add updateSpecimenType mutation (#7017)

* get initial wiring added

* add update type and endpoint

* add tests and move some error handling around

* lint codegen file

* update comment and switch error handling order

* update error message

* typo

* typo v2

* fix code smells

backend/src/main/java/gov/cdc/usds/simplereport/api/devicetype/SpecimenTypeMutationResolver.java

@@ -1,6 +1,7 @@
 package gov.cdc.usds.simplereport.api.devicetype;
 
 import gov.cdc.usds.simplereport.api.model.CreateSpecimenType;
+import gov.cdc.usds.simplereport.api.model.UpdateSpecimenType;
 import gov.cdc.usds.simplereport.api.model.errors.IllegalGraphqlArgumentException;
 import gov.cdc.usds.simplereport.db.model.SpecimenType;
 import gov.cdc.usds.simplereport.service.SpecimenTypeService;
@@ -20,4 +21,10 @@ public SpecimenType createSpecimenType(@Argument CreateSpecimenType input)
       throws IllegalGraphqlArgumentException {
     return specimenTypeService.createSpecimenType(input);
   }
+
+  @MutationMapping
+  public SpecimenType updateSpecimenType(@Argument UpdateSpecimenType input)
+      throws IllegalGraphqlArgumentException {
+    return specimenTypeService.updateSpecimenType(input);
+  }
 }

backend/src/main/java/gov/cdc/usds/simplereport/api/model/UpdateSpecimenType.java

@@ -0,0 +1,15 @@
+package gov.cdc.usds.simplereport.api.model;
+
+import lombok.Builder;
+import lombok.Getter;
+
+@Getter
+@Builder
+public class UpdateSpecimenType {
+  private final String name;
+  private final String typeCode;
+  private final String collectionLocationName;
+  private final String collectionLocationCode;
+
+  // can potentially add isDeleted here if needed in the future
+}

backend/src/main/java/gov/cdc/usds/simplereport/api/model/errors/UnidentifiedSpecimenTypeException.java

@@ -0,0 +1,28 @@
+package gov.cdc.usds.simplereport.api.model.errors;
+
+import graphql.ErrorClassification;
+import graphql.ErrorType;
+import graphql.GraphQLError;
+import graphql.language.SourceLocation;
+import java.util.Collections;
+import java.util.List;
+
+/** Exception to throw when a specimen type code can't be found */
+public class UnidentifiedSpecimenTypeException extends RuntimeException implements GraphQLError {
+
+  private static final long serialVersionUID = 1L;
+
+  public UnidentifiedSpecimenTypeException(String typeCode) {
+    super("Specimen with type code " + typeCode + " wasn't found. Make sure that type code exists");
+  }
+
+  @Override // should-be-defaulted unused interface method
+  public List<SourceLocation> getLocations() {
+    return Collections.emptyList();
+  }
+
+  @Override
+  public ErrorClassification getErrorType() {
+    return ErrorType.ExecutionAborted;
+  }
+}

backend/src/main/java/gov/cdc/usds/simplereport/config/GraphQlConfig.java

@@ -15,6 +15,7 @@
 import gov.cdc.usds.simplereport.api.model.errors.RestrictedAccessUserException;
 import gov.cdc.usds.simplereport.api.model.errors.TestEventSerializationFailureException;
 import gov.cdc.usds.simplereport.api.model.errors.UnidentifiedFacilityException;
+import gov.cdc.usds.simplereport.api.model.errors.UnidentifiedSpecimenTypeException;
 import gov.cdc.usds.simplereport.config.scalars.datetime.DateTimeScalar;
 import gov.cdc.usds.simplereport.config.scalars.localdate.LocalDateScalar;
 import graphql.validation.rules.OnValidationErrorStrategy;
@@ -120,6 +121,12 @@ public DataFetcherExceptionResolver dataFetcherExceptionResolver() {
         return Mono.just(singletonList(new GenericGraphqlException(errorMessage, errorPath)));
       }
 
