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* add program exception model * add route with controller * add exception servicen and typings file * exception db funcs * 422 status code util * exception util file * clean up exception repo file * fix req error handling * fix record error handling for promise behaviour * add swagger * remove unused util file * use enum for exception values * fix up types * add no emit typecheck command * add no program exception record type guard * rename req body check func * change HTTP status code Co-authored-by: Ciaran Schutte <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| /* | ||
| * Copyright (c) 2022 The Ontario Institute for Cancer Research. All rights reserved | ||
| * | ||
| * This program and the accompanying materials are made available under the terms of | ||
| * the GNU Affero General Public License v3.0. You should have received a copy of the | ||
| * GNU Affero General Public License along with this program. | ||
| * If not, see <http://www.gnu.org/licenses/>. | ||
| * | ||
| * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY | ||
| * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES | ||
| * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT | ||
| * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, | ||
| * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED | ||
| * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; | ||
| * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER | ||
| * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN | ||
| * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| */ | ||
|
|
||
| import { Request, Response } from 'express'; | ||
| import { HasFullWriteAccess } from '../decorators'; | ||
| import { loggerFor } from '../logger'; | ||
| import { ControllerUtils, TsvUtils } from '../utils'; | ||
| import * as exceptionService from './exception-service'; | ||
| import { isProgramExceptionRecord, isReadonlyArrayOf } from './types'; | ||
|
|
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| const L = loggerFor(__filename); | ||
|
|
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| enum ProgramExceptionErrorMessage { | ||
| TSV_PARSING_FAILED = `This file is formatted incorrectly`, | ||
| } | ||
|
|
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| class ExceptionController { | ||
| @HasFullWriteAccess() | ||
| async createProgramException(req: Request, res: Response) { | ||
| if (!requestContainsFile(req, res)) { | ||
| return false; | ||
| } | ||
|
|
||
| const programId = req.params.programId; | ||
| const file = req.file; | ||
|
|
||
| try { | ||
| const records = await TsvUtils.tsvToJson(file.path); | ||
| if (records.length === 0) { | ||
| throw new Error('TSV has no records!'); | ||
| } | ||
|
|
||
| if (!isReadonlyArrayOf(records, isProgramExceptionRecord)) { | ||
| throw new Error('TSV is incorrectly structured'); | ||
| } | ||
|
|
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| const result = await exceptionService.operations.createProgramException({ | ||
| programId, | ||
| records, | ||
| }); | ||
|
|
||
| if (!result.successful) { | ||
| return res.status(422).send(result); | ||
| } | ||
| return res.status(201).send(result); | ||
| } catch (err) { | ||
| L.error(`Program Exception TSV_PARSING_FAILED`, err); | ||
| return ControllerUtils.unableToProcess(res, ProgramExceptionErrorMessage.TSV_PARSING_FAILED); | ||
| } | ||
| } | ||
| } | ||
|
|
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| const requestContainsFile = (req: Request, res: Response): boolean => { | ||
| if (req.file === undefined || req.file.size <= 0) { | ||
| L.debug(`File missing`); | ||
| ControllerUtils.badRequest(res, `Program exception file upload required`); | ||
| return false; | ||
| } | ||
| return true; | ||
| }; | ||
|
|
||
| export default new ExceptionController(); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,158 @@ | ||
| /* | ||
| * Copyright (c) 2022 The Ontario Institute for Cancer Research. All rights reserved | ||
| * | ||
| * This program and the accompanying materials are made available under the terms of | ||
| * the GNU Affero General Public License v3.0. You should have received a copy of the | ||
| * GNU Affero General Public License along with this program. | ||
| * If not, see <http://www.gnu.org/licenses/>. | ||
| * | ||
| * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY | ||
| * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES | ||
| * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT | ||
| * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, | ||
| * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED | ||
| * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; | ||
| * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER | ||
| * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN | ||
| * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| */ | ||
|
|
||
| import { DeepReadonly } from 'deep-freeze'; | ||
| import * as dictionaryManager from '../dictionary/manager'; | ||
| import { SchemaWithFields } from '../dictionary/manager'; | ||
| import { programExceptionRepository } from './exception-repo'; | ||
| import { ExceptionValue, ProgramException, ProgramExceptionRecord } from './types'; | ||
|
|
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| const recordsToException = ( | ||
