Merge branch 'master' into dependabot/github_actions/actions/setup-py…

…thon-5
SciCatProject · Sep 30, 2024 · 84e48a9 · 84e48a9
2 parents d1420aa + 2c55165
commit 84e48a9
Show file tree

Hide file tree

Showing 10 changed files with 60 additions and 40 deletions.
diff --git a/src/config/configuration.ts b/src/config/configuration.ts
@@ -59,7 +59,7 @@ const configuration = () => {
 
   const config = {
     versions: {
-      api: "v3",
+      api: "3",
     },
     swaggerPath: process.env.SWAGGER_PATH || "explorer",
     loggerConfigs: jsonConfigMap.loggers || [defaultLogger],

diff --git a/src/datasets/datasets.controller.ts b/src/datasets/datasets.controller.ts
@@ -409,22 +409,22 @@ export class DatasetsController {
       version: "v3",
     };
 
+    if ("proposalId" in inputObsoleteDataset) {
+      propertiesModifier.proposalIds = [
+        (inputObsoleteDataset as CreateRawDatasetObsoleteDto).proposalId,
+      ];
+    }
     if (
       inputObsoleteDataset instanceof CreateRawDatasetObsoleteDto ||
       inputObsoleteDataset instanceof UpdateRawDatasetObsoleteDto ||
       inputObsoleteDataset instanceof PartialUpdateRawDatasetObsoleteDto
     ) {
-      if ("proposalId" in inputObsoleteDataset) {
-        propertiesModifier.proposalIds = [
-          (inputObsoleteDataset as CreateRawDatasetObsoleteDto).proposalId,
-        ];
-      }
       if ("sampleId" in inputObsoleteDataset) {
         propertiesModifier.sampleIds = [
           (inputObsoleteDataset as CreateRawDatasetObsoleteDto).sampleId,
         ];
       }
-      if ("instrumentIds" in inputObsoleteDataset) {
+      if ("instrumentId" in inputObsoleteDataset) {
         propertiesModifier.instrumentIds = [
           (inputObsoleteDataset as CreateRawDatasetObsoleteDto).instrumentId,
         ];
@@ -476,15 +476,15 @@ export class DatasetsController {
     const propertiesModifier: Record<string, unknown> = {};
     if (inputDataset) {
       if ("proposalIds" in inputDataset) {
-        propertiesModifier.proposalIds = inputDataset.proposalIds![0];
+        propertiesModifier.proposalId = inputDataset.proposalIds![0];
       }
       if ("sampleIds" in inputDataset) {
-        propertiesModifier.sampleIds = inputDataset.sampleIds![0];
+        propertiesModifier.sampleId = inputDataset.sampleIds![0];
       }
       if ("instrumentIds" in inputDataset) {
-        propertiesModifier.instrumentIds = inputDataset.instrumentIds![0];
+        propertiesModifier.instrumentId = inputDataset.instrumentIds![0];
       }
-      if (inputDataset.type == "raw") {
+      if (inputDataset.type == "derived") {
         if ("investigator" in inputDataset) {
           propertiesModifier.investigator = inputDataset.principalInvestigator;
         }
@@ -499,7 +499,7 @@ export class DatasetsController {
     return outputDataset;
   }
 
-  // POST /datasets
+  // POST https://scicat.ess.eu/api/v3/datasets
   @UseGuards(PoliciesGuard)
   @CheckPolicies("datasets", (ability: AppAbility) =>
     ability.can(Action.DatasetCreate, DatasetClass),
@@ -557,7 +557,6 @@ export class DatasetsController {
         obsoleteDatasetDto,
       ) as CreateDatasetDto;
       const createdDataset = await this.datasetsService.create(datasetDto);
-
       const outputObsoleteDatasetDto =
         this.convertCurrentToObsoleteSchema(createdDataset);
 
@@ -740,13 +739,15 @@ export class DatasetsController {
     ) as IFilters<DatasetDocument, IDatasetFields>;
 
     // this should be implemented at database level
-    const datasets = (await this.datasetsService.findAll(
-      mergedFilters,
-    )) as OutputDatasetObsoleteDto[];
+    const datasets = await this.datasetsService.findAll(mergedFilters);
+    let outputDatasets: OutputDatasetObsoleteDto[] = [];
     if (datasets && datasets.length > 0) {
       const includeFilters = mergedFilters.include ?? [];
+      outputDatasets = datasets.map((dataset) =>
+        this.convertCurrentToObsoleteSchema(dataset),
+      );
       await Promise.all(
-        datasets.map(async (dataset) => {
+        outputDatasets.map(async (dataset) => {
           if (includeFilters) {
             await Promise.all(
               includeFilters.map(async ({ relation }) => {
@@ -781,7 +782,7 @@ export class DatasetsController {
         }),
       );
     }
-    return datasets;
+    return outputDatasets;
   }
 
   // GET /datasets/fullquery

diff --git a/src/datasets/dto/output-dataset-obsolete.dto.ts b/src/datasets/dto/output-dataset-obsolete.dto.ts
@@ -92,15 +92,6 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
   @IsString()
   readonly dataFormat?: string;
 
