collation links - e.g. getting rid of "method" => deliveryKeys where …

…needed
progenetix · Sep 20, 2024 · 61c2f85 · 61c2f85
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Showing 6 changed files with 24 additions and 25 deletions.
diff --git a/docs/use-cases.md b/docs/use-cases.md
@@ -89,8 +89,8 @@ queries and may lead to a time-out.
 
 ![Example query-based CNV histogram](http://progenetix.org/services/sampleplots/?referenceName=9&variantType=EFO:0030067&start=21500000&start=21975098&end=21967753&end=22500000&filters=NCIT:C3058&filters=pgx:cohort-celllines&output=histoplot)
 
-* [progenetix.org/services/sampleplots/?referenceName=9&variantType=EFO:0030067&start=21500000&start=21975098&end=21967753&end=22500000&filters=NCIT:C3058&filters=pgx:cohort-celllines&output=histoplot](http://progenetix.org/services/sampleplots/?referenceName=9&variantType=EFO:0030067&start=21500000&start=21975098&end=21967753&end=22500000&filters=NCIT:C3058&filters=pgx:cohort-celllines&output=histoplot)
-    - a search for samples with focal deletion in the _CDKN2A_ locus, limited to glioblastoma cell lines 
+* [progenetix.org/services/sampleplots/?geneId=CDKN2A&variantType=EFO:0030067&variantMaxLength=2000000&filters=NCIT:C3058&output=histoplot](http://progenetix.org/services/sampleplots/?geneId=CDKN2A&variantType=EFO:0030067&variantMaxLength=2000000&filters=NCIT:C3058&output=histoplot)
+    - a search for glioblastoma samples with a focal (here <= 2Mb) deletion in the _CDKN2A_ locus
 
 
 ### Example Procedure - Download CNV Frequencies
@@ -104,14 +104,14 @@ local, disease-specific CNV frequencies.
 
 All cancer codes for a given classification system can be retrieved though:
 
-* NCIT
-    - [progenetix.org/services/collations?filters=NCIT&output=text](http://progenetix.org/services/collations?filters=NCIT&output=text)
-* ICD-O Morphologies
-    - [progenetix.org/services/collations?filters=icdom&method=counts&output=text](http://progenetix.org/services/collations?filters=icdom&method=counts&output=text)
+* NCIt cancer codes `NCIT`
+    - [progenetix.org/services/collations?collationTypes=NCIT&deliveryKeys=id,label,count](http://progenetix.org/services/collations?collationTypes=NCIT&deliveryKeys=id,label,count)
+* ICD-O Morphologies `icdom`
+    - [progenetix.org/services/collations?collationTypes=icdom&deliveryKeys=id,label,count](http://progenetix.org/services/collations?collationTypes=icdom&deliveryKeys=id,label,count)
     - please be aware that we have to use transformed ICD-O codes; e.g.
   "ICD-O 8500/3" is represented as `pgx:icdom-85003` (`s/^(\d{4})\/(\d)$/pgx:icdom-$1$2/`)
-* ICD-O Topographies
-    - [progenetix.org/services/collations?filters=icdot&method=counts&output=text](http://progenetix.org/services/collations?filters=icdot&method=counts&output=text)
+* ICD-O Topographies `icdot`
+    - [progenetix.org/services/collations?collationTypes=icdot&deliveryKeys=id,label,count](http://progenetix.org/services/collations?collationTypes=icdot&deliveryKeys=id,label,count)
 
 #### Download the data file
 
@@ -134,8 +134,8 @@ added (single) collation code.
 
 ##### Examples
 
-* [progenetix.org/services/collationPlots/?id=pgx:icdom-85003](http://progenetix.org/services/collationPlots/?id=pgx:icdom-85003)
-* [progenetix.org/services/collationPlots/?id=PMID:22824167](http://progenetix.org/services/collationPlots/?id=PMID:22824167)
+* [progenetix.org/services/collationplots/?id=pgx:icdom-85003](http://progenetix.org/services/collationplots/?id=pgx:icdom-85003)
+* [progenetix.org/services/collationplots/?id=PMID:22824167](http://progenetix.org/services/collationplots/?id=PMID:22824167)
 
