From 6f7738a022c76dce730f8d004da2b8b7d9b53172 Mon Sep 17 00:00:00 2001 From: "bart.charbon" Date: Fri, 7 Jun 2024 13:10:31 +0200 Subject: [PATCH] Add sample decision tree --- package.json | 2 +- pnpm-lock.yaml | 2743 ++++++++++++++----------------- src/Api.d.ts | 1 + src/ApiClient.ts | 6 + src/__tests__/ApiClient.test.ts | 6 + src/__tests__/sampleTree.json | 123 ++ 6 files changed, 1396 insertions(+), 1485 deletions(-) create mode 100644 src/__tests__/sampleTree.json diff --git a/package.json b/package.json index 6e022d1..9c5fb83 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@molgenis/vip-report-api", - "version": "5.0.4", + "version": "5.1.0", "description": "TypeScript Report API for Variant Call Format (VCF) Report Templates", "scripts": { "build": "tsc --build", diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 0432689..7c6c4f2 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -1,379 +1,553 @@ -lockfileVersion: '9.0' - -settings: - autoInstallPeers: true - 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word-wrap@1.2.5: {} + /yallist@4.0.0: + resolution: {integrity: sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==} + dev: true - wrappy@1.0.2: {} + /yocto-queue@0.1.0: + resolution: {integrity: sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==} + engines: {node: '>=10'} + dev: true - yocto-queue@0.1.0: {} + /yocto-queue@1.0.0: + resolution: {integrity: sha512-9bnSc/HEW2uRy67wc+T8UwauLuPJVn28jb+GtJY16iiKWyvmYJRXVT4UamsAEGQfPohgr2q4Tq0sQbQlxTfi1g==} + engines: {node: '>=12.20'} + dev: true - yocto-queue@1.0.0: {} +settings: + autoInstallPeers: true + excludeLinksFromLockfile: false diff --git a/src/Api.d.ts b/src/Api.d.ts index 2f7b855..b677804 100644 --- a/src/Api.d.ts +++ b/src/Api.d.ts @@ -13,6 +13,7 @@ export interface Api { getHtsFileMetadata(): Promise; getAppMetadata(): Promise; getDecisionTree(): Promise; + getSampleTree(): Promise; // testing purposes only isDatasetSupport(): boolean; diff --git a/src/ApiClient.ts b/src/ApiClient.ts index de7cf6e..8bd5a84 100644 --- a/src/ApiClient.ts +++ b/src/ApiClient.ts @@ -30,6 +30,7 @@ export interface ReportData { data: Data; binary: BinaryReportData; decisionTree?: DecisionTree; + sampleTree?: DecisionTree; vcfMeta?: ExternalMetadata; } @@ -118,6 +119,11 @@ export class ApiClient implements Api { return Promise.resolve(decisionTree ? decisionTree : null); } + getSampleTree(): Promise { + const sampleTree = this.reportData.sampleTree; + return Promise.resolve(sampleTree ? sampleTree : null); + } + isDatasetSupport(): boolean { return false; } diff --git a/src/__tests__/ApiClient.test.ts b/src/__tests__/ApiClient.test.ts index 38bb1fb..1576d19 100644 --- a/src/__tests__/ApiClient.test.ts +++ b/src/__tests__/ApiClient.test.ts @@ -174,6 +174,7 @@ beforeEach(() => { }, }, decisionTree: JSON.parse(readFileSync(path.join(__dirname, "decisionTree.json"), "utf8")) as DecisionTree, + sampleTree: JSON.parse(readFileSync(path.join(__dirname, "sampleTree.json"), "utf8")) as DecisionTree, }; const vcf = parseVcf(new TextDecoder().decode(reportData.binary.vcf)); @@ -891,3 +892,8 @@ test("getDecisionTree", async () => { const decisionTree = await api.getDecisionTree(); expect(decisionTree).not.toBe(null); }); + +test("getSampleTree", async () => { + const decisionTree = await api.getSampleTree(); + expect(decisionTree).not.toBe(null); +}); diff --git a/src/__tests__/sampleTree.json b/src/__tests__/sampleTree.json new file mode 100644 index 0000000..b051211 --- /dev/null +++ b/src/__tests__/sampleTree.json @@ -0,0 +1,123 @@ +{ + "rootNode": "gt", + "nodes": { + "gt": { + "description": "Genotype", + "type": "CATEGORICAL", + "field": "FORMAT/GENOTYPE/TYPE", + "outcomeMap": { + "HET": { + "nextNode": "gq" + }, + "HOM_REF": { + "nextNode": "exit_u3" + }, + "HOM_VAR": { + "nextNode": "gq" + }, + "MIXED": { + "nextNode": "gq" + }, + "NO_CALL": { + "nextNode": "exit_u3" + }, + "UNAVAILABLE": { + "nextNode": "exit_u3" + } + }, + "outcomeMissing": { + "nextNode": "gq" + }, + "outcomeDefault": { + "nextNode": "gq" + } + }, + "gq": { + "type": "BOOL", + "description": "Genotype quality", + "query": { + "field": "FORMAT/GQ", + "operator": ">=", + "value": 20 + }, + "outcomeTrue": { + "nextNode": "dp" + }, + "outcomeFalse": { + "nextNode": "exit_u3" + }, + "outcomeMissing": { + "nextNode": "dp" + } + }, + "dp": { + "type": "BOOL", + "description": "Sequencing depth", + "query": { + "field": "FORMAT/DP", + "operator": ">=", + "value": 10 + }, + "outcomeTrue": { + "nextNode": "vim" + }, + "outcomeFalse": { + "nextNode": "exit_u3" + }, + "outcomeMissing": { + "nextNode": "vim" + } + }, + "vim": { + "type": "BOOL", + "description": "Inheritance match", + "query": { + "field": "FORMAT/VIG", + "operator": "contains", + "value": "field:INFO/CSQ/Gene" + }, + "outcomeTrue": { + "nextNode": "exit_u1" + }, + "outcomeFalse": { + "nextNode": "vid" + }, + "outcomeMissing": { + "nextNode": "exit_u2" + } + }, + "vid": { + "type": "BOOL", + "description": "Inheritance denovo", + "query": { + "field": "FORMAT/VID", + "operator": "==", + "value": 1 + }, + "outcomeTrue": { + "nextNode": "exit_u1" + }, + "outcomeFalse": { + "nextNode": "exit_u3" + }, + "outcomeMissing": { + "nextNode": "exit_u2" + } + }, + "exit_u1": { + "description": "Usable: probably", + "type": "LEAF", + "class": "U1" + }, + "exit_u2": { + "description": "Usable: maybe", + "type": "LEAF", + "class": "U2" + }, + "exit_u3": { + "description": "Usable: probably not", + "type": "LEAF", + "class": "U3" + } + } +} \ No newline at end of file