Merge pull request #630 from ao508/crdb-timeout

CRDB service query timeout
mskcc · Mar 3, 2022 · 76d0d59 · 76d0d59
2 parents df74364 + 6609e5b
commit 76d0d59
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Showing 5 changed files with 75 additions and 14 deletions.
diff --git a/service/src/main/java/org/mskcc/cmo/metadb/service/impl/CrdbMappingServiceImpl.java b/service/src/main/java/org/mskcc/cmo/metadb/service/impl/CrdbMappingServiceImpl.java
@@ -1,12 +1,22 @@
 package org.mskcc.cmo.metadb.service.impl;
 
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
 import org.mskcc.cmo.metadb.persistence.jpa.CrdbRepository;
 import org.mskcc.cmo.metadb.service.CrdbMappingService;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
 
 @Component
 public class CrdbMappingServiceImpl implements CrdbMappingService {
+    @Value("${crdb.query_timeout_seconds:5}")
+    private int crdbQueryTimeoutSeconds;
+
+    private ExecutorService executor = Executors.newCachedThreadPool();
 
     @Autowired
     private CrdbRepository crdbRepository;
@@ -19,11 +29,40 @@ public CrdbMappingServiceImpl(CrdbRepository crdbRepository) {
 
     @Override
     public String getCmoPatientIdbyDmpId(String dmpId) {
-        return crdbRepository.getCmoPatientIdbyDmpId(dmpId).toString();
+        Callable<Object> task = new Callable<Object>() {
+            @Override
+            public Object call() {
+                return crdbRepository.getCmoPatientIdbyDmpId(dmpId);
+            }
+        };
+        Object result = runQueryWithForcedTimeout(task);
+        if (result != null) {
+            return result.toString();
+        }
+        return null;
     }
 
     @Override
     public String getCmoPatientIdByInputId(String inputId) {
-        return crdbRepository.getCmoPatientIdByInputId(inputId).toString();
+        Callable<Object> task = new Callable<Object>() {
+            @Override
+            public Object call() {
+                return crdbRepository.getCmoPatientIdByInputId(inputId);
+            }
+        };
+        Object result = runQueryWithForcedTimeout(task);
+        if (result != null) {
+            return result.toString();
+        }
+        return null;
+    }
+
+    private Object runQueryWithForcedTimeout(Callable<Object> task) {
+        Future<Object> future = executor.submit(task);
+        try {
+            return future.get(crdbQueryTimeoutSeconds, TimeUnit.SECONDS);
+        } catch (Exception e) {
+            return null;
+        }
     }
 }
diff --git a/service/src/test/java/org/mskcc/cmo/metadb/service/CrdbMappingServiceTest.java b/service/src/test/java/org/mskcc/cmo/metadb/service/CrdbMappingServiceTest.java
@@ -24,6 +24,7 @@ public class CrdbMappingServiceTest {
     @Autowired
     private CrdbRepository crdbRepository;
 
+    @Autowired
     private CrdbMappingServiceImpl crdbMappingService;
 
     /**
@@ -34,10 +35,9 @@ public void before() {
         for (Map.Entry<String, String> entry : mockDataUtils.mockedDmpPatientMapping.entrySet()) {
             String dmpId = entry.getKey();
             String cmoId = entry.getValue();
-            Mockito.when(crdbRepository.getCmoPatientIdbyDmpId(dmpId))
+            Mockito.when(crdbMappingService.getCmoPatientIdbyDmpId(dmpId))
                     .thenReturn(cmoId);
         }
-        this.crdbMappingService = new CrdbMappingServiceImpl(crdbRepository);
     }
 
     /**
@@ -46,9 +46,8 @@ public void before() {
      */
     @Test
     public void testMadeUpDmpIdThrowsNullPointerException() {
-        Assertions.assertThatExceptionOfType(NullPointerException.class).isThrownBy(() -> {
-            crdbMappingService.getCmoPatientIdbyDmpId("MADEUPVALUE");
-        });
+        Assertions.assertThat(crdbMappingService.getCmoPatientIdbyDmpId("MADEUPVALUE"))
+                .isNull();
     }
 
