Adding tests for origDatablocks

.github/workflows/test.yml

@@ -105,7 +105,7 @@ jobs:
           ACCESS_GROUPS_STATIC_VALUES: "ess"
           CREATE_DATASET_WITH_PID_GROUPS: "group2,group3"
           DATASET_CREATION_VALIDATION_ENABLED: true
-          DATASET_CREATION_VALIDATION_REGEX: "^[0-9A-F]{8}-[0-9A-F]{4}-4[0-9A-F]{3}-[89AB][0-9A-F]{3}-[0-9A-F]{12}$"
+          DATASET_CREATION_VALIDATION_REGEX: "^[0-9A-Fa-f]{8}-[0-9A-Fa-f]{4}-4[0-9A-Fa-f]{3}-[89ABab][0-9A-Fa-f]{3}-[0-9A-Fa-f]{12}$"
 
         # Start mongo container and app before running api tests
         run: |

src/common/dto/ownable.dto.ts

@@ -1,15 +1,31 @@
+import { ApiProperty } from "@nestjs/swagger";
 import { IsOptional, IsString } from "class-validator";
 
 export class OwnableDto {
+  @ApiProperty({
+    type: String,
+    required: true,
+    description: "Name of the group owning this item.",
+  })
   @IsString()
   readonly ownerGroup: string;
 
+  @ApiProperty({
+    type: [String],
+    required: false,
+    description: "List of groups which have access to this item.",
+  })
   @IsOptional()
   @IsString({
     each: true,
   })
   readonly accessGroups?: string[];
 
+  @ApiProperty({
+    type: String,
+    required: false,
+    description: "Group of the instrument which this item was acquired on.",
+  })
   @IsOptional()
   @IsString()
   readonly instrumentGroup?: string;

src/datasets/datasets.controller.ts

@@ -756,7 +756,7 @@ export class DatasetsController {
             }
             case "origdatablocks": {
               dataset.origdatablocks = await this.origDatablocksService.findAll(
-                { datasetId: dataset.pid },
+                { where: { datasetId: dataset.pid } },
               );
               break;
             }
@@ -1388,7 +1388,7 @@ export class DatasetsController {
   ): Promise<OrigDatablock[]> {
     await this.checkPermissionsForDataset(request, id);
 
-    return this.origDatablocksService.findAll({ datasetId: id });
+    return this.origDatablocksService.findAll({ where: { datasetId: id } });
   }
 
   // PATCH /datasets/:id/origdatablocks/:fk
@@ -1500,7 +1500,7 @@ export class DatasetsController {
       });
       // all the remaing orig datablocks for this dataset
       const odb = await this.origDatablocksService.findAll({
-        datasetId: datasetId,
+        where: { datasetId: datasetId },
       });
       // update dataset size and files number
       const updateDatasetDto: PartialUpdateDatasetDto = {

src/datasets/datasets.module.ts

@@ -48,6 +48,7 @@ import { PoliciesModule } from "src/policies/policies.module";
                 this.accessGroups,
                 this.ownerEmail ?? "",
                 av,
+                this.createdBy,
               );
             }
             this.classification = `IN=medium,AV=${av},CO=low`;

src/origdatablocks/dto/create-origdatablock.dto.ts

@@ -35,7 +35,7 @@ export class CreateOrigDatablockDto extends OwnableDto {
     type: String,
     required: false,
     description:
-      "Name of the hasing algorithm used to compute the hash for each file.",
+      "Name of the hashing algorithm used to compute the hash for each file.",
   })
   @IsOptional()
   @IsString()
@@ -46,12 +46,22 @@ export class CreateOrigDatablockDto extends OwnableDto {
     type: "array",
     items: { $ref: getSchemaPath(DataFile) },
     required: true,
-    description:
-      "Name of the hasing algorithm used to compute the hash for each file.",
+    description: "List of the files contained in this orig datablock.",
   })
   @IsArray()
   @ArrayNotEmpty()
   @ValidateNested({ each: true })
   @Type(() => DataFileDto)
   readonly dataFileList: DataFile[];
+
+  @ApiProperty({
+    type: String,
+    required: false,
+    description:
+      "Name of the group owning this item. If it is not specified, the datasets owner group is used.",
+  })
+  @IsOptional()
+  @IsString()
+  @IsNotEmpty()
+  readonly ownerGroup: string;
 }

