr("transform")).translate,c=Math.min(this.options.marginLeft,Math.max(t+d[0],i)),p=Math.min(this.options.marginTop,Math.max(a+d[1],u));l?this.g.transition().duration(this.options.transitionDuration).attr("transform","translate(".concat([c,p],")")):this.g.attr("transform","translate(".concat([c,p],")"));var m=h.default.transform(this.gRowLabels.attr("transform")).translate,g=(0,C.clamp)(0,-i+this.options.marginLeft,m[0]-t);this.placeRowLabelContainers(g),this.renderColumnMetadata(g,!1),this.renderRowAddLink(g),this.renderPinColumnLink(g);var v=h.default.transform(this.gColumnLabels.attr("transform")).translate,y=(0,C.clamp)(this.columnLabelsHeight,this.columnLabelsHeight+this.options.marginTop-u,v[1]-a);this.placeColumnLabelAndMetadataContainers(y,l),this.placePinColumnLinkContainer(y,l),this.placeAddRowLinkContainer(y,l)}},{key:"placeRowLabelContainers",value:function placeRowLabelContainers(t){var a=this.totalMetadataHeight,l=this.totalRowAddLinkHeight;this.gRowLabels.attr("transform","translate(".concat(t,", ").concat(this.columnLabelsHeight+a+l,")")),this.rowLabelsBackgroun

1d.attr("x",t-this.options.marginLeft).attr("y",this.columnLabelsHeight+a),this.metadataLabelsBackground.attr("x",t-this.options.marginLeft)}},{key:"placeColumnLabelAndMetadataContainers",value:function placeColumnLabelAndMetadataContainers(t){var a=arguments.length>1&&void 0!==arguments[1]&&arguments[1];this.gColumnLabels.transition().duration(a?this.options.transitionDuration:0).attr("transform","translate(".concat(this.rowLabelsWidth,",").concat(t,")")),this.gColumnMetadata.transition().duration(a?this.options.transitionDuration:0).attr("transform","translate(0, ".concat(t,")")),this.columnLabelsBackground.transition().duration(a?this.options.transitionDuration:0).attr("y",t-this.columnLabelsHeight-this.options.marginTop),this.metadataLabelsBackground.transition().duration(a?this.options.transitionDuration:0).attr("y",t-this.columnLabelsHeight-this.options.marginTop)}},{key:"placeAddRowLinkContainer",value:function placeAddRowLinkContainer(t){var a=arguments.length>1&&void 0!==arguments[1]&&arguments[1];this.gAddRow.transition().duration(a?this.options.transitionDuration:0).attr("transform","translate(0, ".concat(t,")")),this.addRowBackground.transition().duration(a?this.options.transitionDuration:0).attr("y",t+this.options.columnMetadata.length*this.options.minCellHeight)}},{key:"placePinColumnLinkContainer",value:function placePinColumnLinkContainer(t){var a=arguments.length>1&&void 0!==arguments[1]&&arguments[1];this.gPinColumn.transition().duration(a?this.options.transitionDuration:0).attr("transform","translate(0, ".concat(t,")"))}},{key:"processMetadata",value:function processMetadata(){var t=this,a=0;this.options.columnMetadata.forEach((function(l){var r=new Set;

1t.columnLabels.forEach((function(t){var a=(t.metadata||{})[l.value];a&&r.add(a)})),a+=r.size}));var l=this.options.metadataColorScale.getNScale(a),r=0;this.metadataColors={},this.options.columnMetadata.forEach((function(a){var o={};t.columnLabels.forEach((function(t){var i=(t.metadata||{})[a.value];i&&!o[i]&&(o[i]=l[r++])})),t.metadataColors[a.value]=o}))}},{key:"cluster",value:function cluster(){var t=this;this.options.shouldSortRows?this.sortRows("asc"):this.options.clustering&&this.clusterRows(),this.columnMetadataSortField?