Skip to content

refactor: simplify job validation and reduce db calls #2714

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
minottic wants to merge 1 commit into
base: master
Choose a base branch
from
Open

refactor: simplify job validation and reduce db calls #2714

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
204 changes: 62 additions & 142 deletions src/jobs/jobs.controller.utils.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,8 @@ import {
import { toObject } from "src/config/job-config/actions/actionutils";
import { loadDatasets } from "src/config/job-config/actions/actionutils";
import { DatasetClass } from "src/datasets/schemas/dataset.schema";
import { validate } from "class-validator";
import { plainToInstance } from "class-transformer";

@Injectable()
export class JobsControllerUtils {
Expand Down Expand Up @@ -81,63 +83,30 @@ export class JobsControllerUtils {
JobParams.DatasetList
] as Array<DatasetListDto>;
// check that datasetList is a non empty array
if (!Array.isArray(datasetList)) {
throw new HttpException(
{
status: HttpStatus.BAD_REQUEST,
message: "Invalid dataset list",
},
HttpStatus.BAD_REQUEST,
);
}
if (datasetList.length == 0) {
throw new HttpException(
{
status: HttpStatus.BAD_REQUEST,
message: "List of passed datasets is empty.",
},
HttpStatus.BAD_REQUEST,
if (!Array.isArray(datasetList))
throw new UnprocessableEntityException("Invalid dataset list");
if (datasetList.length == 0)
throw new UnprocessableEntityException(
"List of passed datasets is empty.",
);
}

// check that datasetList is of type DatasetListDto[]
const datasetListDtos: DatasetListDto[] = datasetList.map((item) => {
return Object.assign(new DatasetListDto(), item);
});
const allowedKeys = [JobParams.Pid, JobParams.Files] as string[];
for (const datasetListDto of datasetListDtos) {
const keys = Object.keys(datasetListDto);
if (
keys.length !== 2 ||
!keys.every((key) => allowedKeys.includes(key))
) {
throw new HttpException(
{
status: HttpStatus.BAD_REQUEST,
message:
"Dataset list is expected to contain sets of pid and files.",
},
HttpStatus.BAD_REQUEST,
);
}
if (typeof datasetListDto[JobParams.Pid] !== "string") {
throw new HttpException(
{
status: HttpStatus.BAD_REQUEST,
message: "In datasetList each 'pid' field should be a string.",
},
HttpStatus.BAD_REQUEST,
);
}
if (!Array.isArray(datasetListDto[JobParams.Files])) {
throw new HttpException(
{
status: HttpStatus.BAD_REQUEST,
message: "In datasetList each 'files' field should be an array.",
},
HttpStatus.BAD_REQUEST,
);
}
const datasetListDtos: DatasetListDto[] = plainToInstance(
DatasetListDto,
datasetList,
);
const nestedErrors = await Promise.all(
datasetListDtos.map((dto) => validate(dto)),
Comment thread
sourcery-ai[bot] marked this conversation as resolved.
);
const validateErrors = nestedErrors.flat();
if (validateErrors.length > 0) {
const minimalErrors = validateErrors.map(({ property, constraints }) => ({
property,
constraints,
}));
throw new UnprocessableEntityException(
"Invalid dataset list. " + JSON.stringify(minimalErrors),
);
}

// check that all requested pids exist
Expand All @@ -152,33 +121,22 @@ export class JobsControllerUtils {
* Check that the dataset pids are valid
*/
async checkDatasetPids(datasetList: DatasetListDto[]): Promise<void> {
interface condition {
where: {
pid: { $in: string[] };
};
}

const datasetIds = datasetList.map((x) => x.pid);
const filter: condition = {
const filter: FilterQuery<DatasetClass> = {
where: {
pid: { $in: datasetIds },
},
fields: ["pid"],
};

const findDatasetsById = await this.datasetsService.findAll(filter);
const findIds = findDatasetsById.map(({ pid }) => pid);
const nonExistIds = datasetIds.filter((x) => !findIds.includes(x));
const datasets = await this.datasetsService.findAll(filter);
const findIds = new Set(datasets.map(({ pid }) => pid));
const nonExistIds = datasetIds.filter((x) => !findIds.has(x));

if (nonExistIds.length != 0) {
throw new HttpException(
{
status: HttpStatus.BAD_REQUEST,
message: `Datasets with pid ${nonExistIds} do not exist.`,
},
HttpStatus.BAD_REQUEST,
);
}
return;
if (nonExistIds.length == 0) return;
throw new UnprocessableEntityException(
`Datasets with pid ${nonExistIds} do not exist.`,
);
}

