Merge remote-tracking branch 'exrna/main'

haynescd · Sep 23, 2024 · 4da2bfa · 4da2bfa
2 parents de83e7d + c951805
commit 4da2bfa
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Showing 6 changed files with 286 additions and 189 deletions.
diff --git a/components/legacy/index.tsx b/components/legacy/index.tsx
@@ -1,12 +1,15 @@
 import { MetaNode } from '@/spec/metanode'
 import { GeneTerm, VariantTerm } from '@/components/core/term'
 import { z } from 'zod'
-import { gene_icon, mygeneinfo_icon } from '@/icons'
+import { gene_icon, mygeneinfo_icon, datafile_icon } from '@/icons'
 import * as array from '@/utils/array'
 import { z_maybe_array } from '@/utils/zod'
 import { resolveVariantCaID, getMyVarintInfoLink, variantIdResolveErrorMessage, alleleRegRespErrorMessage } from '@/components/service/variantinfo/variantUtils'
 import { getAlleleRegistryVariantInfo } from '@/components/service/variantinfo/variantInfoSources/alleleRegistryVariantInfo'
 import { getVariantInfoFromMyVariantInfo } from '@/components/service/variantinfo/variantInfoSources/myVariantInfo'
+import { MyRegulatoryElementSetInfoC } from '@/components/service/regulatoryElementInfo/reUtils'
+import { Table, Cell, Column} from '@/app/components/Table'
+import { downloadBlob } from '@/utils/download'
 
 export const MyVariantInfoC = z.object({
   _id: z.string(),
@@ -119,3 +122,46 @@ export const VariantInfoFromVariantTermMyVarintInfo = MetaNode('VariantInfoFromV
     legend: `The closest gene to ${props.inputs?.variant ? props.inputs.variant : 'the variant'}, as reported by MyVariant.info [\\ref{doi:10.1186/s13059-016-0953-9}\\ref{doi:10.1093/bioinformatics/btac017}.`,
   }))
   .build()
+
+  export const RegulatoryElementSetInfo = MetaNode('RegulatoryElementSetInfo')
+  .meta({
+    label: 'Regulatory Element Set Info',
+    description: '',
+    icon: [datafile_icon],
+    hidden: true,
+  })
+  .codec(MyRegulatoryElementSetInfoC)
+  .view(regulatoryElementSet => {
+    return( 
+      <>
+        <p style={{fontSize: '14px'}}><b>Note:</b> In order to view all data, if avaliable, please expand the table rows!</p>
+        <Table
+          height={500}
+          cellRendererDependencies={[regulatoryElementSet]}
+          numRows={regulatoryElementSet.length}
+          enableGhostCells
+          enableFocusedCell
+          downloads={{
+            JSON: () => downloadBlob(new Blob([JSON.stringify(regulatoryElementSet)], { type: 'application/json;charset=utf-8' }), 'data.json')
+          }}>
+          <Column
+            name="Entity id"
+            cellRenderer={row => <Cell key={row+''}>{regulatoryElementSet[row].entId}</Cell>}
+          />
+          <Column
+            name="Chromosome"
+            cellRenderer={row => <Cell key={row+''}>{regulatoryElementSet[row].entContent.coordinates.chromosome}</Cell>}
+          />
+          <Column
+            name="Start Pos."
+            cellRenderer={row => <Cell key={row+''}>{regulatoryElementSet[row].entContent.coordinates.start}</Cell>}
+          />
+          <Column
+            name="End Pos."
+            cellRenderer={row => <Cell key={row+''}>{regulatoryElementSet[row].entContent.coordinates.end}</Cell>}
+          />
+        </Table>
+      </>
+    )
+  })
+  .build()
diff --git a/components/service/ldh/index.tsx b/components/service/ldh/index.tsx
@@ -1,10 +1,11 @@
 import { MetaNode } from '@/spec/metanode'
 import { GeneTerm } from '@/components/core/term'
-import { GeneSet } from '@/components/core/set'
-import { RegulatoryElementSetInfo, RegulatoryElementSetForGeneSetInfo, setGenomicPositionsForRegulatoryElementSet, MyGeneToRegulatoryElementSetInfo, MyRegulatoryElementSetInfo } from '@/components/service/regulatoryElementInfo'
+import { GeneSet, RegulatoryElementSet } from '@/components/core/set'
+import { RegulatoryElementSetForGeneSetInfo, MyGeneToRegulatoryElementSetInfo, MyRegulatoryElementSetInfo } from '@/components/service/regulatoryElementInfo'
 import { GeneInfo, GeneInfoFromGeneTerm } from '@/components/service/mygeneinfo'
 import { linkeddatahub_icon } from '@/icons'
 import { z } from 'zod'
+import { describe } from 'node:test'
 