(this.columnClustering=null,this.options.onPinColumnClick?(0,y.orderBy)(this.columnLabels,[function(t){return t.pinned},function(a){if(!a.pinned)return a.metadata&&a.metadata[t.columnMetadataSortField]||"ZZZ"},function(t){return t.label}],["desc",this.columnMetadataSortAsc?"asc":"desc","asc"]).forEach((function(t,a){t.pos=a})):(0,y.orderBy)(this.columnLabels,(function(a){return a.metadata&&a.metadata[t.columnMetadataSortField]||"ZZZ"}),this.columnMetadataSortAsc?"asc":"desc").forEach((function(t,a){t.pos=a}))):this.options.shouldSortColumns?this.sortColumns("asc"):this.options.clustering&&this.clusterColumns()}},{key:"update",value:function update(){this.renderHeatmap(),this.renderRowLabels(),this.renderColumnLabels(),this.renderPinColumnLink(),this.renderColumnMetadata(),this.renderRowAddLink(0),this.options.clustering&&(this.renderRowDendrogram(),this.renderColumnDendrogram()),this.options.onUpdateFinished&&this.options.onUpdateFinished()}},{key:"getScale",value:function getScale(){return this.scaleType().domain([this.limits.min,this.limits.max]).range([0,1])}},{key:"getRows",value:function getRows(){for(var t=this.getScale(),a=[],l=0;l<this.rowLabels.length;l++)if(!this.rowLabels[l].hidden){for(var r=this.data.values[l].slice(),o=0;o<this.columnLabels.length;o++)r[o]=t(r[o]||this.options.nullValue);r.idx=l,a.push(r)}return a}},{key:"getColumns",value:function getColumns(){for(var t=this.getScale(),a=[],l=0;l<this.columnLabels.length;l++)for(var r=0;r<this.rowLabels.length;r++)this.rowLabels[r].hidden||(a[l]||(a[l]=[],a[l].idx=l),a[l].push(t(this.data.values[r][l]||this.options.nullValue)));return a}},{key:"getPinnedColumns",value:function getPinnedColumns(){return this.columnLabels.filter((function(t){return t.pinned}))}},{key:"getUnpinnedColumns",value:function getUnpinnedColumns(){return this.columnLabels.filter((function(t){return!t.pinned}))}},{key:"getUnpinnedColumnValues",value:function getUnpinnedColumnValues(){for(var t=this.getScale(),a=[],l=0;l<this.columnLabels.length;l++)for(var r=0;r<this.rowLabels.length;r++)this.rowLabels[r].hidden||this.columnLabels[l].pinned||(a[l]||(a[l]=[],a[l].idx=l),a[l].push(t(this.data.values[r][l]||this.options.nullValue)));return(0,y.compact)(a)}},{key:"getCursorLocation",value:function getCursorLocation(){return{left:h.default.event.pageX,top:h.default.event.pageY}}},{key:"getCellFromCursorLocation",value:function getCellFromCursorLocation(){var t=this.gCells[0][0].getBoundingClientRect(),a=h.default.event.clientX-t.left,l=h.default.event.clientY-t.top,r=Math.floor(a/t.width*this.columnLabels.length),o=Math.floor(l/t.height*this.rowLabels.length);if(r<0||o<0)return null;var i=(0,C.find)({pos:r},this.columnLabels).columnIndex,u=(0,C.find)({pos:o},this.rowLabels).rowIndex;return(0,C.find)({columnIndex:i,rowIndex:u},this.cells)}},{key:"sortTree",value:function sortTree(t){if(t)for(var a=this.getScale(),l=[];;){for(;t;)t.right&&l.push(t.right),l.push(t),t=t.left;if((t=l.pop()).right&&l[l.length-1]===t.right)l.pop(),l.push(t),t=t.right;else{if(t.value)t.mean=(0,C.mean)(t.value.map((function(t){return a(t)})));else{if(t.left.mean<t.right.mean){var r=[t.right,t.left];t.left=r[0],t.right=r[1]}t.mean=t.left.mean}t=null}if(!l.length)break}}},{key:"getDepth",value:function getDepth(t){if(!t)return 0;for(var a=[[t,0]],l=0;a.length;){var r=a.pop(),o=(0,i.default)(r,2),u=o[0],d=o[1];l=d>l?d:l,u.left&&a.push([u.left,d+1]),u.right&&a.push([u.right,d+1])}return l}},{key:"setOrder",value:function setOrder(t,a){for(var l=[],r=!1,o=arguments.length>2&&void 0!==arguments[2]?arguments[2]:0;!r;