+      if (exception instanceof UnidentifiedSpecimenTypeException) {
+        String errorMessage =
+            "header: Error updating specimen type details; body: " + exception.getMessage();
+        return Mono.just(singletonList(new GenericGraphqlException(errorMessage, errorPath)));
+      }
+
       return Mono.just(singletonList(new GenericGraphqlException((errorPath))));
     };
   }

backend/src/main/java/gov/cdc/usds/simplereport/service/SpecimenTypeService.java

@@ -1,17 +1,25 @@
 package gov.cdc.usds.simplereport.service;
 
 import gov.cdc.usds.simplereport.api.model.CreateSpecimenType;
+import gov.cdc.usds.simplereport.api.model.UpdateSpecimenType;
+import gov.cdc.usds.simplereport.api.model.errors.IllegalGraphqlArgumentException;
+import gov.cdc.usds.simplereport.api.model.errors.UnidentifiedSpecimenTypeException;
 import gov.cdc.usds.simplereport.config.AuthorizationConfiguration;
 import gov.cdc.usds.simplereport.db.model.SpecimenType;
 import gov.cdc.usds.simplereport.db.repository.SpecimenTypeRepository;
 import java.util.List;
 import java.util.UUID;
+import lombok.extern.slf4j.Slf4j;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
 
 @Service
+@Slf4j
 public class SpecimenTypeService {
   private SpecimenTypeRepository _specimenTypeRepo;
 
+  private static final String NUMERIC_REGEX = "^[0-9]*$";
+
   public SpecimenTypeService(SpecimenTypeRepository specimenTypeRepo) {
     _specimenTypeRepo = specimenTypeRepo;
   }
@@ -33,4 +41,28 @@ public SpecimenType createSpecimenType(CreateSpecimenType input) {
             input.getCollectionLocationName(),
             input.getCollectionLocationCode()));
   }
+
+  @Transactional(readOnly = false)
+  @AuthorizationConfiguration.RequireGlobalAdminUser
+  public SpecimenType updateSpecimenType(UpdateSpecimenType input) {
+    boolean collectionCodeValid =
+        input.getCollectionLocationCode() == null
+            || input.getCollectionLocationCode().matches(NUMERIC_REGEX);
+    if (!collectionCodeValid) {
+      throw new IllegalGraphqlArgumentException(
+          "If specified, collection location code needs to be a numeric string");
+    }
+
+    String typeCodeToMatch = input.getTypeCode();
+    SpecimenType specimenToUpdate =
+        _specimenTypeRepo
+            .findByTypeCode(typeCodeToMatch)
+            .orElseThrow(() -> new UnidentifiedSpecimenTypeException(typeCodeToMatch));
+
+    specimenToUpdate.setName(input.getName());
+    specimenToUpdate.setCollectionLocationCode(input.getCollectionLocationCode());
+    specimenToUpdate.setCollectionLocationName(input.getCollectionLocationName());
+
+    return _specimenTypeRepo.save(specimenToUpdate);
+  }
 }

backend/src/main/resources/graphql/admin.graphqls

@@ -14,6 +14,7 @@ extend type Mutation {
   createDeviceType(input: CreateDeviceType!): DeviceType
   updateDeviceType(input: UpdateDeviceType!): DeviceType
   createSpecimenType(input: CreateSpecimenType!): SpecimenType
+  updateSpecimenType(input: UpdateSpecimenType!): SpecimenType
   addUser( # used in AddOrganizationAdminFormContainer
     user: UserInput!
   ): User

backend/src/main/resources/graphql/main.graphqls

@@ -117,6 +117,13 @@ input CreateSpecimenType {
   collectionLocationCode: String
 }
 
+input UpdateSpecimenType {
+  name: String!
+  typeCode: String!
+  collectionLocationName: String
+  collectionLocationCode: String
+}
+
 type SpecimenType {
   internalId: ID!
   name: String!

backend/src/test/java/gov/cdc/usds/simplereport/service/SpecimenTypeServiceTest.java

