Merge pull request #15 from apache/feature/13-Implement-TypeSystemMod…

…e.MINIMAL

Issue #13: Implement TypeSystemMode.MINIMAL

src/main/java/org/apache/uima/json/jsoncas2/model/FeatureStructures.java

@@ -18,26 +18,40 @@
  */
 package org.apache.uima.json.jsoncas2.model;
 
+import static java.util.Comparator.comparing;
 import static java.util.stream.Collectors.toList;
 
 import java.util.Collection;
-import java.util.Comparator;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Set;
 
 import org.apache.uima.cas.FeatureStructure;
+import com.fasterxml.jackson.databind.DatabindContext;
 
 public class FeatureStructures implements Iterable<FeatureStructure> {
+  public static final String ALL_FEATURE_STRUCTURES = "UIMA.AllFeatureStructures";
+
   private final List<FeatureStructure> featureStructures;
 
+  private final Set<String> typeNames;
+
   public FeatureStructures(Collection<FeatureStructure> aFeatureStructures) {
+    typeNames = new HashSet<>();
     featureStructures = aFeatureStructures.stream() //
-            .sorted(Comparator.comparing(fs -> {
-              return fs.getType().getName();
-            })) //
+            .map(fs -> {
+              typeNames.add(fs.getType().getName());
+              return fs;
+            }) //
+            .sorted(comparing(fs -> fs.getType().getName())) //
             .collect(toList());
   }
 
+  public boolean existsAnnotationOfType(String aTypeName) {
+    return typeNames.contains(aTypeName);
+  }
+
   @Override
   public Iterator<FeatureStructure> iterator() {
     return featureStructures.iterator();
@@ -46,4 +60,12 @@ public Iterator<FeatureStructure> iterator() {
   public boolean isEmpty() {
     return featureStructures.isEmpty();
   }
+
+  public static void set(DatabindContext aProvider, FeatureStructures aAllFs) {
+    aProvider.setAttribute(ALL_FEATURE_STRUCTURES, aAllFs);
+  }
+
+  public static FeatureStructures get(DatabindContext aProvider) {
+    return (FeatureStructures) aProvider.getAttribute(ALL_FEATURE_STRUCTURES);
+  }
 }

src/main/java/org/apache/uima/json/jsoncas2/ser/CasSerializer.java

@@ -68,9 +68,12 @@ public void serialize(CAS aCas, JsonGenerator aJg, SerializerProvider aProvider)
 
     serializeHeader(aCas, aJg, aProvider);
 
+    FeatureStructures allFSes = findAllFeatureStructures(aCas);
+    FeatureStructures.set(aProvider, allFSes);
+
     serializeTypes(aCas, aJg, aProvider);
 
-    serializeFeatureStructures(aCas, aJg, aProvider);
+    serializeFeatureStructures(allFSes, aJg, aProvider);
 
     serializeViews(aCas, aJg, aProvider);
 
@@ -94,13 +97,12 @@ private void serializeTypes(CAS aCas, JsonGenerator aJg, SerializerProvider aPro
     }
   }
 
-  private void serializeFeatureStructures(CAS aCas, JsonGenerator aJg, SerializerProvider aProvider)
+  private void serializeFeatureStructures(FeatureStructures aAllFSes, JsonGenerator aJg, SerializerProvider aProvider)
           throws IOException {
-    FeatureStructures allFSes = findAllFeatureStructures(aCas);
-    FeatureStructureToViewIndex.set(aProvider, new FeatureStructureToViewIndex(allFSes));
-    if (!allFSes.isEmpty()) {
+    FeatureStructureToViewIndex.set(aProvider, new FeatureStructureToViewIndex(aAllFSes));
+    if (!aAllFSes.isEmpty()) {
       aJg.writeFieldName(FEATURE_STRUCTURES_FIELD);
-      aProvider.defaultSerializeValue(allFSes, aJg);
+      aProvider.defaultSerializeValue(aAllFSes, aJg);
     }
   }
 

src/main/java/org/apache/uima/json/jsoncas2/ser/TypeSerializer.java

@@ -20,6 +20,7 @@
 
 import static java.util.stream.Collectors.toList;
 import static org.apache.uima.json.jsoncas2.JsonCas2Names.ELEMENT_TYPE_FIELD;
+import static org.apache.uima.json.jsoncas2.JsonCas2Names.NAME_FIELD;
 import static org.apache.uima.json.jsoncas2.JsonCas2Names.SUPER_TYPE_FIELD;
 