1)t?(l.push(t),t=t.left):l.length?((t=l.pop()).value&&(a[t.value.idx].pos=o++),t=t.right):r=!0;return a}},{key:"clusterRows",value:function clusterRows(){var t=this.getRows();this.rowClustering=m.default.hcluster(t),this.sortTree(this.rowClustering),this.setOrder(this.rowClustering,this.rowLabels)}},{key:"clusterColumns",value:function clusterColumns(){if(this.options.onPinColumnClick){(0,y.orderBy)(this.columnLabels,[function(t){return t.pinned},function(t){return t.label}],["desc","asc"]).forEach((function(t,a){t.pos=a}));var t=this.getUnpinnedColumnValues();this.columnClustering=m.default.hcluster(t),this.sortTree(this.columnClustering),this.setOrder(this.columnClustering,this.columnLabels,this.getPinnedColumns().length)}else{var a=this.getColumns();this.columnClustering=m.default.hcluster(a),this.sortTree(this.columnClustering),this.setOrder(this.columnClustering,this.columnLabels)}}},{key:"sortColumns",value:function sortColumns(t){this.columnClustering=null,this.options.onPinColumnClick?(0,y.orderBy)(this.columnLabels,[function(t){return t.pinned},function(t){return t.label}],["desc",t]).forEach((function(t,a){t.pos=a})):(0,y.orderBy)(this.columnLabels,(function(t){return t.label}),t).forEach((function(t,a){t.pos=a}))}},{key:"sortRows",value:function sortRows(t){this.rowClustering=null,(0,y.orderBy)(this.filteredRowLabels,(function(t){return t.sortKey||t.label}

1),t),this.filteredRowLabels.forEach((function(t,a){t.pos=a}))}},{key:"range",value:function range(t){return Array.apply(null,{length:t}).map(Number.call,Number)}},{key:"download",value:function download(t){var a=this;this.expandColumnLabels(),setTimeout((function(){a.svg.classed(L.default.printMode,!0),a.showPrintCaption(),a.svgSaver.asSvg(a.svg.node(),"heatmap.svg"),a.svg.classed(L.default.printMode,!1),t("truncated"),a.hidePrintCaption()}),100)}},{key:"downloadAsPng",value:function downloadAsPng(t){var a=this;this.expandColumnLabels(),setTimeout((function(){a.svg.classed(L.default.printMode,!0),a.showPrintCaption(),a.svgSaver.asPng(a.svg.node(),"heatmap.png"),a.svg.classed(L.default.printMode,!1),t("truncated"),a.hidePrintCaption()}),100)}},{key:"computeCurrentHeatmapViewValuesForCSV",value:function computeCurrentHeatmapViewValuesForCSV(t){var a=this,l=t.headers,r=void 0===l?[]:l,i=(0,o.default)(r),u=[],d=(0,C.sortBy)(["pos"],this.rowLabels),c=(0,C.sortBy)(["pos"],this.columnLabels);return d.forEach((function(t){return u.push([t.label].concat((0,o.default)(r.includes("Genus")?[t.genusName]:[])))})),c.forEach((function(t){i.push(t.label),d.forEach((function(l){var r,o=t.columnIndex,i=l.rowIndex,d=(0,C.find)({columnIndex:o,rowIndex:i},a.filteredCells);r=d?d.meetsUserFilters?d.value:"NA":0,u[l.pos].push(r)}))})),u=u.map((function(t){return[(0,w.sanitizeCSVRow)(t).join()]})),[[(0,w.sanitizeCSVRow)(i).join()],u]}},{key:"handleColumnMetadataLabelClick",value:function handleColumnMetadataLabelClick(t){var