Merge branch 'main' of https://github.com/progenetix/cancercelllines-web

progenetix · Oct 25, 2023 · 5d573b7 · 5d573b7
2 parents a2406e7 + 93f2ec5
commit 5d573b7
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Showing 4 changed files with 9 additions and 104 deletions.
diff --git a/src/components/SVGloaders.js b/src/components/SVGloaders.js
@@ -25,7 +25,7 @@ export default function SVGloader({ apiReply }) {
   )
 }
 
-export function SubsetHistogram({ id, filter, datasetIds, plotRegionLabels, plotGeneSymbols, plotCytoregionLabels, title, description, size: givenSize }) {
+export function SubsetHistogram({ id, datasetIds, plotRegionLabels, plotGeneSymbols, plotCytoregionLabels, title, description, size: givenSize }) {
   const componentRef = useRef()
   const { width } = useContainerDimensions(componentRef)
   const size = givenSize || width
@@ -35,7 +35,6 @@ export function SubsetHistogram({ id, filter, datasetIds, plotRegionLabels, plot
         apiReply={useSubsethistogram({
           datasetIds,
           id,
-          filter,
           plotRegionLabels,
           plotGeneSymbols,
           plotCytoregionLabels,
@@ -74,7 +73,7 @@ export function SubsetHistogram({ id, filter, datasetIds, plotRegionLabels, plot
 export function BiosamplePlot({ biosid, datasetIds, plotRegionLabels, plotChros}) {
   const componentRef = useRef()
   const { width } = useContainerDimensions(componentRef)
-  const url = `${SITE_DEFAULTS.API_PATH}beacon/biosamples/${biosid}/?datasetIds=${datasetIds}&output=samplesplot&plot_width=${width}&plotRegionLabels=${plotRegionLabels}&plotChros=${plotChros}&forceEmptyPlot=true`
+  const url = `${SITE_DEFAULTS.API_PATH}services/sampleplots/${biosid}?plotType=samplesplot&datasetIds=${datasetIds}&plot_width=${width}&plotRegionLabels=${plotRegionLabels}&plotChros=${plotChros}&forceEmptyPlot=true`
   // width > 0 to make sure the component is mounted and avoid double fetch
   const dataEffect = useExtendedSWR(width > 0 && url, svgFetcher)
   return (
@@ -87,7 +86,7 @@ export function BiosamplePlot({ biosid, datasetIds, plotRegionLabels, plotChros}
 export function CallsetHistogram({ csid, datasetIds }) {
   const componentRef = useRef()
   const { width } = useContainerDimensions(componentRef)
-  const url = `${SITE_DEFAULTS.API_PATH}beacon/biosamples/?analysisIds=${csid}&datasetIds=${datasetIds}&output=samplesplot&plot_width=${width}`
+  const url = `${SITE_DEFAULTS.API_PATH}services/sampleplots/?analysisIds=${csid}&datasetIds=${datasetIds}&plot_width=${width}`
   // width > 0 to make sure the component is mounted and avoid double fetch
   const dataEffect = useExtendedSWR(width > 0 && url, svgFetcher)
   return (
@@ -99,6 +98,5 @@ export function CallsetHistogram({ csid, datasetIds }) {
 
 SubsetHistogram.propTypes = {
   id: PropTypes.string.isRequired,
-  filter: PropTypes.string,
   background: PropTypes.bool
 }
diff --git a/src/hooks/api.js b/src/hooks/api.js
@@ -273,20 +273,6 @@ export function useProgenetixRefPublicationList({ geoCity, geodistanceKm }) {
   return useProgenetixApi(url)
 }
 
-export const ontologymapsBaseUrl = `${SITE_DEFAULTS.API_PATH}services/ontologymaps?`
-
-export function ontologymapsUrl({ filters, filterPrecision }) {
-  let params = new URLSearchParams({ filters: filters })
-  if (filterPrecision) {
-    params.append("filterPrecision", filterPrecision)
-  }
-  return `${ontologymapsBaseUrl}${params.toString()}`
-}
-
-export function ontologymapsPrefUrl({ prefixes, filters }) {
-  return `${ontologymapsBaseUrl}filters=${prefixes},${filters}&filterPrecision=start`
-}
-
 export function useDataItemDelivery(id, entity, datasetIds) {
   return useProgenetixApi(getDataItemUrl(id, entity, datasetIds))
 }
@@ -303,17 +289,11 @@ export function getServiceItemUrl(id, collection, datasetIds) {
   return `${SITE_DEFAULTS.API_PATH}services/${collection}?id=${id}&datasetIds=${datasetIds}`
 }
 
-export function getDataItemPageUrl(id, entity, datasetIds) {
-  return `${SITE_DEFAULTS.API_PATH}${entity}/?datasetIds=${datasetIds}&id=${id}`
-}
-
 export function NoResultsHelp(id, entity) {
-  const url = getDataItemPageUrl(id, entity, SITE_DEFAULTS.DATASETID)
   return (
     <div className="notification is-size-5">
-      This page will only show content if called with a specific biosample ID
-      which already exists in Progenetix {" "}
-      <strong>{entity}</strong> database, e.g. <a href={url}>{url}</a>.
+      This page will only show content if called with an existing {entity} ID;{" "}
+      is not valid.
     </div>
   )
 }
@@ -326,15 +306,14 @@ export function useCytomapper(querytext) {
   return useProgenetixApi(url)
 }
 
