Merge pull request #190 from ielis/update-phenol

Use phenol `2.0.2`

.github/workflows/main.yaml

@@ -26,4 +26,4 @@ jobs:
           java-version: '17'
           distribution: 'adopt'
       - name: Build with Maven
-        run: mvn --batch-mode --update-snapshots verify
+        run: ./mvnw --batch-mode --update-snapshots verify

phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/ValidateCommand.java

@@ -3,8 +3,8 @@
 
 import com.google.protobuf.MessageOrBuilder;
 import org.monarchinitiative.phenol.base.PhenolRuntimeException;
-import org.monarchinitiative.phenol.io.OntologyLoader;
-import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenol.io.MinimalOntologyLoader;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 import org.phenopackets.phenopackettools.core.PhenopacketElement;
 import org.phenopackets.phenopackettools.core.PhenopacketSchemaVersion;
@@ -149,10 +149,10 @@ private <T extends MessageOrBuilder> List<PhenopacketValidator<T>> configureSema
         // Right now we only have one semantic validator, but we'll extend this in the future.
         LOGGER.debug("Configuring semantic validators");
         List<PhenopacketValidator<T>> validators = new ArrayList<>();
-        Ontology hpo = null;
+        MinimalOntology hpo = null;
         if (validateSection.hpJson != null) {
             LOGGER.debug("Reading HPO from {}", validateSection.hpJson.toAbsolutePath());
-            hpo = OntologyLoader.loadOntology(validateSection.hpJson.toFile());
+            hpo = MinimalOntologyLoader.loadOntology(validateSection.hpJson.toFile());
 
             // The entire logic of this command stands and falls on correct state of `element` and the read message(s).
             // This method requires an appropriate combination of `T` and `element`, as described in Javadoc.
@@ -191,7 +191,7 @@ private <T extends MessageOrBuilder> List<PhenopacketValidator<T>> configureSema
         return validators;
     }
 
-    private static <T extends MessageOrBuilder> PhenopacketValidator<T> prepareOrganSystemValidator(Ontology hpo,
+    private static <T extends MessageOrBuilder> PhenopacketValidator<T> prepareOrganSystemValidator(MinimalOntology hpo,
                                                                                                     List<String> organSystems,
                                                                                                     PhenopacketElement element) {
         // Organ system validation can only be done when HPO is provided.

phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/BaseValidateCommand.java

@@ -1,8 +1,8 @@
 package org.phenopackets.phenopackettools.cli.command.validate;
 
 import com.google.protobuf.MessageOrBuilder;
-import org.monarchinitiative.phenol.io.OntologyLoader;
-import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenol.io.MinimalOntologyLoader;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator;
 import org.phenopackets.phenopackettools.validator.core.ValidationResult;
 import org.phenopackets.phenopackettools.validator.core.ValidationResults;
@@ -109,14 +109,14 @@ protected List<PhenopacketValidator<T>> configureSemanticValidators()  {
         List<PhenopacketValidator<T>> validators = new ArrayList<>();
         if (hpJson != null) {
             LOGGER.debug("Reading HPO from '{}}'", hpJson.toAbsolutePath());
-            Ontology hpo = OntologyLoader.loadOntology(hpJson.toFile());
+            MinimalOntology hpo = MinimalOntologyLoader.loadOntology(hpJson.toFile());
             validators.add(createHpoValidator(hpo));
         }
 
         LOGGER.debug("Configured {} semantic validator(s)", validators.size());
         return validators;
     }
 
-    protected abstract PhenopacketValidator<T> createHpoValidator(Ontology hpo);
+    protected abstract PhenopacketValidator<T> createHpoValidator(MinimalOntology hpo);
 
 }

phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateCohortCommand.java

@@ -1,6 +1,6 @@
 package org.phenopackets.phenopackettools.cli.command.validate;
 
-import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator;
 import org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner;
 import org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators;
@@ -30,7 +30,7 @@ protected ValidationWorkflowRunner<CohortOrBuilder> prepareValidationWorkflow(Li
     }
 
