Flatten Molecule so all fields are deserialized

pom.xml

@@ -150,9 +150,8 @@
 							<generate>true</generate>
 						</sourceReferences>
 						<format>'v'yyyyMMddHHmm</format>
-						<!-- Uncomment to package with uncommited code
+						<!-- Uncomment to package with uncommited code-->
 						<jgit.dirtyWorkingTree>warning</jgit.dirtyWorkingTree>
-						-->
 					</configuration>
 				</plugin>
 			</plugins>

server/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/server/api/Molecule.java

@@ -1,41 +1,50 @@
 package nl.esciencecenter.e3dchem.knime.molviewer.server.api;
 
+import java.io.Serializable;
 import java.util.Objects;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
+
 import io.swagger.annotations.ApiModelProperty;
 
-public class Molecule extends AnonymousMolecule {
-	public Molecule(String data, String format) {
-		super(data, format);
-	}
-
-	public Molecule() {
-		super();
-	}
-
-	private static final long serialVersionUID = 8195661028979524114L;
-
-	@ApiModelProperty(required = true, value = "Identifier")
-	public String id;
-	@ApiModelProperty(required = true, value = "Label")
-	public String label;
-
-
-	@Override
-	public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (getClass() != obj.getClass()) {
-			return false;
-		}
-		final Molecule other = (Molecule) obj;
-		return Objects.equals(this.id, other.id) && Objects.equals(this.label, other.label)
-				&& Objects.equals(this.format, other.format) && Objects.equals(this.data, other.data);
-	}
-
-	@Override
-	public int hashCode() {
-		return Objects.hash(id, label, format, data);
-	}
+public class Molecule implements Serializable {
+    public Molecule(String data, String format) {
+        this.data = data;
+        this.format = format;
+    }
+
+    public Molecule() {
+        super();
+    }
+
+    private static final long serialVersionUID = 8195661028979524114L;
+
+    @ApiModelProperty(required = true, value = "Data format", allowableValues = "mol2, pdb, phar, sdf")
+    public String format = null;
+    @ApiModelProperty(required = true, value = "Data of molecule aka atoms/bonds in specified format")
+    public String data = null;
+    @ApiModelProperty(required = false, value = "Identifier")
+    @JsonInclude(JsonInclude.Include.NON_EMPTY)
+    public String id = null;
+    @ApiModelProperty(required = false, value = "Label")
+    @JsonInclude(JsonInclude.Include.NON_EMPTY)
+    public String label = null;
+
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final Molecule other = (Molecule) obj;
+        return Objects.equals(this.id, other.id) && Objects.equals(this.label, other.label)
+                && Objects.equals(this.format, other.format) && Objects.equals(this.data, other.data);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(id, label, format, data);
+    }
 }

server/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/server/api/PharmacophoreContainer.java

@@ -14,11 +14,11 @@ public class PharmacophoreContainer implements Serializable {
 	@ApiModelProperty(required = true, value = "Label")
 	public String label;
 	@ApiModelProperty(required = true, value = "Pharmacophore")
-	public AnonymousMolecule pharmacophore;
+    public Molecule pharmacophore;
 	@ApiModelProperty(required = false, value = "Protein")
-	public AnonymousMolecule protein;
+    public Molecule protein;
 	@ApiModelProperty(required = false, value = "Ligand")
-	public AnonymousMolecule ligand;
+    public Molecule ligand;
 	@ApiModelProperty(required = false, value = "Transformation matrix")
 	public double[] transform = new double[] { 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1 };
 

tests/src/java/nl/esciencecenter/e3dchem/knime/molviewer/MolViewerServerTest.java

@@ -15,10 +15,9 @@
 import org.junit.Test;
 
 import nl.esciencecenter.e3dchem.knime.molviewer.server.LigandsAndProteinsViewerServer;
-import nl.esciencecenter.e3dchem.knime.molviewer.server.MolViewerServer;
 
 public class MolViewerServerTest {
-	private MolViewerServer server;
+    private LigandsAndProteinsViewerServer server;
 
 	@Before
 	public void setUp() throws Exception {

tests/src/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerServerTest.java

@@ -1,12 +1,15 @@
 package nl.esciencecenter.e3dchem.knime.molviewer.ligandsandproteins;
 
+import static org.hamcrest.core.IsNot.not;
 import static org.hamcrest.core.StringContains.containsString;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 
 import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.http.HttpResponse;
 import org.apache.http.client.ClientProtocolException;
@@ -18,6 +21,7 @@
 import org.knime.core.node.property.hilite.HiLiteHandler;
 
 import nl.esciencecenter.e3dchem.knime.molviewer.server.LigandsAndProteinsViewerServer;
+import nl.esciencecenter.e3dchem.knime.molviewer.server.api.Molecule;
 
 public class LigandsAndProteinsViewerServerTest {
 	private LigandsAndProteinsViewerServer server;
@@ -75,4 +79,39 @@ public void testSwaggerJson() throws URISyntaxException, ClientProtocolException
 		assertThat(response, containsString("hilite"));
 	}
 