/**
Expand All @@ -187,74 +145,36 @@ export class JobsControllerUtils {
async checkDatasetFiles(datasetList: DatasetListDto[]): Promise<void> {
const datasetsToCheck = datasetList.filter((x) => x.files.length > 0);
const ids = datasetsToCheck.map((x) => x.pid);
if (ids.length > 0) {
const filter = {
fields: {
pid: true,
datasetId: true,
dataFileList: true,
},
where: {
pid: {
$in: ids,
},
},
};
// Indexing originDataBlock with pid and create set of files for each dataset
const datasets = await this.datasetsService.findAll(filter);
// Include origdatablocks
let datasetOrigDatablocks: OrigDatablock[] = [];
await Promise.all(
datasets.map(async (dataset) => {
datasetOrigDatablocks = await this.origDatablocksService.findAll({
where: { datasetId: dataset.pid },
});
}),
);
const result: Record<string, Set<string>> = datasets.reduce(
(acc: Record<string, Set<string>>, dataset) => {
// Using Set make searching more efficient
const files = datasetOrigDatablocks.reduce((acc, block) => {
block.dataFileList.forEach((file) => {
acc.add(file.path);
});
return acc;
}, new Set<string>());
acc[dataset.pid] = files;
return acc;
},
{},
);
// Get a list of requested files that were not found
const checkResults = datasetsToCheck.reduce(
(acc: { pid: string; nonExistFiles: string[] }[], x) => {
const pid = x.pid;
const referenceFiles = result[pid];
const nonExistFiles = x.files.filter((f) => !referenceFiles.has(f));
if (nonExistFiles.length > 0) {
acc.push({ pid, nonExistFiles });
}
return acc;
},
[],
);
if (checkResults.length > 0) {
throw new HttpException(
{
status: HttpStatus.BAD_REQUEST,
message: "At least one requested file could not be found.",
error: JSON.stringify(
checkResults.map(({ pid, nonExistFiles }) => ({
pid,
nonExistFiles,
})),
),
},
HttpStatus.BAD_REQUEST,
);
}
}
return;
if (ids.length == 0) return;
// Indexing originDataBlock with pid and create set of files for each dataset
const datasetOrigDatablocks: OrigDatablock[] =
await this.origDatablocksService.findAll({
where: { datasetId: { $in: ids } },
fields: ["datasetId", "dataFileList.path"],
});

const origsMappedByDatasetId = datasetOrigDatablocks.reduce(
(acc, orig) => {
const set = (acc[orig.datasetId] ??= new Set<string>());
orig.dataFileList.forEach((file) => set.add(file.path));
return acc;
},
{} as Record<string, Set<string>>,
);
// Get a list of requested files that were not found
const checkResults = datasetsToCheck
.map(({ pid, files }) => {
const referenceFiles = origsMappedByDatasetId[pid] ?? new Set<string>();
const nonExistFiles = files.filter((f) => !referenceFiles.has(f));
return { pid, nonExistFiles };
})
.filter((result) => result.nonExistFiles.length > 0);

if (checkResults.length == 0) return;
throw new UnprocessableEntityException({
message: "At least one requested file could not be found.",
error: JSON.stringify(checkResults),
});
}

/**
Expand Down
2 changes: 1 addition & 1 deletion test/Jobs.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -253,7 +253,7 @@ describe("1110: Jobs: Test New Job Model: possible real configurations", () => {
.send(newJob)
.set("Accept", "application/json")
.set({ Authorization: `Bearer ${accessTokenUser51}` })
.expect(TestData.BadRequestStatusCode)
.expect(TestData.UnprocessableEntityStatusCode)
.expect("Content-Type", /json/)
.then((res) => {
res.body.should.not.have.property("id");
Expand Down
4 changes: 2 additions & 2 deletions test/JobsAll.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -174,7 +174,7 @@ describe("1120: Jobs: Test New Job Model Authorization for all_access jobs type"
.send(newJob)
.set("Accept", "application/json")
.set({ Authorization: `Bearer ${accessTokenAdmin}` })
.expect(TestData.BadRequestStatusCode)
.expect(TestData.UnprocessableEntityStatusCode)
.expect("Content-Type", /json/)
.then((res) => {
res.body.should.not.have.property("id");
Expand Down Expand Up @@ -202,7 +202,7 @@ describe("1120: Jobs: Test New Job Model Authorization for all_access jobs type"
.send(newJob)
.set("Accept", "application/json")
.set({ Authorization: `Bearer ${accessTokenAdmin}` })
.expect(TestData.BadRequestStatusCode)
.expect(TestData.UnprocessableEntityStatusCode)
.expect("Content-Type", /json/)
.then((res) => {
res.body.should.not.have.property("id");
Expand Down
Loading
Loading