@molgenis/vip-report-template 2.6.4 → 2.7.3

package/src/types/Consequence.ts

@@ -3,6 +3,7 @@ import { Vcf } from '@molgenis/vip-report-api';
 export interface ConsequenceMetadata {
   effect: Vcf.InfoMetadata;
   symbol: Vcf.InfoMetadata;
+  incompletePenetrance: Vcf.InfoMetadata;
   inheritance: Vcf.InfoMetadata;
   hgvsC: Vcf.InfoMetadata;
   hgvsP: Vcf.InfoMetadata;
@@ -17,6 +18,7 @@ export interface Consequence {
   alleleIndex: number | null;
   effect: string[];
   symbol: string | null;
+  incompletePenetrance: boolean | false;
   inheritance: string[];
   hgvsC: string | null;
   hgvsP: string | null;

package/src/types/DecisionTree.d.ts

@@ -12,7 +12,7 @@ type BoolOutcome = {
 type Query = {
   field: string;
   operator: string;
-  value: string;
+  value: string | string[] | number | number[];
 };
 
 type BoolNode = {
@@ -21,6 +21,22 @@ type BoolNode = {
   outcomeMissing?: Outcome;
 } & BoolOutcome;
 
+type MultiOperator = 'AND' | 'OR';
+
+type BoolMultiQuery = {
+  operator?: MultiOperator;
+  queries: Query[];
+  outcomeTrue: Outcome;
+};
+
+type BoolMultiNode = {
+  type: 'BOOL_MULTI';
+  fields: string[];
+  outcomes: BoolMultiQuery[];
+  outcomeMissing?: Outcome;
+  outcomeDefault?: Outcome;
+};
+
 type ExistsNode = {
   type: Exists;
   field: string;
@@ -32,8 +48,8 @@ type CategoricalNode = {
   outcomeMap: {
     [key: string]: Outcome;
   };
-  outcomeMissing: Outcome;
-  outcomeDefault: Outcome;
+  outcomeMissing?: Outcome;
+  outcomeDefault?: Outcome;
 };
 
 type ExitNode = {
@@ -45,10 +61,11 @@ type NodeDescription = { description: string };
 
 type NodeWithSimpleOutcome = NodeDescription & (BoolNode | ExistsNode);
 type NodeWithCategoricalOutcome = NodeDescription & CategoricalNode;
+type NodeWithBoolMultiOutcome = NodeDescription & BoolMultiNode;
 
 type Edge = { from: string; to: string; label: string };
 
-export type NodeWithOutcome = NodeWithSimpleOutcome | NodeWithCategoricalOutcome;
+export type NodeWithOutcome = NodeWithSimpleOutcome | NodeWithCategoricalOutcome | NodeWithBoolMultiOutcome;
 
 export type Node = NodeWithOutcome | ExitNode;
 

package/src/types/Gene.ts

@@ -0,0 +1,4 @@
+export interface Gene {
+  symbol: string | null;
+  incompletePenetrance: boolean | false;
+}

