issue #121 test #20

draeger-lab · Aug 2, 2022 · 876bec7 · 876bec7
1 parent ebb4f05
commit 876bec7
Showing 1 changed file with 68 additions and 38 deletions.
diff --git a/src/test/java/edu/ucsd/sbrg/bigg/annotation/BiGGAnnotationTest.java b/src/test/java/edu/ucsd/sbrg/bigg/annotation/BiGGAnnotationTest.java
@@ -10,48 +10,78 @@
 
 import static edu.ucsd.sbrg.TestUtils.assertCVTermIsPresent;
 import static edu.ucsd.sbrg.TestUtils.initParameters;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.*;
 
 public class BiGGAnnotationTest extends BiGGDBTest {
 
-  @Test
-  public void annotatePublication() {
-    initParameters(Map.of(
-            ModelPolisherOptions.ANNOTATE_WITH_BIGG.getOptionName(),
-            "true",
-            ModelPolisherOptions.INCLUDE_ANY_URI.getOptionName(),
-            "true"));
-    var sbml = new SBMLDocument(3, 2);
-    var m = new Model("iJO1366", 3,2);
-    sbml.setModel(m);
-    var annotater = new BiGGAnnotation();
-
-    assertFalse(m.isSetMetaId());
-    assertTrue(m.getCVTerms().isEmpty());
-
-    annotater.annotate(sbml);
-
-    assertTrue(m.isSetMetaId());
-    assertCVTermIsPresent(m,
-            CVTerm.Type.MODEL_QUALIFIER,
-            CVTerm.Qualifier.BQM_IS_DESCRIBED_BY,
-            "https://identifiers.org/pubmed/21988831",
-            "Expected pubmed publication reference 21988831 not present on the model.");
+    @Test
+    public void annotatePublication() {
+        initParameters(Map.of(
+                ModelPolisherOptions.ANNOTATE_WITH_BIGG.getOptionName(),
+                "true",
+                ModelPolisherOptions.INCLUDE_ANY_URI.getOptionName(),
+                "true"));
+        var sbml = new SBMLDocument(3, 2);
+        var m = new Model("iJO1366", 3, 2);
+        sbml.setModel(m);
+        var annotater = new BiGGAnnotation();
+
+        assertFalse(m.isSetMetaId());
+        assertTrue(m.getCVTerms().isEmpty());
+
+        annotater.annotate(sbml);
+
+        assertTrue(m.isSetMetaId());
+        assertCVTermIsPresent(m,
+                CVTerm.Type.MODEL_QUALIFIER,
+                CVTerm.Qualifier.BQM_IS_DESCRIBED_BY,
+                "https://identifiers.org/pubmed/21988831",
+                "Expected pubmed publication reference 21988831 not present on the model.");
+    }
+
+    @Test
+    public void getBiGGIdFromResourcesTest() {
+        initParameters(Map.of(
+                ModelPolisherOptions.ANNOTATE_WITH_BIGG.getOptionName(),
+                "true",
+                ModelPolisherOptions.INCLUDE_ANY_URI.getOptionName(),
+                "true"));
+        var sbml = new SBMLDocument(3, 2);
+        var m = new Model("iJO1366", 3, 2);
+        sbml.setModel(m);
+        var s1 = m.createSpecies("some_name");
+        var s2 = m.createSpecies("some_other_name");
+
+        // this is kegg.compound for H20
+        s1.addCVTerm(new CVTerm(
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "https://identifiers.org/kegg.compound/C00001"));
+
+        // this is biocyc for ATP
+        s2.addCVTerm(new CVTerm(
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "https://identifiers.org/biocyc/META:ATP"));
+
+        var annotater = new BiGGAnnotation();
+        annotater.annotate(sbml);
+
+        assertEquals("some_name", s1.getId());
+        assertEquals("", s1.getName());
+        assertEquals(1, s1.getCVTermCount());
+        assertCVTermIsPresent(s1,
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "https://identifiers.org/kegg.compound/C00001");
+        assertEquals("some_other_name", s2.getId());
+        assertEquals("ATP C10H12N5O13P3", s2.getName());
+        assertEquals(1, s2.getCVTermCount());
+        assertCVTermIsPresent(s2,
+                CVTerm.Type.BIOLOGICAL_QUALIFIER,
+                CVTerm.Qualifier.BQB_IS,
+                "https://identifiers.org/biocyc/META:ATP");
     }
 
-//  @Test
-//  public void getBiGGIdFromResourcesTest() {
-//    for (Species species : doc.getModel().getListOfSpecies()) {
-//      Species obfuscated = species.clone();
-//      obfuscated.setId("random");
-//      BiGGAnnotation biGGAnnotation = new BiGGAnnotation();
-//      String originalId = biGGAnnotation.checkId(species).map(BiGGId::toBiGGId).get();
-//      String obfuscatedId = biGGAnnotation.checkId(species).map(BiGGId::toBiGGId).get();
-//      assertEquals(originalId, obfuscatedId);
-//    }
-//  }
-//
-//
 
 }