src/origdatablocks/origdatablocks.controller.ts

@@ -20,6 +20,7 @@ import {
   ApiBearerAuth,
   ApiBody,
   ApiOperation,
+  ApiParam,
   ApiQuery,
   ApiResponse,
   ApiTags,
@@ -38,6 +39,8 @@ import { AllowAny } from "src/auth/decorators/allow-any.decorator";
 import { plainToInstance } from "class-transformer";
 import { validate, ValidationError } from "class-validator";
 import { DatasetsService } from "src/datasets/datasets.service";
+import { PartialUpdateDatasetDto } from "src/datasets/dto/update-dataset.dto";
+import { filterDescription, filterExample } from "src/common/utils";
 
 @ApiBearerAuth()
 @ApiTags("origdatablocks")
@@ -53,7 +56,7 @@ export class OrigDatablocksController {
   @CheckPolicies((ability: AppAbility) =>
     ability.can(Action.Create, OrigDatablock),
   )
-  @HttpCode(HttpStatus.OK)
+  @HttpCode(HttpStatus.CREATED)
   @Post()
   @ApiOperation({
     summary: "It creates a new orig datablock for the specified dataset.",
@@ -68,7 +71,8 @@ export class OrigDatablocksController {
   @ApiResponse({
     status: 201,
     type: OrigDatablock,
-    description: "Create a new dataset and return its representation in SciCat",
+    description:
+      "Create a new origdataset and return its representation in SciCat",
   })
   async create(
     @Body() createOrigDatablockDto: CreateOrigDatablockDto,
@@ -79,7 +83,47 @@ export class OrigDatablocksController {
     if (!dataset) {
       throw new BadRequestException("Invalid datasetId");
     }
-    return this.origDatablocksService.create(createOrigDatablockDto);
+
+    createOrigDatablockDto = {
+      ...createOrigDatablockDto,
+      ownerGroup: createOrigDatablockDto.ownerGroup
+        ? createOrigDatablockDto.ownerGroup
+        : dataset.ownerGroup,
+      accessGroups: createOrigDatablockDto.accessGroups
+        ? createOrigDatablockDto.accessGroups
+        : JSON.parse(JSON.stringify(dataset.accessGroups)),
+      instrumentGroup: createOrigDatablockDto.instrumentGroup
+        ? createOrigDatablockDto.instrumentGroup
+        : dataset.instrumentGroup,
+    };
+
+    const origdatablock = await this.origDatablocksService.create(
+      createOrigDatablockDto,
+    );
+
+    await this.updateDatasetSizeAndFiles(dataset.pid);
+
+    return origdatablock;
+  }
+
+  async updateDatasetSizeAndFiles(pid: string) {
+    // updates datasets size
+    const parsedFilters: IFilters<OrigDatablockDocument, IOrigDatablockFields> =
+      { where: { datasetId: pid } };
+    const datasetOrigdatablocks = await this.origDatablocksService.findAll(
+      parsedFilters,
+    );
+
+    const updateDatasetDto: PartialUpdateDatasetDto = {
+      size: datasetOrigdatablocks
+        .map((od) => od.size)
+        .reduce((ps, a) => ps + a, 0),
+      numberOfFiles: datasetOrigdatablocks
+        .map((od) => od.dataFileList.length)
+        .reduce((ps, a) => ps + a, 0),
+    };
+
+    await this.datasetsService.findByIdAndUpdate(pid, updateDatasetDto);
   }
 
   @AllowAny()
@@ -129,19 +173,23 @@ export class OrigDatablocksController {
       "It returns a list of orig datablocks. The list returned can be modified by providing a filter.",
   })
   @ApiQuery({
-    name: "filters",
-    description: "Database filters to apply when retrieving all origdatablocks",
+    name: "filter",
+    description:
+      "Database filters to apply when retrieving all origdatablocks\n" +
+      filterDescription,
     required: false,
+    type: String,
+    example: filterExample,
   })
   @ApiResponse({
     status: 200,
     type: OrigDatablock,
     isArray: true,
     description: "Return the orig datablocks requested",
   })
-  async findAll(@Query("filters") filters?: string): Promise<OrigDatablock[]> {
+  async findAll(@Query("filter") filter?: string): Promise<OrigDatablock[]> {
     const parsedFilters: IFilters<OrigDatablockDocument, IOrigDatablockFields> =
-      JSON.parse(filters ?? "{}");
+      JSON.parse(filter ?? "{}");
     return this.origDatablocksService.findAll(parsedFilters);
   }
 
