Merge branch 'master' into dependabot/npm_and_yarn/mocha-11.0.1

.github/workflows/upload-sdk-artifact.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches:
       - master
+  pull_request:
+    branches:
+      - master
 
 env:
   NODE_VERSION: 20.x
@@ -75,6 +78,17 @@ jobs:
             )
 
       - uses: actions/upload-artifact@v4
+        if: github.event_name == 'push'
         with:
           name: sdk-${{ matrix.generator }}-${{ github.sha }}
           path: ./sdk
+
+  cleanup-artifacts:
+    runs-on: ubuntu-latest
+    needs:
+      - generate-and-upload-sdk
+    if: github.event_name != 'push'
+    steps:
+      - uses: geekyeggo/delete-artifact@v5
+        with:
+          name: swagger-*

README.md

@@ -185,8 +185,8 @@ Valid environment variables for the .env file. See [.env.example](/.env.example)
 | `ES_REFRESH` | string | | If set to `wait_for`, Elasticsearch will wait till data is inserted into the specified index before returning a response. | false |
 | `LOGGERS_CONFIG_FILE` | string | | The file name for loggers configuration, located in the project root directory. | "loggers.json" |
 | `PROPOSAL_TYPES_FILE` | string | | The file name for proposal types configuration, located in the project root directory. | "proposalTypes.json" |
-| `SWAGGER_PATH` | string | Yes | swaggerPath is the path where the swagger UI will be available| "explorer"|
-| `MAX_FILE_UPLOAD_SIZE` | string | Yes | Maximum allowed file upload size | "16mb"|
+| `SWAGGER_PATH` | string | Yes | swaggerPath is the path where the swagger UI will be available. | "explorer"|
+| `MAX_FILE_UPLOAD_SIZE` | string | Yes | Maximum allowed file upload size. | "16mb"|
 
 ## Migrating from the old SciCat Backend
 

src/datasets/datasets.service.ts

@@ -287,7 +287,7 @@ export class DatasetsService {
       const datasets = this.datasetModel.find({}, { _id: 0 }).lean().exec();
       return datasets;
     } catch (error) {
-      throw new NotFoundException();
+      throw new NotFoundException(error);
     }
   }
   // Get metadata keys

src/datasets/dto/create-derived-dataset-obsolete.dto.ts

@@ -24,4 +24,13 @@ export class CreateDerivedDatasetObsoleteDto extends UpdateDerivedDatasetObsolet
   @IsOptional()
   @IsString()
   readonly version?: string;
+
+  @ApiProperty({
+    type: String,
+    required: true,
+    description:
+      "A name for the dataset, given by the creator to carry some semantic meaning. Useful for display purposes e.g. instead of displaying the pid.",
+  })
+  @IsString()
+  declare readonly datasetName: string;
 }

src/datasets/dto/create-raw-dataset-obsolete.dto.ts

@@ -24,4 +24,13 @@ export class CreateRawDatasetObsoleteDto extends UpdateRawDatasetObsoleteDto {
   @IsOptional()
   @IsString()
   readonly version?: string;
+
+  @ApiProperty({
+    type: String,
+    required: true,
+    description:
+      "A name for the dataset, given by the creator to carry some semantic meaning. Useful for display purposes e.g. instead of displaying the pid.",
+  })
+  @IsString()
+  declare readonly datasetName: string;
 }

src/datasets/dto/output-dataset-obsolete.dto.ts

@@ -17,7 +17,7 @@ import { Datablock } from "src/datablocks/schemas/datablock.schema";
 export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
   @ApiProperty({
     type: String,
-    required: false,
+    required: true,
     description: "Persistent identifier of the dataset.",
   })
   @IsString()
@@ -44,7 +44,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
 
   @ApiProperty({
     type: String,
-    required: true,
+    required: false,
     description:
       "First name and last name of principal investigator(s). If multiple PIs are present, use a semicolon separated list. This field is required if the dataset is a Raw dataset.",
   })
@@ -74,7 +74,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
 
   @ApiProperty({
     type: String,
-    required: true,
+    required: false,
     description:
       "Unique location identifier where data was taken, usually in the form /Site-name/facility-name/instrumentOrBeamline-name. This field is required if the dataset is a Raw dataset.",
   })
@@ -112,7 +112,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
 
