Cleanup unused request logger (#59)

Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Jul 23, 2024 · 5e5c7eb · 5e5c7eb
1 parent 4749375
commit 5e5c7eb
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Showing 7 changed files with 16 additions and 148 deletions.
diff --git a/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java
@@ -18,7 +18,6 @@
 import org.mskcc.cmo.messaging.MessageConsumer;
 import org.mskcc.smile.service.PromotedRequestMsgHandlingService;
 import org.mskcc.smile.service.ValidRequestChecker;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
@@ -45,9 +44,6 @@ public class PromotedRequestMsgHandlingServiceImpl implements PromotedRequestMsg
     @Autowired
     private ValidRequestChecker validRequestChecker;
 
-    @Autowired
-    private RequestStatusLogger requestStatusLogger;
-
     private final ObjectMapper mapper = new ObjectMapper();
     private static boolean initialized = false;
     private static volatile boolean shutdownInitiated;
@@ -162,12 +158,6 @@ public void onMessage(Message msg, Object message) {
                 } catch (Exception e) {
                     LOG.error("Exception during processing of request on topic: "
                             + VALIDATE_PROMOTED_REQUEST_TOPIC, e);
-                    try {
-                        requestStatusLogger.logRequestStatus(message.toString(),
-                                RequestStatusLogger.StatusType.REQUEST_PARSING_ERROR);
-                    } catch (IOException ex) {
-                        LOG.error("Error during attempt to write request status to logger file", ex);
-                    }
                 }
             }
         });

diff --git a/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java b/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java
@@ -17,7 +17,6 @@
 import org.mskcc.cmo.messaging.MessageConsumer;
 import org.mskcc.smile.service.RequestFilterMessageHandlingService;
 import org.mskcc.smile.service.ValidRequestChecker;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
@@ -44,9 +43,6 @@ public class RequestFilterMsgHandlingServiceIml implements RequestFilterMessageH
     @Autowired
     private ValidRequestChecker validRequestChecker;
 
-    @Autowired
-    private RequestStatusLogger requestStatusLogger;
-
     private final ObjectMapper mapper = new ObjectMapper();
     private static boolean initialized = false;
     private static volatile boolean shutdownInitiated;
@@ -183,12 +179,6 @@ public void onMessage(Message msg, Object message) {
                 } catch (Exception e) {
                     LOG.error("Exception during processing of request on topic: "
                             + IGO_REQUEST_FILTER_TOPIC, e);
-                    try {
-                        requestStatusLogger.logRequestStatus(message.toString(),
-                                RequestStatusLogger.StatusType.REQUEST_PARSING_ERROR);
-                    } catch (IOException ex) {
-                        LOG.error("Error during attempt to write request status to logger file", ex);
-                    }
                 }
             }
         });

diff --git a/src/main/java/org/mskcc/smile/service/impl/ValidRequestCheckerImpl.java b/src/main/java/org/mskcc/smile/service/impl/ValidRequestCheckerImpl.java
@@ -19,17 +19,13 @@
 import org.mskcc.smile.commons.enums.SampleType;
 import org.mskcc.smile.commons.enums.SpecimenType;
 import org.mskcc.smile.service.ValidRequestChecker;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
 
 @Component
 public class ValidRequestCheckerImpl implements ValidRequestChecker {
 
-    @Autowired
-    private RequestStatusLogger requestStatusLogger;
-
     @Value("${igo.cmo_request_filter:false}")
     private Boolean igoCmoRequestFilter;
 
@@ -136,11 +132,11 @@ public Map<String, Object> generatePromotedRequestValidationMap(String requestJs
             }
         }
         if (validPromotedSampleCount < sampleList.length) {
+            String requestId = getRequestId(requestJson);
             LOG.warn("One or more sample(s) is missing one or a combination of the following: igoId or "
                     + "primaryId, cmoPatientId or cmoSampleIdFields --> normalizedPatientId - this "
-                    + "information must be added for promoted requests & samples");
-            requestStatusLogger.logRequestStatus(requestJson,
-                RequestStatusLogger.StatusType.PROMOTED_SAMPLES_MISSING_IDS);
+                    + "information must be added for promoted requests & samples: requestId = "
+                    + requestId + ", " + requestJson);
         }
         if (validPromotedSampleCount == 0) {
             requestStatus.put("validationStatus", Boolean.FALSE);
@@ -206,19 +202,15 @@ public Map<String, Object> generateRequestStatusValidationMap(String requestJson
 