@@ -252,6 +300,20 @@ export class OrigDatablocksController {
     ability.can(Action.Read, OrigDatablock),
   )
   @Get("/:id")
+  @ApiOperation({
+    summary: "It retrieve the origdatablock.",
+    description: "It retrieve the original datablock with the id specified.",
+  })
+  @ApiParam({
+    name: "id",
+    description: "Id of the origdatablock to be retrieved",
+    type: String,
+  })
+  @ApiResponse({
+    status: 200,
+    description: "The origdatablock requested",
+    type: OrigDatablock,
+  })
   async findById(@Param("id") id: string): Promise<OrigDatablock | null> {
     return this.origDatablocksService.findOne({ _id: id });
   }
@@ -262,23 +324,67 @@ export class OrigDatablocksController {
     ability.can(Action.Update, OrigDatablock),
   )
   @Patch("/:id")
+  @ApiOperation({
+    summary: "It updates the origdatablock.",
+    description: "It updates the original datablock with the id specified.",
+  })
+  @ApiParam({
+    name: "id",
+    description: "Id of the origdatablock to be updated",
+    type: String,
+  })
+  @ApiBody({
+    description:
+      "OrigDatablock object that needs to be updated. Only the origdatablock object fields that needs to be updated, should be passed in.",
+    required: true,
+    type: UpdateOrigDatablockDto,
+  })
+  @ApiResponse({
+    status: 200,
+    description: "The updated origdatablock",
+    type: OrigDatablock,
+  })
   async update(
     @Param("id") id: string,
     @Body() updateOrigDatablockDto: UpdateOrigDatablockDto,
   ): Promise<OrigDatablock | null> {
-    return this.origDatablocksService.update(
+    const origdatablock = (await this.origDatablocksService.update(
       { _id: id },
       updateOrigDatablockDto,
-    );
+    )) as OrigDatablock;
+
+    await this.updateDatasetSizeAndFiles(origdatablock.datasetId);
+
+    return origdatablock;
   }
 
   // DELETE /origdatablocks/:id
-  @UseGuards()
+  @UseGuards(PoliciesGuard)
   @CheckPolicies((ability: AppAbility) =>
     ability.can(Action.Delete, OrigDatablock),
   )
   @Delete("/:id")
+  @ApiOperation({
+    summary: "It deletes the origdatablock.",
+    description:
+      "It delete the original datablock specified through the id specified.",
+  })
+  @ApiParam({
+    name: "id",
+    description: "Id of the origdatablock to be deleted",
+    type: String,
+  })
+  @ApiResponse({
+    status: 200,
+    description: "No value is returned",
+  })
   async remove(@Param("id") id: string): Promise<unknown> {
-    return this.origDatablocksService.remove({ _id: id });
+    const origdatablock = (await this.origDatablocksService.remove({
+      _id: id,
+    })) as OrigDatablock;
+
+    await this.updateDatasetSizeAndFiles(origdatablock.datasetId);
+
+    return origdatablock;
   }
 }

src/origdatablocks/origdatablocks.service.ts

@@ -42,7 +42,20 @@ export class OrigDatablocksService {
   async findAll(
     filter: FilterQuery<OrigDatablockDocument>,
   ): Promise<OrigDatablock[]> {
-    return this.origDatablockModel.find(filter).exec();
+    const whereFilter: FilterQuery<OrigDatablockDocument> = filter.where ?? {};
+    const fieldsProjection: FilterQuery<OrigDatablockDocument> =
+      filter.fields ?? {};
+    const { limit, skip, sort } = parseLimitFilters(filter.limits);
+
+    const origdatablockPromise = this.origDatablockModel
+      .find(whereFilter, fieldsProjection)
+      .limit(limit)
+      .skip(skip)
+      .sort(sort);
+
+    const origdatablock = await origdatablockPromise.exec();
+
+    return origdatablock;
   }
 
   async findOne(