Chore / Move Clinical Service Types (#1185)

* Resolve circular import errors

* Update Imports

* Remove unused variable declaration

* Import fixes; updated switch syntax + comment

src/clinical/api/clinical-api.ts

@@ -19,7 +19,7 @@
 
 import { Request, Response } from 'express';
 import * as service from '../clinical-service';
-import { ClinicalDataQuery } from '../clinical-service';
+import { ClinicalDataQuery } from '../types';
 import { getExceptionManifestRecords } from '../../submission/exceptions/exceptions';
 import { ExceptionManifestRecord } from '../../exception/exception-manifest/types';
 import {

src/clinical/clinical-service.ts

@@ -24,12 +24,9 @@ import {
 import { DeepReadonly } from 'deep-freeze';
 import _ from 'lodash';
 import {
-	ClinicalDataSortType,
-	ClinicalDataSortTypes,
 	ClinicalEntityErrorRecord,
 	ClinicalEntitySchemaNames,
 	ClinicalErrorsResponseRecord,
-	EntityAlias,
 	aliasEntityNames,
 	allEntityNames,
 } from '../common-model/entities';
@@ -54,40 +51,16 @@ import { ClinicalEntityData, Donor, Sample } from './clinical-entities';
 import { DONOR_DOCUMENT_FIELDS, donorDao } from './donor-repo';
 import { runTaskInWorkerThread } from './service-worker-thread/runner';
 import { WorkerTasks } from './service-worker-thread/tasks';
-import { CompletionState } from './api/types';
+import {
+	ClinicalDataQuery,
+	ClinicalDataSortType,
+	ClinicalDataSortTypes,
+	ClinicalDonorEntityQuery,
+	PaginationQuery,
+} from './types';
 
 const L = loggerFor(__filename);
 
-// Base type for Clinical Data Queries
-export type ClinicalDonorEntityQuery = {
-	donorIds: number[];
-	submitterDonorIds: string[];
-	entityTypes: EntityAlias[];
-};
-
-export type PaginationQuery = {
-	page: number;
-	pageSize?: number;
-	sort: string;
-};
-
-export type ClinicalDataPaginatedQuery = ClinicalDonorEntityQuery & PaginationQuery;
-
-export type ClinicalDataQuery = ClinicalDataPaginatedQuery & {
-	completionState?: {};
-};
-
-// GQL Query Arguments
-// Submitted Data Table, SearchBar, Sidebar, etc.
-export type ClinicalDataApiFilters = ClinicalDataPaginatedQuery & {
-	completionState?: CompletionState;
-};
-
-export type ClinicalDataVariables = {
-	programShortName: string;
-	filters: ClinicalDataApiFilters;
-};
-
 export async function updateDonorSchemaMetadata(
 	donor: DeepReadonly<Donor>,
 	migrationId: string,

src/clinical/donor-repo.ts

@@ -18,7 +18,7 @@
  */
 
 import { Donor } from './clinical-entities';
-import { ClinicalDataQuery, ClinicalDonorEntityQuery } from './clinical-service';
+import { ClinicalDataQuery, ClinicalDonorEntityQuery } from './types';
 import { getRequiredDonorFieldsForEntityTypes } from '../common-model/functions';
 import mongoose, { PaginateModel } from 'mongoose';
 import mongoosePaginate from 'mongoose-paginate-v2';

src/clinical/service-worker-thread/tasks.ts

@@ -20,8 +20,6 @@
 import { DeepReadonly } from 'deep-freeze';
 import _, { isEmpty } from 'lodash';
 import {
-	ClinicalDataSortType,
-	ClinicalDataSortTypes,
 	ClinicalEntitySchemaNames,
 	ClinicalErrorsResponseRecord,
 	EntityAlias,
@@ -36,7 +34,12 @@ import {
 	getSampleRegistrationDataFromDonor,
 } from '../../common-model/functions';
 import { notEmpty } from '../../utils';
-import { ClinicalDonorEntityQuery, PaginationQuery } from '../clinical-service';
+import {
+	ClinicalDonorEntityQuery,
+	ClinicalDataSortType,
+	ClinicalDataSortTypes,
+	PaginationQuery,
+} from '../types';
 import {
 	ClinicalEntityData,
 	ClinicalInfo,
@@ -178,17 +181,21 @@ const mapEntityDocuments = (
 	let records = results;
 
