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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| import { useFilterTreesByType } from "../hooks/api" | ||
| import { WithData } from "./Loader" | ||
| import React from "react" | ||
| import { keyBy } from "lodash" | ||
| import { buildTree, TreePanel } from "./classificationTree/TreePanel" | ||
|
|
||
| export default function SubsetsHierarchyLoader({ collationTypes, datasetIds, defaultTreeDepth }) { | ||
| const collationsHierarchyReply = useFilterTreesByType({ | ||
| datasetIds, | ||
| collationTypes | ||
| }) | ||
|
|
||
| return ( | ||
| <WithData | ||
| apiReply={collationsHierarchyReply} | ||
| background | ||
| render={(collationsHierarchyReply) => ( | ||
| <SubsetsResponse | ||
| collationsHierarchies={collationsHierarchyReply.response.filteringTerms} | ||
| datasetIds={datasetIds} | ||
| defaultTreeDepth={defaultTreeDepth} | ||
| /> | ||
| )} | ||
| /> | ||
| ) | ||
| } | ||
|
|
||
| function SubsetsResponse({ collationsHierarchies, datasetIds, defaultTreeDepth }) { | ||
| const subsetById = keyBy(collationsHierarchies, "id") | ||
| const { tree, size } = buildTree(collationsHierarchies, subsetById) | ||
|
|
||
| return ( | ||
| <TreePanel | ||
| datasetIds={datasetIds} | ||
| subsetById={subsetById} | ||
| tree={tree} | ||
| size={size} | ||
| defaultTreeDepth={defaultTreeDepth} | ||
| sampleFilterScope="allTermsFilters" | ||
| /> | ||
| ) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,111 @@ | ||
| import { useCollationsByType, useCollationsById } from "../hooks/api" | ||
| import { WithData } from "./Loader" | ||
| import React from "react" | ||
| import { keyBy, merge } from "lodash" | ||
| import { | ||
| SITE_DEFAULTS, | ||
| useServiceItemDelivery, | ||
| sampleSearchPageFiltersLink, | ||
| NoResultsHelp | ||
| } from "../hooks/api" | ||
| import { Loader } from "./Loader" | ||
| import { SubsetHistogram } from "./SVGloaders" | ||
| import { buildTree, buildTreeForDetails, TreePanel } from "./classificationTree/TreePanel" | ||
| // import { ShowJSON } from "./RawData" | ||
| import { ExternalLink, InternalLink } from "./helpersShared/linkHelpers" | ||
|
|
||
| export default function SubsetsLoader({ collationTypes, datasetIds, defaultTreeDepth }) { | ||
| const bioSubsetsHierarchiesReply = useCollationsByType({ | ||
| datasetIds, | ||
| method: "paths", | ||
| collationTypes | ||
| }) | ||
| const service = "collations" | ||
|
|
||
| const allBioSubsetsReply = useCollationsById({ | ||
| export function SubsetLoader({ id, datasetIds }) { | ||
| const { data, error, isLoading } = useServiceItemDelivery( | ||
| id, | ||
| service, | ||
| datasetIds | ||
| }) | ||
|
|
||
| ) | ||
| return ( | ||
| <WithData | ||
| apiReply={bioSubsetsHierarchiesReply} | ||
| background | ||
| render={(bioSubsetsHierarchiesResponse) => ( | ||
| <WithData | ||
| apiReply={allBioSubsetsReply} | ||
| background | ||
| render={(allBioSubsetsResponse) => ( | ||
| <SubsetsResponse | ||
| bioSubsetsHierarchies={bioSubsetsHierarchiesResponse.response.results} | ||
| allBioSubsets={allBioSubsetsResponse.response.results} | ||
| datasetIds={datasetIds} | ||
| defaultTreeDepth={defaultTreeDepth} | ||
| /> | ||
| )} | ||
| /> | ||
| <Loader isLoading={isLoading} hasError={error} background> | ||
| {data && ( | ||
| <SubsetResponse response={data} id={id} datasetIds={datasetIds} /> | ||
