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fix: fix dataset output dto #1432

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merged 4 commits into from
Sep 27, 2024
Merged

fix: fix dataset output dto #1432

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1d381be
fixing the dataset output dto
nitrosx Sep 24, 2024
441374f
updated raw datasets to include instrument and sample id
nitrosx Sep 24, 2024
2e9763b
fixed obsolete dataset dtos
nitrosx Sep 25, 2024
dc99292
removed commented field from dataset dto
nitrosx Sep 27, 2024
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32 changes: 17 additions & 15 deletions src/datasets/datasets.controller.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -409,16 +409,16 @@ export class DatasetsController {
version: "v3",
};

if ("proposalId" in inputObsoleteDataset) {
propertiesModifier.proposalIds = [
(inputObsoleteDataset as CreateRawDatasetObsoleteDto).proposalId,
];
}
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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,
Expand Down Expand Up @@ -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;
}
Expand All @@ -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),
Expand Down Expand Up @@ -739,13 +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 }) => {
Expand Down Expand Up @@ -780,7 +782,7 @@ export class DatasetsController {
}),
);
}
return datasets;
return outputDatasets;
}

// GET /datasets/fullquery
Expand Down
16 changes: 8 additions & 8 deletions src/datasets/dto/output-dataset-obsolete.dto.ts
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Expand Up @@ -92,14 +92,14 @@ 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,
// description: "The ID of the proposal to which the dataset belongs.",
// })
// @IsOptional()
// @IsString()
// readonly proposalId?: string;
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@ApiProperty({
type: String,
Expand Down
9 changes: 9 additions & 0 deletions src/datasets/dto/update-dataset-obsolete.dto.ts
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Expand Up @@ -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(
Expand Down
16 changes: 8 additions & 8 deletions src/datasets/dto/update-raw-dataset-obsolete.dto.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
3 changes: 3 additions & 0 deletions test/DerivedDataset.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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"];
});
});
Expand Down
1 change: 0 additions & 1 deletion test/OrigDatablockForRawDataset.js
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Expand Up @@ -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)
Expand Down
3 changes: 3 additions & 0 deletions test/RawDataset.js
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Expand Up @@ -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"]);
});
});
Expand Down
5 changes: 5 additions & 0 deletions test/TestData.js
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Expand Up @@ -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"],
},
Expand Down Expand Up @@ -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: {
Expand Down
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