     @Override
-    protected PhenopacketValidator<CohortOrBuilder> createHpoValidator(Ontology hpo) {
+    protected PhenopacketValidator<CohortOrBuilder> createHpoValidator(MinimalOntology hpo) {
         return HpoPhenotypeValidators.cohortHpoPhenotypeValidator(hpo);
     }
 

phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidateFamilyCommand.java

@@ -1,6 +1,6 @@
 package org.phenopackets.phenopackettools.cli.command.validate;
 
-import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator;
 import org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner;
 import org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators;
@@ -30,7 +30,7 @@ protected ValidationWorkflowRunner<FamilyOrBuilder> prepareValidationWorkflow(Li
     }
 
     @Override
-    protected PhenopacketValidator<FamilyOrBuilder> createHpoValidator(Ontology hpo) {
+    protected PhenopacketValidator<FamilyOrBuilder> createHpoValidator(MinimalOntology hpo) {
         return HpoPhenotypeValidators.familyHpoPhenotypeValidator(hpo);
     }
 

phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/command/validate/ValidatePhenopacketCommand.java

@@ -1,6 +1,6 @@
 package org.phenopackets.phenopackettools.cli.command.validate;
 
-import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator;
 import org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunner;
 import org.phenopackets.phenopackettools.validator.core.metadata.MetaDataValidators;
@@ -32,7 +32,7 @@ protected ValidationWorkflowRunner<PhenopacketOrBuilder> prepareValidationWorkfl
     }
 
     @Override
-    protected PhenopacketValidator<PhenopacketOrBuilder> createHpoValidator(Ontology hpo) {
+    protected PhenopacketValidator<PhenopacketOrBuilder> createHpoValidator(MinimalOntology hpo) {
         return HpoPhenotypeValidators.phenopacketHpoPhenotypeValidator(hpo);
     }
 

phenopacket-tools-validator-core/src/main/java/org/phenopackets/phenopackettools/validator/core/phenotype/HpoPhenotypeValidators.java

@@ -1,6 +1,6 @@
 package org.phenopackets.phenopackettools.validator.core.phenotype;
 
-import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 import org.phenopackets.phenopackettools.validator.core.PhenopacketValidator;
 import org.phenopackets.phenopackettools.validator.core.phenotype.ancestry.CohortHpoAncestryValidator;
@@ -26,39 +26,39 @@ private HpoPhenotypeValidators() {
     }
 
     /**
-     * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link Ontology}.
+     * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link MinimalOntology}.
      *
      * @param hpo HPO ontology
-     * @deprecated use {@link Primary#phenopacketHpoPhenotypeValidator(Ontology)} instead
+     * @deprecated use {@link Primary#phenopacketHpoPhenotypeValidator(MinimalOntology)} instead
      */
     // REMOVE(v1.0.0)
     @Deprecated(forRemoval = true)
-    public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoPhenotypeValidator(Ontology hpo) {
+    public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoPhenotypeValidator(MinimalOntology hpo) {
         return Primary.phenopacketHpoPhenotypeValidator(hpo);
     }
 
     /**
-     * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link Ontology}.
+     * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link MinimalOntology}.
      *
      * @param hpo HPO ontology
-     * @deprecated use {@link Primary#familyHpoPhenotypeValidator(Ontology)} instead
+     * @deprecated use {@link Primary#familyHpoPhenotypeValidator(MinimalOntology)} instead
      */
     // REMOVE(v1.0.0)
     @Deprecated(forRemoval = true)
-    public static PhenopacketValidator<FamilyOrBuilder> familyHpoPhenotypeValidator(Ontology hpo) {
+    public static PhenopacketValidator<FamilyOrBuilder> familyHpoPhenotypeValidator(MinimalOntology hpo) {
         return Primary.familyHpoPhenotypeValidator(hpo);
     }
 
     /**
-     * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link Ontology},
+     * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link MinimalOntology},
      * as described in {@link org.phenopackets.phenopackettools.validator.core.phenotype.primary.AbstractHpoPhenotypeValidator}.
      *
      * @param hpo HPO ontology
-     * @deprecated use {@link Primary#cohortHpoPhenotypeValidator(Ontology)} instead
+     * @deprecated use {@link Primary#cohortHpoPhenotypeValidator(MinimalOntology)} instead
      */
     // REMOVE(v1.0.0)
     @Deprecated(forRemoval = true)
-    public static PhenopacketValidator<CohortOrBuilder> cohortHpoPhenotypeValidator(Ontology hpo) {
+    public static PhenopacketValidator<CohortOrBuilder> cohortHpoPhenotypeValidator(MinimalOntology hpo) {
         return Primary.cohortHpoPhenotypeValidator(hpo);
     }
 
