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Merge pull request #141 from ProgrammingLife2016/test/test-model-classes
Add tests for the model classes
2 parents 8ee34b5 + 63c6ff8 commit 8177674

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9 files changed

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-51
lines changed

9 files changed

+793
-51
lines changed

‎PL2/PL2-shared/pom.xml‎

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@@ -25,5 +25,10 @@
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<version>4.10</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.mockito</groupId>
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<artifactId>mockito-core</artifactId>
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<version>1.10.19</version>
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</dependency>
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</dependencies>
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</project>

‎PL2/PL2-shared/src/main/java/nl/tudelft/pl2016gr2/model/AbstractNode.java‎

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package nl.tudelft.pl2016gr2.model;
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import nl.tudelft.pl2016gr2.thirdparty.testing.utility.TestId;
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import java.util.ArrayList;
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import java.util.Collection;
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*/
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public abstract class AbstractNode implements Node {
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private final int identifier;
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@TestId(id = "id_field")
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private int identifier;
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/**
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* Construct a bare abstract node with an ID.
@@ -66,6 +69,6 @@ assert getOutEdges().contains(
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@Override
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public String toString() {
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return "id: " + identifier;
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return "id: " + getId();
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}
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}

‎PL2/PL2-shared/src/main/java/nl/tudelft/pl2016gr2/model/HashGraph.java‎

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@@ -147,7 +147,7 @@ public Iterator<GraphNode> iterator() {
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public String toString() {
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StringBuilder sb = new StringBuilder();
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for (GraphNode node : nodes.values()) {
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sb.append(node).append('\n');
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sb.append(node.toString()).append('\n');
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}
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return sb.toString();
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}

‎PL2/PL2-shared/src/main/java/nl/tudelft/pl2016gr2/model/SequenceNode.java‎

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@@ -88,6 +88,9 @@ public void setSequence(BaseSequence sequence) {
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@Override
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public String getSequence() {
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if (sequence == null) {
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return null;
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}
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return sequence.getBaseSequence();
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}
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@@ -119,7 +122,7 @@ public void addInEdge(int identifier) {
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public void removeInEdge(int identifier) {
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assert inEdges.contains(
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identifier) : "Removing non-existent in-edge: " + identifier + ". NodeID: " + this.getId();
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inEdges.remove(identifier);
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inEdges.remove((Integer) identifier);
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}
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/**
@@ -150,7 +153,7 @@ public void addOutEdge(int identifier) {
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public void removeOutEdge(int identifier) {
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assert outEdges.contains(
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identifier) : "Removing non-existent out-edge: " + identifier + ". NodeID: " + this.getId();
153-
outEdges.remove(identifier);
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outEdges.remove((Integer) identifier);
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}
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@Override

