@sjcrh/proteinpaint-server 2.39.4 → 2.39.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.39.4",
+  "version": "2.39.6",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",

package/routes/gdc.topMutatedGenes.ts

@@ -1,62 +1,299 @@
-import { GdcTopMutatedGeneResponse } from '#shared/types/routes/gdc.topMutatedGenes.ts'
-import path from 'path'
+import { GdcTopMutatedGeneRequest, GdcTopMutatedGeneResponse, Gene } from '#shared/types/routes/gdc.topMutatedGenes.ts'
+import { mclasscnvgain, mclasscnvloss, dtsnvindel } from '#shared/common.js'
 import got from 'got'
 
+// TODO change to /termdb/topMutatedGenes
+
 const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
+const apihostGraphql = apihost + (apihost.includes('/v0') ? '' : '/v0') + '/graphql'
 
 export const api = {
 	endpoint: 'gdc/topMutatedGenes',
 	methods: {
-		get: {
-			init({ genomes }) {
-				/*
-				genomes parameter is currently not used
-				could be used later to:
-				- verify hg38/GDC is on this instance and otherwise disable this route..
-				- perform conversion on gene name/id for future on needs
-				*/
-
-				return async (req: any, res: any): Promise<void> => {
-					try {
-						const genes = await getGenes(req.query)
-						const payload = { genes } as GdcTopMutatedGeneResponse
-						res.send(payload)
-					} catch (e: any) {
-						res.send({ status: 'error', error: e.message || e })
-					}
-				}
-			},
+		all: {
+			init,
 			request: {
-				typeId: null
-				//valid: default to type checker
+				typeId: 'GdcTopMutatedGeneRequest'
 			},
 			response: {
 				typeId: 'GdcTopMutatedGeneResponse'
-				// will combine this with type checker
-				//valid: (t) => {}
 			}
 		}
 	}
 }
 
-/*
-req.query {
-	filter0 // optional gdc GFF cohort filter, invisible and read only
-		FIXME should there be pp filter too?
-	geneFilter?: str
-	maxGenes: int
+function init() {
+	/*
+	genomes parameter is currently not used
+	could be used later to:
+	- verify hg38/GDC is on this instance and otherwise disable this route..
+	- perform conversion on gene name/id for future on needs
+	*/
+	return async (req: any, res: any): Promise<void> => {
+		const q: GdcTopMutatedGeneRequest = req.query
+		try {
+			const genes = await getGenesGraphql(q)
+			const payload: GdcTopMutatedGeneResponse = { genes }
+			res.send(payload)
+		} catch (e: any) {
+			res.send({ status: 'error', error: e.message || e })
+		}
+	}
 }
 
