Clear clinical submission resolver

src/app.ts

@@ -44,6 +44,14 @@ process.title = 'clinical';
 
 // Create Express server
 const app = express();
+
+export type GlobalGqlContext = {
+  isUserRequest: boolean;
+  egoToken: string;
+  Authorization: string;
+  dataLoaders: {};
+};
+
 app.set('port', process.env.PORT || 3000);
 app.set('graphqlPort', process.env.GRAPHQLPORT || 3001);
 app.use(bodyParser.json());

src/dictionary/api.ts

@@ -33,7 +33,7 @@ class SchemaController {
   async update(req: Request, res: Response) {
     const version: string = req.body.version;
     const sync: boolean = req.query.sync;
-    const initiator = ControllerUtils.getUserFromToken(req);
+    const initiator = ControllerUtils.getUserFromRequest(req);
     const migration = await manager.instance().updateSchemaVersion(version, initiator, sync);
     return res.status(200).send(migration);
   }
@@ -49,7 +49,7 @@ class SchemaController {
   @HasFullWriteAccess()
   async dryRunUpdate(req: Request, res: Response) {
     const version: string = req.body.version;
-    const initiator = ControllerUtils.getUserFromToken(req);
+    const initiator = ControllerUtils.getUserFromRequest(req);
     const migration = await manager.instance().dryRunSchemaUpgrade(version, initiator);
     return res.status(200).send(migration);
   }

src/schemas/clinical-resolvers/clearClinicalSubmissionResolver.ts

@@ -0,0 +1,43 @@
+/*
+ * Copyright (c) 2023 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 { GlobalGqlContext } from '../../app';
+import submissionAPI from '../../submission/submission-api';
+import { convertClinicalSubmissionDataToGql } from '../utils';
+
+const clearClinicalSubmissionResolver = {
+  clearClinicalSubmission: async (
+    obj: unknown,
+    args: { programShortName: string; fileType: string; version: string },
+    contextValue: any,
+  ) => {
+    const { programShortName, fileType, version } = args;
+    const response = await submissionAPI.clearFileDataFromActiveSubmission(
+      programShortName,
+      fileType,
+      version,
+      (<GlobalGqlContext>contextValue).egoToken,
+    );
+    return convertClinicalSubmissionDataToGql(programShortName, {
+      submission: response,
+    });
+  },
+};
+
+export default clearClinicalSubmissionResolver;

src/schemas/clinical-resolvers/clinicalSubmissionDataResolver.ts

@@ -21,7 +21,7 @@ import submissionAPI from '../../submission/submission-api';
 import get from 'lodash/get';
 import { ActiveClinicalSubmission } from '../../submission/submission-entities';
 import { DeepReadonly } from 'deep-freeze';
-import { convertClinicalFileErrorToGql, convertClinicalSubmissionEntityToGql } from '../utils';
+import { convertClinicalSubmissionDataToGql } from '../utils';
 import { getClinicalEntitiesData } from '../../dictionary/api';
 
 const clinicalSubmissionResolver = {
@@ -35,35 +35,4 @@ const clinicalSubmissionResolver = {
   },
 };
 
-const convertClinicalSubmissionDataToGql = (
-  programShortName: string,
-  data: {
-    submission: DeepReadonly<ActiveClinicalSubmission> | undefined;
-    batchErrors?: { message: string; batchNames: string[]; code: string }[];
-  },
-) => {
-  const submission = get(data, 'submission', {} as Partial<typeof data.submission>);
-  const fileErrors = get(data, 'batchErrors', [] as typeof data.batchErrors);
-  const clinicalEntities = get(submission, 'clinicalEntities');
-  return {
-    id: submission?._id || undefined,
-    programShortName,
-    state: submission?.state || undefined,
-    version: submission?.version || undefined,
-    updatedBy: submission?.updatedBy || undefined,
-    updatedAt: submission?.updatedAt ? submission.updatedAt : undefined,
-    clinicalEntities: async () => {
-      const clinicalSubmissionTypeList = await getClinicalEntitiesData('false'); // to confirm for true or false
-      const filledClinicalEntities = clinicalSubmissionTypeList.map(clinicalType => ({
-        clinicalType,
-        ...(clinicalEntities ? clinicalEntities[clinicalType.name] : {}),
-      }));
-      return filledClinicalEntities.map(clinicalEntity =>
-        convertClinicalSubmissionEntityToGql(clinicalEntity?.clinicalType.name, clinicalEntity),
-      );
-    },
-    fileErrors: fileErrors?.map(convertClinicalFileErrorToGql),
-  };
-};
-
 export default clinicalSubmissionResolver;

src/schemas/gqlTypeDefs.ts

@@ -37,6 +37,18 @@ const typeDefs = gql`
     clinicalSubmissions(programShortName: String!): ClinicalSubmissionData!
   }
 
