@molgenis/vip-report-template 2.7.3 → 3.0.0

package/src/mocks/MockApiClient.ts

@@ -0,0 +1,375 @@
+import { ApiClient, ReportData } from "@molgenis/vip-report-api/src/ApiClient";
+import { parseVcf } from "@molgenis/vip-report-vcf/src/VcfParser";
+import {
+  Api,
+  AppMetadata,
+  DecisionTree,
+  HtsFileMetadata,
+  Item,
+  Metadata,
+  PagedItems,
+  Params,
+  Phenotype,
+  Sample,
+} from "@molgenis/vip-report-api/src/Api";
+import { samples1, samples100 } from "./static";
+import {
+  bam as bamGRCh37,
+  decisionTree as decisionTreeGRCh37,
+  fastaGz as fastaGzGRCh37,
+  genesGz as genesGzGRCh37,
+  samplesFamily as samplesFamilyGRCh37,
+  vcfFamily as vcfFamilyGRCh37,
+  vcfNoVep as vcfNoVepGRCh37,
+  vcfSamples0 as vcfSamples0GRCh37,
+  vcfSamples1 as vcfSamples1GRCh37,
+  vcfSamples100 as vcfSamples100GRCh37,
+} from "./GRCh37/static";
+import {
+  bam as bamGRCh38,
+  decisionTree as decisionTreeGRCh38,
+  fastaGz as fastaGzGRCh38,
+  genesGz as genesGzGRCh38,
+  samplesFamily as samplesFamilyGRCh38,
+  vcfFamily as vcfFamilyGRCh38,
+  vcfNoVep as vcfNoVepGRCh38,
+  vcfSamples0 as vcfSamples0GRCh38,
+  vcfSamples1 as vcfSamples1GRCh38,
+  vcfSamples100 as vcfSamples100GRCh38,
+} from "./GRCh38/static";
+import { Metadata as RecordMetadata, Record } from "@molgenis/vip-report-vcf/src/Vcf";
+
+/**
+ * API client that uses mocked data as data source.
+ */
+export class MockApiClient implements Api {
+  private apiClient: Api;
+  private readonly datasets: { [key: string]: ReportData };
+
+  constructor() {
+    this.datasets = MockApiClient.createDatasets();
+    this.apiClient = this.createApiClient(this.getDatasetIds()[0]);
+  }
+
+  getFastaGz(contig: string, pos: number): Promise<Uint8Array | null> {
+    return this.apiClient.getFastaGz(contig, pos);
+  }
+
+  getGenesGz(): Promise<Uint8Array | null> {
+    return this.apiClient.getGenesGz();
+  }
+
+  getBam(sampleId: string): Promise<Uint8Array | null> {
+    return this.apiClient.getBam(sampleId);
+  }
+
+  getDecisionTree(): Promise<DecisionTree | null> {
+    return this.apiClient.getDecisionTree();
+  }
+
+  getHtsFileMetadata(): Promise<HtsFileMetadata> {
+    return this.apiClient.getHtsFileMetadata();
+  }
+
+  getAppMetadata(): Promise<AppMetadata> {
+    return this.apiClient.getAppMetadata();
+  }
+
+  getPhenotypes(params: Params): Promise<PagedItems<Phenotype>> {
+    return this.apiClient.getPhenotypes(params);
+  }
+
+  getRecordById(id: number): Promise<Item<Record>> {
+    return this.apiClient.getRecordById(id);
+  }
+
+  getRecords(params: Params): Promise<PagedItems<Record>> {
+    return this.apiClient.getRecords(params);
+  }
+
+  getRecordsMeta(): Promise<RecordMetadata> {
+    return this.apiClient.getRecordsMeta();
+  }
+
+  getSampleById(id: number): Promise<Item<Sample>> {
+    return this.apiClient.getSampleById(id);
+  }
+
+  getSamples(params: Params): Promise<PagedItems<Sample>> {
+    return this.apiClient.getSamples(params);
+  }
+
+  isDatasetSupport(): boolean {
+    return true;
+  }
+
+  getDatasetIds(): string[] {
+    return Object.keys(this.datasets);
+  }
+
+  selectDataset(id: string): void {
+    this.apiClient = this.createApiClient(id);
+  }
+
+  private static createDatasets() {
+    const mockReportData: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b37_vip.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b37_vip.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh37",
+        },
+      } as Metadata,
+      data: samplesFamilyGRCh37,
+      binary: {
+        vcf: vcfFamilyGRCh37,
+        fastaGz: fastaGzGRCh37,
+        genesGz: genesGzGRCh37,
+        bam: {
+          Patient: bamGRCh37,
+        },
+      },
+      decisionTree: decisionTreeGRCh37,
+    };
+
+    const mockReportDataNoVep: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b37.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b37.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh37",
+        },
+      } as Metadata,
+      data: samplesFamilyGRCh37,
+      binary: {
+        vcf: vcfNoVepGRCh37,
+        fastaGz: fastaGzGRCh37,
+        genesGz: genesGzGRCh37,
+        bam: {
+          Patient: bamGRCh37,
+        },
+      },
+      decisionTree: decisionTreeGRCh37,
+    };
+
+    const mockReportData1Sample: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b37_1Sample.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b37_1Sample.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh37",
+        },
+      } as Metadata,
+      data: samples1,
+      binary: {
+        vcf: vcfSamples1GRCh37,
+        fastaGz: fastaGzGRCh37,
+        genesGz: genesGzGRCh37,
+        bam: {
+          SAMPLE1: bamGRCh37,
