Fix regression to guess local catalog file

robot-command/src/main/java/org/obolibrary/robot/CommandLineHelper.java

@@ -478,7 +478,17 @@ public static OWLOntology getInputOntology(
     }
 
     if (!inputOntologyPaths.isEmpty()) {
-      return ioHelper.loadOntology(inputOntologyPaths.get(0), catalogPath, inputFormat);
+      String ontologyPath = inputOntologyPaths.get(0);
+      // When the ontology file is local,
+      // but the catalog path is null at this step,
+      // then we want to guess the catalog file.
+      if (catalogPath == null) {
+        File ontologyFile = new File(ontologyPath);
+        File catalogFile = ioHelper.guessCatalogFile(ontologyFile);
+        return ioHelper.loadOntology(ontologyFile, catalogFile, inputFormat);
+      } else {
+        return ioHelper.loadOntology(ontologyPath, catalogPath, inputFormat);
+      }
     } else if (!inputOntologyIRIs.isEmpty()) {
       return ioHelper.loadOntology(IRI.create(inputOntologyIRIs.get(0)), catalogPath, inputFormat);
     } else {

robot-command/src/test/java/org/obolibrary/robot/CommandLineHelperTest.java

@@ -5,6 +5,8 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
 import org.junit.Test;
 
 /** Tests for CommandLineHelper. */
@@ -49,4 +51,21 @@ public void testParseArgs() throws Exception {
           CommandLineHelper.parseArgList("unbalanced 'quotes");
         });
   }
+
+  /**
+   * Test handling an input ontology that requires a catalog file.
+   *
+   * @throws Exception on parsing problem
+   */
+  @Test
+  public void testGetInputOntology() throws Exception {
+    String[] args = {"--input", "../robot-core/src/test/resources/catalog_test.owl"};
+    Options o = CommandLineHelper.getCommonOptions();
+    o.addOption("i", "input", true, "load ontology from a file");
+    o.addOption("I", "input-iri", true, "load ontology from an IRI");
+    CommandLine line = CommandLineHelper.getCommandLine("usage", o, args);
+    IOHelper ioHelper = CommandLineHelper.getIOHelper(line);
+    CommandLineHelper.getInputOntology(ioHelper, line);
+    assert true;
+  }
 }

robot-core/src/main/java/org/obolibrary/robot/IOHelper.java

@@ -358,7 +358,7 @@ public OWLOntology loadOntology(String ontologyPath, boolean useCatalog, String
    */
   public OWLOntology loadOntology(String ontologyPath, String catalogPath) throws IOException {
     File ontologyFile = new File(ontologyPath);
-    File catalogFile = new File(catalogPath);
+    File catalogFile = catalogPath != null ? new File(catalogPath) : null;
     return loadOntology(ontologyFile, catalogFile);
   }
 

robot-core/src/test/java/org/obolibrary/robot/IOHelperTest.java

@@ -19,6 +19,7 @@
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLLiteral;
 import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.UnloadableImportException;
 import org.semanticweb.owlapi.util.DefaultPrefixManager;
 
 /** Tests for IOHelper. */
@@ -414,4 +415,41 @@ public void testExplicitInputFormat() throws IOException {
     }
     assert error;
   }
+
+  /**
+   * Test loading an ontology and without using a catalog.
+   *
+   * @throws IOException on error creating IOHelper
+   */
+  @Test
+  public void testCatalog() throws IOException {
+    IOHelper ioHelper = new IOHelper();
+
+    // This file should fail to load without using a catalog file.
+    boolean error = false;
+    try {
+      ioHelper.loadOntology("src/test/resources/catalog_test.owl", false);
+    } catch (UnloadableImportException e) {
+      error = true;
+    }
+    assert error;
+
+    // The file should load if we specify the catalog file.
+    ioHelper.loadOntology(
+        "src/test/resources/catalog_test.owl", "src/test/resources/catalog-v001.xml");
+    assert true;
+
+    // If no argument is passed, catalog file should be automatically detected.
+    ioHelper.loadOntology("src/test/resources/catalog_test.owl");
+    assert true;
+
+    // If a null argument is passed, the catalog file will not be detected.
+    error = false;
+    try {
+      ioHelper.loadOntology("src/test/resources/catalog_test.owl", null);
+    } catch (UnloadableImportException e) {
+      error = true;
+    }
+    assert error;
+  }
 }

robot-core/src/test/resources/catalog-v001.xml

@@ -19,4 +19,7 @@
     <uri id="User Entered Import Resolution" name="https://github.com/ontodev/robot/robot-core/src/test/resources/without_redundant_subclasses.owl" uri="./without_redundant_subclasses.owl"/>
     <uri id="User Entered Import Resolution" name="https://github.com/ontodev/robot/robot-core/src/test/resources/non-reasoned.owl" uri="./non-reasoned.owl"/>
     <uri id="User Entered Import Resolution" name="https://github.com/ontodev/robot/robot-core/src/test/resources/import_test.owl" uri="./import_test.owl"/>
+
+    <!-- Used to test catalog_test.owl -->
+    <uri id="User Entered Import Resolution" name="http://example.com/does_not_exist.owl" uri="./simple.owl"/>
 </catalog>

robot-core/src/test/resources/catalog_test.owl

@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<rdf:RDF
+     xmlns:dc="http://purl.org/dc/elements/1.1/"
+     xmlns:foaf="http://xmlns.com/foaf/0.1/"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+  >
+  <owl:Ontology rdf:about="https://github.com/ontodev/robot/robot-core/src/test/resources/catalog_test.owl">
+    <owl:imports rdf:resource="http://example.com/does_not_exist.owl"/>
+  </owl:Ontology>
+</rdf:RDF>
+