 export const MyGeneInfoByTermC = z.object({
   data: z.object({
@@ -60,23 +61,31 @@ export const GetRegulatoryElementsInfoForGeneInfo = MetaNode('GetRegulatoryEleme
     pagerank: 1,
   })
   .inputs({ geneInfo: GeneInfo })
-  .output(RegulatoryElementSetInfo)
+  .output(RegulatoryElementSet)
   .resolve(async (props) => {
     const response =  await myGeneInfoFromLinkDataHub(props.inputs.geneInfo.symbol);
     if(response.data == null || response.data.ld == null){
       throw new Error("Unable to get data from Linked Data Hub API, please try again or wait a few minutes before the next atempt!");
     }
 
-    let reObjSet: any = response.data.ld.RegulatoryElement;
+    let reObjSet = response.data.ld.RegulatoryElement;
     if(reObjSet == null || reObjSet.length == 0){
       throw new Error("Unable to get Regulatory Element data for gene "+props.inputs.geneInfo.symbol+" from Linked Data Hub API, please try again or wait a few minutes before the next atempt!");
     }
-    let reInfoSet = getREPositionDataFromLinkDataHub(reObjSet);
-    if(reInfoSet == null || reInfoSet.length == 0){
-      throw new Error("Unable to get Regulatory Element(s) coordinates for gene "+props.inputs.geneInfo.symbol+" from Linked Data Hub API, please try again or wait a few minutes before the next atempt!");
-    }
 
-    return reInfoSet;
+    let reIdentifiersSet = [];
+    for(let i in reObjSet){
+      reIdentifiersSet.push(reObjSet[i].entId);
+    }
+    if(reIdentifiersSet.length == 0){
+      throw new Error("Unable to get Regulatory Element data for gene "+props.inputs.geneInfo.symbol+" from Linked Data Hub API, please try again or wait a few minutes before the next atempt!");
+    }
+
+    let tempObj = {
+      description:"Regulatory Elements Set",
+      set: reIdentifiersSet
+    }
+    return tempObj;
   })
   .story(props => ({
     abstract: `Regulatory elements in 10kbps region upstream or downstream of gene ${props.inputs ? ` ${props.inputs.geneInfo.symbol}` : ''}.`

diff --git a/components/service/regulatoryElementInfo/reUtils.tsx b/components/service/regulatoryElementInfo/reUtils.tsx
@@ -2,15 +2,16 @@ import { MetaNode } from '@/spec/metanode'
 import { z } from 'zod'
 
 //General RE info
-
 export const RegulatoryElementInfoC = z.object({
     data: z.object({
       entId: z.string(),
       entType: z.string(),
-      coordinates: z.object({
-        "chromosome": z.string(),
-        "start": z.number(),
-        "end": z.number()
+      entContent: z.object({
+        coordinates: z.object({
+          chromosome: z.string(),
+          start: z.number(),
+          end: z.number()
+        }),
       }),
       ld: z.object({
         ENCODERegulatoryElementEvidence: z.array(z.object({
@@ -33,46 +34,107 @@ export const RegulatoryElementInfoC = z.object({
 
   export type RegulatoryElementInfo = z.infer<typeof RegulatoryElementInfoC>
 
-export async function myRegElemInfo_query(regElemId: string): Promise<RegulatoryElementInfo> {
+export async function myRegElemInfoFromLDH(regElemId: string): Promise<RegulatoryElementInfo> {
     const res = await fetch(`https://ldh.genome.network/cfde/ldh/RegulatoryElement/id/${encodeURIComponent(regElemId)}`)
     return await res.json()
 }
 
+//positional data from Weng Lab
+export const RE_PositionalDataWengLabC = z.object({
+  data: z.object({
+    cCREQuery: z.array(z.object({
+      coordinates: z.object({
+        chromosome: z.string(),
+        start: z.number(),
+        end: z.number()
+      })
+    }))
+  })
+});
+type RE_PositionalDataWengLab = z.infer<typeof RE_PositionalDataWengLabC>
 