   @ApiProperty({
     type: String,
-    required: true,
+    required: false,
     description:
       "First name and last name of the person or people pursuing the data analysis. The string may contain a list of names, which should then be separated by semicolons.",
   })
@@ -122,7 +122,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
 
   @ApiProperty({
     type: [String],
-    required: true,
+    required: false,
     description:
       "Array of input dataset identifiers used in producing the derived dataset. Ideally these are the global identifier to existing datasets inside this or federated data catalogs.",
   })
@@ -134,7 +134,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
 
   @ApiProperty({
     type: [String],
-    required: true,
+    required: false,
     description:
       "A list of links to software repositories which uniquely identifies the pieces of software, including versions, used for yielding the derived data.",
   })
@@ -183,6 +183,9 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
     description:
       "Containers that list all files and their attributes which make up a dataset. Usually filled at the time the dataset's metadata is created in the data catalog. Can be used by subsequent archiving processes to create the archived datasets.",
   })
+  @IsOptional()
+  @IsArray()
+  @Type(() => OrigDatablock)
   origdatablocks?: OrigDatablock[];
 
   @ApiProperty({
@@ -192,6 +195,9 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
     description:
       "When archiving a dataset, all files contained in the dataset are listed here together with their checksum information. Several datablocks can be created if the file listing is too long for a single datablock. This partitioning decision is done by the archiving system to allow for chunks of datablocks with manageable sizes. E.g a datasets consisting of 10 TB of data could be split into 10 datablocks of about 1 TB each. The upper limit set by the data catalog system itself is given by the fact that documents must be smaller than 16 MB, which typically allows for datasets of about 100000 files.",
   })
+  @IsOptional()
+  @IsArray()
+  @Type(() => Datablock)
   datablocks?: Datablock[];
 
   @ApiProperty({
@@ -200,6 +206,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
     description:
       "Indicate the user who created this record. This property is added and maintained by the system.",
   })
+  @IsString()
   createdBy: string;
 
   @ApiProperty({
@@ -208,6 +215,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
     description:
       "Indicate the user who updated this record last. This property is added and maintained by the system.",
   })
+  @IsString()
   updatedBy: string;
 
   @ApiProperty({
@@ -216,6 +224,7 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
     description:
       "Date and time when this record was created. This field is managed by mongoose with through the timestamp settings. The field should be a string containing a date in ISO 8601 format (2024-02-27T12:26:57.313Z)",
   })
+  @IsDateString()
   createdAt: Date;
 
   @ApiProperty({
@@ -224,5 +233,6 @@ export class OutputDatasetObsoleteDto extends UpdateDatasetObsoleteDto {
     description:
       "Date and time when this record was updated last. This field is managed by mongoose with through the timestamp settings. The field should be a string containing a date in ISO 8601 format (2024-02-27T12:26:57.313Z)",
   })
+  @IsDateString()
   updatedAt: Date;
 }

src/datasets/dto/update-dataset-obsolete.dto.ts

@@ -123,12 +123,12 @@ export class UpdateDatasetObsoleteDto extends OwnableDto {
   @ApiProperty({
     type: Number,
     default: 0,
-    required: true,
+    required: false,
     description: "Total number of files in all Datablocks for this dataset.",
   })
   @IsOptional()
   @IsInt()
-  readonly numberOfFilesArchived?: number;
+  readonly numberOfFilesArchived?: number = 0;
 
   @ApiProperty({
     type: Date,

src/datasets/dto/update-dataset.dto.ts

@@ -30,7 +30,7 @@ import { HistoryClass } from "../schemas/history.schema";
 export class UpdateDatasetDto extends OwnableDto {
   @ApiProperty({
     type: String,
-    required: true,
+    required: false,
     description:
       "Owner or custodian of the dataset, usually first name + last name. The string may contain a list of persons, which should then be separated by semicolons.",
   })
@@ -125,7 +125,7 @@ export class UpdateDatasetDto extends OwnableDto {
   @ApiProperty({
     type: Number,
     default: 0,
-    required: true,
+    required: false,
     description: "Total number of files in all Datablocks for this dataset.",
   })
   @IsOptional()
@@ -152,7 +152,8 @@ export class UpdateDatasetDto extends OwnableDto {
   readonly validationStatus?: string;
 