a=this.options.onColumnMetadataSortChange;this.columnMetadataSortField===t?this.columnMetadataSortAsc?this.columnMetadataSortAsc=!1:(this.columnMetadataSortField=null,this.columnMetadataSortAsc=!0):(this.columnMetadataSortField=t,this.columnMetadataSortAsc=!0),this.processData("cluster"),a&&a(this.columnMetadataSortField,this.columnMetadataSortAsc)}},{key:"applyScale",value:function applyScale(t,a,l,r){return a=Math.min(Math.max(a,l),r),Math.round(t(a))}},{key:"cellYPosition",value:function cellYPosition(t){return t.pos*this.cell.height}},{key:"renderHeatmap",value:function renderHeatmap(){var t=this,a=this.scaleType().domain([this.scaleLimits.min,this.scaleLimits.max]).range([0,this.options.colors.length-1]),l=function applyFormat(l){l.attr("width",t.cell.width-2).attr("height",t.cell.height-2).attr("x",(function(a){return t.columnLabels[a.columnIndex].pos*t.cell.width+1})).attr("y",(function(a){return t.cellYPosition(t.rowLabels[a.rowIndex])+1})).style("fill",(function(l){if(!l.value&&0!==l.value)return t.options.colorNoValue;var r=t.applyScale(a,l.value,t.scaleLimits.min,t.scaleLimits.max);return t.options.customColorCallback?t.options.customColorCallback(l.value,l,t.options.colors[r],t.options.colors,t.options.colorNoValue):t.options.colors[r]}))};this.bgPattern&&this.bgPattern.remove(),this.bgPattern=this.defs.append("pattern").attr("id","pattern-grid").attr("patternUnits","userSpaceOnUse").attr("width",this.cell.width).attr("height",this.cell.height),this.bgPattern.append("rect").style("fill","rgb(234, 234, 234)").attr("height",this.cell.height-2).attr("width",this.cell.width-2).attr("x",1).attr("y",1);var r=this.cell.width*this.columnLabels.length,o=this.cell.height*this.filteredRowLabels.length;null!=this.bgGrid&&this.bgGrid.remove(),this.bgGrid=this.gCells.append("rect").lower(),this.bgGrid.attr("width",r).attr("height",o).attr("style","fill: url(#pattern-grid)").on("mousemove",(function(){var a=t.getCellFromCursorLocation();a&&((0,C.isEqual)(t.previousNullHover,a)||(t.previousNullHover&&t.handleCellMouseLeave(t.previousNullHover),t.previousNullHover=a,t.handleCellMouseOver(a)))})).on("mouseleave",(function(){t.previousNullHover&&(t.handleCellMouseLeave(t.previousNullHover),t.previousNullHover=null)})).on("click",(function(){var a=t.getCellFromCursorLocation();a&&t.handleCellClick(a)})),this.gCellHover&&this.gCellHover.remove(),this.gCellHover=this.gCells.append("rect").lower(),this.gCellHover.style("fill-opacity",0).style("stroke",O).attr("height",this.cell.height).attr("width",this.cell.width).attr("visibility","hidden");var i=this.gCells.selectAll(".".concat(L.default.cell)).data(this.filteredCells,(function(t){return t.id}));

1i.exit().lower().transition().duration(this.options.transitionDuration).style("opacity",0).remove(),l(i.transition().duration(this.options.transitionDuration)),l(i.enter().append("rect").attr("class",(function(){return L.default.cell})).on("mouseover",this.handleCellMouseOver).on("mouseleave",this.handleCellMouseLeave).on("click",this.handleCellClick))}},{key:"renderRowLabels",value:function renderRowLabels(){var t=this,a=function applyFormat(a){a.attr("transform",(function(a){return"translate(0, ".concat(t.cellYPosition(a),")")})),a.select("rect").attr("width",t.rowLabelsWidth),a.select("text").attr("data-testid","row-label").attr("transform","translate(".concat(t.rowLabelsWidth-t.options.spacing,", ").concat(t.cell.height/2,")"))};this.gRowLabels.classed(L.default.rowClustering,this.rowClustering);var