Latest changes from Keyang

components/service/ldh/index.tsx

@@ -1,7 +1,7 @@
 import { MetaNode } from '@/spec/metanode'
 import { GeneTerm } from '@/components/core/term'
 import { GeneSet } from '@/components/core/set'
-import { RegulatoryElementSetInfo, RegulatoryElementSetForGeneSetInfo, setGenomicPositionsForRegulatoryElementSet, MyGeneToRegulatoryElementSetInfo } from '@/components/service/regulatoryElementInfo'
+import { RegulatoryElementSetInfo, RegulatoryElementSetForGeneSetInfo, setGenomicPositionsForRegulatoryElementSet, MyGeneToRegulatoryElementSetInfo, MyRegulatoryElementSetInfo } from '@/components/service/regulatoryElementInfo'
 import { GeneInfo, GeneInfoFromGeneTerm } from '@/components/service/mygeneinfo'
 import { linkeddatahub_icon } from '@/icons'
 import { z } from 'zod'
@@ -24,6 +24,34 @@ export async function myGeneInfoFromLinkDataHub(geneTerm: string): Promise<MyGen
   return await res.json()
 }
 
+
+function getREPositionDataFromLinkDataHub(reObjSet: any){
+  let response: MyRegulatoryElementSetInfo = [];
+  for(let i in reObjSet){
+    let rgObj: any = reObjSet[i];
+
+    let coordinates = null;
+    if(rgObj.entContent != null && rgObj.entContent.coordinates != null){
+      coordinates = rgObj.entContent.coordinates;
+    }else{
+      coordinates = {
+          chromosome: "",
+          start: 0,
+          end: 0
+      };
+    }
+    let tempObj = {
+      entId: rgObj.entId,
+      ldhId: rgObj.ldhId,
+      entContent: {
+        coordinates: coordinates
+      }
+    }
+    response.push(tempObj);
+  }
+  return response;
+}
+
 export const GetRegulatoryElementsInfoForGeneInfo = MetaNode('GetRegulatoryElementsInfoForGeneInfo')
   .meta({
     label: 'Identify regulatory element in the vicinity of given gene',
@@ -38,8 +66,17 @@ export const GetRegulatoryElementsInfoForGeneInfo = MetaNode('GetRegulatoryEleme
     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 reNamesSet: string[] = response.data.ld.RegulatoryElement.map(({ entId }) => entId );
-    return await setGenomicPositionsForRegulatoryElementSet(reNamesSet);
+
+    let reObjSet: any = 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;
   })
   .story(props => ({
     abstract: `Regulatory elements in 10kbps region upstream or downstream of gene ${props.inputs ? ` ${props.inputs.geneInfo.symbol}` : ''}.`
@@ -81,9 +118,14 @@ export const GetRegulatoryElementsInfoForGeneInfo = MetaNode('GetRegulatoryEleme
         continue;
       }
 
-      let reNamesSet: string[] = response.data.ld.RegulatoryElement.map(({ entId }) => entId );
-      let reInfoSet = await setGenomicPositionsForRegulatoryElementSet(reNamesSet);
-
+      let reObjSet: any = response.data.ld.RegulatoryElement;
+      if(reObjSet == null || reObjSet.length == 0){
+        continue;
+      }
+      let reInfoSet = getREPositionDataFromLinkDataHub(reObjSet);
+      if(reInfoSet == null || reInfoSet.length == 0){
+        continue;
+      }
       let temp = {
         gene: g,
         regulatoryElements: reInfoSet

components/service/regulatoryElementInfo/service.tsx

@@ -81,7 +81,6 @@ export const GetGenesForRegulatoryElementInfo = MetaNode('GetGenesForRegulatoryE
     legend: `A list of genes in the vicinity of given regulatory element`,
   })).build()
 
-
   export const REGeneSet = MetaNode('REGeneSet')
   .meta({
     label: 'Genes Set For Each Regulatory Element In Set',
@@ -161,7 +160,6 @@ export const GetGenesForRegulatoryElementInfo = MetaNode('GetGenesForRegulatoryE
   .story(props => ({ abstract: `Genes linked to the regulatory element set.` }))
   .build()
 