@@ -4,6 +4,9 @@
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
 import gov.cdc.usds.simplereport.api.model.CreateSpecimenType;
+import gov.cdc.usds.simplereport.api.model.UpdateSpecimenType;
+import gov.cdc.usds.simplereport.api.model.errors.IllegalGraphqlArgumentException;
+import gov.cdc.usds.simplereport.api.model.errors.UnidentifiedSpecimenTypeException;
 import gov.cdc.usds.simplereport.db.repository.SpecimenTypeRepository;
 import gov.cdc.usds.simplereport.test_util.SliceTestConfiguration;
 import org.junit.jupiter.api.Test;
@@ -68,4 +71,68 @@ void createNewSpecimenType_failsWithTooShortLoinc() {
             });
     assert (exception.getMessage()).contains("Could not commit JPA transaction");
   }
+
+  @Test
+  @SliceTestConfiguration.WithSimpleReportSiteAdminUser
+  void updateNewSpecimenType_success() {
+    _service.createSpecimenType(
+        CreateSpecimenType.builder()
+            .name("Nasal swab")
+            .typeCode("012345678")
+            .collectionLocationName("Nasopharangyal Structure")
+            .collectionLocationCode("123456789")
+            .build());
+
+    _service.updateSpecimenType(
+        UpdateSpecimenType.builder()
+            .build()
+            .builder()
+            .name("Nasal swab with updates")
+            .typeCode("012345678")
+            .collectionLocationName("Nasopharangyal Structure with updates")
+            .collectionLocationCode("123456788")
+            .build());
+
+    assertEquals(1, _service.fetchSpecimenTypes().size());
+    assertEquals("Nasal swab with updates", _service.fetchSpecimenTypes().get(0).getName());
+    assertEquals(
+        "Nasopharangyal Structure with updates",
+        _service.fetchSpecimenTypes().get(0).getCollectionLocationName());
+    assertEquals("123456788", _service.fetchSpecimenTypes().get(0).getCollectionLocationCode());
+  }
+
+  @Test
+  @SliceTestConfiguration.WithSimpleReportSiteAdminUser
+  void updateNewSpecimenType_throws_UnidentifiedSpecimenTypeError_withBadTypeCode() {
+    UpdateSpecimenType updateSpecimen = UpdateSpecimenType.builder().typeCode("012345678").build();
+    assertThrows(
+        UnidentifiedSpecimenTypeException.class,
+        () -> {
+          _service.updateSpecimenType(updateSpecimen);
+        });
+  }
+
+  @Test
+  @SliceTestConfiguration.WithSimpleReportSiteAdminUser
+  void
+      updateNewSpecimenType_throws_IllegalGraphQlArgumentError_withNonNumericCollectionLocationCode() {
+    _service.createSpecimenType(
+        CreateSpecimenType.builder()
+            .name("Nasal swab")
+            .typeCode("012345678")
+            .collectionLocationName("Nasopharangyal Structure")
+            .collectionLocationCode("123456789")
+            .build());
+
+    UpdateSpecimenType updateSpecimen =
+        UpdateSpecimenType.builder()
+            .typeCode("012345678")
+            .collectionLocationCode("some non numeric string")
+            .build();
+    assertThrows(
+        IllegalGraphqlArgumentException.class,
+        () -> {
+          _service.updateSpecimenType(updateSpecimen);
+        });
+  }
 }

frontend/src/generated/graphql.tsx

@@ -231,6 +231,7 @@ export type Mutation = {
   updateOrganization?: Maybe<Scalars["String"]["output"]>;
   updatePatient?: Maybe<Patient>;
   updateRegistrationLink?: Maybe<Scalars["String"]["output"]>;
+  updateSpecimenType?: Maybe<SpecimenType>;
   updateTimeOfTestQuestions?: Maybe<Scalars["String"]["output"]>;
   updateUser?: Maybe<User>;
   updateUserEmail?: Maybe<User>;
@@ -506,6 +507,10 @@ export type MutationUpdateRegistrationLinkArgs = {
   newLink: Scalars["String"]["input"];
 };
 
+export type MutationUpdateSpecimenTypeArgs = {
+  input: UpdateSpecimenType;
+};
+
 export type MutationUpdateTimeOfTestQuestionsArgs = {
   genderOfSexualPartners?: InputMaybe<
     Array<InputMaybe<Scalars["String"]["input"]>>
@@ -1034,6 +1039,13 @@ export type UpdateFacilityInput = {
   phone?: InputMaybe<Scalars["String"]["input"]>;
 };
 
+export type UpdateSpecimenType = {
+  collectionLocationCode?: InputMaybe<Scalars["String"]["input"]>;
+  collectionLocationName?: InputMaybe<Scalars["String"]["input"]>;
+  name: Scalars["String"]["input"];
+  typeCode: Scalars["String"]["input"];
+};
+
 export type UploadResponse = {
   __typename?: "UploadResponse";
   createdAt: Scalars["DateTime"]["output"];