l=this.gRowLabels.selectAll(".".concat(L.default.rowLabel)).data(this.filteredRowLabels,(function(t){return t.label})).order();l.exit().lower().transition().duration(this.options.transitionDuration).style("opacity",0).remove(),a(l.transition().duration(this.options.transitionDuration));var r=l.enter().append("g").attr("class",L.default.rowLabel).on("mouseenter",this.handleRowLabelMouseEnter).on("mouseleave",this.handleRowLabelMouseLeave);r.append("rect").attr("class",L.default.hoverTarget).attr("width",this.rowLabelsWidth).attr("height",this.cell.height).style(N,"end"),r.append("text").text((function(t){return t.label})).style("dominant-baseline","central").style(N,"end").on("click",(function(a){return t.options.onRowLabelClick&&t.options.onRowLabelClick(a.label,h.default.event)})),a(r),r.append("line").attr("x1",0).attr("x2",this.rowLabelsWidth).attr("y1",this.cell.height).attr("y2",this.cell.height).attr("class",L.default.genusBorder).classed(L.default.hideGenusBorder,(function(a,l){var r=t.filteredRowLabels[l+1];return!r||a.sortKey===r.sortKey})),r.append("svg:image").attr("class",L.default.removeIcon).attr("width",this.options.spacing).attr("height",this.options.spacing).attr("transform","translate(".concat(this.options.spacing,",\n        ").concat((this.cell.height-this.options.spacing)/2,")")).attr(k,"".concat(this.options.iconPath,"/IconCloseSmall.svg")).on("click",this.removeRow),a(r)}},{key:"renderRowAddLink",value:function renderRowAddLink(t){var a=this;if(this.options.onAddRowClick){var l=function handleAddRowClick(){a.options.onAddRowClick(d.node(),{x:a.rowLabelsWidth-10,y:u})},r=this.gAddRow.selectAll(".".concat(L.default.columnMetadataAdd)).data([1]),o=function applyFormat(t){t.select("text").attr("x",a.rowLabelsWidth-a.options.marginAddLink),t.select("image").attr("x",a.rowLabelsWidth-a.options.marginAddLinkImg)};o(r.transition().duration(this.options.transitionDuration));var i=r.enter().append("g").attr("class",L.default.columnMetadataAdd),u=this.options.metadataAddLinkHeight/2;i.append("rect"),i.append("text").text((function(){return"Add Taxon"})).attr("class",L.default.metadataAddLabel).attr("y",11).on("click",l),o(i);var d=i.append("g").attr("class",L.default.metadataAddTrigger).on("click",l);d.append("svg:image").attr("class",L.default.metadataAddIcon).attr("width",this.options.metadataAddLinkHeight).attr("height",this.options.metadataAddLinkHeight).attr(k,"".concat(this.options.iconPath,"/plus.svg")),o(d),d.size()&&(this.addRowTrigger=d.node()),r.attr("transform","translate(".concat(t,", ").concat((1+this.options.columnMetadata.length)*this.options.minCellHeight,")")),r.select("rect").attr("width",this.rowLabelsWidth+this.columnLabels.length*this.cell.width).attr("height",this.options.metadataAddLinkHeight)}}},{key:"renderPinColumnLink",value:function renderPinColumnLink(){var t=this,a=arguments.length>0&&void 0!==arguments[0]?arguments[0]:0;if(this.options.onPinColumnClick){var l=function handlePinColumnClick(){t.options.onPinColumnClick(d.node(),{x:t.rowLabelsWidth-10,y:u})},r=function applyFormat(a){a.select("text").attr("x",t.rowLabelsWidth-t.options.marginAddLink),a.select("image").attr("x",t.rowLabelsWidth-t.options.marginAddLinkImg),a.select("rect").attr("width",t.rowLabelsWidth+t.columnLabels.length*t.cell.width).attr("height",t.options.metadataAddLinkHeight)},o=this.gPinColumn.selectAll(".".concat(L.default.columnMetadataAdd)

