Merge branch 'release-3.x.x' into TASK-7531

Author: juanfeSanahuja

opencga-core/src/main/java/org/opencb/opencga/core/common/JacksonUtils.java

@@ -18,9 +18,11 @@
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.core.JsonFactory;
+import com.fasterxml.jackson.databind.BeanDescription;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.introspect.BeanPropertyDefinition;
 import com.fasterxml.jackson.databind.util.TokenBuffer;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 import org.apache.avro.generic.GenericRecord;
@@ -49,6 +51,8 @@
 import javax.ws.rs.ext.ContextResolver;
 import java.io.IOException;
 import java.io.UncheckedIOException;
+import java.util.HashMap;
+import java.util.Map;
 
 public class JacksonUtils {
 
@@ -202,6 +206,13 @@ public static <T> T copySafe(T instance, Class<T> clazz) {
         }
     }
 
+    public static <T> T copy(T instance) throws IOException {
+        if (instance == null) {
+            return null;
+        }
+        return copy(instance, (Class<T>) instance.getClass());
+    }
+
     public static <T> T copy(T instance, Class<T> clazz) throws IOException {
         if (instance == null) {
             return null;
@@ -226,4 +237,18 @@ public static <T> void update(T valueToUpdate, Object overrides) throws IOExcept
         defaultObjectMapper.updateValue(valueToUpdate, overrides);
     }
 
+    public static Map<String, Class<?>> getFields(Class<?> aClass) {
+        return getFields(aClass, getDefaultObjectMapper());
+    }
+
+    public static Map<String, Class<?>> getFields(Class<?> aClass, ObjectMapper objectMapper) {
+        BeanDescription beanDescription = objectMapper.getSerializationConfig().introspect(objectMapper.constructType(aClass));
+        Map<String, Class<?>> fields = new HashMap<>(beanDescription.findProperties().size());
+        for (BeanPropertyDefinition property : beanDescription.findProperties()) {
+            Class<?> rawPrimaryType = property.getRawPrimaryType();
+            fields.put(property.getName(), rawPrimaryType);
+        }
+        return fields;
+    }
+
 }

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/models/ProjectMetadata.java

@@ -4,6 +4,7 @@
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException;
 
 import java.util.*;
@@ -40,6 +41,14 @@ public VariantAnnotationSets(VariantAnnotationMetadata current, List<VariantAnno
             this.saved = saved;
         }
 
+        public VariantAnnotationSets(VariantAnnotationSets other) {
+            this.current = other.current == null ? null : new VariantAnnotationMetadata(other.current);
+            this.saved = new ArrayList<>(other.saved.size());
+            for (VariantAnnotationMetadata saved : other.saved) {
+                this.saved.add(new VariantAnnotationMetadata(saved));
+            }
+        }
+
         public VariantAnnotationMetadata getCurrent() {
             return current;
         }
@@ -114,6 +123,19 @@ public VariantAnnotationMetadata(int id, String name, Date creationDate, Variant
             this.privateSources = privateSources;
         }
 
+        public VariantAnnotationMetadata(VariantAnnotationMetadata other) {
+            this.id = other.id;
+            this.name = other.name;
+            this.creationDate = other.creationDate;
+            this.annotator = other.annotator;
+            this.sourceVersion = new ArrayList<>(other.sourceVersion.size());
+            for (ObjectMap source : other.sourceVersion) {
+                this.sourceVersion.add(new ObjectMap(source));
+            }
+            this.dataRelease = other.dataRelease == null ? null : JacksonUtils.copySafe(other.dataRelease, DataRelease.class);
+            this.privateSources = other.privateSources != null ? new ArrayList<>(other.privateSources) : null;
+        }
+
         public int getId() {
             return id;
         }
@@ -293,9 +315,18 @@ public ProjectMetadata(String species, String assembly, String dataRelease, int
         this.counters = counters != null ? counters : new HashMap<>();
     }
 
+    public ProjectMetadata(ProjectMetadata other) {
+        this.species = other.species;
+        this.assembly = other.assembly;
+        this.dataRelease = other.dataRelease;
+        this.release = other.release;
+        this.attributes = other.attributes != null ? new ObjectMap(other.attributes) : new ObjectMap();
+        this.annotation = other.annotation != null ? new VariantAnnotationSets(other.annotation) : new VariantAnnotationSets();
+        this.counters = other.counters != null ? new HashMap<>(other.counters) : new HashMap<>();
+    }
+
     public ProjectMetadata copy() {
-        return new ProjectMetadata(species, assembly, dataRelease, release, new ObjectMap(attributes), new HashMap<>(counters),
-                annotation);
+        return new ProjectMetadata(this);
     }
 
     public String getSpecies() {

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java

@@ -474,6 +474,11 @@ public void deleteAnnotation(String name, ObjectMap params) throws StorageEngine
         newVariantAnnotationManager(params).deleteAnnotation(name, params);
     }
 
+    public DataResult<VariantAnnotation> getAnnotation(Query query, QueryOptions options) throws StorageEngineException {
+        options = addDefaultLimit(options, getOptions());
+        return getDBAdaptor().getAnnotation(VariantAnnotationManager.CURRENT, query, options);
+    }
+
     public DataResult<VariantAnnotation> getAnnotation(String name, Query query, QueryOptions options) throws StorageEngineException {
         options = addDefaultLimit(options, getOptions());
         return getDBAdaptor().getAnnotation(name, query, options);

