[JN-417] Implement basic kit management UI (#477)

Co-authored-by: Matt Bemis <[email protected]>

Author: breilly2

api-admin/src/main/java/bio/terra/pearl/api/admin/controller/enrollee/EnrolleeController.java

@@ -3,6 +3,7 @@
 import bio.terra.pearl.api.admin.api.EnrolleeApi;
 import bio.terra.pearl.api.admin.service.AuthUtilService;
 import bio.terra.pearl.api.admin.service.enrollee.EnrolleeExtService;
+import bio.terra.pearl.core.model.EnvironmentName;
 import bio.terra.pearl.core.model.admin.AdminUser;
 import bio.terra.pearl.core.model.kit.KitRequest;
 import bio.terra.pearl.core.model.participant.Enrollee;
@@ -79,5 +80,17 @@ public ResponseEntity<Object> getKitRequests(
     return ResponseEntity.ok(kitRequests);
   }
 
+  @Override
+  public ResponseEntity<Object> enrolleesWithKits(
+      String portalShortcode, String studyShortcode, String envName) {
+    AdminUser adminUser = authUtilService.requireAdminUser(request);
+    EnvironmentName environmentName = EnvironmentName.valueOfCaseInsensitive(envName);
+
+    var enrollees =
+        enrolleeExtService.findForKitManagement(
+            adminUser, portalShortcode, studyShortcode, environmentName);
+    return ResponseEntity.ok(enrollees);
+  }
+
   public record WithdrawnResponse(UUID withdrawnEnrolleeId) {}
 }

api-admin/src/main/java/bio/terra/pearl/api/admin/controller/kit/KitController.java

@@ -0,0 +1,37 @@
+package bio.terra.pearl.api.admin.controller.kit;
+
+import bio.terra.pearl.api.admin.api.KitApi;
+import bio.terra.pearl.api.admin.service.AuthUtilService;
+import bio.terra.pearl.api.admin.service.kit.KitExtService;
+import bio.terra.pearl.core.model.EnvironmentName;
+import bio.terra.pearl.core.model.admin.AdminUser;
+import javax.servlet.http.HttpServletRequest;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+
+@Controller
+public class KitController implements KitApi {
+  private final AuthUtilService authUtilService;
+  private final KitExtService kitExtService;
+  private final HttpServletRequest request;
+
+  public KitController(
+      AuthUtilService authUtilService, KitExtService kitExtService, HttpServletRequest request) {
+    this.authUtilService = authUtilService;
+    this.kitExtService = kitExtService;
+    this.request = request;
+  }
+
+  @Override
+  public ResponseEntity<Object> kitsByStudyEnvironment(
+      String portalShortcode, String studyShortcode, String envName) {
+    AdminUser adminUser = authUtilService.requireAdminUser(request);
+    EnvironmentName environmentName = EnvironmentName.valueOfCaseInsensitive(envName);
+
+    var kits =
+        kitExtService.getKitRequestsByStudyEnvironment(
+            adminUser, portalShortcode, studyShortcode, environmentName);
+
+    return ResponseEntity.ok(kits);
+  }
+}

api-admin/src/main/java/bio/terra/pearl/api/admin/service/enrollee/EnrolleeExtService.java

@@ -63,6 +63,15 @@ public List<EnrolleeSearchResult> search(
     return enrolleeSearchService.search(studyShortcode, environmentName, facets);
   }
 
+  public List<Enrollee> findForKitManagement(
+      AdminUser user,
+      String portalShortcode,
+      String studyShortcode,
+      EnvironmentName environmentName) {
+    authUtilService.authUserToStudy(user, portalShortcode, studyShortcode);
+    return enrolleeService.findForKitManagement(studyShortcode, environmentName);
+  }
+
   public Enrollee findWithAdminLoad(AdminUser user, String enrolleeShortcode) {
     Enrollee enrollee = authUtilService.authAdminUserToEnrollee(user, enrolleeShortcode);
     return enrolleeService.loadForAdminView(enrollee);
@@ -90,6 +99,6 @@ public KitRequest requestKit(AdminUser adminUser, String enrolleeShortcode, Stri
 
   public Collection<KitRequest> getKitRequests(AdminUser adminUser, String enrolleeShortcode) {
     Enrollee enrollee = authUtilService.authAdminUserToEnrollee(adminUser, enrolleeShortcode);
-    return kitRequestService.getKitRequests(adminUser, enrollee);
+    return kitRequestService.getKitRequests(enrollee);
   }
 }

