diff --git a/data/pom.xml b/data/pom.xml index 298160fc..f4afa848 100644 --- a/data/pom.xml +++ b/data/pom.xml @@ -8,6 +8,10 @@ 1.0-SNAPSHOT + + 2.15.2 + + data data @@ -26,12 +30,16 @@ commons-csv - org.codehaus.jackson - jackson-core-asl + com.fasterxml.jackson.core + jackson-core + + + com.fasterxml.jackson.core + jackson-databind - org.codehaus.jackson - jackson-mapper-asl + com.fasterxml.jackson.core + jackson-annotations edu.harvard.hms.dbmi.avillach 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 index 3831c31c..98d2fa8d 100644 --- 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 index ebf2760b..8b835346 100644 --- a/docker/pic-sure-hpds/server.xml +++ b/docker/pic-sure-hpds/server.xml @@ -27,6 +27,7 @@ + diff --git a/pom.xml b/pom.xml index 879eeaf9..67701777 100644 --- a/pom.xml +++ b/pom.xml @@ -17,7 +17,7 @@ client-api - 1.8.6 + 2.15.2 UTF-8 1.4.10 @@ -245,13 +245,18 @@ 3.2.5 - org.codehaus.jackson - jackson-core-asl + com.fasterxml.jackson.core + jackson-core ${jackson.version} - org.codehaus.jackson - jackson-mapper-asl + com.fasterxml.jackson.core + jackson-databind + ${jackson.version} + + + com.fasterxml.jackson.core + jackson-annotations ${jackson.version} @@ -275,8 +280,8 @@ 1.1.1 - org.codehaus.jackson - jackson-jaxrs + com.fasterxml.jackson.jaxrs + jackson-jaxrs-json-provider ${jackson.version} diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java index e67d24cb..0a196f5b 100644 --- a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java +++ b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java @@ -273,7 +273,12 @@ private void addIdSetsForAnyRecordOf(List anyRecordOfFilters, ArrayList< addIdSetsForVariantSpecCategoryFilters(new String[]{"0/1", "1/1"}, path, patientsInScope, bucketCache); return patientsInScope.stream(); } else { - return (Stream) getCube(path).keyBasedIndex().stream(); + try { + return (Stream) 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/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java b/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java index e22bea5e..47153ee3 100644 --- a/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java +++ b/processing/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> 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 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 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 variantInfoFilters = List.of(variantInfoFilter); + + Query query = new Query(); + query.setVariantInfoFilters(variantInfoFilters); + + TreeSet 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 argumentCaptor = ArgumentCaptor.forClass(VariantIndex.class); + ArgumentCaptor>> listArgumentCaptor = ArgumentCaptor.forClass(List.class); + when(patientVariantJoinHandler.getPatientIdsForIntersectionOfVariantSets(listArgumentCaptor.capture(), argumentCaptor.capture())).thenReturn(List.of(Set.of(42))); + + Map 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 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 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 argumentCaptor = ArgumentCaptor.forClass(VariantIndex.class); + ArgumentCaptor>> listArgumentCaptor = ArgumentCaptor.forClass(List.class); + when(patientVariantJoinHandler.getPatientIdsForIntersectionOfVariantSets(listArgumentCaptor.capture(), argumentCaptor.capture())).thenReturn(List.of(Set.of(42))); + + Map 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 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 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 index 734e3a94..267d3092 100644 --- a/service/pom.xml +++ b/service/pom.xml @@ -45,12 +45,16 @@ guava - org.codehaus.jackson - jackson-core-asl + com.fasterxml.jackson.core + jackson-core - org.codehaus.jackson - jackson-mapper-asl + com.fasterxml.jackson.core + jackson-databind + + + com.fasterxml.jackson.core + jackson-annotations javax.xml.bind @@ -69,8 +73,8 @@ activation - org.codehaus.jackson - jackson-jaxrs + com.fasterxml.jackson.jaxrs + jackson-jaxrs-json-provider org.springframework diff --git a/service/src/main/resources/jaxrs-context.xml b/service/src/main/resources/jaxrs-context.xml index 08a237bf..006ed56d 100644 --- a/service/src/main/resources/jaxrs-context.xml +++ b/service/src/main/resources/jaxrs-context.xml @@ -14,7 +14,7 @@ - + diff --git a/war/src/main/webapp/WEB-INF/web.xml b/war/src/main/webapp/WEB-INF/web.xml index 04fbef21..dfa1d2ee 100644 --- a/war/src/main/webapp/WEB-INF/web.xml +++ b/war/src/main/webapp/WEB-INF/web.xml @@ -31,4 +31,12 @@ true + + 404 + /error-404.html + + + 500 + /error-500.html +