Merge pull request #434 from monarch-initiative/release_v2.0.1

Release v2.0.1

CHANGELOG.rst

@@ -2,6 +2,20 @@
 Changelog
 =========
 
+------
+latest
+------
+
+------
+v2.0.1
+------
+
+Minor changes
+#############
+
+- Use Jackson annotations to configure serialization of `TermId` and `Identified`
+- update dependencies
+
 ------
 v2.0.0
 ------

README.md

@@ -14,7 +14,7 @@ associate phenotype annotation files.
 
 - **Language/Platform:** Java >=11
 - **License:** BSD 3-Clause Clear
-- **Version:** 2.0.0
+- **Version:** 2.0.1
 - **Authors:**
     - Sebastian Bauer
     - Peter N. Robinson
@@ -39,7 +39,7 @@ We recommend indicating the phenol version in the `properties` section of the po
 ```
 <properties>
   (...)
-  <phenol.version>2.0.0</phenol.version>
+  <phenol.version>2.0.1</phenol.version>
 </properties>
 ```
 

phenol-analysis/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
   </parent>
 
   <artifactId>phenol-analysis</artifactId>
@@ -25,6 +25,11 @@
       <version>${commons-codec.version}</version>
     </dependency>
 
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>com.h2database</groupId>
       <artifactId>h2</artifactId>

phenol-annotations/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
   </parent>
 
   <artifactId>phenol-annotations</artifactId>

phenol-cli/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
   </parent>
 
   <artifactId>phenol-cli</artifactId>

phenol-cli/src/main/java/module-info.java

@@ -2,7 +2,7 @@
   requires org.monarchinitiative.phenol.io;
   requires org.monarchinitiative.phenol.analysis;
 
-  requires commons.csv;
+  requires org.apache.commons.csv;
   requires info.picocli;
   requires org.slf4j;
 

phenol-cli/src/main/java/org/monarchinitiative/phenol/cli/Main.java

@@ -9,7 +9,7 @@
 
 @CommandLine.Command(name = "phenol demo",
   mixinStandardHelpOptions = true,
-  version = "2.0.0",
+  version = "2.0.1",
   description = "phenol demo programs")
 public class Main implements Callable<Integer> {
   private static final Logger LOGGER = LoggerFactory.getLogger(Main.class);

phenol-core/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
   </parent>
 
   <artifactId>phenol-core</artifactId>
@@ -18,6 +18,11 @@
       <groupId>org.jgrapht</groupId>
       <artifactId>jgrapht-core</artifactId>
     </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+      <scope>provided</scope>
+    </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.dataformat</groupId>
       <artifactId>jackson-dataformat-yaml</artifactId>

phenol-core/src/main/java/module-info.java

@@ -8,5 +8,9 @@
   exports org.monarchinitiative.phenol.utils;
 
   requires transitive org.jgrapht.core; // due to DefaultDirectedGraph being exposed in MinimalOntology
+  requires com.fasterxml.jackson.databind; // for annotating model classes
   requires org.slf4j;
+
+  // To enable custom `TermId` serialization
+  opens org.monarchinitiative.phenol.ontology.serialize;
 }

phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/data/Identified.java

@@ -1,16 +1,21 @@
 package org.monarchinitiative.phenol.ontology.data;
 
+import com.fasterxml.jackson.annotation.JsonGetter;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 /**
  * The interface implemented by entities that have an identifier.
  */
 public interface Identified {
 
+  @JsonGetter
   TermId id();
 
   /**
    * @deprecated the getter will be removed in <code>v3.0.0</code>, use {@link #id()} instead.
    */
   @Deprecated(forRemoval = true, since = "2.0.0-RC2")
+  @JsonIgnore
   default TermId getId() {
     return id();
   }

phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/data/TermId.java

@@ -1,6 +1,8 @@
 package org.monarchinitiative.phenol.ontology.data;
 
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import org.monarchinitiative.phenol.base.PhenolRuntimeException;
+import org.monarchinitiative.phenol.ontology.serialize.TermIdSerializer;
 
 import java.io.Serializable;
 import java.util.Objects;
@@ -11,6 +13,7 @@
  * @author <a href="mailto:[email protected]">Manuel Holtgrewe</a>
  * @author <a href="mailto:[email protected]">Peter Robinson</a>
  */
+@JsonSerialize(using = TermIdSerializer.class)
 public final class TermId implements Comparable<TermId>, Serializable {
 
   /** Serial UId for serialization. */

phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/serialize/TermIdSerializer.java