 import java.io.IOException;
@@ -28,8 +29,6 @@
 import org.apache.uima.cas.Feature;
 import org.apache.uima.cas.Type;
 import org.apache.uima.cas.impl.TypeImpl;
-import org.apache.uima.json.jsoncas2.JsonCas2Names;
-
 import com.fasterxml.jackson.core.JsonGenerator;
 import com.fasterxml.jackson.databind.SerializerProvider;
 import com.fasterxml.jackson.databind.ser.std.StdSerializer;
@@ -46,7 +45,7 @@ public void serialize(Type aType, JsonGenerator aJg, SerializerProvider aProvide
           throws IOException {
     aJg.writeStartObject(aType);
 
-    aJg.writeStringField(JsonCas2Names.NAME_FIELD, aType.getName());
+    aJg.writeStringField(NAME_FIELD, aType.getName());
 
     Type parent = ((TypeImpl) aType).getSuperType();
     if (parent != null) {
@@ -57,13 +56,12 @@ public void serialize(Type aType, JsonGenerator aJg, SerializerProvider aProvide
       aJg.writeStringField(ELEMENT_TYPE_FIELD, aType.getComponentType().getName());
     }
 
-    List<Feature> newFeatures = aType.getFeatures().stream().filter(f -> f.getDomain() == aType)
+    List<Feature> localFeatures = aType.getFeatures().stream() //
+            .filter(f -> f.getDomain() == aType) //
             .collect(toList());
-    if (!newFeatures.isEmpty()) {
-      for (Feature feature : newFeatures) {
-        aJg.writeFieldName(feature.getShortName());
-        aProvider.defaultSerializeValue(feature, aJg);
-      }
+    for (Feature feature : localFeatures) {
+      aJg.writeFieldName(feature.getShortName());
+      aProvider.defaultSerializeValue(feature, aJg);
     }
 
     aJg.writeEndObject();

src/main/java/org/apache/uima/json/jsoncas2/ser/TypeSystemSerializer.java

@@ -24,14 +24,19 @@
 import static java.util.stream.Collectors.toList;
 
 import java.io.IOException;
+import java.util.ArrayDeque;
+import java.util.Deque;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.stream.StreamSupport;
 
 import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.Feature;
 import org.apache.uima.cas.Type;
 import org.apache.uima.cas.TypeSystem;
+import org.apache.uima.json.jsoncas2.mode.TypeSystemMode;
+import org.apache.uima.json.jsoncas2.model.FeatureStructures;
 import org.apache.uima.json.jsoncas2.ref.ReferenceCache;
 
 import com.fasterxml.jackson.core.JsonGenerator;
@@ -41,7 +46,7 @@
 public class TypeSystemSerializer extends StdSerializer<TypeSystem> {
   private static final long serialVersionUID = -4369127219437592227L;
 
-  private final Set<String> BUILT_IN_TYPES = unmodifiableSet(new HashSet<>(asList(
+  private static final Set<String> BUILT_IN_TYPES = unmodifiableSet(new HashSet<>(asList(
           CAS.TYPE_NAME_ANNOTATION, CAS.TYPE_NAME_ANNOTATION_BASE, CAS.TYPE_NAME_ARRAY_BASE,
           CAS.TYPE_NAME_BOOLEAN, CAS.TYPE_NAME_BOOLEAN_ARRAY, CAS.TYPE_NAME_BYTE,
           CAS.TYPE_NAME_BYTE_ARRAY, CAS.TYPE_NAME_DOCUMENT_ANNOTATION, CAS.TYPE_NAME_DOUBLE,
@@ -65,11 +70,9 @@ public void serialize(TypeSystem aTypeSystem, JsonGenerator jg, SerializerProvid
           throws IOException {
     ReferenceCache refCache = ReferenceCache.get(aProvider);
 
-    jg.writeStartObject(aTypeSystem);
+    List<Type> types = findTypesToSerialize(aTypeSystem, aProvider);
 