-export function useSubsethistogram({ datasetIds, id, filter, plotRegionLabels, plotGeneSymbols, plotCytoregionLabels, size, chr2plot }) {
+export function useSubsethistogram({ datasetIds, id, plotRegionLabels, plotGeneSymbols, plotCytoregionLabels, size, plotChros }) {
   const svgbaseurl = subsetHistoBaseLink(id, datasetIds)
   const params = []
-  filter && params.push(["filter", filter])
   plotRegionLabels && params.push(["plotRegionLabels", plotRegionLabels])
   plotGeneSymbols && params.push(["plotGeneSymbols", plotGeneSymbols])
   plotCytoregionLabels && params.push(["plotCytoregionLabels", plotCytoregionLabels])
   size && params.push(["plotWidth", size])
-  chr2plot && params.push(["chr2plot", chr2plot])
+  plotChros && params.push(["plotChros", plotChros])
   const searchQuery = new URLSearchParams(params).toString()
   return useExtendedSWR(size > 0 && `${svgbaseurl}&${searchQuery}`, svgFetcher)
 }
@@ -390,7 +369,7 @@ export function useGeneSymbol({ geneId }) {
 }
 
 export function subsetHistoBaseLink(id, datasetIds) {
-  return `${SITE_DEFAULTS.API_PATH}services/intervalFrequencies/?datasetIds=${datasetIds}&id=${id}&output=histoplot`
+  return `${SITE_DEFAULTS.API_PATH}services/collationplots/?datasetIds=${datasetIds}&id=${id}`
 }
 
 // the targets are resolved by `bycon` (bycon/services/ids.py)

diff --git a/src/modules/details-pages/variantPage.js b/src/modules/details-pages/variantPage.js
@@ -14,78 +14,6 @@ import React from "react"
 const entity = "variants"
 const exampleId = "5bab576a727983b2e00b8d32"
 
-// import '@fontsource/roboto'
-// import {
-//     createViewState,
-//     JBrowseLinearGenomeView,
-// } from '@jbrowse/react-linear-genome-view'
-//
-// const defaultSession = {
-//     name: 'My session',
-//     view: {
-//         id: 'linearGenomeView',
-//         type: 'LinearGenomeView',
-//         tracks: [
-//             {
-//                 type: 'ReferenceSequenceTrack',
-//                 configuration: 'GRCh38-ReferenceSequenceTrack',
-//                 displays: [
-//                     {
-//                         type: 'LinearReferenceSequenceDisplay',
-//                         configuration:
-//                             'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
-//                     },
-//                 ],
-//             },
-//         ],
-//     },
-// }
-//
-// const assembly = {
-//     name: 'GRCh38',
-//     sequence: {
-//         type: 'ReferenceSequenceTrack',
-//         trackId: 'GRCh38-ReferenceSequenceTrack',
-//         adapter: {
-//             type: 'BgzipFastaAdapter',
-//             fastaLocation: {
-//                 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz',
-//                 locationType: 'UriLocation',
-//             },
-//             faiLocation: {
-//                 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai',
-//                 locationType: 'UriLocation',
-//             },
-//             gziLocation: {
-//                 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi',
-//                 locationType: 'UriLocation',
-//             },
-//         },
-//     },
-//     aliases: ['hg38'],
-//     refNameAliases: {
-//         adapter: {
-//             type: 'RefNameAliasAdapter',
-//             location: {
-//                 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt',
-//                 locationType: 'UriLocation',
-//             },
-//         },
-//     },
-// }
-// function View() {
-//     const state = createViewState({
-//         assembly,
-//         // tracks,
-//         location: '10:29,838,737..29,838,819',
-//         // location: '1:11,127,738-11,127,739',
-//         defaultSession,
-//     })
-//
-//     return <JBrowseLinearGenomeView viewState={state} />;
-// }
-
-
 const VariantDetailsPage = withUrlQuery(({ urlQuery }) => {
   var { id } = urlQuery
   var datasetIds = SITE_DEFAULTS.DATASETID

diff --git a/src/modules/service-pages/dataVisualizationPage.js b/src/modules/service-pages/dataVisualizationPage.js
@@ -135,7 +135,7 @@ function DataVisualizationForm({ isQuerying, sampleCount, onSubmit }) {
       <div className="columns">
         <div className="column">
           <InputField
-            name="chr2plot"
+            name="plotChros"
             label="Chromosomes"
             infoText="The chromosomes to be included in the plot, in the order they should appear. The values should just be the comma-separated chromosome numbers (e.g. '1,3,19,X' - unquoted, no spaces). The default is chr 1-22."
             errors={errors}