         // if requestId is blank then nothing to do, return null
         if (!hasRequestId) {
-            LOG.warn("CMO request failed sanity checking - missing requestId...");
-            requestStatusLogger.logRequestStatus(requestJson,
-                    RequestStatusLogger.StatusType.REQUEST_MISSING_REQUEST_ID);
+            LOG.warn("CMO request failed sanity checking - missing requestId. " + requestJson);
             validationReport.put("requestId", "IGO Request ID is missing from the request JSON received.");
             validationStatus = Boolean.FALSE;
         }
 
         // if cmo filter is enabled then skip request if it is non-cmo
         if (igoCmoRequestFilter && !isCmoRequest) {
             LOG.warn("CMO request filter enabled - skipping non-CMO request: "
-                    + getRequestId(requestJsonMap));
-            requestStatusLogger.logRequestStatus(requestJson,
-                    RequestStatusLogger.StatusType.CMO_REQUEST_FILTER_SKIPPED_REQUEST);
+                    + getRequestId(requestJsonMap) + ", " + requestJson);
             validationReport.put("isCmo", "SMILE CMO request filter is enabled and request JSON received has"
                     + " 'cmoRequest': false. This value must be set to true for import into SMILE.");
             validationStatus = Boolean.FALSE;
@@ -599,21 +591,20 @@ private Boolean hasNormalizedPatientId(Map<String, Object> sampleMap)
     }
 
     private Boolean requestHasSamples(String requestJson) throws JsonProcessingException, IOException {
+        String requestId = getRequestId(requestJson);
         Map<String, Object> requestJsonMap = mapper.readValue(requestJson, Map.class);
         if (!requestJsonMap.containsKey("samples")) {
-            LOG.warn("Skipping request that is missing 'samples' in JSON");
-            requestStatusLogger.logRequestStatus(requestJson,
-                    RequestStatusLogger.StatusType.REQUEST_WITH_MISSING_SAMPLES);
+            LOG.warn("Skipping request that is missing 'samples' in JSON for request ID: "
+                    + requestId + ", " + requestJson);
             return Boolean.FALSE;
         }
 
         // extract sample list from request json and check size is non-zero
         Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"),
                 Object[].class);
         if (sampleList.length == 0) {
-            LOG.warn("Skipping request without any sample data in 'samples' JSON field");
-            requestStatusLogger.logRequestStatus(requestJson,
-                    RequestStatusLogger.StatusType.REQUEST_WITH_MISSING_SAMPLES);
+            LOG.warn("Skipping request without any sample data in 'samples' JSON field: "
+                    + requestId + ", " + requestJson);
             return Boolean.FALSE;
         }
         return Boolean.TRUE;

diff --git a/src/main/java/org/mskcc/smile/service/impl/ValidateUpdatesMsgHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/ValidateUpdatesMsgHandlingServiceImpl.java
@@ -17,7 +17,6 @@
 import org.mskcc.cmo.messaging.MessageConsumer;
 import org.mskcc.smile.service.ValidRequestChecker;
 import org.mskcc.smile.service.ValidateUpdatesMessageHandlingService;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
@@ -45,9 +44,6 @@ public class ValidateUpdatesMsgHandlingServiceImpl implements ValidateUpdatesMes
     @Autowired
     private ValidRequestChecker validRequestChecker;
 
