Add tests for the kgcl:mint command.

Adds a text fixture for the `kgcl:mint` command. We test re-allocating IDs on a dummy ontology that contains only one entity with a temporary identifier, so that we don't run into reproducibility issue because we can't control the order in which entities are iterated over.
gouttegd · Mar 27, 2024 · 7f1dde7 · 7f1dde7
1 parent 26df19a
commit 7f1dde7
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diff --git a/robot/src/test/java/org/incenp/obofoundry/kgcl/robot/ApplyCommandTest.java b/robot/src/test/java/org/incenp/obofoundry/kgcl/robot/ApplyCommandTest.java
@@ -22,13 +22,8 @@
 import java.io.IOException;
 
 import org.apache.commons.io.FileUtils;
-import org.geneontology.owl.differ.Differ;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
-import org.obolibrary.robot.CommandManager;
-import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 
 public class ApplyCommandTest {
 
@@ -120,65 +115,8 @@ void testCreateNewOntology() {
                 "create relation EX:0101 'object property 1'", "--kgcl", "create edge EX:0001 EX:0101 EX:0002");
     }
 
-    /*
-     * Try running a KGCL-Apply command and check that the output ontology matches
-     * what we expect.
-     * 
-     * inputFile: the input ontology (filename relative to
-     * {,../core}/src/test/resources). outputFile: expected output file (likewise);
-     * if null, ignore the output.
-     */
     private void runCommand(String inputFile, String outputFile, String... extra) {
-        File input = new File("/src/test/resources/" + inputFile);
-        if ( !input.exists() ) {
-            input = new File("../core/src/test/resources/" + inputFile);
-        }
-
-        File expectedOutput = null;
-        File actualOutput = null;
-        if ( outputFile != null ) {
-            expectedOutput = new File("src/test/resources/" + outputFile);
-            if ( !expectedOutput.exists() ) {
-                expectedOutput = new File("../core/src/test/resources/" + outputFile);
-            }
-            actualOutput = new File("src/test/resources/output-" + outputFile);
-        } else {
-            actualOutput = new File("dont-care.ofn");
-        }
-
-        String[] args = new String[1 + 2 + 2 + extra.length];
-        args[0] = "kgcl-apply";
-        args[1] = "--input";
-        args[2] = input.getPath();
-        args[3] = "--output";
-        args[4] = actualOutput.getPath();
-        for ( int i = 0; i < extra.length; i++ ) {
-            args[i + 5] = extra[i];
-        }
-
-        CommandManager robot = new CommandManager();
-        robot.addCommand("kgcl-apply", new ApplyCommand());
-        robot.main(args);
-
-        if ( outputFile != null ) {
-            compareOntologies(expectedOutput, actualOutput);
-        } else if ( actualOutput.exists() ) {
-            actualOutput.delete();
-        }
-    }
-
-    private void compareOntologies(File expected, File actual) {
-        try {
-            OWLOntology expectedOntology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(expected);
-            OWLOntology actualOntology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(actual);
-            Differ.BasicDiff diff = Differ.diff(expectedOntology, actualOntology);
-            Assertions.assertTrue(diff.isEmpty());
-            if ( diff.isEmpty() ) {
-                actual.delete();
-            }
-        } catch ( OWLOntologyCreationException e ) {
-            Assertions.fail(e);
-        }
+        TestUtils.runCommand("apply", inputFile, outputFile, extra);
     }
 