package/src/utils/treeBuilder.ts

@@ -63,19 +63,49 @@ export const retrieveEdges = (inputTree: DecisionTree): TreeEdgesArray => {
   let edges: TreeEdgesObj = {};
   Object.keys(inputTree.nodes).forEach((key) => {
     const node: Node = inputTree.nodes[key];
-    if ('outcomeTrue' in node) {
-      edges = createSimpleEdge('True', node, key, edges);
-      edges = createSimpleEdge('False', node, key, edges);
-      if ('outcomeMissing' in node) {
-        edges = createSimpleEdge('Missing', node, key, edges);
-      }
-    } else if ('outcomeMap' in node) {
-      Object.keys(node.outcomeMap).forEach((category) => {
-        const nextNode = node.outcomeMap[category].nextNode;
-        edges = createEdge(nextNode, category, key, edges);
-      });
-      edges = createSimpleEdge('Missing', node, key, edges);
-      edges = createSimpleEdge('Default', node, key, edges);
+    switch (node.type) {
+      case 'BOOL':
+        edges = createSimpleEdge('True', node, key, edges);
+        edges = createSimpleEdge('False', node, key, edges);
+        if ('outcomeMissing' in node) {
+          edges = createSimpleEdge('Missing', node, key, edges);
+        }
+        break;
+      case 'BOOL_MULTI':
+        node.outcomes.forEach((outcome) => {
+          const nextNode = outcome.outcomeTrue.nextNode;
+          const label = outcome.queries
+            .map((query) => `${query.field} ${query.operator} ${query.value}`)
+            .join(` ${outcome.operator} `);
+          edges = createEdge(nextNode, label, key, edges);
+        });
+        if ('outcomeMissing' in node) {
+          edges = createSimpleEdge('Missing', node, key, edges);
+        }
+        if ('outcomeDefault' in node) {
+          edges = createSimpleEdge('Default', node, key, edges);
+        }
+        break;
+      case 'CATEGORICAL':
+        Object.keys(node.outcomeMap).forEach((category) => {
+          const nextNode = node.outcomeMap[category].nextNode;
+          edges = createEdge(nextNode, category, key, edges);
+        });
+        if ('outcomeMissing' in node) {
+          edges = createSimpleEdge('Missing', node, key, edges);
+        }
+        if ('outcomeDefault' in node) {
+          edges = createSimpleEdge('Default', node, key, edges);
+        }
+        break;
+      case 'EXISTS':
+        edges = createSimpleEdge('True', node, key, edges);
+        edges = createSimpleEdge('False', node, key, edges);
+        break;
+      case 'LEAF':
+        break;
+      default:
+        throw new Error('unknown node type');
     }
   });
   return Object.keys(edges).map((k) => edges[k]);

package/tests/unit/globals/utils.spec.ts

@@ -6,6 +6,12 @@ import { Consequence } from '@/types/Consequence';
 const expectedMetadata = {
   effect: { id: 'Consequence', type: 'STRING', number: { type: 'OTHER' }, description: 'Consequence' },
   symbol: { id: 'SYMBOL', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'SYMBOL' },
+  incompletePenetrance: {
+    id: 'IncompletePenetrance',
+    type: 'FLAG',
+    number: { type: 'NUMBER', count: 1 },
+    description: 'IncompletePenetrance'
+  },
   inheritance: {
     id: 'InheritanceModesGene',
     type: 'STRING',
@@ -169,6 +175,7 @@ test('get consequences in case of CSQ info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -183,6 +190,7 @@ test('get consequences in case of CSQ info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -243,6 +251,7 @@ test('get consequences in case of CSQ info with extended info', () => {
         gnomAD: 0.1234,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: ['12345678', '23456789'],
         clinVar: ['likely_pathogenic', 'pathogenic'],
         vkgl: 'B',
@@ -257,6 +266,7 @@ test('get consequences in case of CSQ info with extended info', () => {
         gnomAD: 0.2345,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: ['12345678'],
         clinVar: ['benign'],
         vkgl: 'VUS',
@@ -289,6 +299,7 @@ test('get consequences in case of ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -303,6 +314,7 @@ test('get consequences in case of ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -336,6 +348,7 @@ test('get consequences in case of CSQ and ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -350,6 +363,7 @@ test('get consequences in case of CSQ and ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -364,6 +378,7 @@ test('get consequences in case of CSQ and ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC2',
         hgvsP: 'hgvsP2',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,

package/tests/unit/store/getters.spec.ts

@@ -517,7 +517,7 @@ test('whether records contain MVL annotations - no meta', () => {
 
 test('whether records contain MVL annotations - no info meta', () => {
   const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { };
+  recordsMetadata.info = {};
 
   const metadata = mock<Api.Metadata>();
   metadata.records = recordsMetadata;

