first commit

src/graphql/fragments/BioRiskFields.graphql

@@ -0,0 +1,4 @@
+fragment BioRiskFields on BioRisk {
+    code
+    enabled
+}

src/graphql/mutations/AddBioRisk.graphql

@@ -0,0 +1,5 @@
+mutation AddBioRisk($code: String!) {
+    addBioRisk(code: $code) {
+        ...BioRiskFields
+    }
+}

src/graphql/mutations/SetBioRiskEnabled.graphql

@@ -0,0 +1,5 @@
+mutation SetBioRiskEnabled($code: String!, $enabled: Boolean!) {
+    setBioRiskEnabled(code: $code, enabled: $enabled) {
+        ...BioRiskFields
+    }
+}

src/graphql/queries/GetBioRisks.graphql

@@ -0,0 +1,5 @@
+query GetBioRisks($includeDisabled: Boolean) {
+    bioRisks(includeDisabled: $includeDisabled) {
+        ...BioRiskFields
+    }
+}

src/graphql/queries/GetConfiguration.graphql

@@ -50,4 +50,7 @@ query GetConfiguration {
   dnapStudies(includeDisabled: true) {
     ...DnapStudyFields
   }
+  bioRisks(includeDisabled: true){
+    ...BioRiskFields
+  }
 }

src/graphql/queries/GetRegistrationInfo.graphql

@@ -27,4 +27,7 @@ query GetRegistrationInfo {
   slotRegions {
     name
   }
+  bioRisks {
+    code
+  }
 }

src/lib/factories/bioRiskFactory.ts

@@ -0,0 +1,9 @@
+import { Factory } from 'fishery';
+import { BioRisk } from '../../types/sdk';
+import { faker } from '@faker-js/faker';
+
+export default Factory.define<BioRisk>(({ params, sequence }) => ({
+  __typename: 'BioRisk',
+  code: faker.lorem.word() + sequence,
+  enabled: params.enabled ?? true
+}));

src/mocks/handlers.ts

@@ -61,6 +61,7 @@ import segmentationHandlers from './handlers/segmentationHandlers';
 import cleanOutHandlers from './handlers/cleanOutHandlers';
 import regionOfInterestHandlers from './handlers/regionOfInterestHandlers';
 import omeroProjectHandlers from './handlers/omeroProjectHandlers';
+import bioRiskHandler from './handlers/bioRiskHandler';
 
 export const handlers = [
   ...labwareHandlers,
@@ -123,5 +124,6 @@ export const handlers = [
   ...cleanOutHandlers,
   ...regionOfInterestHandlers,
   ...projectHandlers,
-  ...omeroProjectHandlers
+  ...omeroProjectHandlers,
+  ...bioRiskHandler
 ];

src/mocks/handlers/bioRiskHandler.ts

@@ -0,0 +1,53 @@
+import { graphql, HttpResponse } from 'msw';
+import {
+  AddBioRiskMutation,
+  AddBioRiskMutationVariables,
+  GetBioRisksQuery,
+  GetBioRisksQueryVariables,
+  SetBioRiskEnabledMutation,
+  SetBioRiskEnabledMutationVariables
+} from '../../types/sdk';
+import { isEnabled } from '../../lib/helpers';
+import BioRiskRepository from '../repositories/bioRiskRepository';
+import bioRiskRepository from '../repositories/bioRiskRepository';
+import bioRiskFactory from '../../lib/factories/bioRiskFactory';
+
+const bioRiskHandler = [
+  graphql.mutation<AddBioRiskMutation, AddBioRiskMutationVariables>('AddBioRisk', ({ variables }) => {
+    const bioRisk = bioRiskFactory.build({
+      code: variables.code
+    });
+    bioRiskRepository.save(bioRisk);
+    return HttpResponse.json({ data: { addBioRisk: bioRisk } }, { status: 200 });
+  }),
+
+  graphql.mutation<SetBioRiskEnabledMutation, SetBioRiskEnabledMutationVariables>(
+    'SetBioRiskEnabled',
+    ({ variables }) => {
+      const comment = bioRiskRepository.find('code', variables.code);
+      if (comment) {
+        comment.enabled = variables.enabled;
+        bioRiskRepository.save(comment);
+        return HttpResponse.json({ data: { setBioRiskEnabled: comment } }, { status: 200 });
+      } else {
+        return HttpResponse.json(
+          { errors: [{ message: `Could not find comment: "${variables.code}"` }] },
+          { status: 404 }
+        );
+      }
+    }
+  ),
+
+  graphql.query<GetBioRisksQuery, GetBioRisksQueryVariables>('GetBioRisks', ({ variables }) => {
+    return HttpResponse.json(
+      {
+        data: {
+          bioRisks: BioRiskRepository.findAll().filter((bioRisk) => variables.includeDisabled || isEnabled(bioRisk))
+        }
+      },
+      { status: 200 }
+    );
+  })
+];
+
+export default bioRiskHandler;