     private void checkOutput(String expectedFile, String actualFile) {

diff --git a/robot/src/test/java/org/incenp/obofoundry/kgcl/robot/MintCommandTest.java b/robot/src/test/java/org/incenp/obofoundry/kgcl/robot/MintCommandTest.java
@@ -0,0 +1,54 @@
+/*
+ * KGCL-Java - KGCL library for Java
+ * Copyright © 2024 Damien Goutte-Gattat
+ * 
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the Gnu General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.incenp.obofoundry.kgcl.robot;
+
+import org.junit.jupiter.api.Test;
+
+public class MintCommandTest {
+
+    private final static String idRangeFile = "../core/src/test/resources/idranges.owl";
+
+    @Test
+    void testReallocateWithExplicitRange() {
+        runCommand("temporary-ids.ofn", "reallocated-ids.ofn", "--minted-id-prefix", "https://example.org/",
+                "--pad-width", "4", "--min-id", "501");
+    }
+
+    @Test
+    void testReallocateWithIDRangePolicy() {
+        runCommand("temporary-ids.ofn", "reallocated-ids.ofn", "--id-range-file", idRangeFile, "--id-range-name",
+                "Bob");
+    }
+
+    @Test
+    void testKeepDeprecated() {
+        runCommand("temporary-ids.ofn", "reallocated-ids-keep-deprecated.ofn", "--id-range-file", idRangeFile,
+                "--id-range-name", "Bob", "--keep-deprecated");
+    }
+
+    @Test
+    void testMintedFrom() {
+        runCommand("temporary-ids.ofn", "reallocated-ids-minted-from.ofn", "--id-range-file", idRangeFile,
+                "--id-range-name", "Bob", "--minted-from-property", "https://example.org/properties#mintedFrom");
+    }
+
+    private void runCommand(String inputFile, String outputFile, String... extra) {
+        TestUtils.runCommand("mint", inputFile, outputFile, extra);
+    }
+}
diff --git a/robot/src/test/java/org/incenp/obofoundry/kgcl/robot/TestUtils.java b/robot/src/test/java/org/incenp/obofoundry/kgcl/robot/TestUtils.java
@@ -0,0 +1,103 @@
+/*
+ * KGCL-Java - KGCL library for Java
+ * Copyright © 2024 Damien Goutte-Gattat
+ * 
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the Gnu General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.incenp.obofoundry.kgcl.robot;
+
+import java.io.File;
+
+import org.geneontology.owl.differ.Differ;
+import org.junit.jupiter.api.Assertions;
+import org.obolibrary.robot.CommandManager;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+/*
+ * Helper methods to test the ROBOT commands.
+ */
+public class TestUtils {
+
+    /*
+     * Tries running a command from the KGCL plugin and checks that the output
+     * ontology matches what we expect.
+     * 
+     * @param command The command to run ("apply", "mint").
+     * 
+     * @param inputFile The input ontology (as a filename relative to {@code
+     * {,../core}/src/test/resources}.
+     * 
+     * @param outputFile The expected output file (likewise). If {@code null}, the
+     * output is ignored.
+     * 
+     * @param extra Any extra arguments to pass to the command.
+     */
+    public static void runCommand(String command, String inputFile, String outputFile, String... extra) {
+        File input = new File("src/test/resources/" + inputFile);
+        if ( !input.exists() ) {
+            input = new File("../core/src/test/resources/" + inputFile);
+        }
+
+        File expectedOutput = null;
+        File actualOutput = null;
+        if ( outputFile != null ) {
+            expectedOutput = new File("src/test/resources/" + outputFile);
+            if ( !expectedOutput.exists() ) {
+                expectedOutput = new File("../core/src/test/resources/" + outputFile);
+            }
+            actualOutput = new File("src/test/resources/output-" + outputFile);
+        } else {
+            actualOutput = new File("dont-care.ofn");
+        }
+
+        String[] args = new String[1 + 2 + 2 + extra.length];
+        args[0] = "kgcl-" + command;
+        args[1] = "--input";
+        args[2] = input.getPath();
+        args[3] = "--output";
+        args[4] = actualOutput.getPath();
+        for ( int i = 0; i < extra.length; i++ ) {
+            args[i + 5] = extra[i];
+        }
+
+        CommandManager robot = new CommandManager();
+        robot.addCommand("kgcl-apply", new ApplyCommand());
+        robot.addCommand("kgcl-mint", new MintCommand());
+        robot.main(args);
+
+        if ( outputFile != null ) {
+            compareOntologies(expectedOutput, actualOutput);
+        } else if ( actualOutput.exists() ) {
+            actualOutput.delete();
+        }
+    }
+
+    private static void compareOntologies(File expected, File actual) {
+        try {
+            OWLOntology expectedOntology = OWLManager.createOWLOntologyManager()
+                    .loadOntologyFromOntologyDocument(expected);
+            OWLOntology actualOntology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(actual);
+            Differ.BasicDiff diff = Differ.diff(expectedOntology, actualOntology);
+            Assertions.assertTrue(diff.isEmpty());
+            if ( diff.isEmpty() ) {
+                actual.delete();
+            }
+        } catch ( OWLOntologyCreationException e ) {
+            Assertions.fail(e);
+        }
+    }
+}
diff --git a/robot/src/test/resources/reallocated-ids-keep-deprecated.ofn b/robot/src/test/resources/reallocated-ids-keep-deprecated.ofn
@@ -0,0 +1,34 @@
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(
+Declaration(Class(<http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394>))
+Declaration(Class(<https://example.org/0001>))
+Declaration(Class(<https://example.org/0501>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394> (obsolete class 2)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394> <https://example.org/0501>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394> "obsolete class 2")
+AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394> "true"^^xsd:boolean)
+
+# Class: <https://example.org/0001> (class 1)
+
+AnnotationAssertion(rdfs:label <https://example.org/0001> "class 1")
+
+# Class: <https://example.org/0501> (class 2)
+
+AnnotationAssertion(rdfs:label <https://example.org/0501> "class 2")
+
+
+)
diff --git a/robot/src/test/resources/reallocated-ids-minted-from.ofn b/robot/src/test/resources/reallocated-ids-minted-from.ofn
@@ -0,0 +1,28 @@
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(
+Declaration(Class(<https://example.org/0001>))
+Declaration(Class(<https://example.org/0501>))
+Declaration(AnnotationProperty(<https://example.org/properties#mintedFrom>))
+
+
+############################
+#   Classes
+############################
+
+# Class: <https://example.org/0001> (class 1)
+
+AnnotationAssertion(rdfs:label <https://example.org/0001> "class 1")
+
+# Class: <https://example.org/0501> (class 2)
+
+AnnotationAssertion(rdfs:label <https://example.org/0501> "class 2")
+AnnotationAssertion(<https://example.org/properties#mintedFrom> <https://example.org/0501> <http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394>)
+
+
+)
diff --git a/robot/src/test/resources/reallocated-ids.ofn b/robot/src/test/resources/reallocated-ids.ofn
@@ -0,0 +1,26 @@
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(
+Declaration(Class(<https://example.org/0001>))
+Declaration(Class(<https://example.org/0501>))
+
+
+############################
+#   Classes
+############################
+
+# Class: <https://example.org/0001> (class 1)
+
+AnnotationAssertion(rdfs:label <https://example.org/0001> "class 1")
+
+# Class: <https://example.org/0501> (class 2)
+
+AnnotationAssertion(rdfs:label <https://example.org/0501> "class 2")
+
+
+)
diff --git a/robot/src/test/resources/temporary-ids.ofn b/robot/src/test/resources/temporary-ids.ofn
@@ -0,0 +1,26 @@
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(
+Declaration(Class(<https://example.org/0001>))
+Declaration(Class(<http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394>))
+
+
+############################
+#   Classes
+############################
+
+# Class <https://example.org/0001> (class 1)
+
+AnnotationAssertion(rdfs:label <https://example.org/0001> "class 1")
+
+# Class: <http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394> (class 2)
+
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/temp#00819d24-4175-43d4-8405-3a1be211a394> "class 2")
+
+
+)