Merge branch 'develop' into pepper-1063

.circleci/main-config.yml

@@ -9,7 +9,7 @@ references:
   tcell_config_file: &tcell_config_file
                        tcell_agent.config
   ci_support_image: &ci_support_image
-                      broadinstitute/study-server-build:2022-06-01A
+                      broadinstitute/study-server-build:2023-03-28C
   root_path: &root_path
                /home/circleci
   repo_path: &repo_path
@@ -48,7 +48,7 @@ references:
 executors:
   test-executor:
     docker:
-      - image: broadinstitute/study-server-build:java-2022-06-01A
+      - image: broadinstitute/study-server-build:2023-03-28C
       # start pubsub emulator
       - image: broadinstitute/study-server-build:pubsub-1
       - image: cimg/redis:5.0

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/DSMServer.java

@@ -69,6 +69,7 @@
 import org.broadinstitute.dsm.jobs.PubSubLookUp;
 import org.broadinstitute.dsm.log.SlackAppender;
 import org.broadinstitute.dsm.model.nonpepperkit.NonPepperKitCreationService;
+import org.broadinstitute.dsm.model.nonpepperkit.NonPepperStatusKitService;
 import org.broadinstitute.dsm.pubsub.AntivirusScanningStatusListener;
 import org.broadinstitute.dsm.pubsub.DSMtasksSubscription;
 import org.broadinstitute.dsm.pubsub.MercuryOrderStatusListener;
@@ -98,7 +99,6 @@
 import org.broadinstitute.dsm.route.FieldSettingsRoute;
 import org.broadinstitute.dsm.route.FilterRoute;
 import org.broadinstitute.dsm.route.InstitutionRoute;
-import org.broadinstitute.dsm.route.JuniperShipKitRoute;
 import org.broadinstitute.dsm.route.KitAuthorizationRoute;
 import org.broadinstitute.dsm.route.KitDeactivationRoute;
 import org.broadinstitute.dsm.route.KitDiscardRoute;
@@ -129,6 +129,8 @@
 import org.broadinstitute.dsm.route.admin.UserRoute;
 import org.broadinstitute.dsm.route.dashboard.NewDashboardRoute;
 import org.broadinstitute.dsm.route.familymember.AddFamilyMemberRoute;
+import org.broadinstitute.dsm.route.juniper.JuniperShipKitRoute;
+import org.broadinstitute.dsm.route.juniper.StatusKitRoute;
 import org.broadinstitute.dsm.route.kit.KitFinalScanRoute;
 import org.broadinstitute.dsm.route.kit.KitInitialScanRoute;
 import org.broadinstitute.dsm.route.kit.KitTrackingScanRoute;
@@ -589,8 +591,13 @@ protected void setupCustomRouting(@NonNull Config cfg) {
         get(apiRoot + RoutePath.CLINICAL_KIT_ENDPOINT, new ClinicalKitsRoute(notificationUtil), new JsonTransformer());
 
         if (!cfg.getBoolean("ui.production")) {
-            NonPepperKitCreationService nonPepperKitCreationService = new NonPepperKitCreationService();
-            post(apiRoot + RoutePath.SHIP_KIT_ENDPOINT, new JuniperShipKitRoute(nonPepperKitCreationService), new JsonTransformer());
+            post(apiRoot + RoutePath.SHIP_KIT_ENDPOINT, new JuniperShipKitRoute(), new JsonTransformer());
+
+            StatusKitRoute statusKitRoute = new StatusKitRoute();
+            get(apiRoot + RoutePath.KIT_STATUS_ENDPOINT_STUDY, statusKitRoute, new JsonTransformer());
+            get(apiRoot + RoutePath.KIT_STATUS_ENDPOINT_JUNIPER_KIT_ID, statusKitRoute, new JsonTransformer());
+            get(apiRoot + RoutePath.KIT_STATUS_ENDPOINT_PARTICIPANT_ID, statusKitRoute, new JsonTransformer());
+            post(apiRoot + RoutePath.KIT_STATUS_ENDPOINT_KIT_IDS, statusKitRoute, new JsonTransformer());
         }
 
