Pepper 1040 unable obtain tissue fix (#2928)

broadinstitute · Aug 22, 2024 · e92bed3 · e92bed3
1 parent e6b7523
commit e92bed3
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Showing 3 changed files with 22 additions and 14 deletions.
diff --git a/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/OncHistoryDetail.java b/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/OncHistoryDetail.java
@@ -91,6 +91,7 @@ public class OncHistoryDetail implements HasDdpInstanceId {
     public static final String STATUS_RETURNED = "returned";
     public static final String STATUS_REQUEST = "request";
     public static final String STATUS_UNABLE_TO_OBTAIN = "unableToObtain";
+    public static final String UNABLE_OBTAIN_TISSUE = "unableObtainTissue";
     public static final String PROBLEM_INSUFFICIENT_PATH = "insufficientPath";
     public static final String PROBLEM_INSUFFICIENT_SHL = "insufficientSHL";
     public static final String PROBLEM_NO_E_SIGN = "noESign";

diff --git a/...stitute/dsm/model/elastic/export/generate/OncHistoryDetailUnableObtainTissueStrategy.java b/...stitute/dsm/model/elastic/export/generate/OncHistoryDetailUnableObtainTissueStrategy.java
@@ -1,7 +1,12 @@
 package org.broadinstitute.dsm.model.elastic.export.generate;
 
+import lombok.extern.slf4j.Slf4j;
+import org.broadinstitute.dsm.db.OncHistoryDetail;
+
+import java.util.HashMap;
 import java.util.Map;
 
+@Slf4j
 public class OncHistoryDetailUnableObtainTissueStrategy extends UnableObtainTissueStrategy {
 
     public OncHistoryDetailUnableObtainTissueStrategy(GeneratorPayload generatorPayload) {
@@ -11,7 +16,9 @@ public OncHistoryDetailUnableObtainTissueStrategy(GeneratorPayload generatorPayl
     @Override
     public Map<String, Object> generate() {
         if (isUnableToObtain()) {
-            return Map.of();
+            Map<String, Object> resultMap = new HashMap<>();
+            resultMap.put(OncHistoryDetail.STATUS_REQUEST, OncHistoryDetail.UNABLE_OBTAIN_TISSUE);
+            return resultMap;
         }
         return super.generate();
     }

diff --git a/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/model/patch/BasePatch.java b/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/model/patch/BasePatch.java
@@ -13,6 +13,7 @@
 import lombok.NonNull;
 import org.apache.commons.lang3.StringUtils;
 import org.broadinstitute.dsm.db.DDPInstance;
+import org.broadinstitute.dsm.db.OncHistoryDetail;
 import org.broadinstitute.dsm.db.dao.ddp.onchistory.OncHistoryDetailDaoImpl;
 import org.broadinstitute.dsm.db.dao.ddp.participant.ParticipantDataDao;
 import org.broadinstitute.dsm.db.dao.queue.EventDao;
@@ -233,7 +234,7 @@ protected boolean isNameValuePairs() {
     protected List<NameValue> setWorkflowRelatedFields(@NonNull Patch patch) {
         List<NameValue> nameValues = new ArrayList<>();
         if (patch.getNameValue().getValue() == null) {
-            // if the date that was sent in is null, we don't want to set the workflow fields
+            // if the value that was sent in is null, we don't want to set the workflow fields
             return nameValues;
         }
         //mr request workflow
@@ -279,18 +280,17 @@ protected List<NameValue> setWorkflowRelatedFields(@NonNull Patch patch) {
                                     patch.getNameValues(), patch.getDdpParticipantId()), "sent"));
                 }
             }
-        } else if (patch.getNameValue().getName().equals("oD.unableObtainTissue") && !(boolean) patch.getNameValue().getValue()) {
-            boolean hasReceivedDate = new OncHistoryDetailDaoImpl().hasReceivedDate(getOncHistoryDetailId(patch));
-
-            if (hasReceivedDate) {
-                nameValues.add(setAdditionalValue("oD.request",
-                        new Patch(patch.getId(), PARTICIPANT_ID, patch.getParentId(), patch.getUser(), patch.getNameValue(),
-                                patch.getNameValues(), patch.getDdpParticipantId()), "received"));
-            } else {
-                nameValues.add(setAdditionalValue("oD.request",
-                        new Patch(patch.getId(), PARTICIPANT_ID, patch.getParentId(), patch.getUser(), patch.getNameValue(),
-                                patch.getNameValues(), patch.getDdpParticipantId()), "sent"));
-            }
+        } else if (patch.getNameValue().getName().equals("oD.unableObtainTissue")) {
+            // if unable to obtain tissue, set request to "unable to obtain"
+            // if not unable to obtain, check if received date exists, if so set request to "received", otherwise set to "sent"
+            String status = (boolean) patch.getNameValue().getValue()
+                    ? OncHistoryDetail.UNABLE_OBTAIN_TISSUE
+                    : new OncHistoryDetailDaoImpl().hasReceivedDate(getOncHistoryDetailId(patch))
+                    ? "received"
+                    : "sent";
+            nameValues.add(setAdditionalValue("oD.request",
+                    new Patch(patch.getId(), PARTICIPANT_ID, patch.getParentId(), patch.getUser(), patch.getNameValue(),
+                            patch.getNameValues(), patch.getDdpParticipantId()), status));
         }
         return nameValues;
     }