+  type Mutation {
+    """
+    Clear Clinical Submission
+    fileType is optional, if it is not provided all fileTypes will be cleared. The values for fileType are the same as the file names from each template (ex. donor, specimen)
+    """
+    clearClinicalSubmission(
+      programShortName: String!
+      version: String!
+      fileType: String
+    ): ClinicalSubmissionData!
+  }
+
   scalar DateTime
 
   """

src/schemas/resolvers.ts

@@ -1,13 +1,17 @@
 import clinicalRegistrationResolver from './clinical-resolvers/clinicalRegistrationData';
 import clinicalSearchResultResolver from './clinical-resolvers/clinicalSearchResults';
 import clinicalSubmissionResolver from './clinical-resolvers/clinicalSubmissionDataResolver';
+import clearClinicalSubmissionResolver from './clinical-resolvers/clearClinicalSubmissionResolver';
 
 const resolvers = {
   Query: {
     ...clinicalRegistrationResolver,
     ...clinicalSearchResultResolver,
     ...clinicalSubmissionResolver,
   },
+  Mutation: {
+    ...clearClinicalSubmissionResolver,
+  },
 };
 
 export default resolvers;

src/schemas/utils.ts

@@ -19,10 +19,12 @@
 
 import get from 'lodash/get';
 import {
+  ActiveClinicalSubmission,
   SubmissionValidationError,
   SubmissionValidationUpdate,
 } from '../submission/submission-entities';
 import { DeepReadonly } from 'deep-freeze';
+import { getClinicalEntitiesData } from '../dictionary/api';
 
 const ARRAY_DELIMITER_CHAR = '|';
 
@@ -209,11 +211,43 @@ const convertClinicalSubmissionUpdateToGql = (updateData: UpdateData) => {
   };
 };
 
+const convertClinicalSubmissionDataToGql = (
+  programShortName: string,
+  data: {
+    submission: DeepReadonly<ActiveClinicalSubmission> | undefined;
+    batchErrors?: { message: string; batchNames: string[]; code: string }[];
+  },
+) => {
+  const submission = get(data, 'submission', {} as Partial<typeof data.submission>);
+  const fileErrors = get(data, 'batchErrors', [] as typeof data.batchErrors);
+  const clinicalEntities = get(submission, 'clinicalEntities');
+  return {
+    id: submission?._id || undefined,
+    programShortName,
+    state: submission?.state || undefined,
+    version: submission?.version || undefined,
+    updatedBy: submission?.updatedBy || undefined,
+    updatedAt: submission?.updatedAt ? submission.updatedAt : undefined,
+    clinicalEntities: async () => {
+      const clinicalSubmissionTypeList = await getClinicalEntitiesData('false'); // to confirm for true or false
+      const filledClinicalEntities = clinicalSubmissionTypeList.map(clinicalType => ({
+        clinicalType,
+        ...(clinicalEntities ? clinicalEntities[clinicalType.name] : {}),
+      }));
+      return filledClinicalEntities.map(clinicalEntity =>
+        convertClinicalSubmissionEntityToGql(clinicalEntity?.clinicalType.name, clinicalEntity),
+      );
+    },
+    fileErrors: fileErrors?.map(convertClinicalFileErrorToGql),
+  };
+};
+
 export {
   convertClinicalRecordToGql,
   convertRegistrationErrorToGql,
   convertClinicalFileErrorToGql,
   convertRegistrationStatsToGql,
   RegistrationErrorData,
   convertClinicalSubmissionEntityToGql,
+  convertClinicalSubmissionDataToGql,
 };

src/server.ts

@@ -16,6 +16,8 @@
  * 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 { token } from 'morgan';
+
 console.time('boot time');
 // Has to import config before any other import uses the configurations
 import { AppConfig, RxNormDbConfig, KafkaConfigurations } from './config';
@@ -29,11 +31,16 @@ import { Server } from 'http';
 // we import here to allow configs to fully load
 import * as bootstrap from './bootstrap';
 import app from './app';
+import { GlobalGqlContext } from './app';
 import { database, up } from 'migrate-mongo';
 
-import { ApolloServer } from '@apollo/server';
-import { startStandaloneServer } from '@apollo/server/standalone';
+import { ApolloServer, ContextFunction } from '@apollo/server';
+import {
+  StandaloneServerContextFunctionArgument,
+  startStandaloneServer,
+} from '@apollo/server/standalone';
 import schema from './schemas/index';
+// import { EgoJwtData } from '@icgc-argo/ego-token-utils/dist/common';
 
 let secrets: any = {};
 let server: Server;
@@ -153,10 +160,36 @@ let server: Server;
   /**
    * Start Graphql server.
    */
-  const apolloServer = new ApolloServer({
+
+  const context: ContextFunction<
+    [StandaloneServerContextFunctionArgument],
+    GlobalGqlContext
+  > = async ({ req, res }) => {
+    // Get the user token from the headers.
+    const authHeader = req.headers.authorization;
+    let userJwtData = undefined;
+    try {
+      if (authHeader) {
+        const jwt = authHeader.replace('Bearer ', '');
+      }
+    } catch (err) {
+      userJwtData = undefined;
+    }
+    // Add the user to the context
+    return {
+      isUserRequest: true,
+      egoToken: (authHeader || '').split('Bearer ').join(''),
+      Authorization: `Bearer ${(authHeader || '').replace(/^Bearer[\s]*!/, '')}` || '',
+      dataLoaders: {},
+    };
+  };
+
+  const apolloServer = new ApolloServer<GlobalGqlContext>({
     schema,
   });
+
   const { url } = await startStandaloneServer(apolloServer, {
+    context,
     listen: { port: app.get('graphqlPort') },
   });
 

