More logging for datadog (#1241)

Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Jul 29, 2024 · b9df516 · b9df516
1 parent 76d1391
commit b9df516
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Showing 6 changed files with 16 additions and 142 deletions.
diff --git a/service/src/main/java/org/mskcc/smile/service/impl/RequestServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/RequestServiceImpl.java
@@ -27,7 +27,6 @@
 import org.mskcc.smile.persistence.neo4j.SmileRequestRepository;
 import org.mskcc.smile.service.SmileRequestService;
 import org.mskcc.smile.service.SmileSampleService;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.annotation.Transactional;
@@ -47,13 +46,7 @@ public class RequestServiceImpl implements SmileRequestService {
     @Autowired
     private SmileSampleService sampleService;
 
-    @Autowired
-    private RequestStatusLogger requestStatusLogger;
-
     private final DateFormat IMPORT_DATE_FORMATTER = initDateFormatter();
-    // 24 hours in milliseconds
-    private final Integer TIME_ADJ_24HOURS_MS = 24 * 60 * 60 * 1000;
-    private Map<String, Date> loggedExistingRequests = new HashMap<>();
     private static final Log LOG = LogFactory.getLog(RequestServiceImpl.class);
     private final ObjectMapper mapper = new ObjectMapper();
 
@@ -79,7 +72,6 @@ public Boolean saveRequest(SmileRequest request) throws Exception {
             requestRepository.save(request);
             return Boolean.TRUE;
         }
-        logDuplicateRequest(request);
         return Boolean.FALSE;
     }
 
@@ -99,46 +91,16 @@ public Boolean saveRequestMetadata(SmileRequest request) {
             StringBuilder builder = new StringBuilder();
             builder.append("Failed to update the Request-level metadata for request id: ")
                     .append(request.getIgoRequestId())
-                    .append("\n\tTotal versions of request metadata -->\n\t\t - before save: ")
+                    .append(" - Total versions of request metadata  - before save: ")
                     .append(currentMetadataList.size())
-                    .append("\n\t\t - after save: ")
+                    .append(" - after save: ")
                     .append(updatedMetadataList.size());
             LOG.error(builder.toString());
             return Boolean.FALSE;
         }
         return Boolean.TRUE;
     }
 
-    /**
-     * Logs duplicate requests.
-     * @param request
-     * @throws IOException
-     */
-    private void logDuplicateRequest(SmileRequest request) throws IOException {
-        // if request has not been logged before then save request to request logger file
-        // otherwise check if new timestamp occurs within 24 hours since the last time
-        // the same request was seen. If it does not then save request to logger file
-        Date newTimestamp = new Date();
-        Boolean logRequest = Boolean.FALSE;
-        if (!loggedExistingRequests.containsKey(request.getIgoRequestId())) {
-            loggedExistingRequests.put(request.getIgoRequestId(), newTimestamp);
-            logRequest = Boolean.TRUE;
-        } else {
-            // check if new timestamp occurs within 24 hours of the reference timestamp
-            // if check does not pass then log the request to the logger file
-            Date referenceTimestamp = loggedExistingRequests.get(request.getIgoRequestId());
-            if (!timestampWithin24Hours(referenceTimestamp, newTimestamp)) {
-                logRequest = Boolean.TRUE;
-                loggedExistingRequests.put(request.getIgoRequestId(), newTimestamp);
-            }
-        }
-
-        if (logRequest) {
-            requestStatusLogger.logRequestStatus(request.getRequestJson(),
-                    RequestStatusLogger.StatusType.DUPLICATE_REQUEST);
-        }
-    }
-
     @Override
     public SmileRequest getSmileRequestById(String requestId) throws Exception {
         SmileRequest request = requestRepository.findRequestById(requestId);
@@ -198,20 +160,6 @@ public Boolean updateRequestMetadata(RequestMetadata requestMetadata, Boolean fr
         return Boolean.FALSE;
     }
 
-    /**
-     * Returns true if new timestamp occurs within 24 hours of the reference timestamp.
-     * @param referenceTimestamp
-     * @param newTimestamp
-     * @return Boolean
-     */
-    private Boolean timestampWithin24Hours(Date referenceTimestamp, Date newTimestamp) {
-        // create reference timestamp shifted 24 hours in milliseconds
-        Calendar adjustedReferenceTimestamp = Calendar.getInstance();
-        adjustedReferenceTimestamp.setTime(referenceTimestamp);
-        adjustedReferenceTimestamp.add(Calendar.MILLISECOND, TIME_ADJ_24HOURS_MS);
-        return newTimestamp.before(adjustedReferenceTimestamp.getTime());
-    }
-
     @Override
     public Boolean requestHasUpdates(SmileRequest existingRequest, SmileRequest request,
             Boolean fromLims) throws Exception {

diff --git a/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java
@@ -254,7 +254,7 @@ public Boolean updateSampleMetadata(SampleMetadata sampleMetadata, Boolean fromL
             SmileRequest request = requestService.getSmileRequestById(sampleMetadata.getIgoRequestId());
             if (request == null) {
                 LOG.error("Failed to persist sample metadata updates, "
-                        + "request does not exist " + sampleMetadata.getIgoRequestId());
+                        + "request does not exist " + sampleMetadata.toString());
                 return Boolean.FALSE;
             }
             LOG.info("Persisting new sample to db: " + sampleMetadata.getPrimaryId());