api-admin/src/main/java/bio/terra/pearl/api/admin/service/kit/KitExtService.java

@@ -0,0 +1,40 @@
+package bio.terra.pearl.api.admin.service.kit;
+
+import bio.terra.pearl.api.admin.service.AuthUtilService;
+import bio.terra.pearl.core.model.EnvironmentName;
+import bio.terra.pearl.core.model.admin.AdminUser;
+import bio.terra.pearl.core.model.kit.KitRequest;
+import bio.terra.pearl.core.model.study.StudyEnvironment;
+import bio.terra.pearl.core.service.kit.KitRequestService;
+import bio.terra.pearl.core.service.study.StudyEnvironmentService;
+import java.util.Collection;
+import org.springframework.stereotype.Service;
+
+@Service
+public class KitExtService {
+  private final AuthUtilService authUtilService;
+  private final KitRequestService kitRequestService;
+  private final StudyEnvironmentService studyEnvironmentService;
+
+  public KitExtService(
+      AuthUtilService authUtilService,
+      KitRequestService kitRequestService,
+      StudyEnvironmentService studyEnvironmentService) {
+    this.authUtilService = authUtilService;
+    this.kitRequestService = kitRequestService;
+    this.studyEnvironmentService = studyEnvironmentService;
+  }
+
+  public Collection<KitRequest> getKitRequestsByStudyEnvironment(
+      AdminUser adminUser,
+      String portalShortcode,
+      String studyShortcode,
+      EnvironmentName environmentName) {
+    authUtilService.authUserToStudy(adminUser, portalShortcode, studyShortcode);
+
+    StudyEnvironment studyEnvironment =
+        studyEnvironmentService.findByStudy(studyShortcode, environmentName).get();
+
+    return kitRequestService.getSampleKitsByStudyEnvironment(studyEnvironment);
+  }
+}

api-admin/src/main/resources/api/openapi.yml

@@ -888,6 +888,37 @@ paths:
                 format: binary
         '500':
           $ref: '#/components/responses/ServerError'
+  /api/portals/v1/{portalShortcode}/studies/{studyShortcode}/env/{envName}/enrolleesWithKits:
+    get:
+      summary: Gets a list of enrollees with tasks and kit requests
+      tags: [ enrollee ]
+      operationId: enrolleesWithKits
+      parameters:
+        - { name: portalShortcode, in: path, required: true, schema: { type: string } }
+        - { name: studyShortcode, in: path, required: true, schema: { type: string } }
+        - { name: envName, in: path, required: true, schema: { type: string } }
+      responses:
+        '200':
+          description: enrollee list
+          content: { application/json: { schema: { type: object } } }
+        '500':
+          $ref: '#/components/responses/ServerError'
+  /api/portals/v1/{portalShortcode}/studies/{studyShortcode}/env/{envName}/kits:
+    get:
+      summary: Gets a list of kits for a study
+      tags: [ kit ]
+      operationId: kitsByStudyEnvironment
+      parameters:
+        - { name: portalShortcode, in: path, required: true, schema: { type: string } }
+        - { name: studyShortcode, in: path, required: true, schema: { type: string } }
+        - { name: envName, in: path, required: true, schema: { type: string } }
+      responses:
+        '200':
+          description: kit list
+          content: { application/json: { schema: { type: object } } }
+        '500':
+          $ref: '#/components/responses/ServerError'
+
 components:
   responses:
     SystemStatusResponse:

api-admin/src/test/java/bio/terra/pearl/api/admin/service/kit/KitExtServiceTests.java

@@ -0,0 +1,34 @@
+package bio.terra.pearl.api.admin.service.kit;
+
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.when;
+
+import bio.terra.pearl.api.admin.BaseSpringBootTest;
+import bio.terra.pearl.api.admin.service.AuthUtilService;
+import bio.terra.pearl.core.model.EnvironmentName;
+import bio.terra.pearl.core.model.admin.AdminUser;
+import bio.terra.pearl.core.service.exception.PermissionDeniedException;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.transaction.annotation.Transactional;
+
+public class KitExtServiceTests extends BaseSpringBootTest {
+  @Autowired private KitExtService kitExtService;
+
+  @Test
+  @Transactional
+  public void testGetKitRequestsForStudyEnvironmentRequiresAdmin() {
+    when(mockAuthUtilService.authUserToStudy(any(), any(), any()))
+        .thenThrow(new PermissionDeniedException(""));
+    AdminUser adminUser = new AdminUser();
+    Assertions.assertThrows(
+        PermissionDeniedException.class,
+        () ->
+            kitExtService.getKitRequestsByStudyEnvironment(
+                adminUser, "someportal", "somestudy", EnvironmentName.sandbox));
+  }
+
+  @MockBean private AuthUtilService mockAuthUtilService;
+}