 --------------------------------------------------------------------------------
 

diff --git a/src/components/SubsetsHierarchyLoader.js b/src/components/SubsetsHierarchyLoader.js
@@ -7,7 +7,7 @@ import { buildTree, TreePanel } from "./classificationTree/TreePanel"
 export default function SubsetsHierarchyLoader({ collationTypes, datasetIds, defaultTreeDepth }) {
   const bioSubsetsHierarchiesReply = useCollationsByType({
     datasetIds,
-    method: "paths",
+    deliveryKeys: "",
     collationTypes
   })
 

diff --git a/src/components/formShared/GenespanUtilities.js b/src/components/formShared/GenespanUtilities.js
@@ -71,5 +71,5 @@ function geneLabel(gene) {
 }
 
 function geneSearchUrl(querytext) {
-  return `${basePath}services/genespans/?geneId=${querytext}&filterPrecision=start&method=genespan`
+  return `${basePath}services/genespans/?geneId=${querytext}&filterPrecision=start&deliveryKeys=symbol,referenceName,start,end`
 }
diff --git a/src/components/searchForm/BiosamplesSearchForm.js b/src/components/searchForm/BiosamplesSearchForm.js
@@ -761,7 +761,7 @@ function useFilteringTerms(watchForm, ct, mode) {
   const datasetIds = watchForm("datasetIds")
   return useFiltersByType({
     datasetIds,
-    method: "counts",
+    deliveryKeys: "id,label,count",
     mode: mode,
     collationTypes: ct
   })

diff --git a/src/hooks/api.js b/src/hooks/api.js
@@ -234,7 +234,7 @@ export function buildDataVisualizationParameters(queryData) {
 }
 
 export function publicationDataUrl(id) {
-  return `${SITE_DEFAULTS.API_PATH}services/publications?filters=${id}&method=details`
+  return `${SITE_DEFAULTS.API_PATH}services/publications?filters=${id}`
 }
 
 export function usePublication(id) {
@@ -358,11 +358,10 @@ export function useSubsethistogram({
   return useExtendedSWR(size > 0 && `${svgbaseurl}&${searchQuery}`, svgFetcher)
 }
 
-// method is "counts" / "child_terms" for smaller payloads
 export function useCollationsById({ datasetIds }) {
   const { data, ...other } = useCollations({
     filters: "",
-    method: "counts",
+    deliveryKeys: "id,label,count",
     datasetIds
   })
 
@@ -379,19 +378,19 @@ export function useCollationsById({ datasetIds }) {
   return { data, ...other }
 }
 
-export function useCollations({ datasetIds, method, filters }) {
-  const url = `${SITE_DEFAULTS.API_PATH}beacon/filtering_terms/?datasetIds=${datasetIds}&method=${method}&filters=${filters}`
+export function useCollations({ datasetIds, deliveryKeys, filters }) {
+  const url = `${SITE_DEFAULTS.API_PATH}beacon/filtering_terms/?datasetIds=${datasetIds}&deliveryKeys=${deliveryKeys}&filters=${filters}`
   return useProgenetixApi(url)
 }
 
-export function useFiltersByType({ datasetIds, method, mode, collationTypes }) {
+export function useFiltersByType({ datasetIds, deliveryKeys, mode, collationTypes }) {
   // TODO: construct URL w/o optional parameters if empty
-  const url = `${SITE_DEFAULTS.API_PATH}beacon/filtering_terms/?datasetIds=${datasetIds}&method=${method}&mode=${mode}&collationTypes=${collationTypes}`
+  const url = `${SITE_DEFAULTS.API_PATH}beacon/filtering_terms/?datasetIds=${datasetIds}&deliveryKeys=${deliveryKeys}&mode=${mode}&collationTypes=${collationTypes}`
   return useProgenetixApi(url)
 }
 
-export function useCollationsByType({ datasetIds, method, collationTypes }) {
-  const url = `${SITE_DEFAULTS.API_PATH}services/collations/?datasetIds=${datasetIds}&method=${method}&collationTypes=${collationTypes}`
+export function useCollationsByType({ datasetIds, deliveryKeys, collationTypes }) {
+  const url = `${SITE_DEFAULTS.API_PATH}services/collations/?datasetIds=${datasetIds}&deliveryKeys=${deliveryKeys}&collationTypes=${collationTypes}`
   return useProgenetixApi(url)
 }
 
@@ -409,7 +408,7 @@ export function useGeoCity({ city }) {
 }
 
 export function useGeneSymbol({ geneId }) {
-  const url = geneId ? `${SITE_DEFAULTS.API_PATH}services/genespans/?geneId=${geneId}&filterPrecision=start&method=genespan` : null
+  const url = geneId ? `${SITE_DEFAULTS.API_PATH}services/genespans/?geneId=${geneId}&filterPrecision=start&deliveryKeys=symbol,referenceName,start,end` : null
   return useProgenetixApi(url)
 }
 

diff --git a/src/pages/index.js b/src/pages/index.js
@@ -104,10 +104,10 @@ export const getStaticProps = async () => {
     `${SITE}services/dbstats/?datasetIds=${SITE_DEFAULTS.DATASETID}`
   )
   const ncitCountReply = await tryFetch(
-    `${SITE}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&method=codematches&collationTypes=NCIT`
+    `${SITE}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&collationTypes=NCIT&includeDescendantTerms=false&requestedGranularity=count`
   )
   const subsetsReply = await tryFetch(
-    `${SITE}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&method=counts&collationTypes=NCIT`
+    `${SITE}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&collationTypes=NCIT&deliveryKeys=count,id,label`
   )
 
   return {