-//Position data
+export async function getRegElemPositionDataWengLab(regElemId: string): Promise<RE_PositionalDataWengLab> {
+  let bodyString = '{\"query\":\"query CCRE{\\n  cCREQuery(assembly: \\"GRCh38\\", accession:\\"'+encodeURIComponent(regElemId)+'\\") {\\n  coordinates {\\n  chromosome\\n  start\\n  end\\n  }\\n  }\\n}"}';
+  const res = await fetch(`https://ga.staging.wenglab.org/graphql`, {
+      method: 'POST',
+      headers: {
+      'Accept-Encoding': 'gzip, deflate, br',
+      'Content-Type': 'application/json',
+      'Accept': 'application/json',
+      'Connection': 'keep-alive',
+      'DNT': '1',
+      'Origin': 'https://ga.staging.wenglab.org'
+      },
+      body: bodyString
+  })
+  return await res.json()
+}
 
-export const RE_PositionalDataC = z.object({
-    data: z.object({
-      cCREQuery: z.array(z.object({
-        coordinates: z.object({
-          chromosome: z.string(),
-          start: z.number(),
-          end: z.number()
-        })
-      }))
-    })
-  });
-type RE_PositionalData = z.infer<typeof RE_PositionalDataC>
-
-export async function getRegElemPositionData(regElemId: string): Promise<RE_PositionalData> {
-    let bodyString = '{\"query\":\"query CCRE{\\n  cCREQuery(assembly: \\"GRCh38\\", accession:\\"'+encodeURIComponent(regElemId)+'\\") {\\n  coordinates {\\n  chromosome\\n  start\\n  end\\n  }\\n  }\\n}"}';
-    const res = await fetch(`https://ga.staging.wenglab.org/graphql`, {
-        method: 'POST',
-        headers: {
-        'Accept-Encoding': 'gzip, deflate, br',
-        'Content-Type': 'application/json',
-        'Accept': 'application/json',
-        'Connection': 'keep-alive',
-        'DNT': '1',
-        'Origin': 'https://ga.staging.wenglab.org'
-        },
-        body: bodyString
-    })
-    return await res.json()
+//positional data from LDH
+export const RegulatoryElementPositionC = z.object({
+    entId: z.string(),
+    coordinates: z.object({
+      "chromosome": z.string(),
+      "start": z.number(),
+      "end": z.number()
+    }) 
+})
+export type RegulatoryElementPosition = z.infer<typeof RegulatoryElementPositionC>
+
+export const RegulatoryElementSetPositionC = z.array( RegulatoryElementPositionC )
+export type RegulatoryElementSetPosition = z.infer<typeof RegulatoryElementSetPositionC>
+
+export async function getRegulatoryElementPosition(reIdentifier: string): Promise<RegulatoryElementPosition>{
+  const ldhResponse = await myRegElemInfoFromLDH(reIdentifier);
+  let coordinatesObject: any = null;
+  if(ldhResponse != null && ldhResponse.data != null && ldhResponse.data.entContent != null){
+    coordinatesObject = ldhResponse.data.entContent.coordinates
+  }else{
+    let wengLabReposne = await getRegElemPositionDataWengLab(reIdentifier);
+    if(wengLabReposne != null && wengLabReposne.data.cCREQuery[0].coordinates != null){
+      coordinatesObject = wengLabReposne.data.cCREQuery[0].coordinates;
+    }
+  }
+  let reCoordinatesObj = {
+    entId: ldhResponse.data.entId,
+    coordinates: coordinatesObject
+  };
+
+  return reCoordinatesObj;
 }
 
-//Unique Regions
+export async function getRegulatoryElementsSetPosition(regElemeIdsSet: string[]): Promise<RegulatoryElementSetPosition>{
+  let reSetCoordinates: RegulatoryElementSetPosition = [];
+  for(let i in regElemeIdsSet){
+      let reId = regElemeIdsSet[i];
+      let coordinatesObjFromLDH = await getRegulatoryElementPosition(reId);
+      if(coordinatesObjFromLDH == null || coordinatesObjFromLDH.coordinates == null){
+        continue;
+      }
+      reSetCoordinates.push(coordinatesObjFromLDH);
+  }
+  return reSetCoordinates;
+}
+
+const MyRegulatoryElementC = z.object({
+  entId: z.string(),
+  ldhId: z.string(),
+  entContent: z.object({
+    coordinates: z.object({    
+      chromosome: z.string(),
+      end: z.any(),
+      start: z.any()
+    })
+  })
+})
+export type MyRegulatoryElement = z.infer<typeof MyRegulatoryElementC>
 
+export const MyRegulatoryElementSetInfoC = z.array(
+  MyRegulatoryElementC
+)
+export type MyRegulatoryElementSetInfo = z.infer<typeof MyRegulatoryElementSetInfoC>
+
+//Unique Regions
 export const RE_UniqueRegionC = z.array(
     z.object({
       '@id': z.string(),