core/src/main/java/bio/terra/pearl/core/dao/BaseJdbiDao.java

@@ -8,6 +8,8 @@
 import java.time.LocalDate;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
 import lombok.Getter;
 import org.apache.commons.lang3.StringUtils;
 import org.jdbi.v3.core.Jdbi;
@@ -248,6 +250,15 @@ protected List<T> findAllByProperty(String columnName, Object columnValue) {
         );
     }
 
+    protected Stream<T> streamAllByProperty(String columnName, Object columnValue) {
+        return jdbi.withHandle(handle ->
+                handle.createQuery("select * from " + tableName + " where " + columnName + " = :columnValue;")
+                        .bind("columnValue", columnValue)
+                        .mapTo(clazz)
+                        .stream()
+        );
+    }
+
     protected List<T> findAllByPropertyCollection(String columnName, Collection<?> columnValues) {
         if (columnValues.isEmpty()) {
             // short circuit this case because bindList errors if list is empty
@@ -261,6 +272,19 @@ protected List<T> findAllByPropertyCollection(String columnName, Collection<?> c
         );
     }
 
+    protected Stream<T> streamAllByPropertyCollection(String columnName, Collection<?> columnValues) {
+        if (columnValues.isEmpty()) {
+            // short circuit this case because bindList errors if list is empty
+            return Stream.empty();
+        }
+        return jdbi.withHandle(handle ->
+                handle.createQuery("select * from " + tableName + " where " + columnName + " IN (<columnValues>);")
+                        .bindList("columnValues", columnValues)
+                        .mapTo(clazz)
+                        .stream()
+        );
+    }
+
     protected List<T> findAllByPropertySorted(String columnName, Object columnValue, String sortProperty, String sortDir) {
         return jdbi.withHandle(handle ->
                 handle.createQuery("select * from " + tableName + " where " + columnName + " = :columnValue"

core/src/main/java/bio/terra/pearl/core/dao/kit/KitRequestDao.java

@@ -6,35 +6,55 @@
 import org.jdbi.v3.core.Jdbi;
 import org.springframework.stereotype.Component;
 
-import java.util.List;
-import java.util.UUID;
+import java.util.*;
+import java.util.stream.Collectors;
 
 @Component
 public class KitRequestDao extends BaseMutableJdbiDao<KitRequest> {
     public KitRequestDao(Jdbi jdbi) {
         super(jdbi);
     }
 
+    private final String BASE_QUERY_BY_STUDY =
+            " select " + prefixedGetQueryColumns("kit") + " from " + tableName + " kit "
+            + " join enrollee on kit.enrollee_id = enrollee.id "
+            + " join study_environment on enrollee.study_environment_id = study_environment.id "
+            + " where study_environment.id = :studyEnvironmentId ";
+
     @Override
     protected Class<KitRequest> getClazz() { return KitRequest.class; }
 
     public List<KitRequest> findByEnrollee(UUID enrolleeId) {
         return super.findAllByProperty("enrollee_id", enrolleeId);
     }
 
+    public Map<UUID, List<KitRequest>> findByEnrolleeIds(Collection<UUID> enrolleeIds) {
+        return streamAllByPropertyCollection("enrollee_id", enrolleeIds)
+                .collect(Collectors.groupingBy(KitRequest::getEnrolleeId, Collectors.toList()));
+    }
+
     /**
      * Find all kits that are not complete (or errored) for a study.
      * This represents the set of in-flight kits that we want to keep an eye on in Pepper.
      */
-    public List<KitRequest> findIncompleteKits(UUID studyEnvironmentId) {
+    public List<KitRequest> findByStatus(UUID studyEnvironmentId, List<KitRequestStatus> statuses) {
+        return jdbi.withHandle(handle ->
+                handle.createQuery(BASE_QUERY_BY_STUDY +
+                                " and kit.status in (<kitStatuses>) ")
+                        .bind("studyEnvironmentId", studyEnvironmentId)
+                        .bindList("kitStatuses", statuses)
+                        .mapTo(clazz)
+                        .list()
+        );
+    }
+
+    /**
+     * Find all kits for a study (environment).
+     */
+    public List<KitRequest> findByStudyEnvironment(UUID studyEnvironmentId) {
         return jdbi.withHandle(handle ->
-                handle.createQuery(" select " + prefixedGetQueryColumns("kit") + " from " + tableName + " kit " +
-                                    " join enrollee on kit.enrollee_id = enrollee.id " +
-                                    " join study_environment on enrollee.study_environment_id = study_environment.id " +
-                                    " where study_environment.id = :studyEnvironmentId " +
-                                    " and kit.status in (<kitStatuses>) ")
+                handle.createQuery(BASE_QUERY_BY_STUDY)
                         .bind("studyEnvironmentId", studyEnvironmentId)
-                        .bindList("kitStatuses", KitRequestStatus.NON_TERMINAL_STATES)
                         .mapTo(clazz)
                         .list()
         );