-
 export const GetVariantsForRegulatoryElementInfo = MetaNode('GetVariantListForRegulatoryElementInfo')
   .meta({
     label: 'Identify Variants Within Regulatory Element',
@@ -586,7 +584,7 @@ export const RegElementSetInfoFromRegElementTerm = MetaNode('RegElementSetInfoFr
   export const GenomicRegionCoordinateTransformationAcrossReferences = MetaNode('GenomicRegionCoordinateTransformationAcrossReferences')
   .meta({
     label: 'Genomic region coordinate transformation across references',
-    description: 'Get unique name for genomic region(s) cross refenrce: GRCh38, GRCh37 and NCBI36.',
+    description: 'Get coordinates for genomic region(s) cross references: GRCh38, GRCh37 and NCBI36.',
     icon: [linkeddatahub_icon],
   })
   .inputs({ regulatoryElement: RegulatoryElementTerm })
@@ -637,10 +635,6 @@ export const RegElementSetInfoFromRegElementTerm = MetaNode('RegElementSetInfoFr
                 name="Regulatory Element id"
                 cellRenderer={row => <Cell key={row+''}>{uniqueRegionsCrossReferenceList[row]?.regElementId}</Cell>}
               />
-              <Column
-                name="Position"
-                cellRenderer={row => <Cell key={row+''}>{uniqueRegionsCrossReferenceList[row]?.rePosition}</Cell>}
-              />
               <Column
                 name="Cross Reference(s)"
                 cellRenderer={row => <Cell key={row+''}>{
@@ -661,7 +655,7 @@ export const RegElementSetInfoFromRegElementTerm = MetaNode('RegElementSetInfoFr
   export const GenomicRegionCoordinateTransformationAcrossReferencesRE_Set = MetaNode('GenomicRegionCoordinateTransformationAcrossReferencesRE_Set')
   .meta({
     label: 'Genomic region coordinate transformation across references',
-    description: 'Get unique name for genomic region(s) cross refenrce: GRCh38, GRCh37 and NCBI36.',
+    description: 'Get coordinates for genomic region(s) cross references: GRCh38, GRCh37 and NCBI36.',
     icon: [linkeddatahub_icon],
   })
   .inputs({ regulatoryElementSet: RegulatoryElementSet })

components/service/variantinfo/externalRecords.tsx

@@ -107,11 +107,12 @@ export const AlleleRegistryExternalRecordsTable = MetaNode('AlleleRegistryExtern
       }
     }
 
+    //id: caid+"("+variantInfoObj.communityStandardTitle[0]+")"
     let arExternalR = {
       name: 'Allele Registry',
       sources: [{
         '@id': variantInfoObj['@id'], 
-        id: caid+"("+variantInfoObj.communityStandardTitle[0]+")"
+        id: caid
       }]
     }
     alleleInfoExternalResources.push(arExternalR);

docker-compose.yaml

@@ -30,7 +30,7 @@ services:
     logging: *default-logging
   # app serves the UI & API, it registers user interactions into the database (pg)
   pwb-app:
-    image: maayanlab/playbook-partnership:0.65.9-ui
+    image: maayanlab/playbook-partnership:0.65.10-ui
     build:
       context: .
       dockerfile: Dockerfile
@@ -80,7 +80,7 @@ services:
   # the workers should be replicated,
   #   they deal with creating "Resolved" entries for submitted Processes.
   pwb-worker:
-    image: maayanlab/playbook-partnership:0.65.9
+    image: maayanlab/playbook-partnership:0.65.10
     build:
       context: .
       dockerfile: Dockerfile
@@ -113,7 +113,7 @@ services:
     logging: *default-logging
   # app-dev serves a dev version of the app
   app-dev:
-    image: maayanlab/playbook-partnership:0.65.9
+    image: maayanlab/playbook-partnership:0.65.10
     build:
       context: .
       dockerfile: Dockerfile
@@ -152,7 +152,7 @@ services:
   # a playbook-partnership development environment
   #  doesn't run in production, just for convenience
   dev:
-    image: maayanlab/playbook-partnership:0.65.9-dev
+    image: maayanlab/playbook-partnership:0.65.10-dev
     build:
       context: .
       dockerfile: Dockerfile

package.json

@@ -1,6 +1,6 @@
 {
   "name": "playbook-workflow-builder",
-  "version": "0.65.9",
+  "version": "0.65.10",
   "description": "A repository for the playbook workflow builder collaboration.",
   "private": true,
   "workspaces": [