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
@@ -123,12 +123,13 @@ public void run() {
                                     tempoService.mergeBamCompleteEventBySamplePrimaryId(primaryId,
                                         bamComplete);
                                 } catch (IncorrectResultSizeDataAccessException e) {
-                                    LOG.error("Encountered error while persisting BAM complete "
-                                            + "event to database: " + bcEvent.toString(), e);
+                                    LOG.error("[TEMPO BAM COMPLETE ERROR] Encountered error while "
+                                            + "persisting BAM complete event to database: "
+                                            + bcEvent.toString(), e);
                                 }
                             }
                         } else {
-                            LOG.error("Sample does not exist by id: " + sampleId);
+                            LOG.error("[TEMPO BAM COMPLETE ERROR] Sample does not exist by id: " + sampleId);
                         }
                     }
                 } catch (InterruptedException e) {
@@ -169,12 +170,12 @@ public void run() {
                                     tempoService.mergeQcCompleteEventBySamplePrimaryId(primaryId,
                                             qcComplete);
                                 } catch (IncorrectResultSizeDataAccessException e) {
-                                    LOG.error("Encountered error while persisting QC complete "
-                                            + "event to database: " + qcEvent.toString(), e);
+                                    LOG.error("[TEMPO QC COMPLETE ERROR] Encountered error while persisting "
+                                            + "QC complete event to database: " + qcEvent.toString(), e);
                                 }
                             }
                         } else {
-                            LOG.error("Sample does not exist by id: " + sampleId);
+                            LOG.error("[TEMPO QC COMPLETE ERROR] Sample does not exist by id: " + sampleId);
                         }
                     }
                 } catch (InterruptedException e) {
@@ -225,12 +226,13 @@ public void run() {
                                     tempoService.mergeMafCompleteEventBySamplePrimaryId(primaryId,
                                             mafComplete);
                                 } catch (IncorrectResultSizeDataAccessException e) {
-                                    LOG.error("Encountered error while persisting MAF complete "
-                                            + "event to database: " + mcEvent.toString(), e);
+                                    LOG.error("[TEMPO MAF COMPLETE ERROR] Encountered error while "
+                                            + "persisting MAF complete event to database: "
+                                            + mcEvent.toString(), e);
                                 }
                             }
                         } else {
-                            LOG.error("Sample does not exist by id: " + sampleId);
+                            LOG.error("[TEMPO MAF COMPLETE ERROR] Sample does not exist by id: " + sampleId);
                         }
                     }
                 } catch (InterruptedException e) {
@@ -327,8 +329,8 @@ public void run() {
                             LOG.info(builder.toString());
                             tempoService.updateSampleBilling(billing);
                         } else {
-                            LOG.error("Cannot update billing information for sample that does not exist: "
-                                    + billing.getPrimaryId());
+                            LOG.error("[TEMPO SAMPLE BILLING ERROR] Cannot update billing information for "
+                                    + "sample that does not exist: " + billing.getPrimaryId());
                         }
                     }
                 } catch (InterruptedException e) {

diff --git a/service/src/main/java/org/mskcc/smile/service/util/RequestStatusLogger.java b/service/src/main/java/org/mskcc/smile/service/util/RequestStatusLogger.java
diff --git a/service/src/test/java/org/mskcc/smile/service/SmileTestApp.java b/service/src/test/java/org/mskcc/smile/service/SmileTestApp.java
@@ -16,7 +16,6 @@
 import org.mskcc.smile.service.impl.SampleServiceImpl;
 import org.mskcc.smile.service.impl.TempoMessageHandlingServiceImpl;
 import org.mskcc.smile.service.impl.TempoServiceImpl;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.domain.EntityScan;
 import org.springframework.boot.test.mock.mockito.MockBean;
@@ -68,9 +67,6 @@ public CohortCompleteService cohortCompleteService() {
     @MockBean
     public CrdbMappingServiceImpl crdbMappingService;
 
-    @MockBean
-    public RequestStatusLogger requestStatusLogger;
-
     @MockBean
     public Gateway messagingGateway;
 

diff --git a/src/main/resources/application.properties.EXAMPLE b/src/main/resources/application.properties.EXAMPLE
@@ -73,9 +73,6 @@ smile.correct_cmoptid_topic=
 # messaging failures filepath
 smile.publishing_failures_filepath=
 
-# request handling failure filepath
-smile.request_handling_failures_filepath=
-
 # tempo topics
 num.tempo_msg_handler_threads=
 tempo.wes_bam_complete_topic=