Merge pull request #243 from SciCatProject/fix-linting-issues

fix linting issues and add back the datasetlifecycle

src/datasets/datasets.controller.ts

@@ -111,7 +111,7 @@ export class DatasetsController {
   @ApiOperation({
     summary: "It creates a new dataset which can be a raw or derived one.",
     description:
-      "It creates a new proposal and returnes it completed with systems fields.",
+      "It creates a new dataset and returns it completed with systems fields.",
   })
   @ApiExtraModels(CreateRawDatasetDto, CreateDerivedDatasetDto)
   @ApiBody({
@@ -127,8 +127,7 @@ export class DatasetsController {
   @ApiResponse({
     status: 201,
     type: DatasetClass,
-    description:
-      "Create a new proposal and return its representation in SciCat",
+    description: "Create a new dataset and return its representation in SciCat",
   })
   async create(
     @Body() createDatasetDto: CreateRawDatasetDto | CreateDerivedDatasetDto,
@@ -214,7 +213,7 @@ export class DatasetsController {
     status: 200,
     type: Boolean,
     description:
-      "Check if the proposal provided pass validation. It return true if the validation is passed",
+      "Check if the dataset provided pass validation. It return true if the validation is passed",
   })
   async isValid(
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
@@ -389,7 +388,7 @@ export class DatasetsController {
     status: 200,
     type: DatasetClass,
     isArray: true,
-    description: "Return proposals requested",
+    description: "Return datasets requested",
   })
   async fullfacet(
     @Query() filters: { fields?: string; facets?: string },
@@ -586,7 +585,7 @@ export class DatasetsController {
   @ApiExtraModels(UpdateRawDatasetDto, UpdateDerivedDatasetDto)
   @ApiBody({
     description:
-      "Fields that needs to be updated in the dataset. Only the fields that needs to be updated have to passed in.",
+      "Fields that needs to be updated in the dataset. Only the fields that needs to be updated have to be passed in.",
     required: true,
     schema: {
       oneOf: [
@@ -609,6 +608,12 @@ export class DatasetsController {
     return this.datasetsService.findByIdAndUpdate(pid, updateDatasetDto);
   }
 
+  /**
+   * NOTE: PUT and PATCH functionality is exactly the same and behaves as a PATCH. They update only the fields that are passed in.
+   * In literature, the PUT method should replace completely the object requested with the values passed in.
+   * Here is an example of a proper implementation: https://wanago.io/2021/09/27/api-nestjs-put-patch-mongodb-mongoose/
+   * There is a ticket open for discussion where we decide how to move forward: https://jira.esss.lu.se/browse/SWAP-2942
+   */
   // PUT /datasets/:id
   @UseGuards(PoliciesGuard)
   @CheckPolicies((ability: AppAbility) =>
@@ -624,38 +629,36 @@ export class DatasetsController {
   @ApiOperation({
     summary: "It updates the dataset.",
     description:
-      "It updates the dataset specified through the pid specified. The full dataset is updated.",
+      "It updates the dataset specified through the pid provided. Only the specified fields are updated(at the moment put and patch behavior is completely the same).",
   })
   @ApiParam({
     name: "pid",
     description: "Id of the dataset to modify",
     type: String,
   })
-  @ApiExtraModels(CreateRawDatasetDto, CreateDerivedDatasetDto)
+  @ApiExtraModels(UpdateRawDatasetDto, UpdateDerivedDatasetDto)
   @ApiBody({
     description:
-      "Complete dataset definition with new values to replace current ones. The complete dataset structure needs to be specified.",
+      "Fields that needs to be updated in the dataset. Only the fields that needs to be updated have to be passed in.",
     required: true,
     schema: {
       oneOf: [
-        { $ref: getSchemaPath(CreateRawDatasetDto) },
-        { $ref: getSchemaPath(CreateDerivedDatasetDto) },
+        { $ref: getSchemaPath(UpdateRawDatasetDto) },
+        { $ref: getSchemaPath(UpdateDerivedDatasetDto) },
       ],
     },
   })
   @ApiResponse({
     status: 200,
     type: DatasetClass,
     description:
-      "Completely update an existing dataset and return its representation in SciCat",
+      "Update an existing dataset and return its representation in SciCat",
   })
   async findByIdReplaceOrCreate(
     @Param("pid") id: string,
-    @Body() replaceDatasetDto: CreateRawDatasetDto | CreateDerivedDatasetDto,
+    @Body() updateDatasetDto: UpdateRawDatasetDto | UpdateDerivedDatasetDto,
   ): Promise<DatasetClass | null> {
-    // validate dataset
-    const validatedDatasetDto = await this.validateDataset(replaceDatasetDto);
-    return this.datasetsService.findByIdAndUpdate(id, validatedDatasetDto);
+    return this.datasetsService.findByIdAndUpdate(id, updateDatasetDto);
   }
 
