[O2B-1200] Add QC flags creation API (#1499)

* refactor * typos * add testS * fix * fix * test * refactor' * fix * refactor * refactor * add controller * test * test * more rigid * mr * cleanup * ceanup * refactor * refactor * cleanup * ref * ch err * test * use default timestamps * refactor * refactor * fix * docs * handle missing timestamps * typo * dates * test * test * test * cleanup * rename * date * syntax * rename * correct * correct * typo * typo
AliceO2Group · Apr 10, 2024 · 0c6da29 · 0c6da29
1 parent dac7be0
commit 0c6da29
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Showing 5 changed files with 712 additions and 7 deletions.
diff --git a/lib/server/controllers/qcFlag.controller.js b/lib/server/controllers/qcFlag.controller.js
@@ -82,7 +82,61 @@ const listQcFlagsHandler = async (req, res) => {
     }
 };
 
+// eslint-disable-next-line valid-jsdoc
+/**
+ * Create QcFlag
+ */
+const createQcFlagHandler = async (req, res) => {
+    const validatedDTO = await dtoValidator(
+        DtoFactory.bodyOnly(Joi.object({
+            from: Joi.number().required().allow(null),
+            to: Joi.number().required().allow(null),
+            comment: Joi.string().optional().allow(null),
+            flagTypeId: Joi.number().required(),
+            runNumber: Joi.number().required(),
+            dplDetectorId: Joi.number().required(),
+            dataPassId: Joi.number(),
+            simulationPassId: Joi.number(),
+        }).xor('dataPassId', 'simulationPassId')),
+        req,
+        res,
+    );
+    if (validatedDTO) {
+        try {
+            const {
+                from,
+                to,
+                comment,
+                flagTypeId,
+                runNumber,
+                dplDetectorId,
+                dataPassId,
+                simulationPassId,
+            } = validatedDTO.body;
+            const parameters = { from, to, comment };
+            const relations = {
+                user: { externalUserId: validatedDTO.session.externalId },
+                flagTypeId,
+                runNumber,
+                dplDetectorId,
+                dataPassId,
+                simulationPassId,
+            };
+            let createdFlag;
+            if (dataPassId) {
+                createdFlag = await qcFlagService.createForDataPass(parameters, relations);
+            } else {
+                createdFlag = await qcFlagService.createForSimulationPass(parameters, relations);
+            }
+            res.status(201).json({ data: createdFlag });
+        } catch (error) {
+            updateExpressResponseFromNativeError(res, error);
+        }
+    }
+};
+
 exports.QcFlagController = {
     getQcFlagByIdHandler,
     listQcFlagsHandler,
+    createQcFlagHandler,
 };
diff --git a/lib/server/routers/qcFlag.router.js b/lib/server/routers/qcFlag.router.js
@@ -25,5 +25,9 @@ exports.qcFlagsRouter = {
             method: 'get',
             controller: QcFlagController.listQcFlagsHandler,
         },
+        {
+            method: 'post',
+            controller: QcFlagController.createQcFlagHandler,
+        },
     ],
 };
diff --git a/lib/server/services/qualityControlFlag/QcFlagService.js b/lib/server/services/qualityControlFlag/QcFlagService.js
@@ -11,11 +11,14 @@
  * or submit itself to any jurisdiction.
  */
 
-const { repositories: { QcFlagRepository } } = require('../../../database/index.js');
+const { repositories: { QcFlagRepository, DplDetectorRepository, RunRepository } } = require('../../../database/index.js');
 const { dataSource } = require('../../../database/DataSource.js');
 const { qcFlagAdapter } = require('../../../database/adapters/index.js');
 const { BadParameterError } = require('../../errors/BadParameterError.js');
 const { NotFoundError } = require('../../errors/NotFoundError.js');
+const { getUserOrFail } = require('../user/getUserOrFail.js');
+
+const NON_QC_DETECTORS = new Set(['TST']);
 
 /**
  * Quality control flags service
@@ -53,6 +56,211 @@ class QcFlagService {
         return qcFlag;
     }
 