     /**
@@ -59,10 +58,7 @@ public void testDmpToCmoIdMapping() {
         for (Map.Entry<String, String> entry : mockDataUtils.mockedDmpPatientMapping.entrySet()) {
             String dmpId = entry.getKey();
             String cmoId = entry.getValue();
-            if (dmpId != null) {
-                Assertions.assertThat(cmoId)
-                        .isEqualTo(crdbMappingService.getCmoPatientIdbyDmpId(dmpId));
-            }
+            Assertions.assertThat(crdbMappingService.getCmoPatientIdbyDmpId(dmpId)).isEqualTo(cmoId);
         }
     }
 

diff --git a/service/src/test/java/org/mskcc/cmo/metadb/service/MetadbTestApp.java b/service/src/test/java/org/mskcc/cmo/metadb/service/MetadbTestApp.java
@@ -7,6 +7,7 @@
 import org.mskcc.cmo.metadb.persistence.jpa.CrdbRepository;
 import org.mskcc.cmo.metadb.service.impl.ClinicalMessageHandlingServiceImpl;
 import org.mskcc.cmo.metadb.service.impl.CorrectCmoPatientHandlingServiceImpl;
+import org.mskcc.cmo.metadb.service.impl.CrdbMappingServiceImpl;
 import org.mskcc.cmo.metadb.service.impl.PatientServiceImpl;
 import org.mskcc.cmo.metadb.service.impl.RequestReplyHandlingServiceImpl;
 import org.mskcc.cmo.metadb.service.impl.RequestServiceImpl;
@@ -51,6 +52,9 @@ public MetadbJsonComparator metadbJsonComparator() {
     @MockBean
     public CrdbRepository crdbRepository;
 
+    @MockBean
+    public CrdbMappingServiceImpl crdbMappingService;
+
     @MockBean
     public RequestStatusLogger requestStatusLogger;
 
@@ -62,10 +66,10 @@ public MetadbJsonComparator metadbJsonComparator() {
 
     @MockBean
     public ResearchMessageHandlingServiceImpl researchMessageHandlingService;
-    
+
     @MockBean
     public ClinicalMessageHandlingServiceImpl clinicalMessageHandlingService;
-    
+
     @MockBean
     public CorrectCmoPatientHandlingServiceImpl patientCorrectionHandlingService;
 

diff --git a/service/src/test/java/org/mskcc/cmo/metadb/service/MockDataUtils.java b/service/src/test/java/org/mskcc/cmo/metadb/service/MockDataUtils.java
@@ -92,7 +92,9 @@ public void mockedDmpPatientMapping() throws IOException {
             } catch (ArrayIndexOutOfBoundsException e) {
                 // do nothing
             }
-            mockedDmpPatientMapping.put(dmpPatientId, cmoPatientId);
+            if (dmpPatientId != null) {
+                mockedDmpPatientMapping.put(dmpPatientId, cmoPatientId);
+            }
         }
         reader.close();
     }

diff --git a/src/main/resources/application.properties.EXAMPLE b/src/main/resources/application.properties.EXAMPLE
@@ -20,6 +20,26 @@ spring.data.neo4j.username=
 spring.data.neo4j.password=
 spring.data.neo4j.uri=
 
+# OracleDB connection settings
+spring.datasource.url=
+spring.datasource.username=
+spring.datasource.password=
+spring.datasource.driver-class-name=
+
+# HikariCP settings
+spring.datasource.hikari.minimumIdle=
+spring.datasource.hikari.maximumPoolSize=
+spring.datasource.hikari.idleTimeout=
+spring.datasource.hikari.maxLifetime=
+spring.datasource.hikari.connectionTimeout=
+spring.datasource.hikari.poolName=
+
+# JPA settings
+spring.jpa.database-platform=
+spring.jpa.hibernate.use-new-id-generator-mappings=
+spring.jpa.hibernate.ddl-auto=
+crdb.query_timeout_seconds=
+
 # new request topics
 num.new_request_handler_threads=
 igo.new_request_topic=