Fix initialized pipeline run dates for TEMPO nodes (#1829)

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

Author: ao508

model/src/main/java/org/mskcc/smile/model/tempo/Tempo.java

@@ -28,8 +28,8 @@ public class Tempo implements Serializable {
     private Boolean billed;
     private String billedBy;
     private String costCenter;
-    private String initialPipelineRunDate;
-    private String embargoDate;
+    private String initialPipelineRunDate; // yyyy-MM-dd
+    private String embargoDate; // yyyy-MM-dd
     @Relationship(type = "HAS_EVENT", direction = Relationship.Direction.OUTGOING)
     private List<BamComplete> bamCompleteEvents;
     @Relationship(type = "HAS_EVENT", direction = Relationship.Direction.OUTGOING)

persistence/src/main/java/org/mskcc/smile/persistence/neo4j/TempoRepository.java

@@ -200,7 +200,10 @@ OPTIONAL MATCH (cc:CohortComplete)<-[:HAS_COHORT_COMPLETE]-(c:Cohort)-[:HAS_COHO
            }[0] AS earliestDeliveryDate
            WITH custodianInformation, s.smileSampleId as smileSampleId, earliestDeliveryDate,
            CASE WHEN (earliestDeliveryDate IS NULL OR earliestDeliveryDate = "")
-            THEN $ccDeliveryDate ELSE earliestDeliveryDate END AS initialPipelineRunDate
+            THEN apoc.date.parse($ccDeliveryDate,"ms","yyyy-MM-dd HH:mm")
+            ELSE apoc.date.parse(earliestDeliveryDate,"ms","yyyy-MM-dd HH:mm") END AS initPipelineRunDatetime
+           WITH custodianInformation, smileSampleId, earliestDeliveryDate,
+            apoc.date.format(initPipelineRunDatetime, "ms", "yyyy-MM-dd") AS initialPipelineRunDate
            WITH custodianInformation, smileSampleId, earliestDeliveryDate, initialPipelineRunDate,
            CASE WHEN (initialPipelineRunDate IS NULL OR initialPipelineRunDate = "") THEN ""
             ELSE  apoc.temporal.format(datetime(apoc.date.format(
@@ -244,17 +247,17 @@ CASE WHEN ((t.initialPipelineRunDate IS NULL OR t.initialPipelineRunDate = "")
               AND (earliestDeliveryDate IS NULL)) THEN ""
             ELSE CASE WHEN (t.initialPipelineRunDate IS NULL OR t.initialPipelineRunDate = ""
               OR earliestDeliveryDate < t.initialPipelineRunDate)
-            THEN earliestDeliveryDate
-            ELSE t.initialPipelineRunDate
+            THEN apoc.date.parse(earliestDeliveryDate,"ms","yyyy-MM-dd HH:mm")
+            ELSE apoc.date.parse(t.initialPipelineRunDate,"ms","yyyy-MM-dd")
             END
-           END AS updatedInitRundate
-           SET t.initialPipelineRunDate = updatedInitRundate
+           END AS updatedInitRundatetime
+           SET t.initialPipelineRunDate = apoc.date.format(updatedInitRundatetime,"ms","yyyy-MM-dd")
            WITH s, t, today,
            CASE WHEN (t.initialPipelineRunDate IS NULL OR t.initialPipelineRunDate = "")
             THEN ""
             ELSE apoc.temporal.format(datetime(
               apoc.date.format(apoc.date.parse(t.initialPipelineRunDate, "ms", "yyyy-MM-dd"),
-              "ms", "yyyy-MM-dd")) + Duration({months:18}), 'YYYY-MM-dd')
+              "ms", "yyyy-MM-dd")) + Duration({months:18}), 'yyyy-MM-dd')
            END as updatedEmbargoDate
            SET t.embargoDate = updatedEmbargoDate
            WITH s,t,today,

service/src/test/java/org/mskcc/smile/service/TempoServiceTest.java

@@ -426,6 +426,26 @@ public void testInitAndSaveDefaultTempoDataWithFallbackToCohortDate() throws Exc
         Assertions.assertEquals("2025-12-01", tempo.getEmbargoDate());
     }
 
+    @Test
+    public void testInitAndSaveBatchTempoDataWithFallbackToCohortDate() throws Exception {
+        // use a tumor sample that doet not belong to an existing cohort
+        String igoId = "MOCKREQUEST1_B_3";
+        Tempo preTempo = tempoService.getTempoDataBySamplePrimaryId(igoId);
+        Assertions.assertNull(preTempo);
+
+        // call batch create tempo nodes for current sample
+        SmileSample sample = sampleService.getSampleByInputId(igoId);
+        String fallbackCohortDate = "2024-06-01 12:00";
+        Integer actual =
+                tempoService.batchCreateTempoNodesForSamplePrimaryIds(
+                        Arrays.asList("MOCKREQUEST1_B_3"), fallbackCohortDate);
+        Assertions.assertEquals(1, actual);
+        Tempo tempo = tempoService.getTempoDataBySampleId(sample);
+        // verify that the tempo dates are set based on the fallback date
+        Assertions.assertEquals("2024-06-01", tempo.getInitialPipelineRunDate());
+        Assertions.assertEquals("2025-12-01", tempo.getEmbargoDate());
+    }
+
     @Test
     public void testCohortCompletePipelineVersionNull() throws Exception {
         CohortCompleteJson ccJson = getCohortEventData("mockCohortCompleteCCSPPPQQQQ");