Merge pull request #59 from julesjacobsen/json-deserialise

Json deserialise
geneontology · Feb 26, 2020 · f56ec14 · f56ec14
2 parents b5eb537 + a38ef83
commit f56ec14
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Showing 20 changed files with 260 additions and 152 deletions.
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.geneontology</groupId>
   <artifactId>obographs</artifactId>
-  <version>0.2.0</version>
+  <version>0.2.1</version>
   <packaging>jar</packaging>
   <name>${project.groupId}:${project.artifactId}</name>
   <description>Reference implementation for Obo Graphs</description>
@@ -168,6 +168,15 @@
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-javadoc-plugin</artifactId>
         <version>2.9.1</version>
+          <configuration>
+            <doclet>ch.raffael.doclets.pegdown.PegdownDoclet</doclet>
+            <docletArtifact>
+              <groupId>ch.raffael.pegdown-doclet</groupId>
+              <artifactId>pegdown-doclet</artifactId>
+              <version>1.1</version>
+            </docletArtifact>
+            <useStandardDocletOptions>true</useStandardDocletOptions>
+          </configuration>
         <executions>
           <execution>
             <id>attach-javadocs</id>
@@ -177,21 +186,6 @@
           </execution>
         </executions>
       </plugin>
-
-      <plugin>
-        <artifactId>maven-javadoc-plugin</artifactId>
-        <version>2.9</version>
-        <configuration>
-          <doclet>ch.raffael.doclets.pegdown.PegdownDoclet</doclet>
-          <docletArtifact>
-            <groupId>ch.raffael.pegdown-doclet</groupId>
-            <artifactId>pegdown-doclet</artifactId>
-            <version>1.1</version>
-          </docletArtifact>
-          <useStandardDocletOptions>true</useStandardDocletOptions>
-        </configuration>
-      </plugin>
-
     </plugins>
   </build>
 

diff --git a/src/main/java/org/geneontology/obographs/io/OgJsonReader.java b/src/main/java/org/geneontology/obographs/io/OgJsonReader.java
@@ -1,27 +1,26 @@
 package org.geneontology.obographs.io;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.geneontology.obographs.model.GraphDocument;
+
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 
-import org.geneontology.obographs.model.Graph;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 public class OgJsonReader {
 
-	public static Graph readFile(String fileName) throws IOException {
+	public static GraphDocument readFile(String fileName) throws IOException {
 		return readFile(new File(fileName));
 	}
 
-	public static Graph readFile(File file) throws IOException {
+	public static GraphDocument readFile(File file) throws IOException {
 		ObjectMapper objectMapper = new ObjectMapper();
-		return objectMapper.readValue(file, Graph.class);
+		return objectMapper.readValue(file, GraphDocument.class);
 	}
 
-	public static Graph readInputStream(InputStream stream) throws IOException {
+	public static GraphDocument readInputStream(InputStream stream) throws IOException {
 		ObjectMapper objectMapper = new ObjectMapper();
-		return objectMapper.readValue(stream, Graph.class);
+		return objectMapper.readValue(stream, GraphDocument.class);
 	}
 
 }
diff --git a/src/main/java/org/geneontology/obographs/model/Edge.java b/src/main/java/org/geneontology/obographs/model/Edge.java
@@ -1,13 +1,16 @@
 package org.geneontology.obographs.model;
 
+import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 
 /**
  * An edge connects two nodes via a predicate
  * 
  * @author cjm
  *
  */
+@JsonDeserialize(builder = Edge.Builder.class)
 public class Edge implements NodeOrEdge {
 
 	private Edge(Builder builder) {
@@ -48,7 +51,15 @@ public String getObj() {
 		return obj;
 	}
 
-
+	@Override
+	public String toString() {
+		return "Edge{" +
+				"sub='" + sub + '\'' +
+				", pred='" + pred + '\'' +
+				", obj='" + obj + '\'' +
+				", meta=" + meta +
+				'}';
+	}
 
 	/**
 	 * @return the meta
@@ -90,6 +101,7 @@ public Builder meta(Meta meta) {
             return this;
         }
 
+        @JsonCreator
         public Edge build() {
         	return new Edge(this);
         }

diff --git a/src/main/java/org/geneontology/obographs/model/Graph.java b/src/main/java/org/geneontology/obographs/model/Graph.java
@@ -1,13 +1,14 @@
 package org.geneontology.obographs.model;
 
-import java.util.List;
-
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import org.geneontology.obographs.model.axiom.DomainRangeAxiom;
 import org.geneontology.obographs.model.axiom.EquivalentNodesSet;
 import org.geneontology.obographs.model.axiom.LogicalDefinitionAxiom;
 import org.geneontology.obographs.model.axiom.PropertyChainAxiom;
 
-import com.fasterxml.jackson.annotation.JsonProperty;
+import java.util.List;
 
 /**
  * A graph object holds a collection of nodes and edges
@@ -33,6 +34,7 @@
  * @author cjm
  *
  */
+@JsonDeserialize(builder = Graph.Builder.class)
 public class Graph {
 
     private Graph(Builder builder) {
@@ -139,6 +141,20 @@ public List<PropertyChainAxiom> getPropertyChainAxioms() {
     }
 
 
+    @Override
+    public String toString() {
+        return "Graph{" +
+                "nodes=" + nodes +
+                ", edges=" + edges +
+                ", id='" + id + '\'' +
+                ", lbl='" + lbl + '\'' +
+                ", meta=" + meta +
+                ", equivalentNodesSets=" + equivalentNodesSets +
+                ", logicalDefinitionAxioms=" + logicalDefinitionAxioms +
+                ", domainRangeAxioms=" + domainRangeAxioms +
+                ", propertyChainAxioms=" + propertyChainAxioms +
+                '}';
+    }
 
     public static class Builder {
 
@@ -202,6 +218,7 @@ public Builder domainRangeAxioms(List<DomainRangeAxiom> domainRangeAxioms) {
             return this;
         }
 