-    @Autowired
-    private RequestStatusLogger requestStatusLogger;
-
     private static boolean initialized = false;
     private static Gateway messagingGateway;
     private static final Log LOG = LogFactory.getLog(RequestFilterMsgHandlingServiceIml.class);
@@ -123,8 +119,6 @@ public void run() {
                         } else {
                             LOG.error("Sanity check failed on Request updates: "
                                     + validRequestChecker.getRequestId(requestJson));
-                            requestStatusLogger.logRequestStatus(requestJson,
-                                    RequestStatusLogger.StatusType.REQUEST_UPDATE_FAILED_SANITY_CHECK);
                         }
                     }
                     if (interrupted && requestUpdateFilterQueue.isEmpty()) {
@@ -158,9 +152,8 @@ public void run() {
                         Map<String, Object> sampleMap = mapper.readValue(sampleJson, Map.class);
                         Boolean hasRequestId = validRequestChecker.hasRequestId(sampleJson);
                         if (!hasRequestId) {
-                            LOG.warn("Cannot extract request ID information from sample update message");
-                            requestStatusLogger.logRequestStatus(sampleJson,
-                                    RequestStatusLogger.StatusType.SAMPLE_UPDATE_FAILED_SANITY_CHECK);
+                            LOG.warn("Cannot extract request ID information from sample update message: "
+                                    + sampleJson);
                             continue;
                         }
 
@@ -175,9 +168,7 @@ public void run() {
                                 messagingGateway.publish(CMO_LABEL_UPDATE_TOPIC,
                                         sampleJson);
                             } else {
-                                LOG.error("Sanity check failed on CMO sample updates ");
-                                requestStatusLogger.logRequestStatus(sampleJson,
-                                        RequestStatusLogger.StatusType.SAMPLE_UPDATE_FAILED_SANITY_CHECK);
+                                LOG.error("Sanity check failed on CMO sample updates: " + sampleJson);
                             }
                         } else {
                             Map<String, Object> sampleStatus =
@@ -190,9 +181,8 @@ public void run() {
                                         SERVER_SAMPLE_UPDATE_TOPIC,
                                         sampleJson);
                             } else {
-                                LOG.error("Sanity check failed on non-CMO sample update received.");
-                                requestStatusLogger.logRequestStatus(sampleJson,
-                                        RequestStatusLogger.StatusType.SAMPLE_UPDATE_FAILED_SANITY_CHECK);
+                                LOG.error("Sanity check failed on non-CMO sample update received: "
+                                        + sampleJson);
                             }
                         }
                     }

diff --git a/src/main/java/org/mskcc/smile/service/util/RequestStatusLogger.java b/src/main/java/org/mskcc/smile/service/util/RequestStatusLogger.java
diff --git a/src/main/resources/application.properties.EXAMPLE b/src/main/resources/application.properties.EXAMPLE
@@ -45,5 +45,3 @@ num.promoted_request_handler_threads=
 # publishing failures filepath
 smile.publishing_failures_filepath=
 
-# detailed consistency checking logger filepath
-req_filter.request_logger_filepath=
diff --git a/src/test/java/org/mskcc/smile/config/MockDataConfig.java b/src/test/java/org/mskcc/smile/config/MockDataConfig.java
@@ -14,7 +14,6 @@
 import org.mskcc.smile.commons.FileUtil;
 import org.mskcc.smile.model.MockJsonTestData;
 import org.mskcc.smile.service.impl.ValidRequestCheckerImpl;
-import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.ComponentScan;
@@ -48,17 +47,12 @@ public ValidRequestCheckerImpl validRequestCheckerImpl() {
         return new ValidRequestCheckerImpl();
     }
 
-    @Bean
-    public RequestStatusLogger requestStatusLogger() {
-        return Mockito.mock(RequestStatusLogger.class);
-    }
-
     private Map<String, MockJsonTestData> mockedRequestJsonDataMap;
 
     /**
      * Generates the mocked request json data map;
      * @return Map
-     * @throws IOException 
+     * @throws IOException
      */
     @Bean(name = "mockedRequestJsonDataMap")
     public Map<String, MockJsonTestData> mockedRequestJsonDataMap() throws IOException {