-mayAddCGC2filter() are copied to
-/utils/gdc/topSSMgenes.js
-and hosted on https://proteinpaint.stjude.org/GDC/
-*/
-async function getGenes(q: any) {
-	let _f = { op: 'and', content: [] } // allow blank filter to test geneset edit ui (without filter)
+const query = `
+query GenesTable_relayQuery(
+  $genesTable_filters: FiltersArgument
+  $genesTable_size: Int
+  $genesTable_offset: Int
+  $score: String
+  $ssmCase: FiltersArgument
+  $geneCaseFilter: FiltersArgument
+  $ssmTested: FiltersArgument
+  $cnvTested: FiltersArgument
+  $cnvGainFilters: FiltersArgument
+  $cnvLossFilters: FiltersArgument
+) {
+  genesTableViewer: viewer {
+    explore {
+      cases {
+        hits(first: 0, filters: $ssmTested) {
+          total
+        }
+      }
+      filteredCases: cases {
+        hits(first: 0, filters: $geneCaseFilter) {
+          total
+        }
+      }
+      cnvCases: cases {
+        hits(first: 0, filters: $cnvTested) {
+          total
+        }
+      }
+      genes {
+        hits(first: $genesTable_size, offset: $genesTable_offset, filters: $genesTable_filters, score: $score) {
+          total
+          edges {
+            node {
+              id
+              numCases: score
+              symbol
+              name
+              cytoband
+              biotype
+              gene_id
+              is_cancer_gene_census
+              ssm_case: case {
+                hits(first: 0, filters: $ssmCase) {
+                  total
+                }
+              }
+              cnv_case: case {
+                hits(first: 0, filters: $cnvTested) {
+                  total
+                }
+              }
+              case_cnv_gain: case {
+                hits(first: 0, filters: $cnvGainFilters) {
+                  total
+                }
+              }
+              case_cnv_loss: case {
+                hits(first: 0, filters: $cnvLossFilters) {
+                  total
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}
+`
+
+async function getGenesGraphql(q: GdcTopMutatedGeneRequest) {
+	// set type "any" to avoid complains
+	const variables: any = {
+		genesTable_filters: {
+			op: 'and',
+			content: []
+		},
+		genesTable_size: q.maxGenes || 50,
+		genesTable_offset: 0,
+		score: 'case.project.project_id',
+		ssmCase: {
+			op: 'and',
+			content: [
+				{
+					op: 'in',
+					content: {
+						field: 'cases.available_variation_data',
+						value: ['ssm']
+					}
+				},
+				{
+					op: 'NOT',
+					content: {
+						field: 'genes.case.ssm.observation.observation_id',
+						value: 'MISSING'
+					}
+				}
+			]
+		},
+		geneCaseFilter: {
+			content: [
+				{
+					content: {
+						field: 'cases.available_variation_data',
+						value: ['ssm']
+					},
+					op: 'in'
+				}
+			],
+			op: 'and'
+		},
+		ssmTested: {
+			content: [
+				{
+					content: {
+						field: 'cases.available_variation_data',
+						value: ['ssm']
+					},
+					op: 'in'
+				}
+			],
+			op: 'and'
+		},
+		cnvTested: {
+			op: 'and',
+			content: [
+				{
+					content: {
+						field: 'cases.available_variation_data',
+						value: ['cnv']
+					},
+					op: 'in'
+				}
+			]
+		},
+		cnvGainFilters: {
+			op: 'and',
+			content: [
+				{
+					content: {
+						field: 'cases.available_variation_data',
+						value: ['cnv']
+					},
+					op: 'in'
+				},
+				{
+					content: {
+						field: 'cnvs.cnv_change',
+						value: ['Gain']
+					},
+					op: 'in'
+				}
+			]
+		},
+		cnvLossFilters: {
+			op: 'and',
+			content: [
+				{
+					content: {
+						field: 'cases.available_variation_data',
+						value: ['cnv']
+					},
+					op: 'in'
+				},
+				{
+					content: {
+						field: 'cnvs.cnv_change',
+						value: ['Loss']
+					},
+					op: 'in'
+				}
+			]
+		}
+	}
+
 	if (q.filter0) {
-		if (typeof q.filter0 != 'object') throw 'filter0 not object'
-		_f = q.filter0
+		variables.genesTable_filters.content.push(JSON.parse(JSON.stringify(q.filter0)))
+		variables.geneCaseFilter.content.push(JSON.parse(JSON.stringify(q.filter0)))
+		variables.cnvTested.content.push(JSON.parse(JSON.stringify(q.filter0)))
+		variables.cnvGainFilters.content.push(JSON.parse(JSON.stringify(q.filter0)))
+		variables.cnvLossFilters.content.push(JSON.parse(JSON.stringify(q.filter0)))
+	}
+
+	if (q.geneFilter == 'CGC') {
+		variables.genesTable_filters.content.push(geneCGC())
+		variables.geneCaseFilter.content.push(geneCGC())
+		variables.cnvTested.content.push(geneCGC())
+		variables.cnvGainFilters.content.push(geneCGC())
+		variables.cnvLossFilters.content.push(geneCGC())
+	}
+
+	const response = await got.post(apihostGraphql, {
+		headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
+		body: JSON.stringify({ query, variables })
+	})
+
+	const re: any = JSON.parse(response.body)
+	const genes: Gene[] = []
+	for (const g of re.data.genesTableViewer.explore.genes.hits.edges) {
+		/* g.node is:
+		{
+		  "biotype": "protein_coding",
+		  "case_cnv_gain": { "hits": { "total": 65 } },
+		  "case_cnv_loss": { "hits": { "total": 93 } },
+		  "cnv_case": { "hits": { "total": 173 } },
+		  "cytoband": [
+			"12q15"
+		  ],
+		  "gene_id": "ENSG00000127329",
+		  "is_cancer_gene_census": true,
+		  "name": "protein tyrosine phosphatase receptor type B",
+		  "numCases": 18,
+		  "ssm_case": { "hits": { "total": 630 } },
+		  "symbol": "PTPRB"
+		}
+		*/
+		if (typeof g.node != 'object') throw 'node missing from re.data.genesTableViewer.explore.genes.hits.edges[]'
+		const mutationStat: any = []
+		if (Number.isInteger(g.node.case_cnv_gain?.hits?.total) && g.node.case_cnv_gain.hits.total > 0)
+			mutationStat.push({ class: mclasscnvgain, count: g.node.case_cnv_gain.hits.total })
+		if (Number.isInteger(g.node.case_cnv_loss?.hits?.total) && g.node.case_cnv_loss.hits.total > 0)
+			mutationStat.push({ class: mclasscnvloss, count: g.node.case_cnv_loss.hits.total })
+		if (Number.isInteger(g.node.ssm_case?.hits?.total) && g.node.ssm_case.hits.total > 0)
+			mutationStat.push({ dt: dtsnvindel, count: g.node.ssm_case.hits.total })
+		genes.push({
+			gene: g.node.symbol,
+			mutationStat
+		})
 	}
+	return genes
+}
+
+function geneCGC() {
+	// return a copy of cgc filter obj each time
+	return {
+		content: {
+			field: 'genes.is_cancer_gene_census',
+			value: ['true']
+		},
+		op: 'in'
+	} as object
+}
+
+/*************************************
+	  below are old code
+      old method to use rest api
+**************************************
+this api only gets ssm-cases and does not account for cnv cases, will not return any gene for ssm-less cohort e.g. APOLLO-LUAD
+thus is replaced by getGenesGraphql
+async function getGenes(q: GdcTopMutatedGeneRequest) {
+	const _f = q.filter0 || { op: 'and', content: [] } // allow blank filter to test geneset edit ui (without filter)
 	const response = await got.post(path.join(apihost, '/analysis/top_mutated_genes_by_project'), {
 		headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
 		body: JSON.stringify({
@@ -73,6 +310,7 @@ async function getGenes(q: any) {
 	}
 	return genes
 }
+*/
 
 /*
 str:
@@ -89,7 +327,6 @@ geneFilter: str
 			}
 		]
 	}
-*/
 function mayAddCGC2filter(f: any, geneFilter?: string) {
 	// reformulate f into f2
 	// f may be "in" or "and". f2 is always "and", in order to join in additional filters
@@ -128,3 +365,4 @@ function mayAddCGC2filter(f: any, geneFilter?: string) {
 
 	return f2
 }
+*/