-    List<Type> types = StreamSupport.stream(aTypeSystem.spliterator(), false)
-            .sorted(comparing(Type::getName))
-            .filter(type -> !BUILT_IN_TYPES.contains(type.getName())).collect(toList());
+    jg.writeStartObject(aTypeSystem);
 
     for (Type type : types) {
       jg.writeFieldName(refCache.typeRef(type));
@@ -79,4 +82,65 @@ public void serialize(TypeSystem aTypeSystem, JsonGenerator jg, SerializerProvid
 
     jg.writeEndObject();
   }
+
+  private List<Type> findTypesToSerialize(TypeSystem aTypeSystem, SerializerProvider aProvider) {
+    Iterable<Type> typesSource = aTypeSystem;
+
+    if (TypeSystemMode.get(aProvider) == TypeSystemMode.MINIMAL) {
+      Deque<Type> queue = collectTypesUsedByFeatureStructures(aTypeSystem, aProvider);
+      typesSource = collectTypesUsedByTypes(aTypeSystem, typesSource, queue);
+    }
+
+    return StreamSupport.stream(typesSource.spliterator(), false) //
+            .filter(type -> !type.isArray()) //
+            .filter(type -> !BUILT_IN_TYPES.contains(type.getName())) //
+            .sorted(comparing(Type::getName)) //
+            .collect(toList());
+  }
+
+  private Set<Type> collectTypesUsedByTypes(TypeSystem aTypeSystem, Iterable<Type> typesSource, Deque<Type> queue) {
+    Set<Type> typeSet = new HashSet<>();
+    while (!queue.isEmpty()) {
+      Type t = queue.poll();
+
+      if (typeSet.contains(t)) {
+        continue;
+      }
+
+      for (Feature f : t.getFeatures()) {
+        Type parent = aTypeSystem.getParent(t);
+        while (parent != null) {
+          if (!typeSet.contains(parent)) {
+            queue.add(parent);
+          }
+          parent = aTypeSystem.getParent(parent);
+        }
+
+        Type range = f.getRange();
+        if (!typeSet.contains(range)) {
+          queue.add(range);
+        }
+
+        Type componentType = range.getComponentType();
+        if (componentType != null && !typeSet.contains(typesSource)) {
+          queue.add(componentType);
+        }
+      }
+
+      typeSet.add(t);
+    }
+    return typeSet;
+  }
+
+  private Deque<Type> collectTypesUsedByFeatureStructures(TypeSystem aTypeSystem,
+          SerializerProvider aProvider) {
+    FeatureStructures allFs = FeatureStructures.get(aProvider);
+    Deque<Type> queue = new ArrayDeque<>();
+    aTypeSystem.forEach(type -> {
+      if (allFs.existsAnnotationOfType(type.getName())) {
+        queue.add(type);
+      }
+    });
+    return queue;
+  }
 }