         if (!cfg.getBoolean("ui.production")) {

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/KitRequestShipping.java

@@ -197,6 +197,13 @@ public class KitRequestShipping extends KitRequest implements HasDdpInstanceId {
                     + "denial_reason = ?, authorized_by = ? WHERE kit.dsm_kit_request_id = ?";
     private static final String MARK_ORDER_AS_TRANSMITTED =
             "update ddp_kit_request set order_transmitted_at = ? where external_order_number = ?";
+
+    private static final String GET_COUNT_KITS_WITH_SAME_COLLABORATOR_SAMPLE_ID_AND_KIT_TYPE =
+            " SELECT count(*) kitRequestCount from ddp_kit_request where bsp_collaborator_sample_id REGEXP \"^%1\" and kit_type_id = ?";
+
+    private static final String GET_FOUND_IF_KIT_WITH_DDP_LABEL_ALREADY_EXISTS =
+            " select 1 from ddp_kit_request req  where req.ddp_label = ? ";
+
     private static final String QUEUE = "queue";
     private static final String ERROR = "error";
     private static final String SENT = "sent";
@@ -924,6 +931,8 @@ public static void addKitRequests(@NonNull String instanceId, @NonNull String ki
     // called by
     // 1. hourly job to add kit requests into db
     // 2. kit upload
+    // 3. Juniper shipKit route
+    // BSP and Mercury dummy kit routes in non-prod
     public static String writeRequest(@NonNull String instanceId, @NonNull String ddpKitRequestId, int kitTypeId,
                                       @NonNull String ddpParticipantId, String bspCollaboratorParticipantId, String collaboratorSampleId,
                                       @NonNull String createdBy, String addressIdTo, String errorMessage, String externalOrderNumber,
@@ -991,19 +1000,17 @@ public static String writeRequest(@NonNull String instanceId, @NonNull String dd
 
             DDPInstanceDto ddpInstanceDto =
                     new DDPInstanceDao().getDDPInstanceByInstanceId(Integer.valueOf(ddpInstance.getDdpInstanceId())).orElseThrow();
-            // update ES only if it's a pepper study
+            // update ES only if it's a pepper study, not for Darwin's arc or Juniper studies
             if (ddpInstanceDto.isESUpdatePossible()) {
                 try {
                     UpsertPainlessFacade.of(DBConstants.DDP_KIT_REQUEST_ALIAS, kitRequestShipping, ddpInstanceDto,
                             ESObjectConstants.DSM_KIT_REQUEST_ID, ESObjectConstants.DOC_ID,
                             Exportable.getParticipantGuid(ddpParticipantId, ddpInstance.getParticipantIndexES()),
                             new PutToNestedScriptBuilder()).export();
                 } catch (Exception e) {
-                    //This error will trigger on studies with no participants, this skips
-                    //the error log if that is the reason for the upsert failure.
-                        logger.error(String.format("Error inserting newly created kit request shipping with dsm kit request id: %s in "
+                    logger.error(String.format("Error inserting newly created kit request shipping with dsm kit request id: %s in "
                                 + "ElasticSearch", kitRequestShipping.getDsmKitRequestId()));
-                        e.printStackTrace();
+                    e.printStackTrace();
                 }
             }
 
@@ -1271,8 +1278,7 @@ public static String generateBspSampleID(@NonNull Connection conn, String collab
     }
 
     public static int getKitCounter(@NonNull Connection conn, String collaboratorSampleId, int kitTypeId) {
-        String query = DSMConfig.getSqlFromConfig(ApplicationConfigConstants.GET_COUNT_KITS_WITH_SAME_COLLABORATOR_SAMPLE_ID_AND_KIT_TYPE)
-                .replace("%1", collaboratorSampleId);
+        String query = GET_COUNT_KITS_WITH_SAME_COLLABORATOR_SAMPLE_ID_AND_KIT_TYPE.replace("%1", collaboratorSampleId);
         try (PreparedStatement stmt = conn.prepareStatement(query, ResultSet.TYPE_SCROLL_SENSITIVE, ResultSet.CONCUR_READ_ONLY)) {
             stmt.setInt(1, kitTypeId);
             try (ResultSet rs = stmt.executeQuery()) {
@@ -1294,8 +1300,7 @@ public static int getKitCounter(@NonNull Connection conn, String collaboratorSam
      * and checking it against db if unique
      */
     public static String generateDdpLabelID() {
-        return generateDdpLabelID(15,
-                DSMConfig.getSqlFromConfig(ApplicationConfigConstants.GET_FOUND_IF_KIT_WITH_DDP_LABEL_ALREADY_EXISTS));
+        return generateDdpLabelID(15, GET_FOUND_IF_KIT_WITH_DDP_LABEL_ALREADY_EXISTS);
     }
 