src/submission/submission-api.ts

@@ -35,6 +35,7 @@ import { HasFullWriteAccess, HasProgramWriteAccess } from '../decorators';
 import _ from 'lodash';
 import { batchErrorMessage } from './submission-error-messages';
 import * as fs from 'fs';
+import { GlobalGqlContext } from '../app';
 
 const L = loggerFor(__filename);
 const fsPromises = fs.promises;
@@ -62,7 +63,7 @@ class SubmissionController {
       return;
     }
     const programId = req.params.programId;
-    const creator = ControllerUtils.getUserFromToken(req);
+    const creator = ControllerUtils.getUserFromRequest(req);
     const file = req.file;
     let records: ReadonlyArray<TsvUtils.TsvRecordAsJsonObj>;
     try {
@@ -136,7 +137,7 @@ class SubmissionController {
       return;
     }
 
-    const user = ControllerUtils.getUserFromToken(req);
+    const user = ControllerUtils.getUserFromRequest(req);
     const newClinicalData: NewClinicalEntity[] = [];
     const tsvParseErrors: SubmissionBatchError[] = [];
     const clinicalFiles = req.files as Express.Multer.File[];
@@ -191,7 +192,7 @@ class SubmissionController {
   async validateActiveSubmission(req: Request, res: Response) {
     if (await submissionSystemIsDisabled(res)) return;
     const { versionId, programId } = req.params;
-    const updater = ControllerUtils.getUserFromToken(req);
+    const updater = ControllerUtils.getUserFromRequest(req);
     const result = await submission.operations.validateMultipleClinical({
       versionId,
       programId,
@@ -207,7 +208,7 @@ class SubmissionController {
   async clearFileFromActiveSubmission(req: Request, res: Response) {
     if (await submissionSystemIsDisabled(res)) return;
     const { programId, versionId, fileType } = req.params;
-    const updater = ControllerUtils.getUserFromToken(req);
+    const updater = ControllerUtils.getUserFromRequest(req);
     L.debug(`Entering clearFileFromActiveSubmission: ${{ programId, versionId, fileType }}`);
     const updatedSubmission = await submission.operations.clearSubmissionData({
       programId,
@@ -219,11 +220,32 @@ class SubmissionController {
     return res.status(200).send(updatedSubmission || {});
   }
 
+  // @HasProgramWriteAccess((programId: string) => programId)
+  async clearFileDataFromActiveSubmission(
+    programId: string,
+    fileType: string,
+    versionId: string,
+    token: string,
+  ) {
+    const submissionSystemDisabled = await persistedConfig.getSubmissionDisabledState();
+    if (submissionSystemDisabled) return;
+    const updater = ControllerUtils.getUserFromToken(token);
+    L.debug(`Entering clearFileDataFromActiveSubmission: ${{ programId, versionId, fileType }}`);
+    const updatedSubmission = await submission.operations.clearSubmissionData({
+      programId,
+      versionId,
+      fileType,
+      updater,
+    });
+    // Handle case where submission was cleared and is now undefined
+    return updatedSubmission;
+  }
+
   @HasProgramWriteAccess((req: Request) => req.params.programId)
   async commitActiveSubmission(req: Request, res: Response) {
     if (await submissionSystemIsDisabled(res)) return;
     const { versionId, programId } = req.params;
-    const updater = ControllerUtils.getUserFromToken(req);
+    const updater = ControllerUtils.getUserFromRequest(req);
     const activeSubmission = await submission2Clinical.commitClinicalSubmission({
       versionId,
       programId,
@@ -247,7 +269,7 @@ class SubmissionController {
   async reopenActiveSubmission(req: Request, res: Response) {
     if (await submissionSystemIsDisabled(res)) return;
     const { versionId, programId } = req.params;
-    const updater = ControllerUtils.getUserFromToken(req);
+    const updater = ControllerUtils.getUserFromRequest(req);
     const activeSubmission = await submission.operations.reopenClinicalSubmission({
       versionId,
       programId,
@@ -299,7 +321,7 @@ class SubmissionController {
     const samplesSubmitterIds =
       req.query.sampleSubmitterIds && req.query.sampleSubmitterIds.split(',');
     const dryRun = req.query.dryRun === 'false' ? false : true;
-    const updater = ControllerUtils.getUserFromToken(req);
+    const updater = ControllerUtils.getUserFromRequest(req);
     L.info(
       `Delete registered samples called, caller ${updater}, ids: ${samplesSubmitterIds}, programId: ${programId}`,
     );