Merge branch 'release/0005' into ALS-5000

hms-dbmi · Oct 30, 2023 · 4d08479 · 4d08479
2 parents ffeac44 + 47b827b
commit 4d08479
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Showing 9 changed files with 129 additions and 24 deletions.
diff --git a/data/pom.xml b/data/pom.xml
@@ -8,6 +8,10 @@
 		<version>1.0-SNAPSHOT</version>
 	</parent>
 
+	<properties>
+		<jackson.version>2.15.2</jackson.version>
+	</properties>
+
 	<artifactId>data</artifactId>
 
 	<name>data</name>
@@ -26,12 +30,16 @@
 			<artifactId>commons-csv</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-core-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-annotations</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.avillach</groupId>

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java
@@ -3,8 +3,8 @@
 import java.io.Serializable;
 import java.util.List;
 
-import org.codehaus.jackson.annotate.JsonIgnore;
-import org.codehaus.jackson.map.annotate.JsonSerialize;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 
 @JsonSerialize(include=JsonSerialize.Inclusion.NON_NULL)
 public class ColumnMeta implements Serializable{

diff --git a/docker/pic-sure-hpds/server.xml b/docker/pic-sure-hpds/server.xml
@@ -27,6 +27,7 @@
 			<Host name="localhost" appBase="/.extract/webapps" unpackWARs="true"
 				autoDeploy="true">
 				<Context path="/" reloadable="true" />
+				<Valve className="org.apache.catalina.valves.ErrorReportValve" showReport="false" showServerInfo="false"/>
 			</Host>
 		</Engine>
 	</Service>

diff --git a/pom.xml b/pom.xml
@@ -17,7 +17,7 @@
     <module>client-api</module>
   </modules>
   <properties>
-    <jackson.version>1.8.6</jackson.version>
+    <jackson.version>2.15.2</jackson.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <dockerfile-maven-version>1.4.10</dockerfile-maven-version>
   </properties>
@@ -245,13 +245,18 @@
         <version>3.2.5</version>
       </dependency>
       <dependency>
-        <groupId>org.codehaus.jackson</groupId>
-        <artifactId>jackson-core-asl</artifactId>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-core</artifactId>
         <version>${jackson.version}</version>
       </dependency>
       <dependency>
-        <groupId>org.codehaus.jackson</groupId>
-        <artifactId>jackson-mapper-asl</artifactId>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-databind</artifactId>
+        <version>${jackson.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-annotations</artifactId>
         <version>${jackson.version}</version>
       </dependency>
       <dependency>
@@ -275,8 +280,8 @@
         <version>1.1.1</version>
       </dependency>
       <dependency>
-        <groupId>org.codehaus.jackson</groupId>
-        <artifactId>jackson-jaxrs</artifactId>
+        <groupId>com.fasterxml.jackson.jaxrs</groupId>
+        <artifactId>jackson-jaxrs-json-provider</artifactId>
         <version>${jackson.version}</version>
       </dependency>
       <dependency>

diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java
@@ -273,7 +273,12 @@ private void addIdSetsForAnyRecordOf(List<String> anyRecordOfFilters, ArrayList<
 					addIdSetsForVariantSpecCategoryFilters(new String[]{"0/1", "1/1"}, path, patientsInScope, bucketCache);
 					return patientsInScope.stream();
 				} else {
-					return (Stream<Integer>) getCube(path).keyBasedIndex().stream();
+					try {
+						return (Stream<Integer>) getCube(path).keyBasedIndex().stream();
+					} catch (InvalidCacheLoadException e) {
+						// return an empty stream if this concept doesn't exist
+						return Stream.empty();
+					}
 				}
 			}).collect(Collectors.toSet());
 			filteredIdSets.add(anyRecordOfPatientSet);

diff --git a/...ng/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java b/...ng/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java
@@ -1,7 +1,10 @@
 package edu.harvard.hms.dbmi.avillach.hpds.processing;
 
 
+import com.google.common.cache.CacheLoader;
+import com.google.common.cache.LoadingCache;
 import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.FileBackedByteIndexedInfoStore;
+import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube;
 import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query;
 import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage;
 import org.junit.Before;
@@ -12,6 +15,7 @@
 import org.mockito.junit.MockitoJUnitRunner;
 
 import java.util.*;
+import java.util.concurrent.ExecutionException;
 
 import static org.mockito.ArgumentMatchers.any;
 import static org.junit.Assert.*;
@@ -33,6 +37,9 @@ public class AbstractProcessorTest {
     @Mock
     private PatientVariantJoinHandler patientVariantJoinHandler;
 