src/mocks/handlers/configurationHandlers.ts

@@ -17,6 +17,7 @@ import programRepository from '../repositories/programRepository';
 import omeroProjectRepository from '../repositories/omeroProjectRepository';
 import dnapStudyRepository from '../repositories/dnapStudyRepository';
 import probePanelRepository from '../repositories/probePanelRepository';
+import bioRiskRepository from '../repositories/bioRiskRepository';
 
 const configurationHandlers = [
   graphql.query<GetConfigurationQuery, GetConfigurationQueryVariables>('GetConfiguration', () => {
@@ -38,7 +39,8 @@ const configurationHandlers = [
         programs: programRepository.findAll(),
         omeroProjects: omeroProjectRepository.findAll(),
         dnapStudies: dnapStudyRepository.findAll(),
-        probePanels: probePanelRepository.findAll()
+        probePanels: probePanelRepository.findAll(),
+        bioRisks: bioRiskRepository.findAll()
       }
     });
   })

src/mocks/handlers/registrationHandlers.ts

@@ -17,6 +17,7 @@ import speciesRepository from '../repositories/speciesRepository';
 import hmdmcRepository from '../repositories/hmdmcRepository';
 import solutionRepository from '../repositories/solutionRepository';
 import slotRegionRepository from '../repositories/slotRegionRepository';
+import bioRiskRepository from '../repositories/bioRiskRepository';
 
 const registrationHandlers = [
   graphql.query<GetRegistrationInfoQuery, GetRegistrationInfoQueryVariables>('GetRegistrationInfo', ({ variables }) => {
@@ -108,7 +109,8 @@ const registrationHandlers = [
           fixatives: [{ name: 'None' }, { name: 'Formalin' }],
           mediums: [{ name: 'OCT' }, { name: 'Paraffin' }, { name: 'None' }],
           solutions: solutionRepository.findAll().filter((sample) => sample.enabled),
-          slotRegions: slotRegionRepository.findAll().filter((region) => region.enabled)
+          slotRegions: slotRegionRepository.findAll().filter((region) => region.enabled),
+          bioRisks: bioRiskRepository.findAll().filter((bioRisk) => bioRisk.enabled)
         }
       },
       { status: 200 }

src/mocks/handlers/userHandlers.ts

@@ -29,7 +29,7 @@ const userHandlers = [
           user: {
             __typename: 'User',
             username,
-            role: UserRole.Normal
+            role: UserRole.Admin
           }
         }
       }
@@ -53,7 +53,7 @@ const userHandlers = [
           user: {
             __typename: 'User',
             username: 'jb1',
-            role: UserRole.Normal
+            role: UserRole.Admin
           }
         }
       });
@@ -63,7 +63,7 @@ const userHandlers = [
           user: {
             __typename: 'User',
             username: currentUser,
-            role: UserRole.Normal
+            role: UserRole.Admin
           }
         }
       });

src/mocks/repositories/bioRiskRepository.ts

@@ -0,0 +1,11 @@
+import { BioRisk } from '../../types/sdk';
+import { createSessionStorageRepository } from './index';
+import bioRiskFactory from '../../lib/factories/bioRiskFactory';
+
+const seeds: Array<BioRisk> = bioRiskFactory.buildList(5);
+seeds.push(bioRiskFactory.build({ enabled: false }));
+seeds.push(bioRiskFactory.build({ code: 'bioRisk1' }));
+
+const bioRiskRepository = createSessionStorageRepository('BIORISKS', 'code', seeds);
+
+export default bioRiskRepository;

src/pages/BlockRegistration.tsx

@@ -44,6 +44,7 @@ export interface RegistrationFormTissue {
   sampleCollectionDate?: Date | string;
   blocks: RegistrationFormBlock[];
   workNumber: string;
+  bioRiskCode: string;
 }
 
 export interface RegistrationFormValues {
@@ -80,7 +81,8 @@ export function getRegistrationFormTissue(): RegistrationFormTissue {
     tissueType: '',
     blocks: [getRegistrationFormBlock()],
     sampleCollectionDate: '',
-    workNumber: ''
+    workNumber: '',
+    bioRiskCode: ''
   };
 }
 