   // DELETE /datasets/:id

src/datasets/datasets.service.ts

@@ -354,7 +354,7 @@ export class DatasetsService {
           previousValue: dataset[updatedField as keyof UpdateDatasetDto],
         };
       });
-      dataset.history = dataset.history ?? []
+      dataset.history = dataset.history ?? [];
       dataset.history.push({
         updatedBy: (req.user as JWTUser).username,
         ...JSON.parse(JSON.stringify(historyItem).replace(/\$/g, "")),

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

@@ -17,7 +17,8 @@ import { ApiProperty, ApiTags, getSchemaPath } from "@nestjs/swagger";
 import { DatasetType } from "../dataset-type.enum";
 import { Type } from "class-transformer";
 import { CreateRelationshipDto } from "./create-relationship.dto";
-import { CreateTechniqueDto } from "./create-technique.dto"
+import { CreateTechniqueDto } from "./create-technique.dto";
+import { LifecycleClass } from "../schemas/lifecycle.schema";
 
 @ApiTags("datasets")
 export class CreateDatasetDto extends OwnableDto {
@@ -82,14 +83,14 @@ export class CreateDatasetDto extends OwnableDto {
     required: false,
     description:
       "DNS host name of file server hosting sourceFolder, optionally including protocol e.g. [protocol://]fileserver1.example.com",
-  })  
+  })
   @IsOptional()
   @IsFQDN()
   readonly sourceFolderHost?: string;
 
   /*
    * size and number of files fields should be managed by the system
-   */ 
+   */
   @ApiProperty({
     type: Number,
     default: 0,
@@ -107,7 +108,7 @@ export class CreateDatasetDto extends OwnableDto {
     required: false,
     description:
       "Total size of all datablock package files created for this dataset",
-  })  
+  })
   @IsOptional()
   @IsInt()
   readonly packedSize?: number = 0;
@@ -273,6 +274,16 @@ export class CreateDatasetDto extends OwnableDto {
   @Type(() => CreateRelationshipDto)
   readonly relationships?: RelationshipClass[];
 
+  @ApiProperty({
+    type: LifecycleClass,
+    required: false,
+    default: {},
+    description:
+      "For each dataset there exists an embedded dataset lifecycle document which describes the current status of the dataset during its lifetime with respect to the storage handling systems",
+  })
+  @IsOptional()
+  readonly datasetlifecycle: LifecycleClass;
+
   @ApiProperty({
     type: Object,
     required: false,
@@ -283,4 +294,3 @@ export class CreateDatasetDto extends OwnableDto {
   @IsObject()
   readonly scientificMetadata?: Record<string, unknown>;
 }
-

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

@@ -7,7 +7,8 @@ export class CreateRawDatasetDto extends CreateDatasetDto {
   @ApiProperty({
     type: String,
     required: true,
-    description: "Email of principal investigator. This field is required if the dataset is a Raw dataset.",
+    description:
+      "Email of principal investigator. This field is required if the dataset is a Raw dataset.",
   })
   @IsString()
   readonly principalInvestigator: string;
@@ -17,7 +18,7 @@ export class CreateRawDatasetDto extends CreateDatasetDto {
     required: false,
     description:
       "Time of end of data taking for this dataset, format according to chapter 5.6 internet date/time format in RFC 3339. Local times without timezone/offset info are automatically transformed to UTC using the timezone of the API server. This field is required if the dataset is a Raw dataset",
-  })  
+  })
   @IsOptional()
   @IsDateString()
   readonly endTime?: Date;

src/datasets/dto/create-technique.dto.ts

@@ -5,7 +5,8 @@ export class CreateTechniqueDto {
   @ApiProperty({
     type: String,
     required: true,
-    description: "Persistent Identifier of the technique. Usually it is a UUIDv4",
+    description:
+      "Persistent Identifier of the technique. Usually it is a UUIDv4",
   })
   @IsString()
   readonly pid: string;

src/datasets/interceptors/fullquery.interceptor.ts

@@ -34,16 +34,21 @@ export class FullQueryInterceptor implements NestInterceptor {
                 scientificMetadata,
                 `${lhs}.value`,
               ) as number;
-              if (unit && currentUnit && currentUnit !== unit) {
+              if (
+                unit &&
+                currentUnit &&
+                currentUnit !== unit &&
+                scientificMetadata
+              ) {
                 const { valueRequested, unitRequested } =
                   convertToRequestedUnit(currentValue, currentUnit, unit);
                 lodash.update(
-                  scientificMetadata as Object,
+                  scientificMetadata,
                   `${lhs}.unit`,
                   () => unitRequested,
                 );
                 lodash.update(
-                  scientificMetadata as Object,
+                  scientificMetadata,
                   `${lhs}.value`,
                   () => valueRequested,
                 );

