TEMPO additional logging (#1142)

Added extra logging to help with debugging. Additonal logs also report whether a cohort attempts to import with samples that are unknown to SMILE. The cohort is still imported but incompletely. Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Apr 11, 2024 · b90e4d5 · b90e4d5
1 parent d556c5e
commit b90e4d5
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Showing 2 changed files with 38 additions and 6 deletions.
diff --git a/service/src/main/java/org/mskcc/smile/service/impl/CohortCompleteServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/CohortCompleteServiceImpl.java
@@ -1,8 +1,10 @@
 package org.mskcc.smile.service.impl;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.mskcc.smile.commons.JsonComparator;
@@ -41,7 +43,8 @@ public class CohortCompleteServiceImpl implements CohortCompleteService {
     public Cohort saveCohort(Cohort cohort, Set<String> samplePrimaryIds) throws Exception {
         // persist new cohort complete event to the db
         cohortCompleteRepository.save(cohort);
-        // create cohort-smaple relationships
+        Set<String> unknownSamples = new HashSet<>(); // tracks unknown samples in smile
+        // create cohort-sample relationships
         for (String primaryId : samplePrimaryIds) {
             // confirm sample exists by primary id and then link to cohort
             if (sampleService.sampleExistsByPrimaryId(primaryId)) {
@@ -50,8 +53,21 @@ public Cohort saveCohort(Cohort cohort, Set<String> samplePrimaryIds) throws Exc
                     tempoService.initAndSaveDefaultTempoData(primaryId);
                 }
                 cohortCompleteRepository.addCohortSampleRelationship(cohort.getCohortId(), primaryId);
+            } else {
+                unknownSamples.add(primaryId);
             }
         }
+        // log and report unknown samples for reference
+        if (!unknownSamples.isEmpty()) {
+            StringBuilder builder = new StringBuilder();
+            builder.append("Could not import ")
+                    .append(unknownSamples.size())
+                    .append(" samnples for cohort ")
+                    .append(cohort.getCohortId())
+                    .append(": ")
+                    .append(StringUtils.join(unknownSamples,", "));
+            LOG.warn(builder.toString());
+        }
         return getCohortByCohortId(cohort.getCohortId());
     }
 

diff --git a/service/src/main/java/org/mskcc/smile/service/impl/TempoMessageHandlingServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/TempoMessageHandlingServiceImpl.java
@@ -35,6 +35,7 @@
 import org.mskcc.smile.service.TempoService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.dao.IncorrectResultSizeDataAccessException;
 import org.springframework.stereotype.Component;
 
 /**
@@ -117,8 +118,13 @@ public void run() {
                             Tempo tempo = tempoService.getTempoDataBySamplePrimaryId(primaryId);
                             if (tempo == null
                                     || !tempo.hasBamCompleteEvent(bamComplete)) {
-                                tempoService.mergeBamCompleteEventBySamplePrimaryId(primaryId,
+                                try {
+                                    tempoService.mergeBamCompleteEventBySamplePrimaryId(primaryId,
                                         bamComplete);
+                                } catch (IncorrectResultSizeDataAccessException e) {
+                                    LOG.error("Encountered error while persisting BAM complete "
+                                            + "event to database: " + bcEvent.toString(), e);
+                                }
                             }
                         } else {
                             LOG.error("Sample with primary id " + primaryId + " does not exist");
@@ -156,8 +162,13 @@ public void run() {
                             Tempo tempo = tempoService.getTempoDataBySamplePrimaryId(primaryId);
                             if (tempo == null
                                     || !tempo.hasQcCompleteEvent(qcComplete)) {
-                                tempoService.mergeQcCompleteEventBySamplePrimaryId(primaryId,
-                                        qcComplete);
+                                try {
+                                    tempoService.mergeQcCompleteEventBySamplePrimaryId(primaryId,
+                                            qcComplete);
+                                } catch (IncorrectResultSizeDataAccessException e) {
+                                    LOG.error("Encountered error while persisting QC complete "
+                                            + "event to database: " + qcEvent.toString(), e);
+                                }
                             }
                         } else {
                             LOG.error("Sample with primary id: " + primaryId + " does not exist");
@@ -195,8 +206,13 @@ public void run() {
                             Tempo tempo = tempoService.getTempoDataBySamplePrimaryId(primaryId);
                             if (tempo == null
                                     || !tempo.hasMafCompleteEvent(mafComplete)) {
-                                tempoService.mergeMafCompleteEventBySamplePrimaryId(primaryId,
-                                        mafComplete);
+                                try {
+                                    tempoService.mergeMafCompleteEventBySamplePrimaryId(primaryId,
+                                            mafComplete);
+                                } catch (IncorrectResultSizeDataAccessException e) {
+                                    LOG.error("Encountered error while persisting MAF complete "
+                                            + "event to database: " + mcEvent.toString(), e);
+                                }
                             }
                         } else {
                             LOG.error("Sample with primary id " + primaryId + " does not exist");