@@ -0,0 +1,27 @@
+package org.monarchinitiative.phenol.ontology.serialize;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.SerializerProvider;
+import com.fasterxml.jackson.databind.ser.std.StdSerializer;
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import java.io.IOException;
+
+/**
+ * Serialize the {@link TermId}'s {@code value} as a {@link String}.
+ */
+public class TermIdSerializer extends StdSerializer<TermId> {
+
+  public TermIdSerializer() {
+    super(TermId.class);
+  }
+
+  public TermIdSerializer(StdSerializer<?> src) {
+    super(src);
+  }
+
+  @Override
+  public void serialize(TermId id, JsonGenerator jsonGenerator, SerializerProvider serializerProvider) throws IOException {
+    jsonGenerator.writeString(id.getValue());
+  }
+}

phenol-core/src/test/java/org/monarchinitiative/phenol/ontology/data/IdentifiedTest.java

@@ -0,0 +1,74 @@
+package org.monarchinitiative.phenol.ontology.data;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.junit.jupiter.api.Test;
+
+import java.util.List;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+
+public class IdentifiedTest {
+
+  /**
+   *
+   * Two-pronged test. First, test that {@link Identified#id()} is serialized as an "id" string field.
+   * Second, test that a list of {@link TermId}s is serialized as a list of string values (NOT JSON objects).
+   */
+  @Test
+  public void testSerialization() throws JsonProcessingException {
+    ObjectMapper mapper = new ObjectMapper();
+
+    Identified id = new SimpleIdentified(
+      TermId.of("BLA:1234567"),
+      List.of(TermId.of("BLA:999"), TermId.of("BLA:888")),
+      "Jimmy",
+      15,
+      true);
+
+
+    String actual = mapper.writeValueAsString(id);
+    assertThat(actual, equalTo("{\"id\":\"BLA:1234567\",\"altTermIds\":[\"BLA:999\",\"BLA:888\"],\"name\":\"Jimmy\",\"age\":15,\"alive\":true}"));
+  }
+
+  public static class SimpleIdentified implements Identified {
+
+    private final TermId id;
+    private final List<TermId> altTermIds;
+    private final String name;
+    private final int age;
+    private final boolean alive;
+
+    private SimpleIdentified(TermId id, List<TermId> altTermIds, String name, int age, boolean alive) {
+      this.id = id;
+      this.altTermIds = altTermIds;
+      this.name = name;
+      this.age = age;
+      this.alive = alive;
+    }
+
+
+    @Override
+    public TermId id() {
+      return id;
+    }
+
+    public List<TermId> getAltTermIds() {
+      return altTermIds;
+    }
+
+    public String getName() {
+      return name;
+    }
+
+    public int getAge() {
+      return age;
+    }
+
+    public boolean isAlive() {
+      return alive;
+    }
+  }
+
+}

phenol-core/src/test/java/org/monarchinitiative/phenol/ontology/data/ImmutableTermIdTest.java

@@ -5,6 +5,7 @@
 import static org.hamcrest.Matchers.lessThan;
 import static org.junit.jupiter.api.Assertions.*;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.phenol.base.PhenolRuntimeException;
 
@@ -60,6 +61,16 @@ public void testQueryFunctions() {
     assertEquals("HP:0000001", termId.getValue());
   }
 
+  /**
+   * Check that the `TermId` is serialized into a simple quoted string and NOT into a JSON object.
+   */
+  @Test
+  public void testSerializeToJson() throws Exception {
+    ObjectMapper mapper = new ObjectMapper();
+    assertEquals("\"HP:0000001\"", mapper.writeValueAsString(termId));
+    assertEquals("\"HP:0000002\"", mapper.writeValueAsString(termId2));
+  }
+
   @Test
   public void testToString() {
     assertEquals("HP:0000001", termId.toString());

phenol-io/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
   </parent>
 
   <artifactId>phenol-io</artifactId>
@@ -23,18 +23,11 @@
        <groupId>org.geneontology.obographs</groupId>
        <artifactId>obographs-core</artifactId>
     </dependency>
+    <!-- We can drop the dependency after obographs-core updates the vulnerable snakeyaml 1.33 to >=2.0. -->
+    <dependency>
+      <groupId>org.yaml</groupId>
+      <artifactId>snakeyaml</artifactId>
+    </dependency>
   </dependencies>
 
-  <build>
-    <plugins>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-surefire-plugin</artifactId>
-        <configuration>
-          <argLine>--add-reads com.fasterxml.jackson.datatype.guava=ALL-UNNAMED </argLine>
-        </configuration>
-      </plugin>
-    </plugins>
-  </build>
-
 </project>