Add test for diff with labels

ontodev · Sep 19, 2018 · 53726c1 · 53726c1
1 parent 49586b8
commit 53726c1
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Showing 5 changed files with 39 additions and 7 deletions.
diff --git a/docs/diff.md b/docs/diff.md
@@ -22,6 +22,8 @@ If `--output` is provided then a report will be written with any differences bet
 
 See <a href="/examples/release-diff.txt" target="_blank">`release-diff.txt`</a> for an example. In the output, 'Ontology 1' corresponds to your `--left` input and 'Ontology 2' corresponds to your `--right` input.
 
+The output is in OWL Manchester syntax, but you can include entity labels with `--labels true`.
+
 You can also compare ontologies by IRI with `--left-iri` and `--right-iri`. You may want to compare a local file to a release, in which case:
 <!-- DO NOT TEST -->
 ```

diff --git a/robot-command/src/main/java/org/obolibrary/robot/DiffCommand.java b/robot-command/src/main/java/org/obolibrary/robot/DiffCommand.java
@@ -47,7 +47,7 @@ public DiffCommand() {
     o.addOption("r", "right", true, "load right ontology from file");
     o.addOption("R", "right-iri", true, "load right ontology from IRI");
     o.addOption("o", "output", true, "save results to file");
-    o.addOption("u", "use-labels", true, "if true, use labels in place of entity IRIs");
+    o.addOption(null, "labels", true, "if true, use labels in place of entity IRIs");
     options = o;
   }
 
@@ -149,7 +149,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception
     }
 
     Map<String, String> options = new HashMap<>();
-    options.put("use-labels", CommandLineHelper.getDefaultValue(line, "use-labels", "false"));
+    options.put("labels", CommandLineHelper.getDefaultValue(line, "labels", "false"));
 
     DiffOperation.compare(leftOntology, rightOntology, ioHelper, writer, options);
     writer.flush();

diff --git a/robot-core/src/main/java/org/obolibrary/robot/DiffOperation.java b/robot-core/src/main/java/org/obolibrary/robot/DiffOperation.java
@@ -32,7 +32,7 @@ public class DiffOperation {
    */
   public static Map<String, String> getDefaultOptions() {
     Map<String, String> options = new HashMap<>();
-    options.put("use-labels", "false");
+    options.put("labels", "false");
     return options;
   }
 
@@ -87,7 +87,7 @@ public static boolean compare(
       Map<String, String> options)
       throws IOException {
 
-    boolean useLabels = OptionsHelper.optionIsTrue(options, "use-labels");
+    boolean useLabels = OptionsHelper.optionIsTrue(options, "labels");
 
     Map<IRI, String> labels = OntologyHelper.getLabels(ontology1);
     labels.putAll(OntologyHelper.getLabels(ontology2));
@@ -160,7 +160,7 @@ public static String addLabels(Map<IRI, String> labels, String axiom) {
       if (id.startsWith(oboBase)) {
         id = id.substring(oboBase.length()).replace("_", ":");
       }
-      String replacement = "<" + iri + ">";
+      String replacement = "<" + id + ">";
       if (labels.containsKey(iri)) {
         replacement = "<" + id + ">[" + labels.get(iri) + "]";
       }
@@ -189,9 +189,12 @@ public static String addLabels(IOHelper ioHelper, Map<IRI, String> labels, Strin
       if (id.startsWith("obo:")) {
         id = id.substring(4).replace("_", ":");
       }
-      String replacement = "<" + iri + ">";
+      if (!id.startsWith("<") && !id.endsWith(">")) {
+        id = "<" + id + ">";
+      }
+      String replacement = id;
       if (labels.containsKey(iri)) {
-        replacement = "<" + id + ">[" + labels.get(iri) + "]";
+        replacement = id + "[" + labels.get(iri) + "]";
       }
       matcher.appendReplacement(sb, replacement);
     }

diff --git a/robot-core/src/test/java/org/obolibrary/robot/DiffOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/DiffOperationTest.java
@@ -5,7 +5,9 @@
 
 import java.io.IOException;
 import java.io.StringWriter;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 import org.apache.commons.io.IOUtils;
 import org.junit.Test;
@@ -54,4 +56,25 @@ public void testCompareModified() throws IOException, OWLOntologyCreationExcepti
     String expected = IOUtils.toString(this.getClass().getResourceAsStream("/simple1.diff"));
     assertEquals(expected, writer.toString());
   }
+
+  /**
+   * Compare one ontology to a modified copy with labels in output.
+   *
+   * @throws IOException on file problem
+   * @throws OWLOntologyCreationException on ontology problem
+   */
+  @Test
+  public void testCompareModifiedWithLabels() throws IOException, OWLOntologyCreationException {
+    OWLOntology simple = loadOntology("/simple.owl");
+    OWLOntology elk = loadOntology("/simple_elk.owl");
+
+    StringWriter writer = new StringWriter();
+    Map<String, String> options = new HashMap<>();
+    options.put("labels", "true");
+    boolean actual = DiffOperation.compare(simple, elk, new IOHelper(), writer, options);
+    System.out.println(writer.toString());
+    assertFalse(actual);
+    String expected = IOUtils.toString(this.getClass().getResourceAsStream("/simple.diff"));
+    assertEquals(expected, writer.toString());
+  }
 }
diff --git a/robot-core/src/test/resources/simple.diff b/robot-core/src/test/resources/simple.diff
@@ -0,0 +1,4 @@
+0 axioms in Ontology 1 but not in Ontology 2:
+
+1 axioms in Ontology 2 but not in Ontology 1:
++ SubClassOf(<https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl#test1>[Test 1] owl:Thing)