   @ApiProperty({
-    type: [String],
+    type: String,
+    isArray: true,
     required: false,
     description:
       "Array of tags associated with the meaning or contents of this dataset. Values should ideally come from defined vocabularies, taxonomies, ontologies or knowledge graphs.",
@@ -226,7 +227,8 @@ export class UpdateDatasetDto extends OwnableDto {
 
   // it needs to be discussed if this fields is managed by the user or by the system
   @ApiProperty({
-    type: [String],
+    type: String,
+    isArray: true,
     required: false,
     default: [],
     description: "List of users that the dataset has been shared with.",
@@ -342,7 +344,8 @@ export class UpdateDatasetDto extends OwnableDto {
   readonly dataFormat?: string;
 
   @ApiProperty({
-    type: [String],
+    type: String,
+    isArray: true,
     required: false,
     description:
       "ID of the proposal or proposals which the dataset belongs to.<br>This dataset might have been acquired under the listed proposals or is derived from datasets acquired from datasets belonging to the listed datasets.",
@@ -354,7 +357,8 @@ export class UpdateDatasetDto extends OwnableDto {
   readonly proposalIds?: string[];
 
   @ApiProperty({
-    type: [String],
+    type: String,
+    isArray: true,
     required: false,
     description:
       "ID of the sample or samples used when collecting the data included or used in this dataset.",
@@ -367,6 +371,7 @@ export class UpdateDatasetDto extends OwnableDto {
 
   @ApiProperty({
     type: String,
+    isArray: true,
     required: false,
     description:
       "ID of the instrument or instruments where the data included or used in this datasets was collected on.",
@@ -378,8 +383,9 @@ export class UpdateDatasetDto extends OwnableDto {
   readonly instrumentIds?: string[];
 
   @ApiProperty({
-    type: [String],
-    required: true,
+    type: String,
+    isArray: true,
+    required: false,
     description:
       "Array of input dataset identifiers used in producing the derived dataset. Ideally these are the global identifier to existing datasets inside this or federated data catalogs.",
   })
@@ -390,7 +396,8 @@ export class UpdateDatasetDto extends OwnableDto {
   readonly inputDatasets?: string[];
 
   @ApiProperty({
-    type: [String],
+    type: String,
+    isArray: true,
     required: false,
     description:
       "A list of links to software repositories which uniquely identifies the pieces of software, including versions, used for yielding the derived data.",

src/datasets/schemas/dataset.schema.ts

@@ -3,7 +3,6 @@ import { ApiProperty, getSchemaPath } from "@nestjs/swagger";
 import { Document } from "mongoose";
 import { OwnableClass } from "src/common/schemas/ownable.schema";
 import { v4 as uuidv4 } from "uuid";
-import { DatasetType } from "../dataset-type.enum";
 import { HistoryClass, HistorySchema } from "./history.schema";
 import { LifecycleClass, LifecycleSchema } from "./lifecycle.schema";
 import { RelationshipClass, RelationshipSchema } from "./relationship.schema";

src/proposals/dto/update-proposal.dto.ts

@@ -4,7 +4,6 @@ import {
   IsArray,
   IsDateString,
   IsEmail,
-  IsEnum,
   IsObject,
   IsOptional,
   IsString,

src/proposals/proposals.controller.ts

@@ -164,7 +164,7 @@ export class ProposalsController {
           return false;
       }
     } catch (error) {
-      throw new InternalServerErrorException();
+      throw new InternalServerErrorException(error);
     }
   }
 

src/samples/samples.controller.ts

@@ -160,7 +160,7 @@ export class SamplesController {
           return false;
       }
     } catch (error) {
-      throw new InternalServerErrorException();
+      throw new InternalServerErrorException(error);
     }
   }
 
@@ -410,7 +410,6 @@ export class SamplesController {
     required: false,
     type: String,
     // NOTE: This is custom example because the service function metadataKeys expects input like the following.
-    // eslint-disable-next-line @/quotes
     example: '{ "fields": { "metadataKey": "chemical_formula" } }',
   })
   @ApiResponse({