+        },
+      },
+      decisionTree: decisionTreeGRCh37,
+    };
+
+    const mockReportData100Samples: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b37_100Samples.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b37_100Samples.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh37",
+        },
+      } as Metadata,
+      data: samples100,
+      binary: {
+        vcf: vcfSamples100GRCh37,
+        fastaGz: fastaGzGRCh37,
+        genesGz: genesGzGRCh37,
+      },
+      decisionTree: decisionTreeGRCh37,
+    };
+
+    const mockReportDataNoSample: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b37_1NoSamples.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b37_NoSamples.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh37",
+        },
+      } as Metadata,
+      data: { samples: [], phenotypes: [] },
+      binary: {
+        vcf: vcfSamples0GRCh37,
+        fastaGz: fastaGzGRCh37,
+        genesGz: genesGzGRCh37,
+      },
+      decisionTree: decisionTreeGRCh37,
+    };
+
+    const mockReportDataFamilyGRCh38: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b38_vip.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b38_vip.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh38",
+        },
+      } as Metadata,
+      data: samplesFamilyGRCh38,
+      binary: {
+        vcf: vcfFamilyGRCh38,
+        fastaGz: fastaGzGRCh38,
+        genesGz: genesGzGRCh38,
+        bam: {
+          Patient: bamGRCh38,
+        },
+      },
+      decisionTree: decisionTreeGRCh38,
+    };
+
+    const mockReportDataNoVepGRCh38: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b38.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b38.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh38",
+        },
+      } as Metadata,
+      data: samplesFamilyGRCh38,
+      binary: {
+        vcf: vcfNoVepGRCh38,
+        fastaGz: fastaGzGRCh38,
+        genesGz: genesGzGRCh38,
+        bam: {
+          Patient: bamGRCh38,
+        },
+      },
+      decisionTree: decisionTreeGRCh38,
+    };
+
+    const mockReportData1SampleGRCh38: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b38_1Sample.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b38_1Sample.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh38",
+        },
+      } as Metadata,
+      data: samples1,
+      binary: {
+        vcf: vcfSamples1GRCh38,
+        fastaGz: fastaGzGRCh38,
+        genesGz: genesGzGRCh38,
+        bam: {
+          SAMPLE1: bamGRCh38,
+        },
+      },
+      decisionTree: decisionTreeGRCh38,
+    };
+
+    const mockReportData100SamplesGRCh38: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b38_100Samples.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b38_100Samples.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh38",
+        },
+      } as Metadata,
+      data: samples100,
+      binary: {
+        vcf: vcfSamples100GRCh38,
+        fastaGz: fastaGzGRCh38,
+        genesGz: genesGzGRCh38,
+      },
+      decisionTree: decisionTreeGRCh38,
+    };
+
+    const mockReportDataNoSampleGRCh38: ReportData = {
+      metadata: {
+        app: {
+          name: "vcf-report",
+          version: "0.0.8",
+          args: "-i testdata_b38_1NoSamples.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
+        },
+        htsFile: {
+          uri: "testdata_b38_NoSamples.vcf",
+          htsFormat: "VCF",
+          genomeAssembly: "GRCh38",
+        },
+      } as Metadata,
+      data: { samples: [], phenotypes: [] },
+      binary: {
+        vcf: vcfSamples0GRCh38,
+        fastaGz: fastaGzGRCh38,
+        genesGz: genesGzGRCh38,
+      },
+      decisionTree: decisionTreeGRCh38,
+    };
+
+    const datasets: { [key: string]: ReportData } = {};
+    datasets["GRCh37 Family"] = mockReportData;
+    datasets["GRCh37 Family no VEP"] = mockReportDataNoVep;
+    datasets["GRCh37 Samples 0"] = mockReportDataNoSample;
+    datasets["GRCh37 Samples 1"] = mockReportData1Sample;
+    datasets["GRCh37 Samples 100"] = mockReportData100Samples;
+    datasets["GRCh38 Family"] = mockReportDataFamilyGRCh38;
+    datasets["GRCh38 Family no VEP"] = mockReportDataNoVepGRCh38;
+    datasets["GRCh38 Samples 0"] = mockReportDataNoSampleGRCh38;
+    datasets["GRCh38 Samples 1"] = mockReportData1SampleGRCh38;
+    datasets["GRCh38 Samples 100"] = mockReportData100SamplesGRCh38;
+    return datasets;
+  }
+
+  private createApiClient(id: string): Api {
+    const reportData = this.datasets[id];
+    const vcf = parseVcf(new TextDecoder().decode(reportData.binary.vcf));
+    reportData.metadata.records = vcf.metadata;
+    reportData.data.records = vcf.data;
+
+    return new ApiClient(reportData);
+  }
+}