+        @JsonCreator
         public Graph build() {
             return new Graph(this);
         }

diff --git a/src/main/java/org/geneontology/obographs/model/GraphDocument.java b/src/main/java/org/geneontology/obographs/model/GraphDocument.java
@@ -1,8 +1,10 @@
 package org.geneontology.obographs.model;
 
-import java.util.List;
-
+import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+
+import java.util.List;
 
 /**
  * Holds a collection of graphs, plus document-level metadata
@@ -23,6 +25,7 @@
  * @author cjm
  *
  */
+@JsonDeserialize(builder = GraphDocument.Builder.class)
 public class GraphDocument {
 
     private GraphDocument(Builder builder) {
@@ -61,21 +64,24 @@ public Meta getMeta() {
     }
 
 
-
-
-
+    @Override
+    public String toString() {
+        return "GraphDocument{" +
+                "graphs=" + graphs +
+                ", meta=" + meta +
+                ", context=" + context +
+                '}';
+    }
 
     public static class Builder {
 
         @JsonProperty
         private Meta meta;
         @JsonProperty
         private List<Graph> graphs;
-        @JsonProperty
+        @JsonProperty("@context")
         private Object context;
 
-
-
         public Builder meta(Meta meta) {
             this.meta = meta;
             return this;
@@ -89,6 +95,7 @@ public Builder context(Object context) {
             return this;
         }
 
+        @JsonCreator
         public GraphDocument build() {
             return new GraphDocument(this);
         }

diff --git a/src/main/java/org/geneontology/obographs/model/Meta.java b/src/main/java/org/geneontology/obographs/model/Meta.java
@@ -1,7 +1,9 @@
 package org.geneontology.obographs.model;
 
+import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import org.geneontology.obographs.model.meta.*;
 
 import java.util.ArrayList;
@@ -25,6 +27,7 @@
  * @author cjm
  *
  */
+@JsonDeserialize(builder = Meta.Builder.class)
 public class Meta {
 
     private Meta(Builder builder) {
@@ -107,6 +110,20 @@ public Boolean getDeprecated() {
         return deprecated;
     }
 
+    @Override
+    public String toString() {
+        return "Meta{" +
+                "definition=" + definition +
+                ", comments=" + comments +
+                ", subsets=" + subsets +
+                ", xrefs=" + xrefs +
+                ", synonyms=" + synonyms +
+                ", basicPropertyValues=" + basicPropertyValues +
+                ", version='" + version + '\'' +
+                ", deprecated=" + deprecated +
+                '}';
+    }
+
     public static class Builder {
 
         @JsonProperty
@@ -205,6 +222,7 @@ public Builder deprecated(Boolean deprecated) {
         }
 
 
+        @JsonCreator
         public Meta build() {
             return new Meta(this);
         }

diff --git a/src/main/java/org/geneontology/obographs/model/Node.java b/src/main/java/org/geneontology/obographs/model/Node.java
@@ -1,6 +1,8 @@
 package org.geneontology.obographs.model;
 
+import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 
 /**
  * A graph node corresponds to a class, individual or property
@@ -19,6 +21,7 @@
  * @author cjm
  *
  */
+@JsonDeserialize(builder = Node.Builder.class)
 public class Node implements NodeOrEdge {
 
     public enum RDFTYPES { CLASS, INDIVIDUAL, PROPERTY };
@@ -77,11 +80,21 @@ public Meta getMeta() {
 		return meta;
 	}
 
-	public static class Builder {
+    @Override
+    public String toString() {
+        return "Node{" +
+                "id='" + id + '\'' +
+                ", label='" + label + '\'' +
+                ", meta=" + meta +
+                ", type=" + type +
+                '}';
+    }
+
+    public static class Builder {
 
         @JsonProperty
         private String id;
-        @JsonProperty
+        @JsonProperty("lbl")
         private String label;
         @JsonProperty
         private Meta meta;
@@ -108,6 +121,7 @@ public Builder type(RDFTYPES type) {
             return this;
         }
 
+        @JsonCreator
         public Node build() {
         	return new Node(this);
         }

diff --git a/src/main/java/org/geneontology/obographs/model/axiom/AbstractAxiom.java b/src/main/java/org/geneontology/obographs/model/axiom/AbstractAxiom.java
@@ -1,11 +1,7 @@
 package org.geneontology.obographs.model.axiom;
 
-import java.util.Set;
-
-import org.geneontology.obographs.model.Meta;
-import org.geneontology.obographs.model.axiom.EquivalentNodesSet.Builder;
-
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.geneontology.obographs.model.Meta;
 
 public abstract class AbstractAxiom implements Axiom {
 
@@ -31,7 +27,7 @@ public static class Builder {
 
         @JsonProperty
         private Meta meta;
-       
+
         public Builder meta(Meta meta) {
             this.meta = meta;
             return this;

diff --git a/src/main/java/org/geneontology/obographs/model/axiom/AbstractExpression.java b/src/main/java/org/geneontology/obographs/model/axiom/AbstractExpression.java
@@ -1,19 +1,11 @@
 package org.geneontology.obographs.model.axiom;
 
-import org.geneontology.obographs.model.Meta;
-import org.geneontology.obographs.model.axiom.AbstractAxiom.Builder;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
 public class AbstractExpression implements Expression {
 
     protected AbstractExpression(Builder builder) {
     }
 
     public static class Builder {
 
-
-
-
     }
 }