@sjcrh/proteinpaint-server 2.39.5 → 2.40.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.39.5",
+  "version": "2.40.0",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",

package/routes/gdc.maf.ts

@@ -90,15 +90,16 @@ async function listMafFiles(q: GdcMafRequest) {
 			{ op: '=', content: { field: 'access', value: 'open' } } // delete if later to support controlled files
 		]
 	}
-
+	const case_filters: any = { op: 'and', content: [] }
 	if (q.filter0) {
-		filters.content.push(q.filter0)
+		case_filters.content.push(q.filter0)
 	}
 
 	const headers = { 'Content-Type': 'application/json', Accept: 'application/json' }
 
 	const data = {
 		filters,
+		case_filters,
 		size: maxFileNumber,
 		fields: [
 			'id',

package/routes/gdc.topMutatedGenes.ts

@@ -1,6 +1,8 @@
-import { GdcTopMutatedGeneRequest, 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'
+import serverconfig from '#src/serverconfig.js'
+import { getheaders } from '#src/mds3.gdc.js'
 
 // TODO change to /termdb/topMutatedGenes
 
@@ -41,7 +43,10 @@ function init() {
 	}
 }
 
-const query = `
+// query string copied from v1, works in v2. but v1 are not "cohort-centric and lacks the case_filters: $caseFilters"
+// delete the v1 after soft launch
+const queryV1: any = {
+	query: `
 query GenesTable_relayQuery(
   $genesTable_filters: FiltersArgument
   $genesTable_size: Int
@@ -111,155 +116,377 @@ query GenesTable_relayQuery(
     }
   }
 }
-`
-
-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']
+`,
+	getVariables: (q: any) => {
+		// 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'
+						}
 					}
-				},
-				{
-					op: 'NOT',
-					content: {
-						field: 'genes.case.ssm.observation.observation_id',
-						value: 'MISSING'
+				]
+			},
+			geneCaseFilter: {
+				content: [
+					{
+						content: {
+							field: 'cases.available_variation_data',
+							value: ['ssm']
+						},
+						op: 'in'
 					}
-				}
-			]
-		},
-		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: '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'
 					},
-					op: 'in'
-				}
-			]
-		},
-		cnvGainFilters: {
-			op: 'and',
-			content: [
-				{
-					content: {
-						field: 'cases.available_variation_data',
-						value: ['cnv']
+					{
+						content: {
+							field: 'cnvs.cnv_change',
+							value: ['Gain']
+						},
+						op: 'in'
+					}
+				]
+			},
+			cnvLossFilters: {
+				op: 'and',
+				content: [
+					{
+						content: {
+							field: 'cases.available_variation_data',
+							value: ['cnv']
+						},
+						op: 'in'
 					},
-					op: 'in'
-				},
-				{
-					content: {
-						field: 'cnvs.cnv_change',
-						value: ['Gain']
+					{
+						content: {
+							field: 'cnvs.cnv_change',
+							value: ['Loss']
+						},
+						op: 'in'
+					}
+				]
+			}
+		}
+
+		if (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())
+		}
+		return variables
+	}
+}
+
+const queryV2: any = {
+	query: `
+          query GenesTable(
+            $caseFilters: FiltersArgument
+            $genesTable_filters: FiltersArgument
+            $genesTable_size: Int
+            $genesTable_offset: Int
+            $score: String
+            $ssmCase: FiltersArgument
+            $geneCaseFilter: FiltersArgument
+            $ssmTested: FiltersArgument
+            $cnvTested: FiltersArgument
+            $cnvGainFilters: FiltersArgument
+            $cnvLossFilters: FiltersArgument
+            $sort: [Sort]
+          ) {
+            genesTableViewer: viewer {
+              explore {
+                cases {
+                  hits(first: 0, case_filters: $ssmTested) {
+                    total
+                  }
+                }
+                filteredCases: cases {
+                  hits(first: 0, case_filters: $geneCaseFilter) {
+                    total
+                  }
+                }
+                cnvCases: cases {
+                  hits(first: 0, case_filters: $cnvTested) {
+                    total
+                  }
+                }
+                genes {
+                  hits(
+                    first: $genesTable_size
+                    offset: $genesTable_offset
+                    filters: $genesTable_filters
+                    case_filters: $caseFilters
+                    score: $score
+                    sort: $sort
+                  ) {
+                    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
+                          }
+                        }
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          }`,
+	getVariables: (q: any) => {
+		const variables: any = {
+			caseFilters: { op: 'and', content: [] },
+			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: 'in'
-				}
-			]
-		},
-		cnvLossFilters: {
-			op: 'and',
-			content: [
-				{
-					content: {
-						field: 'cases.available_variation_data',
-						value: ['cnv']
+					{
+						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'
 					},
-					op: 'in'
-				},
-				{
-					content: {
-						field: 'cnvs.cnv_change',
-						value: ['Loss']
+					{
+						content: {
+							field: 'cnvs.cnv_change',
+							value: ['Gain']
+						},
+						op: 'in'
+					}
+				]
+			},
+			cnvLossFilters: {
+				op: 'and',
+				content: [
+					{
+						content: {
+							field: 'cases.available_variation_data',
+							value: ['cnv']
+						},
+						op: 'in'
 					},
-					op: 'in'
-				}
-			]
+					{
+						content: {
+							field: 'cnvs.cnv_change',
+							value: ['Loss']
+						},
+						op: 'in'
+					}
+				]
+			}
+		}
+
+		if (q.filter0) {
+			variables.caseFilters.content.push(JSON.parse(JSON.stringify(q.filter0)))
+			variables.geneCaseFilter.content.push(JSON.parse(JSON.stringify(q.filter0)))
+			variables.cnvLossFilters.content.push(JSON.parse(JSON.stringify(q.filter0)))
+			variables.cnvGainFilters.content.push(JSON.parse(JSON.stringify(q.filter0)))
+			variables.cnvTested.content.push(JSON.parse(JSON.stringify(q.filter0)))
 		}
-	}
 