1).data([1]);r(o.transition().duration(this.options.transitionDuration));var i=o.enter().append("g").attr("class",L.default.columnMetadataAdd),u=this.options.metadataAddLinkHeight/2;i.append("rect"),i.append("text").text((function(){return"Pin Samples"})).attr("class",L.default.metadataAddLabel).attr("y",11).on("click",l),r(i);var d=i.append("g").attr("class",L.default.metadataAddTrigger).on("click",l);d.append("svg:image").attr("class",L.default.metadataAddIcon).attr("width",this.options.metadataAddLinkHeight).attr("height",this.options.metadataAddLinkHeight).attr(k,"".concat(this.options.iconPath,"/plus.svg")),r(d),d.size()&&(this.pinColumnTrigger=d.node()),o.attr("transform","translate(".concat(a,", ").concat(2*-this.options.metadataAddLinkHeight,")"))}}},{key:"renderColumnLabels",value:function renderColumnLabels(){var t=this;this.gColumnLabels.selectAll("*").remove();var a=this.gColumnLabels.selectAll(".".concat(L.default.columnLabel)).data(this.columnLabels,(function(t){return t.id})),l=function applyFormat(a){a.attr("transform",(function(a){return"translate(".concat(a.pos*t.cell.width,",-").concat(t.options.spacing,")")}))};l(a.transition().duration(this.options.transitionDuration));var r=a.enter().append("g").attr("class",L.default.columnLabel).on("mouseenter",this.handleColumnLabelMouseEnter).on("mouseleave",this.handleColumnLabelMouseLeave);r.append("text").text((function(t){return t.label})).style(N,"left").attr("transform","translate(".concat(this.cell.width/2,",-").concat(this.options.spacing,") rotate (").concat(this.options.textRotation,")")).on("mousein",this.options.onColumnLabelMouseIn).on("mouseout",this.options.onColumnLabelMouseOut).on("mouseover",(function(a){t.options.onColumnLabelHover&&t.options.onColumnLabelHover(a)})).on("mouseleave",this.options.onColumnLabelOut).on("click",(function(a){return t.options.onColumnLabelClick&&t.options.onColumnLabelClick(a.id,h.default.event)})),r.append("svg:image").attr("class",L.default.pinIcon).attr("transform","translate(".concat(this.cell.width/2-7,", 0)")).attr(k,"".concat(this.options.iconPath,"/IconPin.svg")).on("mouseenter",this.options.onPinIconHover).on("mouseleave",this.options.onPinIconExit).on("click",this.unpinColumn),l(r),a.select(".".concat(L.default.pinIcon)).attr("display",(function(t){return t.pinned?"default":"none"}))}},{key:"renderColumnMetadata",value:function renderColumnMetadata(){var t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:0,a=!(arguments.length>1&&void 0!==arguments[1])||arguments[1];this.renderColumnMetadataCells(),this.renderColumnMetadataAddLink(t),this.renderColumnMetadataLabels(t,a)}},{key:"getColumnMetadataLabelOffset",value:function getColumnMetadataLabelOffset(t){return t.value===this.columnMetadataSortField?this.options.metadataSortIconSize+this.options.spacing:0}},{key:"renderColumnMetadataLabels",value:function renderColumnMetadataLabels(t){var a=this,l=!(arguments.length>1&&void 0!