Update dependencies

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

@@ -3,13 +3,14 @@
 import org.monarchinitiative.phenol.io.MinimalOntologyLoader;
 import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 
-import java.nio.file.Path;
+import java.io.File;
+import java.net.URL;
+import java.util.Objects;
 
-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 class TestData {
 
-    public static final MinimalOntology HPO = MinimalOntologyLoader.loadOntology(HPO_MODULE_PATH.toFile());
+    private static final URL HP_MODULE_URL = TestData.class.getResource("hp.module.json");
+    public static final MinimalOntology HPO = MinimalOntologyLoader.loadOntology(new File(Objects.requireNonNull(HP_MODULE_URL.getPath())));
 
 }

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

@@ -36,7 +36,7 @@ public void testValidInput() {
             // Has some Abnormality of finger but no Arachnodactyly.
             Phenopacket pp = createPhenopacket(
                     "example-phenopacket", "example-subject",
-                    createPhenotypicFeature("HP:0001167", "Abnormality of finger", false),
+                    createPhenotypicFeature("HP:0001167", "Abnormal finger morphology", false),
                     createPhenotypicFeature("HP:0001166", "Arachnodactyly", true)
             ).build();
 
@@ -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

@@ -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:0001182 in proband A not found in 2026-06-06"));
         }
 
         @Test

phenopacket-tools-validator-core/src/test/resources/org/phenopackets/phenopackettools/validator/core/README.md

@@ -4,5 +4,71 @@ The folder contains test resources.
 
 ## HPO
 The `hp.module.json` contains Human Phenotype Ontology module in Obographs format. For the *Phenotypic abnormality* 
-subhierarchy, the module contains *Arachnodactyly* (`HP:0001166`) and the ancestors. The module contains all other HPO
-subhierarchies.
+subhierarchy, the module contains *Arachnodactyly* (`HP:0001166`), *Focal clonic seizure* (`HP:0002266`),
+and their ancestors. The module contains all other HPO subhierarchies.
+
+Run the following to prepare the module:
+
+```shell
+module load robot/1.9.8
+
+HPO=https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2026-06-06/hp.obo
+
+wget $HPO
+
+# Arachnodactyly HP:0001166
+robot extract --input hp.obo --method BOT --term HP:0001166 \
+  convert --output arachnodactyly.hp.obo
+
+# Focal clonic seizure HP:0002266  
+robot extract --input hp.obo --method BOT --term HP:0002266 \
+  convert --output fcs.hp.obo
+
+# We use a kind of a hack to include both
+# Clinical modifier HP:0012823
+robot extract --input hp.obo --method BOT --term HP:0012823 \
+  convert --output cm.bot.hp.obo
+robot extract --input hp.obo --method TOP --term HP:0012823 \
+  convert --output cm.top.hp.obo
+
+# Frequency HP:0040279
+robot extract --input hp.obo --method BOT --term HP:0040279 \
+  convert --output freq.bot.hp.obo
+robot extract --input hp.obo --method TOP --term HP:0040279 \
+  convert --output freq.top.hp.obo
+
+# Mode of inheritance HP:0000005
+robot extract --input hp.obo --method BOT --term HP:0000005 \
+  convert --output moi.bot.hp.obo
+robot extract --input hp.obo --method TOP --term HP:0000005 \
+  convert --output moi.top.hp.obo
+
+# Past medical history HP:0032443
+robot extract --input hp.obo --method BOT --term HP:0032443 \
+  convert --output pmh.bot.hp.obo
+robot extract --input hp.obo --method TOP --term HP:0032443 \
+  convert --output pmh.top.hp.obo
+
+# Blood group HP:0032223
+robot extract --input hp.obo --method BOT --term HP:0032223 \
+  convert --output bg.bot.hp.obo
+robot extract --input hp.obo --method TOP --term HP:0032223 \
+  convert --output bg.top.hp.obo
+
+# Merge into one file
+robot merge --input arachnodactyly.hp.obo \
+  --input fcs.hp.obo \
+  --input cm.bot.hp.obo \
+  --input cm.top.hp.obo \
+  --input freq.bot.hp.obo \
+  --input freq.top.hp.obo \
+  --input moi.bot.hp.obo \
+  --input moi.top.hp.obo \
+  --input pmh.bot.hp.obo \
+  --input pmh.top.hp.obo \
+  --input bg.bot.hp.obo \
+  --input bg.top.hp.obo \
+  --output hp.module.json
+
+rm *.obo
+```