-	if (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.cnvLossFilters.content.push(geneCGC())
+			variables.cnvGainFilters.content.push(geneCGC())
+		}
+		return variables
 	}
+}
+
+async function getGenesGraphql(q: GdcTopMutatedGeneRequest) {
+	let query: string, variables: object
 
-	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())
+	if (serverconfig.features?.geneExpHost) {
+		// quick fix! this is only set on local dev machines, meaning it's using v1 api; delete this after soft launch!!
+		query = queryV1.query
+		variables = queryV1.getVariables(q)
+	} else {
+		// this is not set and should be in qa-orange. it should be like this after softlaunch
+		query = queryV2.query
+		variables = queryV2.getVariables(q)
 	}
 
 	const response = await got.post(apihostGraphql, {
-		headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
+		headers: getheaders(q),
 		body: JSON.stringify({ query, variables })
 	})
 
 	const re: any = JSON.parse(response.body)
-	const genes: string[] = []
+	const genes: Gene[] = []
 	for (const g of re.data.genesTableViewer.explore.genes.hits.edges) {
-		/*
+		/* g.node is:
 		{
-		  node: {
-			biotype: 'protein_coding',
-			case_cnv_gain: { hits: [Object] },
-			case_cnv_loss: { hits: [Object] },
-			cnv_case: { hits: [Object] },
-			cytoband: [ '17q11.2' ],
-			gene_id: 'ENSG00000196712',
-			is_cancer_gene_census: true,
-			name: 'neurofibromin 1',
-			numCases: 93,
-			ssm_case: { hits: [Object] },
-			symbol: 'NF1'
-		  }
+		  "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"
 		}
 		*/
-		genes.push(g.node.symbol)
+		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
 }
@@ -276,11 +503,11 @@ function geneCGC() {
 }
 
 /*************************************
+	  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'), {
@@ -299,6 +526,7 @@ async function getGenes(q: GdcTopMutatedGeneRequest) {
 	}
 	return genes
 }
+*/
 
 /*
 str:
@@ -315,7 +543,6 @@ 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
@@ -354,3 +581,4 @@ function mayAddCGC2filter(f: any, geneFilter?: string) {
 
 	return f2
 }
+*/

package/routes/hicdata.ts

@@ -86,7 +86,7 @@ function handle_hicdata(q: HicdataRequest) {
 			}
 			const n1 = Number.parseInt(l[0])
 			const n2 = Number.parseInt(l[1])
-			const v = Number.parseFloat(l[2])
+			const v = q.matrixType == 'oe' ? Math.log(Number.parseFloat(l[2])) : Number.parseFloat(l[2])
 			if (Number.isNaN(n1) || Number.isNaN(n2) || Number.isNaN(v)) {
 				fieldnotnumerical++
 				return

package/routes/termdb.singleSampleMutation.ts

@@ -25,7 +25,7 @@ export const api: any = {
 
 function init({ genomes }) {
 	return async (req: any, res: any): Promise<void> => {
-		const q = req.query as TermdbSingleSampleMutationRequest
+		const q: TermdbSingleSampleMutationRequest = req.query
 		let result
 		try {
 			const g = genomes[q.genome]

package/routes/termdb.violin.ts

@@ -42,7 +42,6 @@ export const api: any = {
 							axisHeight: 60,
 							rightMargin: 50,
 							unit: 'abs',
-							plotThickness: 150,
 							termid: 'agedx'
 						}
 					},