==arguments[1])||arguments[1],r=function applyFormat(l){l.attr("transform",(function(l,r){var o=a.getColumnMetadataLabelOffset(l);return"translate(".concat(t-o,", ").concat(a.options.metadataAddLinkHeight+(1+r*a.options.minCellHeight),")")})),l.select("text").attr("transform","translate(".concat(a.rowLabelsWidth-a.options.spacing,", ").concat(a.options.minCellHeight/2,")")),l.select("rect").attr("width",(function(t){var l=a.getColumnMetadataLabelOffset(t);return a.rowLabelsWidth+a.options.marginLeft+l})),l.select("image").attr("transform","translate(".concat(a.rowLabelsWidth,",").concat((a.options.minCellHeight+a.options.metadataSortIconSize)/2,")"))},o=this.gColumnMetadata.selectAll(".".concat(L.default.columnMetadataLabel)).data(this.options.columnMetadata,(function(t){return t.value}));o.exit().lower().transition().duration(this.options.transitionDuration).style("opacity",0).remove();var i=o.transition().duration(this.options.transitionDuration);r(l?i:o);var u=o.enter().append("g").attr("class",L.default.columnMetadataLabel).on("mousein",this.options.onColumnMetadataLabelMouseIn).on("mouseout",this.options.onColumnMetadataLabelMouseOut);u.append("rect").attr("class",L.default.hoverTarget).attr("x",-this.options.marginLeft).attr("y",-1).attr("height",this.options.minCellHeight+1).style(N,"end").style("fill","white"),r(u);var d=function handleColumnMetadataLabelClick(t){a.options.onColumnMetadataLabelClick?a.options.onColumnMetadataLabelClick(t.value,h.default.event):a.handleColumnMetadataLabelClick(t.value),u.selectAll("rect").attr("width",(function(t){var l=a.getColumnMetadataLabelOffset(t);return a.rowLabelsWidth+a.options.marginLeft+l}))};u.append("text").text((function(t){return t.label})).style("dominant-baseline","central").style(N,"end").on("click",d).on("mouseover",(function(t){a.options.onColumnMetadataLabelHover&&a.options.onColumnMetadataLabelHover(t)})).on("mouseleave",(function(t){a.options.onColumnMetadataLabelOut&&a.options.onColumnMetadataLabelOut(t)})),r(u),u.append("g").append("svg:image").attr("class","metadataSortIcon").attr("width",this.options.metadataSortIconSize).attr("height",this.options.metadataSortIconSize).attr("transform","rotate(-90)").on("click",d),r(u),o.select(".metadataSortIcon").attr(k,(function(t){return t.value===a.columnMetadataSortField?"".concat(a.options.iconPath,"/sort_").concat(a.columnMetadataSortAsc?"asc":"desc",".svg"):""}))}},{key:"renderColumnMetadataCells",value:function renderColumnMetadataCells(){var t=this,a=function applyFormatForCells(a){a.attr("width",t.cell.width-2).attr("height",t.options.minCellHeight-2).attr("transform",(function(a){return"translate(".concat(a.pos*t.cell.width+t.rowLabelsWidth+1,", 0)")}))},l=function applyFormatForRows(a){a.attr("transform",(function(a,l){return"translate(0, ".concat(t.options.metadataAddLinkHeight+t.options.minCellHeight*l,")")}))},r=this.gColumnMetadata.selectAll(".columnMetadataCells").data(this.options.columnMetadata,(function(t){return t.value}));r.exit().lower().transition().duration(this.options.transitionDuration).style("opacity",0).remove(),l(r.transition().duration(this.options.transitionDuration)),l(r.enter().append("g").attr("class",(function(t){return(0,p.default)("columnMetadataCells",t.value.replace(/ 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handleAddColumnMetadataClick(){a.options.onAddColumnMetadataClick(d.node(),{x:a.rowLabelsWidth-10,y:u})},r=this.gColumnMetadata.selectAll(".".concat(L.default.columnMetadataAdd)

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