 	switch (sortType) {
-		case ClinicalDataSortTypes.defaultDonor:
+		case ClinicalDataSortTypes.defaultDonor: {
 			records = results.sort(sortDocs(sort, completionStats, sortDonorRecordsByCompletion));
 			break;
-		case ClinicalDataSortTypes.invalidEntity:
+		}
+		case ClinicalDataSortTypes.invalidEntity: {
 			records = sortInvalidRecords(errors, results, entityName);
 			break;
+		}
+		// Column Sort is the default, fallback here is intentional
 		case ClinicalDataSortTypes.columnSort:
-		default:
+		default: {
 			const sortKey = sort[0] === '-' ? sort.split('-')[1] : sort;
 			const key = sortKey === 'donorId' ? DONOR_ID_FIELD : sortKey;
 			records = results.sort(sortDocs(sort, key, sortRecordsByColumn));
+		}
 	}
 
 	if (records.length > pageSize) {

src/clinical/types.ts

@@ -0,0 +1,63 @@
+/*
+ * Copyright (c) 2024 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 { EntityAlias } from '../common-model/entities';
+import { CompletionState } from './api/types';
+import { Values } from '../utils/objectTypes';
+
+// Types Specific to Clinical Service and Related Tasks
+
+// Base type for Clinical Data Queries
+export type ClinicalDonorEntityQuery = {
+	donorIds: number[];
+	submitterDonorIds: string[];
+	entityTypes: EntityAlias[];
+};
+
+// Types related to sorting, filtering, pagination, etc
+export type PaginationQuery = {
+	page: number;
+	pageSize?: number;
+	sort: string;
+};
+
+export type ClinicalDataPaginatedQuery = ClinicalDonorEntityQuery & PaginationQuery;
+
+export type ClinicalDataQuery = ClinicalDataPaginatedQuery & {
+	completionState?: {};
+};
+
+export const ClinicalDataSortTypes = {
+	defaultDonor: 'defaultDonor',
+	invalidEntity: 'invalidEntity',
+	columnSort: 'columnSort',
+};
+
+export type ClinicalDataSortType = Values<typeof ClinicalDataSortTypes>;
+
+// GQL Query Arguments
+// Submitted Data Table, SearchBar, Sidebar, etc.
+export type ClinicalDataApiFilters = ClinicalDataPaginatedQuery & {
+	completionState?: CompletionState;
+};
+
+export type ClinicalDataVariables = {
+	programShortName: string;
+	filters: ClinicalDataApiFilters;
+};

src/common-model/entities.ts

@@ -19,7 +19,6 @@
 
 import { z as zod } from 'zod';
 import { entities as dictionaryEntities } from '@overturebio-stack/lectern-client';
-import { Values } from '../utils/objectTypes';
 
 // this is temporary to keep code compiling until surgery is ready in dictionary, to be removed in favor of
 // the surgery in ClinicalEntitySchemaNames
@@ -95,14 +94,6 @@ export interface ClinicalErrorsResponseRecord {
 	errors: ClinicalEntityErrorRecord[];
 }
 
-export const ClinicalDataSortTypes = {
-	defaultDonor: 'defaultDonor',
-	invalidEntity: 'invalidEntity',
-	columnSort: 'columnSort',
-};
-
-export type ClinicalDataSortType = Values<typeof ClinicalDataSortTypes>;
-
 export type ClinicalFields =
 	| DonorFieldsEnum
 	| SpecimenFieldsEnum

src/schemas/clinical-resolvers/clinicalData.ts

@@ -16,7 +16,9 @@
  * 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 { getPaginatedClinicalData, ClinicalDataVariables } from '../../clinical/clinical-service';
+
+import { ClinicalDataVariables } from '../../clinical/types';
+import { getPaginatedClinicalData } from '../../clinical/clinical-service';
 import { ClinicalEntityData, ClinicalInfo } from '../../clinical/clinical-entities';
 import { completionFilters } from '../../clinical/api/clinical-api';
 import { ClinicalErrorsResponseRecord } from '../../common-model/entities';

src/schemas/clinical-resolvers/clinicalSearchResults.ts

@@ -16,7 +16,9 @@
  * 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 { getClinicalSearchResults, ClinicalDataVariables } from '../../clinical/clinical-service';
+
+import { ClinicalDataVariables } from '../../clinical/types';
+import { getClinicalSearchResults } from '../../clinical/clinical-service';
 
 const clinicalSearchResults = async (obj: unknown, args: ClinicalDataVariables) => {
 	const { programShortName, filters } = args;

src/submission/validation-clinical/therapy.ts

@@ -36,7 +36,7 @@ import {
 import { getSingleClinicalObjectFromDonor } from '../../common-model/functions';
 import { donorDao } from '../../clinical/donor-repo';
 import { ClinicalInfo, Donor, Treatment } from '../../clinical/clinical-entities';
-import { ClinicalDataQuery } from '../../clinical/clinical-service';
+import { ClinicalDataQuery } from '../../clinical/types';
 import featureFlags from '../../feature-flags';
 import { isValueEqual } from '../../utils';