+    @Mock
+    private LoadingCache<String, PhenoCube<?>> mockLoadingCache;
+
     public static final String GENE_WITH_VARIANT_KEY = "Gene_with_variant";
     private static final String VARIANT_SEVERITY_KEY = "Variant_severity";
     public static final List<String> EXAMPLE_GENES_WITH_VARIANT = List.of("CDH8", "CDH9", "CDH10");
@@ -61,7 +68,7 @@ public void setup() {
                         new TreeMap<>(),
                         new TreeSet<>()
                 ),
-                null,
+                mockLoadingCache,
                 infoStores,
                 null,
                 variantService,
@@ -125,20 +132,87 @@ public void getPatientSubsetForQuery_twoVariantCategoryFilters_intersectFilters(
         when(patientVariantJoinHandler.getPatientIdsForIntersectionOfVariantSets(any(), argumentCaptor.capture())).thenReturn(List.of(Set.of(42)));
 
         Map<String, String[]> categoryVariantInfoFilters = Map.of(
-            GENE_WITH_VARIANT_KEY, new String[] {EXAMPLE_GENES_WITH_VARIANT.get(0)},
-            VARIANT_SEVERITY_KEY, new String[] {EXAMPLE_VARIANT_SEVERITIES.get(0)}
+                GENE_WITH_VARIANT_KEY, new String[] {EXAMPLE_GENES_WITH_VARIANT.get(0)},
+                VARIANT_SEVERITY_KEY, new String[] {EXAMPLE_VARIANT_SEVERITIES.get(0)}
+        );
+        Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter();
+        variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters;
+
+        List<Query.VariantInfoFilter> variantInfoFilters = List.of(variantInfoFilter);
+
+        Query query = new Query();
+        query.setVariantInfoFilters(variantInfoFilters);
+
+        TreeSet<Integer> patientSubsetForQuery = abstractProcessor.getPatientSubsetForQuery(query);
+        assertFalse(patientSubsetForQuery.isEmpty());
+        // Expected result is the intersection of the two filters
+        assertEquals(argumentCaptor.getValue(), new SparseVariantIndex(Set.of(4, 6)));
+    }
+
+    @Test
+    public void getPatientSubsetForQuery_anyRecordOf_applyOrLogic() throws ExecutionException {
+        when(variantIndexCache.get(GENE_WITH_VARIANT_KEY, EXAMPLE_GENES_WITH_VARIANT.get(0))).thenReturn(new SparseVariantIndex(Set.of(2, 4, 6)));
+        when(variantIndexCache.get(VARIANT_SEVERITY_KEY, EXAMPLE_VARIANT_SEVERITIES.get(0))).thenReturn(new SparseVariantIndex(Set.of(4, 5, 6, 7)));
+
+        ArgumentCaptor<VariantIndex> argumentCaptor = ArgumentCaptor.forClass(VariantIndex.class);
+        ArgumentCaptor<List<Set<Integer>>> listArgumentCaptor = ArgumentCaptor.forClass(List.class);
+        when(patientVariantJoinHandler.getPatientIdsForIntersectionOfVariantSets(listArgumentCaptor.capture(), argumentCaptor.capture())).thenReturn(List.of(Set.of(42)));
+
+        Map<String, String[]> categoryVariantInfoFilters = Map.of(
+                GENE_WITH_VARIANT_KEY, new String[] {EXAMPLE_GENES_WITH_VARIANT.get(0)},
+                VARIANT_SEVERITY_KEY, new String[] {EXAMPLE_VARIANT_SEVERITIES.get(0)}
         );
         Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter();
         variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters;
 
         List<Query.VariantInfoFilter> variantInfoFilters = List.of(variantInfoFilter);
 