package/tests/unit/utils/treeBuilder.spec.ts

@@ -28,6 +28,55 @@ describe('treeBuilder', () => {
           nextNode: 'existsNode'
         }
       },
+      boolMultiNode: {
+        type: 'BOOL_MULTI',
+        description: 'Bool multi type node',
+        fields: ['my_multi_1', 'my_multi_2'],
+        outcomeDefault: {
+          nextNode: 'exit_t'
+        },
+        outcomeMissing: {
+          nextNode: 'exit_f'
+        },
+        outcomes: [
+          {
+            operator: 'AND',
+            queries: [
+              {
+                field: 'my_multi_1',
+                operator: '>',
+                value: 0.1
+              },
+              {
+                field: 'my_multi_1',
+                operator: '<=',
+                value: 0.2
+              }
+            ],
+            outcomeTrue: {
+              nextNode: 'exit_f'
+            }
+          },
+          {
+            operator: 'OR',
+            queries: [
+              {
+                field: 'my_multi_2',
+                operator: '<',
+                value: 0.1
+              },
+              {
+                field: 'my_multi_2',
+                operator: '>',
+                value: 0.2
+              }
+            ],
+            outcomeTrue: {
+              nextNode: 'exit_t'
+            }
+          }
+        ]
+      },
       existsNode: {
         type: 'EXISTS',
         description: 'check some field exists',
@@ -82,6 +131,11 @@ describe('treeBuilder', () => {
         label: 'boolNode\n(== val)',
         type: 'BOOL'
       },
+      {
+        id: 'boolMultiNode',
+        label: 'boolMultiNode',
+        type: 'BOOL_MULTI'
+      },
       {
         id: 'existsNode',
         label: 'existsNode\n(exists)',
@@ -181,6 +235,16 @@ describe('treeBuilder', () => {
         to: 'existsNode',
         label: 'False\nMissing'
       },
+      {
+        from: 'boolMultiNode',
+        to: 'exit_f',
+        label: 'my_multi_1 > 0.1 AND my_multi_1 <= 0.2\nMissing'
+      },
+      {
+        from: 'boolMultiNode',
+        to: 'exit_t',
+        label: 'my_multi_2 < 0.1 OR my_multi_2 > 0.2\nDefault'
+      },
       {
         from: 'existsNode',
         to: 'categorical_field',
@@ -199,4 +263,58 @@ describe('treeBuilder', () => {
     ];
     expect(outcome).toStrictEqual(expected);
   });
+  it('should generate edges for CATEGORICAL node without default/missing', () => {
+    const decisionTree: DecisionTree = {
+      files: {
+        panel: {
+          path: 'path/to/tsv'
+        }
+      },
+      rootNode: 'ROOT',
+      nodes: {
+        categoricalField: {
+          type: 'CATEGORICAL',
+          description: 'check categorical field',
+          field: 'FIELD_TO_CHECK',
+          outcomeMap: {
+            P: {
+              nextNode: 'exit_t'
+            },
+            LP: {
+              nextNode: 'exit_t'
+            },
+            LB: {
+              nextNode: 'exit_f'
+            },
+            B: {
+              nextNode: 'exit_f'
+            }
+          }
+        },
+        exit_t: {
+          type: 'LEAF',
+          class: 'T'
+        },
+        exit_f: {
+          type: 'LEAF',
+          class: 'F'
+        }
+      }
+    };
+
+    const outcome = retrieveEdges(decisionTree);
+    const expected = [
+      {
+        from: 'categoricalField',
+        to: 'exit_t',
+        label: 'P\nLP'
+      },
+      {
+        from: 'categoricalField',
+        to: 'exit_f',
+        label: 'LB\nB'
+      }
+    ];
+    expect(outcome).toStrictEqual(expected);
+  });
 });

package/tests/unit/utils/treeDrawer.spec.ts

@@ -1,4 +1,4 @@
-import treeDrawer, { calculateScaleToFit, getGraphScale } from '@/utils/treeDrawer';
+import treeDrawer from '@/utils/treeDrawer';
 