| )} | ||
| /> | ||
| </Loader> | ||
| ) | ||
| } | ||
|
|
||
| function SubsetsResponse({ bioSubsetsHierarchies, allBioSubsets, datasetIds, defaultTreeDepth }) { | ||
| const isDetailPage = bioSubsetsHierarchies.length === 1 | ||
| // We merge both subsets from hierarchies and subsets from allSubsets. | ||
| // This is because some children in the bioSubsetsHierarchies don't have labels or sample count information. | ||
| const subsetById = merge(keyBy(bioSubsetsHierarchies, "id"), allBioSubsets) | ||
| const { tree, size } = isDetailPage | ||
| ? buildTreeForDetails(bioSubsetsHierarchies, subsetById) | ||
| : buildTree(bioSubsetsHierarchies, subsetById) | ||
| function SubsetResponse({ response, datasetIds }) { | ||
| if (!response.response.results[0]) { | ||
| return NoResultsHelp("subsetdetails") | ||
| } | ||
| return <Subset subset={response.response.results[0]} datasetIds={datasetIds} /> | ||
| } | ||
|
|
||
| function Subset({ subset, datasetIds }) { | ||
|
|
||
| const filters = subset.id | ||
| const sampleFilterScope = "allTermsFilters" | ||
|
|
||
| return ( | ||
| <section className="content"> | ||
| <h2> | ||
| {subset.label} ({subset.id}) | ||
| </h2> | ||
|
|
||
| {subset.type && ( | ||
| <> | ||
| {isDetailPage && ( | ||
| <div className="mb-3"> | ||
| <SubsetHistogram | ||
| id={bioSubsetsHierarchies[0].id} | ||
| datasetIds={datasetIds} | ||
| loaderProps={{ | ||
| background: true, | ||
| colored: true | ||
| }} | ||
| <h5>Subset Type</h5> | ||
| <ul> | ||
| <li> | ||
| {subset.type}{" "} | ||
| <ExternalLink | ||
| href={subset.reference} | ||
| label={subset.id} | ||
| /> | ||
| </div> | ||
| )} | ||
| <TreePanel | ||
| datasetIds={datasetIds} | ||
| subsetById={subsetById} | ||
| tree={tree} | ||
| size={size} | ||
| defaultTreeDepth={defaultTreeDepth} | ||
| sampleFilterScope="allTermsFilters" | ||
| /> | ||
| </li> | ||
| </ul> | ||
| </> | ||
| )} | ||
|
|
||
| <h5>Sample Counts</h5> | ||
| <ul> | ||
| <li>{subset.count} samples</li> | ||
| <li>{subset.codeMatches} direct <i>{subset.id}</i> code matches</li> | ||
| {subset.cnvAnalyses && ( | ||
| <li>{subset.cnvAnalyses} CNV analyses</li> | ||
| )} | ||
| {subset.frequencymapCnvAnalyses && ( | ||
| <li> | ||
| {subset.frequencymapCnvAnalyses} {" CNV analyses used in frequency calculations"} | ||
| </li> | ||
| )} | ||
| </ul> | ||
| <h5>CNV Histogram</h5> | ||
| <div className="mb-3"> | ||
| <SubsetHistogram | ||
| id={subset.id} | ||
| datasetIds={datasetIds} | ||
| loaderProps={{background: true, colored: true}} | ||
| /> | ||
| </div> | ||
|
|
||
| <h5> | ||
| <InternalLink | ||
| href={`${SITE_DEFAULTS.API_PATH}services/intervalFrequencies/${subset.id}/?output=pgxfreq`} | ||
| label="Download CNV frequencies" | ||
| /> | ||
| </h5> | ||
| <p> | ||
| Download CNV frequency data for genomic 1Mb bins. | ||
| </p> | ||
|
|
||
| <h5> | ||
| <InternalLink | ||
| href={ sampleSearchPageFiltersLink({datasetIds, sampleFilterScope, filters}) } | ||
| label={`Search for ${subset.id} Samples`} | ||
| rel="noreferrer" | ||
| target="_blank" | ||
| /> | ||
| </h5> | ||
| <p> | ||
| Select samples through the search form, e.g. by querying for specific | ||
| genomic variants or phenotypes. | ||
| </p> | ||
|
|
||
| {/*<ShowJSON data={subset} />*/} | ||
|
|
||
| </section> | ||
| ) | ||
| } |
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