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManager.java

@@ -18,6 +18,7 @@
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
@@ -153,7 +154,7 @@ protected final VariantAnnotationMetadata checkCurrentAnnotation(ProjectMetadata
             if (current.getDataRelease() == null) {
                 // Missing current dataRelease. Continue.
             } else {
-                if (!current.getDataRelease().equals(newVariantAnnotationMetadata.getDataRelease())) {
+                if (!dataReleaseEquals(current.getDataRelease(), newVariantAnnotationMetadata.getDataRelease())) {
                     String msg = "DataRelease has changed. "
                             + "Existing annotation calculated with dataRelease " + current.getDataRelease().getRelease()
                             + ", attempting to annotate with " + newVariantAnnotationMetadata.getDataRelease().getRelease();
@@ -194,6 +195,30 @@ protected final VariantAnnotationMetadata checkCurrentAnnotation(ProjectMetadata
         return current;
     }
 
+    /**
+     * Check if two DataRelease are equal.
+     *
+     * Fields to compare:
+     * - release
+     * - date
+     * - collections
+     * - sources
+     *
+     * Ignored fields:
+     * - active
+     * - activeByDefaultIn
+     *
+     * @param current Current DataRelease
+     * @param other Other DataRelease
+     * @return true if both DataRelease are equal
+     */
+    public static boolean dataReleaseEquals(DataRelease current, DataRelease other) {
+        return current.getRelease() == other.getRelease()
+                && Objects.equals(current.getDate(), other.getDate())
+                && Objects.equals(current.getCollections(), other.getCollections())
+                && Objects.equals(current.getSources(), other.getSources());
+    }
+
     private static String removePatchFromVersion(String version) {
         String[] split = StringUtils.split(version, '.');
         if (split.length <= 1) {

opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageBaseTest.java

@@ -116,7 +116,6 @@ public abstract class VariantStorageBaseTest extends GenericTest implements Vari
     protected static URI corruptedInputUri;
 
     public static final String ANNOTATOR_EXTENSION_VCF_TEST_FILE_NAME = "variant-test-file-annotator-extension.vcf.gz";
-    protected static URI annotatorExtensionInputUri;
 
     protected static URI outputUri;
     protected VariantStorageEngine variantStorageEngine;
@@ -146,20 +145,16 @@ public static void _beforeClass() throws Exception {
         Path inputPath = rootDir.resolve(VCF_TEST_FILE_NAME);
         Path smallInputPath = rootDir.resolve(SMALL_VCF_TEST_FILE_NAME);
         Path corruptedInputPath = rootDir.resolve(VCF_CORRUPTED_FILE_NAME);
-        Path annotatorExtensionInputPath = rootDir.resolve(ANNOTATOR_EXTENSION_VCF_TEST_FILE_NAME);
         Files.copy(VariantStorageEngineTest.class.getClassLoader().getResourceAsStream(VCF_TEST_FILE_NAME), inputPath,
                 StandardCopyOption.REPLACE_EXISTING);
         Files.copy(VariantStorageEngineTest.class.getClassLoader().getResourceAsStream(SMALL_VCF_TEST_FILE_NAME), smallInputPath,
                 StandardCopyOption.REPLACE_EXISTING);
         Files.copy(VariantStorageEngineTest.class.getClassLoader().getResourceAsStream(VCF_CORRUPTED_FILE_NAME), corruptedInputPath,
                 StandardCopyOption.REPLACE_EXISTING);
-        Files.copy(VariantStorageEngineTest.class.getClassLoader().getResourceAsStream(ANNOTATOR_EXTENSION_VCF_TEST_FILE_NAME),
-                annotatorExtensionInputPath, StandardCopyOption.REPLACE_EXISTING);
 
         inputUri = inputPath.toUri();
         smallInputUri = smallInputPath.toUri();
         corruptedInputUri = corruptedInputPath.toUri();
-        annotatorExtensionInputUri = annotatorExtensionInputPath.toUri();
         outputUri = rootDir.toUri();
 //        logger.info("count: " + count.getAndIncrement());
 

opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyVariantAnnotationManagerTest.java

@@ -0,0 +1,23 @@
+package org.opencb.opencga.storage.core.variant.annotation;
+
+import org.junit.Assume;
+import org.junit.experimental.categories.Category;
+import org.opencb.opencga.core.testclassification.duration.ShortTests;
+import org.opencb.opencga.storage.core.variant.dummy.DummyVariantStorageTest;
+
+
+@Category(ShortTests.class)
+public class DummyVariantAnnotationManagerTest extends VariantAnnotationManagerTest implements DummyVariantStorageTest {
+
+    @Override
+    public void testMultiAnnotations() throws Exception {
+        Assume.assumeTrue("Multi annotations not supported in DummyVariantStorageEngine", false);
+        super.testMultiAnnotations();
+    }
+
+    @Override
+    public void testCosmicAnnotatorExtensionWithCosmicAnnotation() throws Exception {
+        Assume.assumeTrue("Can not check actual results", false);
+        super.testCosmicAnnotatorExtensionWithCosmicAnnotation();
+    }
+}