@@ -149,7 +151,8 @@ export function buildRegisterTissuesMutationVariables(
               ? tissue.sampleCollectionDate instanceof Date
                 ? tissue.sampleCollectionDate.toLocaleDateString()
                 : tissue.sampleCollectionDate
-              : undefined
+              : undefined,
+            bioRiskCode: tissue.bioRiskCode
           };
 
           if (!ignoreExistingTissues && existingTissues.includes(blockRegisterRequest.externalIdentifier)) {

src/pages/Configuration.tsx

@@ -23,6 +23,7 @@ export default function Configuration() {
 
   //Listed in alphabetical order
   const configElements = [
+    'Biological Risk Assessment Numbers',
     'Comments',
     'Cost Codes',
     'Destruction Reasons',
@@ -58,6 +59,29 @@ export default function Configuration() {
   //Fill in the Config panels in same order as config Elements
   const configPanels = React.useMemo(() => {
     return [
+      /**BioRisk Codes**/
+      <div data-testid="config">
+        <Heading level={2}>Biological Risk Assessment Numbers</Heading>
+        <p className="mt-3 mb-6 text-lg" />
+        <EntityManager
+          initialEntities={configuration.bioRisks}
+          displayKeyColumnName={'code'}
+          valueColumnName={'enabled'}
+          onChangeValue={(entity, value) => {
+            const enabled = typeof value === 'boolean' ? value : false;
+            return stanCore
+              .SetBioRiskEnabled({
+                enabled,
+                code: entity.code
+              })
+              .then((res) => res.setBioRiskEnabled);
+          }}
+          valueFieldComponentInfo={{
+            type: 'CHECKBOX'
+          }}
+          onCreate={(code) => stanCore.AddBioRisk({ code }).then((res) => res.addBioRisk)}
+        />
+      </div>,
       /**Comments**/
       <div className="space-y-8">
         {Object.keys(groupedComments)

src/pages/OriginalSampleRegistration.tsx

@@ -82,7 +82,8 @@ export function getRegistrationFormTissueSample(): RegistrationFormOriginalSampl
     tissueType: '',
     blocks: [getRegistrationFormSample()],
     sampleCollectionDate: '',
-    workNumber: ''
+    workNumber: '',
+    bioRiskCode: ''
   };
 }
 

src/pages/ProbeHybridisationXenium.tsx

@@ -252,7 +252,7 @@ const ProbeHybridisationXenium: React.FC = () => {
                                 <FormikInput
                                   label={'Sample Prep Reagent Lot'}
                                   name={'samplePrepReagentLot'}
-                                  onChange={async (e: React.ChangeEvent<HTMLSelectElement>) => {
+                                  onChange={async (e: React.ChangeEvent<HTMLInputElement>) => {
                                     await setValues((prev) => ({
                                       ...prev,
                                       samplePrepReagentLot: e.target.value,

src/pages/registration/RegistrationForm.tsx

@@ -152,6 +152,15 @@ const RegistrationForm = <T extends TissueValues<B>, B>({
                 options={selectOptionValues(registrationInfo.tissueTypes, 'name', 'name')}
                 value={values.tissues[currentIndex].tissueType}
               />
+              <CustomReactSelect
+                label="Biological Risk Assessment Numbers"
+                emptyOption
+                name={`tissues.${currentIndex}.bioRiskCode`}
+                className="mt-2"
+                dataTestId="bioRisks"
+                options={selectOptionValues(registrationInfo.bioRisks, 'code', 'code')}
+                value={values.tissues[currentIndex].bioRiskCode}
+              />
             </motion.div>
 
             <motion.div variants={variants.fadeInWithLift} className="space-y-4">