‎PL2/PL2-shared/src/test/java/nl/tudelft/pl2016gr2/model/AbstractNodeTest.java‎

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@@ -0,0 +1,110 @@
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package nl.tudelft.pl2016gr2.model;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNull;
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import static org.junit.Assert.assertTrue;
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import static org.mockito.Matchers.any;
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import static org.mockito.Mockito.mock;
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import nl.tudelft.pl2016gr2.thirdparty.testing.utility.AccessPrivate;
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import org.junit.Before;
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import org.junit.Rule;
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import org.junit.Test;
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import org.junit.rules.ExpectedException;
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import org.mockito.Mockito;
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import java.util.Arrays;
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/**
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* Tests the {@link AbstractNode} class.
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*
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* @author Wouter Smit
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*/
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public class AbstractNodeTest {
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@Rule
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public final ExpectedException exception = ExpectedException.none();
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private AbstractNode instance;
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/**
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* Sets up the abstract spied class.
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*/
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@Before
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public void setUp() {
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instance = mock(AbstractNode.class);
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Mockito.when(instance.getId()).thenCallRealMethod();
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Mockito.when(instance.hasChildren()).thenCallRealMethod();
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Mockito.when(instance.getChildren()).thenCallRealMethod();
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Mockito.when(instance.size()).thenCallRealMethod();
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Mockito.when(instance.toString()).thenCallRealMethod();
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Mockito.when(instance.getGenomesOverEdge(any())).thenCallRealMethod();
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}
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@Test
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public void testConstructor() {
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AbstractNode extendedNode = new SequenceNode(5);
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assertEquals(5, extendedNode.getId());
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}
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@Test
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public void getId() {
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AccessPrivate.setFieldValue("id_field", AbstractNode.class, instance, 5);
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assertEquals(5, instance.getId());
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}
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57+
@Test
58+
public void hasChildren() {
59+
assertFalse(instance.hasChildren());
60+
}
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@Test
63+
public void getChildren() {
64+
assertNull(instance.getChildren());
65+
}
66+
67+
@Test
68+
public void size() {
69+
Mockito.when(instance.getSequence()).thenReturn("ACTG");
70+
assertEquals(4, instance.size());
71+
}
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73+
@Test
74+
public void getGenomesOverEdge() {
75+
GraphNode otherNode = mock(GraphNode.class);
76+
77+
Mockito.when(otherNode.getId()).thenReturn(2);
78+
AccessPrivate.setFieldValue("id_field", AbstractNode.class, instance, 5);
79+
80+
Mockito.when(instance.getGenomes()).thenReturn(Arrays.asList("equal", "gen0"));
81+
Mockito.when(otherNode.getGenomes()).thenReturn(Arrays.asList("equal", "gen1"));
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83+
Mockito.when(otherNode.getInEdges()).thenReturn(Arrays.asList(1, 5, 8));
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Mockito.when(instance.getOutEdges()).thenReturn(Arrays.asList(2, 10, 15));
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86+
assertTrue(instance.getGenomesOverEdge(otherNode).contains("equal"));
87+
assertEquals(1, instance.getGenomesOverEdge(otherNode).size());
88+
}
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90+
@Test
91+
public void getGenomesOverEdgeThrowsAssertionWhenNotSuccessor() {
92+
GraphNode otherNode = mock(GraphNode.class);
93+
94+
Mockito.when(otherNode.getId()).thenReturn(2);
95+
AccessPrivate.setFieldValue("id_field", AbstractNode.class, instance, 5);
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97+
Mockito.when(otherNode.getInEdges()).thenReturn(Arrays.asList(1, 8));
98+
Mockito.when(instance.getOutEdges()).thenReturn(Arrays.asList(10, 15));
99+
100+
exception.expect(AssertionError.class);
101+
instance.getGenomesOverEdge(otherNode);
102+
}
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@Test
105+
public void testToString() {
106+
AccessPrivate.setFieldValue("id_field", AbstractNode.class, instance, 5);
107+
assertEquals("id: 5", instance.toString());
108+
}
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110+
}

‎PL2/PL2-shared/src/test/java/nl/tudelft/pl2016gr2/model/HashGraphTest.java‎

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@@ -0,0 +1,67 @@
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package nl.tudelft.pl2016gr2.model;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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import org.junit.Before;
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import org.junit.Test;
9+
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import java.util.ArrayList;
11+
import java.util.Arrays;
12+
import java.util.Collection;
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import java.util.HashMap;
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import java.util.Map;
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16+
/**
17+
* Tests the {@link HashGraph} class.
18+
*
19+
* @author Wouter Smit
20+
*/
21+
public class HashGraphTest {
22+
private Map<Integer, GraphNode> nodes = new HashMap<>();
23+
private Collection<String> genomes = new ArrayList<>();
24+
25+
/**
26+
* Sets up the graph structure with mocked nodes.
27+
*/
28+
@Before
29+
public void setUp() {
30+
for (int i = 0; i < 5; i++) {
31+
nodes.put(i, SequenceGraphTest.mockNode(i, false));
32+
}
33+
int rootId = 5;
34+
nodes.put(rootId, SequenceGraphTest.mockNode(rootId, true));
35+
36+
for (int i = 0; i < 5; i++) {
37+
genomes.add("genome" + i);
38+
}
39+
}
40+
41+
@Test
42+
public void testHashGraphConstructorForNodesAndGenomes() {
43+
HashGraph graph = new HashGraph(nodes, genomes);
44+
45+
nodes.forEach((id, node) -> assertTrue(graph.contains(id)));
46+
assertTrue(graph.getGenomes().containsAll(genomes));
47+
}
48+
49+
@Test
50+
public void testHashGraphConstructorIncludingRootNodes() {
51+
Collection<Integer> rootNodes = new ArrayList<>(Arrays.asList(5, 10, 25));
52+
HashGraph graph = new HashGraph(nodes, rootNodes, genomes);
53+
54+
nodes.forEach((id, node) -> assertTrue(graph.contains(id)));
55+
assertTrue(graph.getGenomes().containsAll(genomes));
56+
assertTrue(graph.getRootNodes().containsAll(rootNodes));
57+
}
58+
59+
@Test
60+
public void testToString() throws Exception {
61+
HashGraph graph = new HashGraph();
62+
assertEquals("", graph.toString());
63+
graph.add(SequenceGraphTest.mockNode(0, false));
64+
assertNotNull(graph.toString());
65+
}
66+
67+
}