 describe('retrieveTreeFromFile', () => {
   it('getLineThickness', () => {

package/.scannerwork/css-bundle/bin/server

@@ -1,15 +0,0 @@
-#!/usr/bin/env node
-
-/*
-* This script expects following arguments
-*
-* port - port number on which server should listen
-* host - host address on which server should listen
-*/
-
-const server = require("../lib/src/server");
-
-const port = process.argv[2];
-const host = process.argv[3];
-
-server.start(port, host);

package/.scannerwork/css-bundle/lib/src/server.d.ts

@@ -1,14 +0,0 @@
-/// <reference types="node" />
-import { Server } from "http";
-export declare function setLogHandlersForTests(logHandler: typeof console.log, errorHandler: typeof console.error): void;
-export declare function start(port?: number, host?: string): Promise<Server>;
-export interface AnalysisInput {
-    filePath: string;
-    fileContent: string | undefined;
-    configFile: string;
-}
-export interface Issue {
-    line: number;
-    rule: string;
-    text: string;
-}

package/.scannerwork/css-bundle/lib/src/server.js

@@ -1,83 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.start = exports.setLogHandlersForTests = void 0;
-const express = require("express");
-const stylelint = require("stylelint");
-const fs = require("fs");
-const bodyParser = require("body-parser");
-// for testing purposes
-let log = console.log;
-let logError = console.error;
-const MAX_REQUEST_SIZE = "50mb";
-function setLogHandlersForTests(logHandler, errorHandler) {
-    log = logHandler;
-    logError = errorHandler;
-}
-exports.setLogHandlersForTests = setLogHandlersForTests;
-function start(port = 0, host = "127.0.0.1") {
-    return new Promise(resolve => {
-        log("DEBUG starting stylelint-bridge server at port", port);
-        const app = express();
-        app.use(bodyParser.json({ limit: MAX_REQUEST_SIZE }));
-        app.post("/analyze", analyzeWithStylelint);
-        app.get("/status", (_, resp) => resp.send("OK!"));
-        app.post("/close", (_req, resp) => {
-            console.log("DEBUG stylelint-bridge server will shutdown");
-            resp.end(() => {
-                server.close();
-            });
-        });
-        // every time something is wrong we log error and send empty response (with 0 issues)
-        // it's important to keep this call last in configuring "app"
-        app.use((error, _req, response, _next) => processError(error, response));
-        const server = app.listen(port, host, () => {
-            log("DEBUG stylelint-bridge server is running at port", server.address().port);
-            resolve(server);
-        });
-    });
-}
-exports.start = start;
-function analyzeWithStylelint(request, response) {
-    const parsedRequest = request.body;
-    const { filePath, fileContent, configFile } = parsedRequest;
-    const code = typeof fileContent == "string" ? fileContent : getFileContent(filePath);
-    const options = {
-        code,
-        codeFilename: filePath,
-        configFile
-    };
-    stylelint
-        .lint(options)
-        .then(result => response.json(toIssues(result.results, filePath)))
-        .catch(error => processError(error, response));
-}
-function processError(error, response) {
-    logError(error);
-    response.json([]);
-}
-function toIssues(results, filePath) {
-    const analysisResponse = [];
-    // we should have only one element in 'results' as we are analyzing only 1 file
-    results.forEach(result => {
-        // to avoid reporting on "fake" source like <input ccs 1>
-        if (result.source !== filePath) {
-            log(`DEBUG For file [${filePath}] received issues with [${result.source}] as a source. They will not be reported.`);
-            return;
-        }
-        result.warnings.forEach(warning => analysisResponse.push({
-            line: warning.line,
-            text: warning.text,
-            rule: warning.rule
-        }));
-    });
-    return analysisResponse;
-}
-function getFileContent(filePath) {
-    const fileContent = fs.readFileSync(filePath, { encoding: "utf8" });
-    // strip BOM
-    if (fileContent.charCodeAt(0) === 0xfeff) {
-        return fileContent.slice(1);
-    }
-    return fileContent;
-}
-//# sourceMappingURL=server.js.map

package/.scannerwork/css-bundle/lib/src/server.js.map

@@ -1 +0,0 @@
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