     public static String generateDdpLabelID(int length, String query) {
@@ -1355,7 +1360,7 @@ public static Address getToAddressId(@NonNull EasyPostUtil easyPostUtil, KitRequ
                                          DDPParticipant participant, DDPInstanceDto ddpInstanceDto) throws Exception {
         Address toAddress = null;
         if (addressId == null && participant == null) { //if both are set to null then it is return label!
-            toAddress = easyPostUtil.createBroadAddress(kitRequestSettings.getReturnName(), kitRequestSettings.getReturnStreet1(),
+            toAddress = easyPostUtil.createAddressWithoutValidation(kitRequestSettings.getReturnName(), kitRequestSettings.getReturnStreet1(),
                     kitRequestSettings.getReturnStreet2(), kitRequestSettings.getReturnCity(), kitRequestSettings.getReturnZip(),
                     kitRequestSettings.getReturnState(), kitRequestSettings.getReturnCountry(), kitRequestSettings.getPhone());
         } else {
@@ -1428,7 +1433,7 @@ public static Shipment getShipment(@NonNull EasyPostUtil easyPostUtil, String bi
         if (kitType != null) {
 
             Address returnAddress =
-                    easyPostUtil.createBroadAddress(kitRequestSettings.getReturnName(), kitRequestSettings.getReturnStreet1(),
+                    easyPostUtil.createAddressWithoutValidation(kitRequestSettings.getReturnName(), kitRequestSettings.getReturnStreet1(),
                             kitRequestSettings.getReturnStreet2(), kitRequestSettings.getReturnCity(), kitRequestSettings.getReturnZip(),
                             kitRequestSettings.getReturnState(), kitRequestSettings.getReturnCountry(), kitRequestSettings.getPhone());
 

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/dao/kit/KitDao.java

@@ -32,10 +32,10 @@ public interface KitDao extends Dao<KitRequestShipping> {
     Integer deleteKit(Long kitId);
 
     Optional<KitRequestShipping> getKitByDdpLabel(String ddpLabel, String kitLabel);
+
     Optional<List<KitRequestShipping>> getSubkitsByDdpLabel(String ddpLabel, String kitLabel);
 
     List<KitRequestShipping> getKitsByHruid(String hruid);
 
     Optional<ScanError> updateKitLabel(KitRequestShipping kitRequestShipping);
-
 }

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/dao/kit/KitDaoImpl.java

@@ -26,8 +26,6 @@
 
 public class KitDaoImpl implements KitDao {
 
-    private static final Logger logger = LoggerFactory.getLogger(KitDaoImpl.class);
-
     public static final String SQL_SELECT_KIT_REQUEST =
             "SELECT * FROM ( SELECT req.upload_reason, kt.kit_type_name, ddp_site.instance_name, ddp_site.ddp_instance_id, "
                     + "ddp_site.base_url, ddp_site.auth0_token, ddp_site.billing_reference, "
@@ -56,7 +54,7 @@ public class KitDaoImpl implements KitDao {
     public static final String KIT_BY_KIT_ID = " and kit.dsm_kit_id = ?";
     public static final String KIT_BY_HRUID = " and bsp_collaborator_participant_id like ? AND not kit_complete <=> 1 "
             + "AND deactivated_date is null";
-
+    private static final Logger logger = LoggerFactory.getLogger(KitDaoImpl.class);
     private static final String SQL_IS_BLOOD_KIT_QUERY = "SELECT kt.requires_insert_in_kit_tracking AS found "
             + "FROM ddp_kit_request request "
             + "LEFT JOIN kit_type kt on (kt.kit_type_id = request.kit_type_id) "
@@ -96,18 +94,20 @@ public class KitDaoImpl implements KitDao {
             + "LEFT JOIN ddp_kit_request_settings AS ks ON ks.kit_type_id = req.kit_type_id AND ks.ddp_instance_id = req.ddp_instance_id "
             + "WHERE req.ddp_label = ?";
 