src/test/java/org/apache/uima/json/jsoncas2/ser/CasSerializerTest.java

@@ -0,0 +1,119 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ * 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.uima.json.jsoncas2.ser;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.apache.uima.UIMAFramework.getResourceSpecifierFactory;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.contentOf;
+
+import java.io.File;
+
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.FeatureStructure;
+import org.apache.uima.json.jsoncas2.JsonCas2Serializer;
+import org.apache.uima.json.jsoncas2.mode.TypeSystemMode;
+import org.apache.uima.resource.metadata.TypeDescription;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.apache.uima.util.CasCreationUtils;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+class CasSerializerTest {
+  private final static String USED_ANNOTATION_TYPE = "custom.UsedAnnotationType";
+
+  private final static String ANNOTATION_TYPE_USED_FROM_RANGE = "custom.AnnotationTypeUsedFromRange";
+
+  private final static String ANNOTATION_TYPE_USED_FROM_COMPONENT = "custom.AnnotationTypeUsedFromComponent";
+
+  private final static String ANNOTATION_TYPE_USED_FROM_PARENT = "custom.AnnotationTypeUsedFromParent";
+
+  private final static String UNUSED_ANNOTATION_TYPE = "custom.UnusedAnnotationType";
+
+  private JsonCas2Serializer sut;
+
+  @BeforeEach
+  void setup() {
+    sut = new JsonCas2Serializer();
+  }
+
+  @Test
+  void thatUnusedTypesAreNotSerializedInMinimalTypeSystemMode(@TempDir
+  File aTemp) throws Exception {
+    CAS cas = CasCreationUtils.createCas(makeTypeSystem(), null, null);
+    createFeatureStructure(USED_ANNOTATION_TYPE, cas);
+
+    File out = new File(aTemp, "out.json");
+    sut.setTypeSystemMode(TypeSystemMode.MINIMAL);
+    sut.serialize(cas, out);
+
+    assertThat(contentOf(out, UTF_8)).isEqualTo(
+            contentOf(getClass().getResource("/CasSerializerTest/minimalTypeSystem.json"), UTF_8));
+  }
+
+  @Test
+  void thatAllTypesAreSerializedInFullTypeSystemMode(@TempDir
+  File aTemp) throws Exception {
+    CAS cas = CasCreationUtils.createCas(makeTypeSystem(), null, null);
+    createFeatureStructure(USED_ANNOTATION_TYPE, cas);
+
+    File out = new File(aTemp, "out.json");
+    sut.setTypeSystemMode(TypeSystemMode.FULL);
+    sut.serialize(cas, out);
+
+    assertThat(contentOf(out, UTF_8)).isEqualTo(
+            contentOf(getClass().getResource("/CasSerializerTest/fullTypeSystem.json"), UTF_8));
+  }
+
+  @Test
+  void thatNoTypesAreSerializedInNoTypeSystemMode(@TempDir
+  File aTemp) throws Exception {
+    CAS cas = CasCreationUtils.createCas(makeTypeSystem(), null, null);
+    createFeatureStructure(USED_ANNOTATION_TYPE, cas);
+
+    File out = new File(aTemp, "out.json");
+    sut.setTypeSystemMode(TypeSystemMode.NONE);
+    sut.serialize(cas, out);
+
+    assertThat(contentOf(out, UTF_8)).isEqualTo(
+            contentOf(getClass().getResource("/CasSerializerTest/noTypeSystem.json"), UTF_8));
+  }
+
+  private TypeSystemDescription makeTypeSystem() {
+    TypeSystemDescription tsd = getResourceSpecifierFactory().createTypeSystemDescription();
+    tsd.addType(ANNOTATION_TYPE_USED_FROM_PARENT, null, CAS.TYPE_NAME_ANNOTATION);
+    tsd.addType(ANNOTATION_TYPE_USED_FROM_RANGE, null, CAS.TYPE_NAME_ANNOTATION);
+    tsd.addType(ANNOTATION_TYPE_USED_FROM_COMPONENT, null, CAS.TYPE_NAME_ANNOTATION);
+    tsd.addType(UNUSED_ANNOTATION_TYPE, null, CAS.TYPE_NAME_ANNOTATION);
+
+    TypeDescription td = tsd.addType(USED_ANNOTATION_TYPE, null, ANNOTATION_TYPE_USED_FROM_PARENT);
+    td.addFeature("feat1", null, ANNOTATION_TYPE_USED_FROM_RANGE);
+    td.addFeature("feat2", null, CAS.TYPE_NAME_FS_ARRAY, ANNOTATION_TYPE_USED_FROM_COMPONENT,
+            false);
+    return tsd;
+  }
+
+  private FeatureStructure createFeatureStructure(String usedAnnotationType, CAS cas) {
+    FeatureStructure fs = cas.createAnnotation(cas.getTypeSystem().getType(usedAnnotationType), 0,
+            0);
+    cas.addFsToIndexes(fs);
+    return fs;
+  }
+}

src/test/java/org/apache/uima/json/jsoncas2/ser/FeatureDeSerializerTest.java

@@ -40,16 +40,11 @@
 import org.apache.uima.util.TypeSystemUtil;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import com.fasterxml.jackson.core.Version;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.module.SimpleModule;
 
 public class FeatureDeSerializerTest {
-  private Logger log = LoggerFactory.getLogger(getClass());
-
   private static final String TYPE = "Type";
   private static final String FEATURE = "feature";
 

src/test/java/org/apache/uima/json/jsoncas2/ser/TypeDeSerializerTest.java

@@ -31,16 +31,11 @@
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.uima.util.CasCreationUtils;
 import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import com.fasterxml.jackson.core.Version;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.module.SimpleModule;
 
 public class TypeDeSerializerTest {
-  private Logger log = LoggerFactory.getLogger(getClass());
-
   @Test
   public void thatTypeDeSerializationWorks() throws Exception {
     ObjectMapper mapper = getMapper();