+    @Test
+    public void test_getLigands_optionalFilled() throws URISyntaxException, ClientProtocolException, IOException {
+        List<Molecule> ligands = new ArrayList<>(1);
+        Molecule ligand = new Molecule();
+        ligand.data = "Some data to render later";
+        ligand.id = "Row1";
+        ligand.label = "Label1";
+        ligand.format = "sdf";
+        ligands.add(ligand);
+        server.updateLigands(ligands);
+
+        URI uri = server.getBaseUri().resolve("/api/ligands");
+        String response = Request.Get(uri).execute().returnContent().asString();
+        assertThat(response, containsString("Row1"));
+        assertThat(response, containsString("Some data to render later"));
+        assertThat(response, containsString("Label1"));
+        assertThat(response, containsString("sdf"));
+    }
+
+    @Test
+    public void test_getLigands_requiredFilled() throws URISyntaxException, ClientProtocolException, IOException {
+        List<Molecule> ligands = new ArrayList<>(1);
+        Molecule ligand = new Molecule();
+        ligand.data = "Some data to render later";
+        ligand.format = "sdf";
+        ligands.add(ligand);
+        server.updateLigands(ligands);
+
+        URI uri = server.getBaseUri().resolve("/api/ligands");
+        String response = Request.Get(uri).execute().returnContent().asString();
+        assertThat(response, containsString("sdf"));
+        assertThat(response, containsString("Some data to render later"));
+        assertThat(response, not(containsString("id")));
+        assertThat(response, not(containsString("label")));
+    }
 }

tests/src/java/nl/esciencecenter/e3dchem/knime/molviewer/pharmacophores/PharmacophoresViewerModelTest.java

@@ -12,7 +12,7 @@
 import org.knime.core.node.CanceledExecutionException;
 import org.knime.core.node.ExecutionMonitor;
 
-import nl.esciencecenter.e3dchem.knime.molviewer.server.api.AnonymousMolecule;
+import nl.esciencecenter.e3dchem.knime.molviewer.server.api.Molecule;
 import nl.esciencecenter.e3dchem.knime.molviewer.server.api.PharmacophoreContainer;
 
 public class PharmacophoresViewerModelTest {
@@ -25,9 +25,9 @@ public void testSaveAndLoad() throws IOException, CanceledExecutionException {
 		PharmacophoreContainer phar = new PharmacophoreContainer();
 		phar.id = "id1";
 		phar.label = "label1";
-		phar.pharmacophore = new AnonymousMolecule("...", "phar");
-		phar.ligand = new AnonymousMolecule("...", "sdf");
-		phar.protein = new AnonymousMolecule("...", "pdb");
+        phar.pharmacophore = new Molecule("...", "phar");
+        phar.ligand = new Molecule("...", "sdf");
+        phar.protein = new Molecule("...", "pdb");
 		node.getPharmacophores().add(phar);
 
 		ExecutionMonitor exec = null;

tests/src/java/nl/esciencecenter/e3dchem/knime/molviewer/server/api/MoleculeTest.java

@@ -176,4 +176,45 @@ public void testHashCodeDiff() {
 
 		assertNotEquals(mol.hashCode(), other.hashCode());
 	}
+
+    @Test
+    public void test_anonymousConstructor() {
+        Molecule mol = new Molecule();
+        assertNull(mol.format);
+        assertNull(mol.data);
+    }
+
+    @Test
+    public void test_constructor() {
+        Molecule mol = new Molecule("data", "format");
+        assertEquals("data", mol.data);
+        assertEquals("format", mol.format);
+    }
+
+    @Test
+    public void testEqualsNull_dataConstructor() {
+        Molecule mol = new Molecule("data", "format");
+
+        assertFalse(mol.equals(null));
+    }
+
+    @Test
+    public void testEqualsString() {
+        Molecule mol = new Molecule("data", "format");
+
+        assertFalse(mol.equals("no mol"));
+    }
+
+    @Test
+    public void testHashCode() {
+        Molecule mol = new Molecule("data", "format");
+        assertEquals(-673444332L, mol.hashCode());
+    }
+
+    @Test
+    public void testEqualsFilledProps_dataConstructor() {
+        Molecule mol = new Molecule("data1", "format1");
+        Molecule other = new Molecule("data1", "format1");
+        assertTrue(mol.equals(other));
+    }
 }

tests/src/java/nl/esciencecenter/e3dchem/knime/molviewer/server/api/PharmacophoreContainerTest.java

@@ -25,9 +25,9 @@ public void testEqualsFilledProps_otherUnset() {
 		PharmacophoreContainer phar = new PharmacophoreContainer();
 		phar.id = "id1";
 		phar.label = "label1";
-		phar.pharmacophore = new AnonymousMolecule("...", "phar");
-		phar.ligand = new AnonymousMolecule("...", "sdf");
-		phar.protein = new AnonymousMolecule("...", "pdb");
+        phar.pharmacophore = new Molecule("...", "phar");
+        phar.ligand = new Molecule("...", "sdf");
+        phar.protein = new Molecule("...", "pdb");
 
 		PharmacophoreContainer other = new PharmacophoreContainer();
 		assertFalse(phar.equals(other));
@@ -38,16 +38,16 @@ public void testEqualsFilledProps_otherSameFill() {
 		PharmacophoreContainer phar = new PharmacophoreContainer();
 		phar.id = "id1";
 		phar.label = "label1";
-		phar.pharmacophore = new AnonymousMolecule("...", "phar");
-		phar.ligand = new AnonymousMolecule("...", "sdf");
-		phar.protein = new AnonymousMolecule("...", "pdb");
+        phar.pharmacophore = new Molecule("...", "phar");
+        phar.ligand = new Molecule("...", "sdf");
+        phar.protein = new Molecule("...", "pdb");
 
 		PharmacophoreContainer other = new PharmacophoreContainer();
 		other.id = "id1";
 		other.label = "label1";
-		other.pharmacophore = new AnonymousMolecule("...", "phar");
-		other.ligand = new AnonymousMolecule("...", "sdf");
-		other.protein = new AnonymousMolecule("...", "pdb");
+        other.pharmacophore = new Molecule("...", "phar");
+        other.ligand = new Molecule("...", "sdf");
+        other.protein = new Molecule("...", "pdb");
 		assertTrue(phar.equals(other));
 	}