core/src/main/java/bio/terra/pearl/core/dao/participant/EnrolleeDao.java

@@ -8,11 +8,15 @@
 import bio.terra.pearl.core.dao.survey.SurveyResponseDao;
 import bio.terra.pearl.core.model.kit.KitRequest;
 import bio.terra.pearl.core.model.participant.Enrollee;
-import java.util.List;
-import java.util.Optional;
-import java.util.UUID;
+
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
 import org.jdbi.v3.core.Jdbi;
+import org.springframework.data.util.Pair;
 import org.springframework.stereotype.Component;
+import org.springframework.transaction.annotation.Transactional;
 
 @Component
 public class EnrolleeDao extends BaseMutableJdbiDao<Enrollee> {
@@ -58,6 +62,11 @@ public List<Enrollee> findByStudyEnvironmentId(UUID studyEnvironmentId) {
         return findAllByProperty("study_environment_id", studyEnvironmentId);
     }
 
+    @Transactional
+    public Stream<Enrollee> streamByStudyEnvironmentId(UUID studyEnvironmentId) {
+        return streamAllByProperty("study_environment_id", studyEnvironmentId);
+    }
+
     public List<Enrollee> findAllByShortcodes(List<String> shortcodes) {
         return findAllByPropertyCollection("shortcode", shortcodes);
     }
@@ -117,6 +126,40 @@ public Enrollee loadForAdminView(Enrollee enrollee) {
         return enrollee;
     }
 
+    /**
+     * Fetches enrollees, loading all details needed for the kit management view -- currently tasks and kits.
+     * Reduces database round-trips by fetching entities from each table and performing in-memory joins.
+     * Uses Streams to reduce the number of iterations over collections of entities:
+     *  - Streams enrollees into two lists: enrollees and enrollee IDs
+     *    - avoids separately collecting IDs from entities
+     *    - retains order of results (not otherwise guaranteed when using something like Collectors.toMap())
+     *  - Streams tasks and kits into maps grouped by enrollee ID
+     *    - avoids separate iteration to build these maps
+     *  All that remains is a single traversal through the enrollee list to attach their tasks and kits.
+     */
+    @Transactional
+    public List<Enrollee> findForKitManagement(UUID studyEnvironmentId) {
+        var enrolleesAndIds = streamByStudyEnvironmentId(studyEnvironmentId).collect(Collectors.teeing(
+                Collectors.toList(),
+                Collectors.mapping(Enrollee::getId, Collectors.toList()),
+                Pair::of
+        ));
+
+        var enrollees = enrolleesAndIds.getFirst();
+        var enrolleeIds = enrolleesAndIds.getSecond();
+
+        var tasksByEnrolleeId = participantTaskDao.findByEnrolleeIds(enrolleeIds);
+        var kitsByEnrolleeId = kitRequestDao.findByEnrolleeIds(enrolleeIds);
+
+        enrollees.forEach(enrollee -> {
+            // Be sure to set empty collections to indicate that they are empty instead of not initialized
+            enrollee.setParticipantTasks(tasksByEnrolleeId.getOrDefault(enrollee.getId(), Collections.emptySet()));
+            enrollee.setKitRequests(kitsByEnrolleeId.getOrDefault(enrollee.getId(), Collections.emptyList()));
+        });
+
+        return enrollees;
+    }
+
     public int countByStudyEnvironment(UUID studyEnvironmentId) {
         return countByProperty("study_environment_id", studyEnvironmentId);
     }