+    /**
+     * Validate QC flag timestamps
+     * If null timestamp was provided, given timestamp is replaced by run's startTime or endTime
+     * @param {{from: number, to: number}} timestamps QC flag timestamps
+     * @param {Run} targetRun run which for QC flag is to be set
+     * @throws {BadParameterError}
+     * @return {{fromTime: number, toTime: number}} prepared timestamps
+     */
+    _prepareQcFlagPeriod({ from, to }, targetRun) {
+        const fromTime = from ?? targetRun.startTime;
+        const toTime = to ?? targetRun.endTime;
+
+        if (!fromTime || !toTime) {
+            if (!fromTime && !toTime) {
+                return { fromTime: null, toTime: null };
+            } else {
+                throw new BadParameterError('Only null QC flag timestamps are accepted as run.startTime or run.endTime is missing');
+            }
+        }
+
+        if (fromTime >= toTime) {
+            throw new BadParameterError('Parameter "to" timestamp must be greater than "from" timestamp');
+        }
+
+        if (fromTime < targetRun.startTime || targetRun.endTime < toTime) {
+            // eslint-disable-next-line max-len
+            throw new BadParameterError(`Given QC flag period (${fromTime}, ${toTime}) is out of run (${targetRun.startTime}, ${targetRun.endTime}) period`);
+        }
+        return { fromTime, toTime };
+    }
+
+    /**
+     * Validate QC flag DPL detector
+     * @param {number} dplDetectorId DPL detector
+     * @throws {BadParameterError}
+     * @return {void}
+     */
+    async _validateQcFlagDplDetector(dplDetectorId) {
+        const dplDetector = await DplDetectorRepository.findOne({ where: { id: dplDetectorId } });
+        if (!dplDetector?.name || NON_QC_DETECTORS.has(dplDetector.name)) {
+            throw new BadParameterError(`Invalid DPL detector (${dplDetector.name})`);
+        }
+        return dplDetector;
+    }
+
+    /**
+     * Create new instance of quality control flags for data pass
+     * @param {Partial<QcFlag>} parameters flag instance parameters
+     * @param {object} [relations] QC Flag Type entity relations
+     * @param {Partial<UserIdentifier>} [relations.user] user identifiers
+     * @param {number} [parameters.flagTypeId] flag type id
+     * @param {number} [parameters.runNumber] associated run's number
+     * @param {number} [parameters.dataPassId] associated dataPass' id
+     * @param {number} [parameters.dplDetectorId] associated dplDetector's id
+     * @return {Promise<QcFlag>} promise
+     * @throws {BadParameterError, NotFoundError}
+     */
+    async createForDataPass(parameters, relations = {}) {
+        const {
+            from = null,
+            to = null,
+            comment,
+        } = parameters;
+        const {
+            user: { userId, externalUserId } = {},
+            flagTypeId,
+            runNumber,
+            dataPassId,
+            dplDetectorId,
+        } = relations;
+
+        return dataSource.transaction(async () => {
+            // Check user
+            const user = await getUserOrFail({ userId, externalUserId });
+
+            // Check associations
+            const dplDetector = await this._validateQcFlagDplDetector(dplDetectorId);
+
+            const targetRun = await RunRepository.findOne({
+                subQuery: false,
+                attributes: ['timeTrgStart', 'timeTrgEnd'],
+                where: { runNumber },
+                include: [
+                    {
+                        association: 'dataPass',
+                        where: { id: dataPassId },
+                        through: { attributes: [] },
+                        attributes: ['id'],
+                        required: true,
+                    },
+                    {
+                        association: 'detectors',
+                        where: { name: dplDetector.name },
+                        through: { attributes: [] },
+                        attributes: [],
+                        required: true,
+                    },
+                ],
+            });
+            if (!targetRun) {
+                // eslint-disable-next-line max-len
+                throw new BadParameterError(`There is not association between data pass with this id (${dataPassId}), run with this number (${runNumber}) and detector with this name (${dplDetector.name})`);
+            }
+
+            const { fromTime, toTime } = this._prepareQcFlagPeriod({ from, to }, targetRun);
+
+            // Insert
+            const newInstance = await QcFlagRepository.insert({
+                from: fromTime,
+                to: toTime,
+                comment,
+                createdById: user.id,
+                flagTypeId,
+                runNumber,
+                dplDetectorId,
+            });
+
+            const createdFlag = await QcFlagRepository.findOne(this.prepareQueryBuilder().where('id').is(newInstance.id));
+
+            await createdFlag.addDataPasses(targetRun.dataPass);
+
+            return qcFlagAdapter.toEntity(createdFlag);
+        });
+    }
+
+    /**
+     * Create new instance of quality control flags for simulation pass
+     * @param {Partial<QcFlag>} parameters flag instance parameters
+     * @param {object} [relations] QC Flag Type entity relations
+     * @param {Partial<UserIdentifier>} [relations.user] user identifiers
+     * @param {number} [parameters.flagTypeId] flag type id
+     * @param {number} [parameters.runNumber] associated run's number
+     * @param {number} [parameters.simulationPassId] associated simulationPass' id
+     * @param {number} [parameters.dplDetectorId] associated dplDetector's id
+     * @return {Promise<QcFlag>} promise
+     * @throws {BadParameterError, NotFoundError}
+     */
+    async createForSimulationPass(parameters, relations = {}) {
+        const {
+            from = null,
+            to = null,
+            comment,
+        } = parameters;
+        const {
+            user: { userId, externalUserId } = {},
+            flagTypeId,
+            runNumber,
+            simulationPassId,
+            dplDetectorId,
+        } = relations;
+
+        return dataSource.transaction(async () => {
+            // Check user
+            const user = await getUserOrFail({ userId, externalUserId });
+
+            // Check associations
+            const dplDetector = await this._validateQcFlagDplDetector(dplDetectorId);
+
+            const targetRun = await RunRepository.findOne({
+                subQuery: false,
+                attributes: ['timeTrgStart', 'timeTrgEnd'],
+                where: { runNumber },
+                include: [
+                    {
+                        association: 'simulationPasses',
+                        where: { id: simulationPassId },
+                        through: { attributes: [] },
+                        attributes: ['id'],
+                        required: true,
+                    },
+                    {
+                        association: 'detectors',
+                        where: { name: dplDetector.name },
+                        through: { attributes: [] },
+                        attributes: [],
+                        required: true,
+                    },
+                ],
+            });
+            if (!targetRun) {
+            // eslint-disable-next-line max-len
+                throw new BadParameterError(`There is not association between simulation pass with this id (${simulationPassId}), run with this number (${runNumber}) and detector with this name (${dplDetector.name})`);
+            }
+
+            const { fromTime, toTime } = this._prepareQcFlagPeriod({ from, to }, targetRun);
+
+            // Insert
+            const newInstance = await QcFlagRepository.insert({
+                from: fromTime,
+                to: toTime,
+                comment,
+                createdById: user.id,
+                flagTypeId,
+                runNumber,
+                dplDetectorId,
+            });
+
+            const createdFlag = await QcFlagRepository.findOne(this.prepareQueryBuilder().where('id').is(newInstance.id));
+
+            await createdFlag.addSimulationPasses(targetRun.simulationPasses);
+
+            return qcFlagAdapter.toEntity(createdFlag);
+        });
+    }
+
     /**
      * Get all quality control flags instances
      * @param {object} [options.filter] filtering defintion