‎PL2/PL2-shared/src/test/java/nl/tudelft/pl2016gr2/model/NodePositionTest.java‎

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@@ -1,46 +1,47 @@
1-
//package nl.tudelft.pl2016gr2.model;
2-
//
3-
//import static org.junit.Assert.assertEquals;
4-
//import static org.junit.Assert.assertTrue;
5-
//
6-
//import org.junit.Before;
7-
//import org.junit.Test;
8-
//
9-
//import java.util.ArrayList;
10-
//
11-
//public class NodePositionTest {
12-
//
13-
// private NodePosition nodePosition;
14-
// private AbstractNode node;
15-
//
16-
// @Before
17-
// public void setup() {
18-
// this.node = new Node(5, 3, new ArrayList<String>(), 2);
19-
// this.nodePosition = new NodePosition(node, 6);
20-
// }
21-
//
22-
// @Test
23-
// public void offsetTest() {
24-
// nodePosition.addPositionOffset(4);
25-
// assertEquals(10, nodePosition.getLevel());
26-
// }
27-
//
28-
// @Test
29-
// public void getNodeTest() {
30-
// assertEquals(node, nodePosition.getNode());
31-
// }
32-
//
33-
// @Test
34-
// public void overlapTest() {
35-
// nodePosition.setOverlapping(true);
36-
// assertTrue(nodePosition.isOverlapping());
37-
// }
38-
//
39-
// @Test
40-
// public void compareTest() {
41-
// AbstractNode other = new Node(5, 3, new ArrayList<String>(), 2);
42-
// NodePosition otherPosition = new NodePosition(other, 2);
43-
// assertEquals(4, nodePosition.compareTo(otherPosition));
44-
// }
45-
//
46-
//}
1+
package nl.tudelft.pl2016gr2.model;
2+
3+
import static org.junit.Assert.assertEquals;
4+
import static org.junit.Assert.assertTrue;
5+
import static org.mockito.Mockito.mock;
6+
7+
import org.junit.Before;
8+
import org.junit.Test;
9+
10+
import java.util.ArrayList;
11+
12+
public class NodePositionTest {
13+
14+
private NodePosition nodePosition;
15+
private GraphNode node;
16+
17+
@Before
18+
public void setup() {
19+
this.node = mock(GraphNode.class);
20+
this.nodePosition = new NodePosition(node, 6);
21+
}
22+
23+
@Test
24+
public void offsetTest() {
25+
nodePosition.addPositionOffset(4);
26+
assertEquals(10, nodePosition.getLevel());
27+
}
28+
29+
@Test
30+
public void getNodeTest() {
31+
assertEquals(node, nodePosition.getNode());
32+
}
33+
34+
@Test
35+
public void overlapTest() {
36+
nodePosition.setOverlapping(true);
37+
assertTrue(nodePosition.isOverlapping());
38+
}
39+
40+
@Test
41+
public void compareTest() {
42+
GraphNode other = mock(GraphNode.class);
43+
NodePosition otherPosition = new NodePosition(other, 2);
44+
assertEquals(4, nodePosition.compareTo(otherPosition));
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}
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}

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