-  @ApiProperty({
-    type: String,
-    required: false,
-    description: "The ID of the proposal to which the dataset belongs.",
-  })
-  @IsOptional()
-  @IsString()
-  readonly proposalId?: string;
-
   @ApiProperty({
     type: String,
     required: false,

diff --git a/src/datasets/dto/update-dataset-obsolete.dto.ts b/src/datasets/dto/update-dataset-obsolete.dto.ts
@@ -288,6 +288,15 @@ export class UpdateDatasetObsoleteDto extends OwnableDto {
   @IsOptional()
   @IsNumber()
   readonly dataQualityMetrics?: number;
+
+  @ApiProperty({
+    type: String,
+    required: false,
+    description: "The ID of the proposal to which the dataset belongs.",
+  })
+  @IsOptional()
+  @IsString()
+  readonly proposalId?: string;
 }
 
 export class PartialUpdateDatasetObsoleteDto extends PartialType(

diff --git a/src/datasets/dto/update-raw-dataset-obsolete.dto.ts b/src/datasets/dto/update-raw-dataset-obsolete.dto.ts
@@ -52,14 +52,14 @@ export class UpdateRawDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
   @IsString()
   readonly dataFormat?: string;
 
-  @ApiProperty({
-    type: String,
-    required: false,
-    description: "The ID of the proposal to which the dataset belongs.",
-  })
-  @IsOptional()
-  @IsString()
-  readonly proposalId?: string;
+  // @ApiProperty({
+  //   type: String,
+  //   required: false,
+  //   description: "The ID of the proposal to which the dataset belongs.",
+  // })
+  // @IsOptional()
+  // @IsString()
+  // readonly proposalId?: string;
 
   @ApiProperty({
     type: String,
@@ -77,7 +77,7 @@ export class UpdateRawDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
   })
   @IsOptional()
   @IsString()
-  readonly instrumentId: string;
+  readonly instrumentId?: string;
 
   @IsOptional()
   investigator?: string;

diff --git a/src/main.ts b/src/main.ts
@@ -7,7 +7,7 @@ import {
   SwaggerModule,
 } from "@nestjs/swagger";
 import { AppModule } from "./app.module";
-import { Logger, ValidationPipe } from "@nestjs/common";
+import { Logger, ValidationPipe, VersioningType } from "@nestjs/common";
 import { ConfigService } from "@nestjs/config";
 import { AllExceptionsFilter, ScicatLogger } from "./loggers/logger.service";
 
@@ -29,11 +29,20 @@ async function bootstrap() {
 
   app.enableCors();
 
-  app.setGlobalPrefix(`api/${apiVersion}`);
+  app.setGlobalPrefix("api");
+
+  // NOTE: This is a workaround to enable versioning for individual routes
+  // Version decorator can be used to specify the version for a route
+  // Read more on https://docs.nestjs.com/techniques/versioning
+  app.enableVersioning({
+    type: VersioningType.URI,
+    defaultVersion: apiVersion,
+  });
+
   const config = new DocumentBuilder()
     .setTitle("SciCat backend API")
     .setDescription("This is the API for the SciCat Backend")
-    .setVersion(`api/${apiVersion}`)
+    .setVersion(`api/v${apiVersion}`)
     .addBearerAuth()
     .build();
 

diff --git a/test/DerivedDataset.js b/test/DerivedDataset.js
@@ -99,6 +99,9 @@ describe("0700: DerivedDataset: Derived Datasets", () => {
           .and.be.equal(TestData.DerivedCorrect.owner);
         res.body.should.have.property("type").and.be.equal("derived");
         res.body.should.have.property("pid").and.be.string;
+        res.body.should.have.property("proposalId").and.be.string;
+        //res.body.should.have.property("sampleId").and.be.string;
+        //res.body.should.have.property("instrumentId").and.be.string;
         pid = res.body["pid"];
       });
   });

diff --git a/test/OrigDatablockForRawDataset.js b/test/OrigDatablockForRawDataset.js
@@ -304,7 +304,6 @@ describe("1200: OrigDatablockForRawDataset: Test OrigDatablocks and their relati
       .expect(TestData.SuccessfulGetStatusCode)
       .expect("Content-Type", /json/)
       .then((res) => {
-        console.log(res.body);
         res.body["pid"].should.be.equal(decodeURIComponent(datasetPid1));
         res.body.origdatablocks.should.be
           .instanceof(Array)

diff --git a/test/RawDataset.js b/test/RawDataset.js
@@ -93,6 +93,9 @@ describe("1900: RawDataset: Raw Datasets", () => {
         res.body.should.have.property("owner").and.be.string;
         res.body.should.have.property("type").and.equal("raw");
         res.body.should.have.property("pid").and.be.string;
+        res.body.should.have.property("instrumentId").and.be.string;
+        res.body.should.have.property("proposalId").and.be.string;
+        res.body.should.have.property("sampleId").and.be.string;
         pid = encodeURIComponent(res.body["pid"]);
       });
   });

diff --git a/test/TestData.js b/test/TestData.js
@@ -232,6 +232,8 @@ const TestData = {
     ownerGroup: "p13388",
     accessGroups: [],
     proposalId: "10.540.16635/20110123",
+    instrumentId: "1f016ec4-7a73-11ef-ae3e-439013069377",
+    sampleId: "20c32b4e-7a73-11ef-9aec-5b9688aa3791i",
     type: "raw",
     keywords: ["sls", "protein"],
   },
@@ -451,6 +453,9 @@ const TestData = {
     ownerGroup: "p34123",
     accessGroups: [],
     type: "derived",
+    proposalId: "10.540.16635/20110123",
+    //instrumentId: "1f016ec4-7a73-11ef-ae3e-439013069377",
+    //sampleId: "20c32b4e-7a73-11ef-9aec-5b9688aa3791i",
   },
 
   DerivedWrong: {