@sjcrh/proteinpaint-server 2.44.0 → 2.46.1

package/routes/gdc.topMutatedGenes.ts

@@ -1,586 +0,0 @@
-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'
-
-// TODO change to /termdb/topMutatedGenes
-
-export const api = {
-	endpoint: 'gdc/topMutatedGenes',
-	methods: {
-		all: {
-			init,
-			request: {
-				typeId: 'GdcTopMutatedGeneRequest'
-			},
-			response: {
-				typeId: 'GdcTopMutatedGeneResponse'
-			}
-		}
-	}
-}
-
-function 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> => {
-		const q: GdcTopMutatedGeneRequest = req.query
-		const g = genomes.hg38
-		if (!g) throw 'hg38 missing'
-		const ds = g.datasets.GDC
-		if (!ds) throw 'hg38 GDC missing'
-		try {
-			const genes = await getGenesGraphql(q, ds)
-			const payload: GdcTopMutatedGeneResponse = { genes }
-			res.send(payload)
-		} catch (e: any) {
-			res.send({ status: 'error', error: e.message || e })
-		}
-	}
-}
-
-// 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
-  $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
-                }
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-}
-`,
-	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'
-						}
-					}
-				]
-			},
-			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) {
-			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: '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) {
-			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.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, ds) {
-	let query: string, variables: object
-	const { host, headers } = ds.getHostHeaders(q)
-
-	// TODO: change this condition to use host.geneExp != host.rest ???
-	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(host.graphql, {
-		headers,
-		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(host.rest, '/analysis/top_mutated_genes_by_project'), {
-		headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
-		body: JSON.stringify({
-			size: q.maxGenes || 50,
-			fields: 'symbol',
-			filters: mayAddCGC2filter(_f, q.geneFilter)
-		})
-	})
-	const re = JSON.parse(response.body)
-	const genes = [] as string[]
-	for (const hit of re.data.hits) {
-		if (!hit.symbol) continue
-		genes.push(hit.symbol)
-	}
-	return genes
-}
-*/
-
-/*
-str:
-	stringified gdc filter object, should not include the "genes.is_cancer_gene_census" filter element
-geneFilter: str
-	if = 'CGC', insert following element into the filter and return stringified obj
-
-	{
-		"op":"and",
-		"content":[
-			{
-				"content":{ "field":"genes.is_cancer_gene_census", "value":["true"] },
-				"op":"in"
-			}
-		]
-	}
-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
-	let f2
-
-	if (f.op == 'in') {
-		// wrap f into f2
-		f2 = { op: 'and', content: [f] }
-	} else if (f.op == 'and') {
-		// no need to wrap
-		f2 = f
-	} else {
-		throw 'f.op not "in" or "and"'
-	}
-
-	// per Phil on 12/16/2022, following filters ensure to return IDH1 as 1st gene for gliomas
-	f2.content.push({
-		op: 'NOT',
-		content: {
-			field: 'ssms.consequence.transcript.annotation.vep_impact',
-			value: 'missing'
-		}
-	})
-	f2.content.push({
-		op: 'in',
-		content: {
-			field: 'ssms.consequence.transcript.consequence_type',
-			value: ['missense_variant', 'frameshift_variant', 'start_lost', 'stop_lost', 'stop_gained']
-		}
-	})
-
-	if (geneFilter == 'CGC') {
-		// using CGC genes, add in filter
-		f2.content.push({ op: 'in', content: { field: 'genes.is_cancer_gene_census', value: ['true'] } })
-	}
-
-	return f2
-}
-*/

package/routes/genelookup.ts

@@ -1,50 +0,0 @@
-import { getResult } from '#src/gene.js'
-import { GeneLookupRequest, GeneLookupResponse } from '#shared/types/routes/genelookup.ts'
-
-function init({ genomes }) {
-	return (req: any, res: any): void => {
-		try {
-			const q = req.query as GeneLookupRequest
-			const g = genomes[req.query.genome]
-			if (!g) throw 'invalid genome name'
-			const result = getResult(g, req.query) as GeneLookupResponse
-			res.send(result)
-		} catch (e: any) {
-			res.send({ error: e.message || e })
-			if (e.stack) console.log(e.stack)
-		}
-	}
-}
-
-export const api: any = {
-	endpoint: 'genelookup',
-	methods: {
-		get: {
-			init,
-			request: {
-				typeId: 'GeneLookupRequest'
-				//valid: default to type checker
-			},
-			response: {
-				typeId: 'GeneLookupResponse'
-				// will combine this with type checker
-				//valid: (t) => {}
-			},
-			examples: [
-				{
-					request: {
-						body: { input: 'kr', genome: 'hg38-test' }
-					},
-					response: {
-						header: { status: 200 },
-						body: { hits: ['KRAS'] }
-					}
-				}
-			]
-		},
-		post: {
-			alternativeFor: 'get',
-			init
-		}
-	}
-}

package/routes/healthcheck.ts

@@ -1,29 +0,0 @@
-import { getStat } from '#src/health.ts'
-import { HealthCheckResponse } from '#shared/types/routes/healthcheck.ts'
-
-export const api = {
-	endpoint: 'healthcheck',
-	methods: {
-		get: {
-			init({ genomes }) {
-				return async (req: undefined, res: any): Promise<void> => {
-					try {
-						const health = (await getStat(genomes)) as HealthCheckResponse
-						res.send(health)
-					} catch (e: any) {
-						res.send({ status: 'error', error: e.message || e })
-					}
-				}
-			},
-			request: {
-				typeId: null
-				//valid: default to type checker
-			},
-			response: {
-				typeId: 'HealthCheckResponse'
-				// will combine this with type checker
-				//valid: (t) => {}
-			}
-		}
-	}
-}