| programId: string, | ||
| records: ReadonlyArray<ProgramExceptionRecord>, | ||
| ): ProgramException => ({ | ||
| programId, | ||
| exceptions: records.map(r => ({ | ||
| schema: r.schema, | ||
| coreField: r.requested_core_field, | ||
| exceptionValue: r.requested_exception_value, | ||
| })), | ||
| }); | ||
|
|
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| interface ProgramExceptionResult { | ||
| programException: undefined | DeepReadonly<ProgramException>; | ||
| errors: ValidationError[]; | ||
| successful: boolean; | ||
| } | ||
| export namespace operations { | ||
| export const createProgramException = async ({ | ||
| programId, | ||
| records, | ||
| }: { | ||
| programId: string; | ||
| records: ReadonlyArray<ProgramExceptionRecord>; | ||
| }): Promise<ProgramExceptionResult> => { | ||
| const errors = await validateExceptionRecords(programId, records); | ||
|
|
||
| if (errors.length > 0) { | ||
| return { | ||
| programException: undefined, | ||
| errors, | ||
| successful: false, | ||
| }; | ||
| } else { | ||
| const exception = recordsToException(programId, records); | ||
|
|
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| const result = await programExceptionRepository.create(exception); | ||
| return { | ||
| programException: result, | ||
| errors: [], | ||
| successful: true, | ||
| }; | ||
| } | ||
| }; | ||
| } | ||
|
|
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| interface ValidationError { | ||
| message: string; | ||
| row: number; | ||
| } | ||
|
|
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| const validateExceptionRecords = async ( | ||
| programId: string, | ||
| records: ReadonlyArray<ProgramExceptionRecord>, | ||
| ): Promise<ValidationError[]> => { | ||
| let errors: ValidationError[] = []; | ||
|
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| for (const [idx, record] of records.entries()) { | ||
| const programErrors = checkProgramId(programId, record, idx); | ||
| const coreFieldErrors = await checkCoreField(record, idx); | ||
| const requestedValErrors = checkRequestedValue(record, idx); | ||
| errors = errors.concat(programErrors, coreFieldErrors, requestedValErrors); | ||
| } | ||
|
|
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| return errors; | ||
| }; | ||
|
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| const createValidationError = (row: number, message: string) => ({ | ||
| row: row + 1, // account for tsc header row | ||
| message, | ||
| }); | ||
|
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| const checkProgramId = (programId: string, record: ProgramExceptionRecord, idx: number) => { | ||
| if (programId !== record.program_name) { | ||
| return [ | ||
| createValidationError( | ||
| idx, | ||
| `submitted program id of ${programId} does not match record program id of ${record.program_name}`, | ||
| ), | ||
| ]; | ||
| } | ||
| return []; | ||
| }; | ||
|
|
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| const checkCoreField = async (record: ProgramExceptionRecord, idx: number) => { | ||
| const currentDictionary = await dictionaryManager.instance(); | ||
|
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| const requestedCoreField = record.requested_core_field; | ||
|
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| if (requestedCoreField === undefined) { | ||
| return [createValidationError(idx, `requested_core_field field is not defined`)]; | ||
| } | ||
|
|
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| const fieldFilter = (field: { name: string; meta?: { core: boolean } }): boolean => { | ||
| return field.name === requestedCoreField && !!field.meta?.core; | ||
| }; | ||
|
|
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| const schemaFilter = (schema: SchemaWithFields): boolean => { | ||
| return schema.name === record.schema; | ||
| }; | ||
|
|
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| const existingDictionarySchema = await currentDictionary.getSchemasWithFields( | ||
| schemaFilter, | ||
| fieldFilter, | ||
| ); | ||
|
|
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| if (existingDictionarySchema[0] && existingDictionarySchema[0].fields.length === 0) { | ||
| return [ | ||
| createValidationError(idx, `core field of ${record.requested_core_field} is not valid`), | ||
| ]; | ||
| } | ||
|
|
||
| return []; | ||
| }; | ||
|
|
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| const checkRequestedValue = (record: ProgramExceptionRecord, idx: number) => { | ||
| const validRequests = Object.values(ExceptionValue); | ||
| const requestedExceptionValue = record.requested_exception_value; | ||
|
|
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| if (requestedExceptionValue === undefined) { | ||
| return [createValidationError(idx, `requested_exception_value field is not defined`)]; | ||
| } else if (typeof requestedExceptionValue !== 'string') { | ||
| return [createValidationError(idx, `requested_exception_value is not a string`)]; | ||
| } else if (!validRequests.includes(requestedExceptionValue)) { | ||
| return [ | ||
| createValidationError( | ||
| idx, | ||
| `requested_exception_value is not valid. must be one of ${validRequests.join(', ')}`, | ||
| ), | ||
| ]; | ||
| } | ||
| return []; | ||
| }; |
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