Update HPO test resource.

Author: ielis

phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/TestData.java

@@ -3,13 +3,25 @@
 import org.monarchinitiative.phenol.io.MinimalOntologyLoader;
 import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 
-import java.nio.file.Path;
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.util.Objects;
+import java.util.zip.GZIPInputStream;
 
 public class TestData {
 
-    public static final Path TEST_BASE_DIR = Path.of("src/test/resources/org/phenopackets/phenopackettools/validator/core");
-    private static final Path HPO_MODULE_PATH = TEST_BASE_DIR.resolve("hp.module.json");
+    public static final MinimalOntology HPO;
 
-    public static final MinimalOntology HPO = MinimalOntologyLoader.loadOntology(HPO_MODULE_PATH.toFile());
+    static {
+        try {
+            HPO = MinimalOntologyLoader.loadOntology(new GZIPInputStream(
+                    new BufferedInputStream(
+                            Objects.requireNonNull(TestData.class.getResourceAsStream("hp.v2026-01-08.json.gz"))
+                    )
+            ));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
 
 }

phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/AncestryHpoValidatorTest.java

@@ -49,7 +49,7 @@ public void testValidInput() {
         public void testFailsIfTermAndAncestorIsObserved() {
             // Has some Abnormality of finger and Arachnodactyly. Only Arachnodactyly should be present.
             Phenopacket pp = createPhenopacket(
-                    "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormality of finger", false),
+                    "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", false),
                     createPhenotypicFeature("HP:0001166", "Arachnodactyly", false)
             ).build();
 
@@ -60,14 +60,14 @@ public void testFailsIfTermAndAncestorIsObserved() {
             assertThat(result.validatorInfo(), equalTo(validator.validatorInfo()));
             assertThat(result.level(), equalTo(ValidationLevel.ERROR));
             assertThat(result.category(), equalTo("Violation of the annotation propagation rule"));
-            assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an observed ancestor (Abnormality of finger, HP:0001167)"));
+            assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an observed ancestor (Abnormal finger morphology, HP:0001167)"));
         }
 
         @Test
         public void testFailsIfTermAndAncestorIsExcluded() {
             // Has neither Abnormality of finger nor Arachnodactyly. Only Abnormality of finger should be present.
             Phenopacket pp = createPhenopacket(
-                    "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormality of finger", true),
+                    "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", true),
                     createPhenotypicFeature("HP:0001166", "Arachnodactyly", true)
             ).build();
 
@@ -77,14 +77,14 @@ public void testFailsIfTermAndAncestorIsExcluded() {
             ValidationResult result = results.get(0);
             assertThat(result.level(), equalTo(ValidationLevel.ERROR));
             assertThat(result.category(), equalTo("Violation of the annotation propagation rule"));
-            assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an excluded term (Abnormality of finger, HP:0001167) and an excluded child (Arachnodactyly, HP:0001166)"));
+            assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an excluded term (Abnormal finger morphology, HP:0001167) and an excluded child (Arachnodactyly, HP:0001166)"));
         }
 
         @Test
         public void testFailsIfTermIsPresentAndAncestorIsExcluded() {
             // Has neither Abnormality of finger nor Arachnodactyly. Only Abnormality of finger should be present.
             Phenopacket pp = createPhenopacket(
-                    "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormality of finger", true),
+                    "example-phenopacket", "example-subject", createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", true),
                     createPhenotypicFeature("HP:0001166", "Arachnodactyly", false)
             ).build();
 
@@ -94,7 +94,7 @@ public void testFailsIfTermIsPresentAndAncestorIsExcluded() {
             ValidationResult result = results.get(0);
             assertThat(result.level(), equalTo(ValidationLevel.ERROR));
             assertThat(result.category(), equalTo("Violation of the annotation propagation rule"));
-            assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an excluded ancestor (Abnormality of finger, HP:0001167)"));
+            assertThat(result.message(), equalTo("Phenotypic features of example-phenopacket must not contain both an observed term (Arachnodactyly, HP:0001166) and an excluded ancestor (Abnormal finger morphology, HP:0001167)"));
         }
     }
 

phenopacket-tools-validator-core/src/test/java/org/phenopackets/phenopackettools/validator/core/phenotype/PrimaryHpoPhenotypeValidatorTest.java

@@ -67,8 +67,8 @@ public void testMissingTermId() throws Exception {
                       },
                       "phenotypicFeatures": [{
                         "type": {
-                          "id": "HP:0001182",
-                          "label": "Tapered finger"
+                          "id": "HP:0000000",
+                          "label": "Nonexistent term"
                         }
                       }, {
                         "type": {
@@ -85,7 +85,7 @@ public void testMissingTermId() throws Exception {
             ValidationResult result = results.get(0);
             assertThat(result.level(), equalTo(ValidationLevel.ERROR));
             assertThat(result.category(), equalTo("Invalid TermId"));
-            assertThat(result.message(), equalTo("HP:0001182 in proband A not found in 2021-06-08"));
+            assertThat(result.message(), equalTo("HP:0000000 in proband A not found in 2026-01-08"));
         }
 
         @Test