-    private static final String SQL_GET_SUB_KIT_BY_DDP_LABEL = "SELECT req.ddp_kit_request_id, req.ddp_instance_id, req.ddp_kit_request_id, "
-            + "req.kit_type_id, req.bsp_collaborator_participant_id, req.bsp_collaborator_sample_id, req.ddp_participant_id, "
-            + "req.ddp_label, req.created_by, req.created_date, req.external_order_number, "
-            + "req.external_order_date, req.external_order_status, req.external_response, req.upload_reason, "
-            + "req.order_transmitted_at, req.dsm_kit_request_id, kit.kit_label, kit.dsm_kit_id,"
-            + "kt.requires_insert_in_kit_tracking, kt.kit_type_name, track.tracking_id, ks.kit_label_prefix, ks.kit_label_length "
-            + "FROM ddp_kit as kit "
-            + "LEFT JOIN ddp_kit_request AS req ON req.dsm_kit_request_id = kit.dsm_kit_request_id "
-            + "LEFT JOIN ddp_kit_tracking AS track ON track.kit_label = ?"
-            + "LEFT JOIN kit_type AS kt ON kt.kit_type_id = req.kit_type_id "
-            + "LEFT JOIN ddp_kit_request_settings AS ks ON ks.kit_type_id = req.kit_type_id AND ks.ddp_instance_id = req.ddp_instance_id "
-            + "WHERE ( req.ddp_label = ? or ddp_label like ? )";
+    private static final String SQL_GET_SUB_KIT_BY_DDP_LABEL =
+            "SELECT req.ddp_kit_request_id, req.ddp_instance_id, req.ddp_kit_request_id, "
+                    + "req.kit_type_id, req.bsp_collaborator_participant_id, req.bsp_collaborator_sample_id, req.ddp_participant_id, "
+                    + "req.ddp_label, req.created_by, req.created_date, req.external_order_number, "
+                    + "req.external_order_date, req.external_order_status, req.external_response, req.upload_reason, "
+                    + "req.order_transmitted_at, req.dsm_kit_request_id, kit.kit_label, kit.dsm_kit_id,"
+                    + "kt.requires_insert_in_kit_tracking, kt.kit_type_name, track.tracking_id, ks.kit_label_prefix, ks.kit_label_length "
+                    + "FROM ddp_kit as kit "
+                    + "LEFT JOIN ddp_kit_request AS req ON req.dsm_kit_request_id = kit.dsm_kit_request_id "
+                    + "LEFT JOIN ddp_kit_tracking AS track ON track.kit_label = ?"
+                    + "LEFT JOIN kit_type AS kt ON kt.kit_type_id = req.kit_type_id "
+                    +
+                    "LEFT JOIN ddp_kit_request_settings AS ks ON ks.kit_type_id = req.kit_type_id AND ks.ddp_instance_id = req.ddp_instance_id "
+                    + "WHERE ( req.ddp_label = ? or ddp_label like ? )";
 
     private static final String INSERT_KIT = "INSERT INTO "
             + "ddp_kit "
@@ -569,7 +569,7 @@ public Optional<ScanError> insertKitTracking(KitRequestShipping kitRequestShippi
             return dbVals;
         });
         if (Objects.nonNull(results.resultValue)) {
-            result = Optional.ofNullable((ScanError)results.resultValue);
+            result = Optional.ofNullable((ScanError) results.resultValue);
         }
         return result;
     }
@@ -666,4 +666,5 @@ public boolean hasKitReceived(Connection connection, String ddpParticipantId) {
         }
         return false;
     }
+
 }