src/datasets/schemas/dataset.schema.ts

@@ -1,12 +1,11 @@
 import { Prop, Schema, SchemaFactory } from "@nestjs/mongoose";
 import { ApiProperty, getSchemaPath } from "@nestjs/swagger";
 import { Document } from "mongoose";
-import { Attachment, AttachmentSchema } from "src/attachments/schemas/attachment.schema";
-/*
 import {
   Attachment,
   AttachmentSchema,
 } from "src/attachments/schemas/attachment.schema";
+import { OwnableClass } from "src/common/schemas/ownable.schema";
 import {
   Datablock,
   DatablockSchema,
@@ -15,10 +14,6 @@ import {
   OrigDatablock,
   OrigDatablockSchema,
 } from "src/origdatablocks/schemas/origdatablock.schema";
-*/
-import { OwnableClass } from "src/common/schemas/ownable.schema";
-import { Datablock, DatablockSchema } from "src/datablocks/schemas/datablock.schema";
-import { OrigDatablock, OrigDatablockSchema } from "src/origdatablocks/schemas/origdatablock.schema";
 import { v4 as uuidv4 } from "uuid";
 import { DatasetType } from "../dataset-type.enum";
 import { HistoryClass, HistorySchema } from "./history.schema";
@@ -104,10 +99,10 @@ export class DatasetClass extends OwnableClass {
     description:
       "Email of contact person for this dataset. The string may contain a list of emails, which should then be seperated by semicolons.",
   })
-  @Prop({ 
-    type: String, 
-    required: true, 
-    index: true 
+  @Prop({
+    type: String,
+    required: true,
+    index: true,
   })
   contactEmail: string;
 
@@ -134,10 +129,10 @@ export class DatasetClass extends OwnableClass {
     description:
       "DNS host name of file server hosting sourceFolder, optionally including protocol e.g. [protocol://]fileserver1.example.com",
   })
-  @Prop({ 
-    type: String, 
+  @Prop({
+    type: String,
     required: false,
-    index: true 
+    index: true,
   })
   sourceFolderHost?: string;
 
@@ -148,11 +143,11 @@ export class DatasetClass extends OwnableClass {
     description:
       "Total size of all source files contained in source folder on disk when unpacked",
   })
-  @Prop({ 
+  @Prop({
     type: Number,
-    required: true, 
-    index: true, 
-    default: 0
+    required: true,
+    index: true,
+    default: 0,
   })
   size: number;
 
@@ -333,10 +328,10 @@ export class DatasetClass extends OwnableClass {
     default: [],
     description: "List of users that the dataset has been shared with",
   })
-  @Prop({ 
+  @Prop({
     type: [String],
     required: false,
-    default: []
+    default: [],
   })
   sharedWith?: string[];
 
@@ -371,7 +366,7 @@ export class DatasetClass extends OwnableClass {
   })
   @Prop({ type: [DatablockSchema], default: [] })
   datablocks: Datablock[];
-  
+
   @ApiProperty({
     type: Object,
     required: false,
@@ -387,7 +382,8 @@ export class DatasetClass extends OwnableClass {
   @ApiProperty({
     type: String,
     required: false,
-    description: "Email of principal investigator. This field is required if the dataset is a Raw dataset.",
+    description:
+      "Email of principal investigator. This field is required if the dataset is a Raw dataset.",
   })
   @Prop({ type: String, required: false })
   principalInvestigator?: string;

src/datasets/schemas/history.schema.ts

@@ -5,15 +5,14 @@ import { v4 as uuidv4 } from "uuid";
 
 export type HistoryDocument = HistoryClass & Document;
 
-@Schema({ 
-  strict: false, 
-  timestamps: { 
-    createdAt: false, 
-    updatedAt: true 
-  }
+@Schema({
+  strict: false,
+  timestamps: {
+    createdAt: false,
+    updatedAt: true,
+  },
 })
 export class HistoryClass {
-
   @ApiProperty({
     type: String,
     required: true,
@@ -25,7 +24,7 @@ export class HistoryClass {
     type: String,
     //unique: true,
     required: true,
-    default: uuidv4()
+    default: uuidv4(),
   })
   /*
   id: string;
@@ -51,26 +50,24 @@ export class HistoryClass {
     type: Date,
     required: true,
     default: Date.now(),
-    description:
-      "Time when update was performed.",
-  })  
-  @Prop({ 
-    type: Date, 
-    required: true, 
-    default: Date.now() 
+    description: "Time when update was performed.",
+  })
+  @Prop({
+    type: Date,
+    required: true,
+    default: Date.now(),
   })
   updatedAt: Date;
 
   @ApiProperty({
     type: Date,
     required: true,
     default: Date.now(),
-    description:
-      "Username of the user that performed the update.",
-  })  
-  @Prop({ 
-    type: String, 
-    required: true 
+    description: "Username of the user that performed the update.",
+  })
+  @Prop({
+    type: String,
+    required: true,
   })
   updatedBy: string;
 }