+        PhenoCube mockPhenoCube = mock(PhenoCube.class);
+        when(mockPhenoCube.keyBasedIndex()).thenReturn(List.of(42, 101));
+        when(mockLoadingCache.get("good concept")).thenReturn(mockPhenoCube);
+        when(mockLoadingCache.get("bad concept")).thenThrow(CacheLoader.InvalidCacheLoadException.class);
+
+        Query query = new Query();
+        query.setVariantInfoFilters(variantInfoFilters);
+        query.setAnyRecordOf(List.of("good concept", "bad concept"));
+
+        TreeSet<Integer> patientSubsetForQuery = abstractProcessor.getPatientSubsetForQuery(query);
+        assertFalse(patientSubsetForQuery.isEmpty());
+        // Expected result is the intersection of the two filters
+        assertEquals(argumentCaptor.getValue(), new SparseVariantIndex(Set.of(4, 6)));
+        assertEquals(listArgumentCaptor.getValue().get(0), Set.of(42, 101));
+    }
+
+
+
+    @Test
+    public void getPatientSubsetForQuery_anyRecordOfInvalidKey_returnEmpty() throws ExecutionException {
+        when(variantIndexCache.get(GENE_WITH_VARIANT_KEY, EXAMPLE_GENES_WITH_VARIANT.get(0))).thenReturn(new SparseVariantIndex(Set.of(2, 4, 6)));
+        when(variantIndexCache.get(VARIANT_SEVERITY_KEY, EXAMPLE_VARIANT_SEVERITIES.get(0))).thenReturn(new SparseVariantIndex(Set.of(4, 5, 6, 7)));
+
+        ArgumentCaptor<VariantIndex> argumentCaptor = ArgumentCaptor.forClass(VariantIndex.class);
+        ArgumentCaptor<List<Set<Integer>>> listArgumentCaptor = ArgumentCaptor.forClass(List.class);
+        when(patientVariantJoinHandler.getPatientIdsForIntersectionOfVariantSets(listArgumentCaptor.capture(), argumentCaptor.capture())).thenReturn(List.of(Set.of(42)));
+
+        Map<String, String[]> categoryVariantInfoFilters = Map.of(
+                GENE_WITH_VARIANT_KEY, new String[] {EXAMPLE_GENES_WITH_VARIANT.get(0)},
+                VARIANT_SEVERITY_KEY, new String[] {EXAMPLE_VARIANT_SEVERITIES.get(0)}
+        );
+        Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter();
+        variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters;
+
+        List<Query.VariantInfoFilter> variantInfoFilters = List.of(variantInfoFilter);
+
+        when(mockLoadingCache.get("bad concept")).thenThrow(CacheLoader.InvalidCacheLoadException.class);
+
         Query query = new Query();
         query.setVariantInfoFilters(variantInfoFilters);
+        query.setAnyRecordOf(List.of("bad concept"));
 
         TreeSet<Integer> patientSubsetForQuery = abstractProcessor.getPatientSubsetForQuery(query);
         assertFalse(patientSubsetForQuery.isEmpty());
         // Expected result is the intersection of the two filters
         assertEquals(argumentCaptor.getValue(), new SparseVariantIndex(Set.of(4, 6)));
+        assertEquals(listArgumentCaptor.getValue().get(0), Set.of());
     }
 }
diff --git a/service/pom.xml b/service/pom.xml
@@ -45,12 +45,16 @@
 			<artifactId>guava</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-core-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-core</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-annotations</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>javax.xml.bind</groupId>
@@ -69,8 +73,8 @@
 			<artifactId>activation</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-jaxrs</artifactId>
+			<groupId>com.fasterxml.jackson.jaxrs</groupId>
+			<artifactId>jackson-jaxrs-json-provider</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>

diff --git a/service/src/main/resources/jaxrs-context.xml b/service/src/main/resources/jaxrs-context.xml
@@ -14,7 +14,7 @@
             <bean class="org.apache.cxf.transport.common.gzip.GZIPOutInterceptor" />
         </jaxrs:outInterceptors>
         <jaxrs:providers>
-            <bean class="org.codehaus.jackson.jaxrs.JacksonJsonProvider" />
+            <bean class="com.fasterxml.jackson.jaxrs.json.JacksonJsonProvider" />
         </jaxrs:providers>
     </jaxrs:server>
 </beans>
diff --git a/war/src/main/webapp/WEB-INF/web.xml b/war/src/main/webapp/WEB-INF/web.xml
@@ -31,4 +31,12 @@
             <http-only>true</http-only>
         </cookie-config>
     </session-config>
+    <error-page>
+        <error-code>404</error-code>
+        <location>/error-404.html</location>
+    </error-page>
+    <error-page>
+        <error-code>500</error-code>
+        <location>/error-500.html</location>
+    </error-page>
 </web-app>