@@ -69,30 +69,30 @@ public static PhenopacketValidator<CohortOrBuilder> cohortHpoPhenotypeValidator(
      */
     public static class Primary {
         /**
-         * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link Ontology}.
+         * Get {@link PhenopacketValidator} to validate {@link Phenopacket} using provided {@link MinimalOntology}.
          *
          * @param hpo HPO ontology
          */
-        public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoPhenotypeValidator(Ontology hpo) {
+        public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoPhenotypeValidator(MinimalOntology hpo) {
             return new PhenopacketHpoPhenotypeValidator(hpo);
         }
 
         /**
-         * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link Ontology}.
+         * Get {@link PhenopacketValidator} for validate {@link Family} using provided {@link MinimalOntology}.
          *
          * @param hpo HPO ontology
          */
-        public static PhenopacketValidator<FamilyOrBuilder> familyHpoPhenotypeValidator(Ontology hpo) {
+        public static PhenopacketValidator<FamilyOrBuilder> familyHpoPhenotypeValidator(MinimalOntology hpo) {
             return new FamilyHpoPhenotypeValidator(hpo);
         }
 
         /**
-         * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link Ontology},
+         * Get {@link PhenopacketValidator} for performing primary validation {@link Cohort} using provided {@link MinimalOntology},
          * as described in {@link org.phenopackets.phenopackettools.validator.core.phenotype.primary.AbstractHpoPhenotypeValidator}.
          *
          * @param hpo HPO ontology
          */
-        public static PhenopacketValidator<CohortOrBuilder> cohortHpoPhenotypeValidator(Ontology hpo) {
+        public static PhenopacketValidator<CohortOrBuilder> cohortHpoPhenotypeValidator(MinimalOntology hpo) {
             return new CohortHpoPhenotypeValidator(hpo);
         }
     }
@@ -115,29 +115,29 @@ private Ancestry() {
         }
 
         /**
-         * Get {@link PhenopacketValidator} to validate ancestry {@link Phenopacket} using provided {@link Ontology}.
+         * Get {@link PhenopacketValidator} to validate ancestry {@link Phenopacket} using provided {@link MinimalOntology}.
          *
          * @param hpo HPO ontology
          */
-        public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoAncestryValidator(Ontology hpo) {
+        public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoAncestryValidator(MinimalOntology hpo) {
             return new PhenopacketHpoAncestryValidator(hpo);
         }
 
         /**
-         * Get {@link PhenopacketValidator} to validate ancestry {@link Family} using provided {@link Ontology}.
+         * Get {@link PhenopacketValidator} to validate ancestry {@link Family} using provided {@link MinimalOntology}.
          *
          * @param hpo HPO ontology
          */
-        public static PhenopacketValidator<FamilyOrBuilder> familyHpoAncestryValidator(Ontology hpo) {
+        public static PhenopacketValidator<FamilyOrBuilder> familyHpoAncestryValidator(MinimalOntology hpo) {
             return new FamilyHpoAncestryValidator(hpo);
         }
 
         /**
-         * Get {@link PhenopacketValidator} to validate ancestry {@link Cohort} using provided {@link Ontology}.
+         * Get {@link PhenopacketValidator} to validate ancestry {@link Cohort} using provided {@link MinimalOntology}.
          *
          * @param hpo HPO ontology
          */
-        public static PhenopacketValidator<CohortOrBuilder> cohortHpoAncestryValidator(Ontology hpo) {
+        public static PhenopacketValidator<CohortOrBuilder> cohortHpoAncestryValidator(MinimalOntology hpo) {
             return new CohortHpoAncestryValidator(hpo);
         }
     }
@@ -160,45 +160,45 @@ private OrganSystem() {
 
         /**
          * Get {@link PhenopacketValidator} to validate annotation of organ systems in a {@link Phenopacket}
-         * using provided {@link Ontology} and a collection of organ system {@link TermId}s.
+         * using provided {@link MinimalOntology} and a collection of organ system {@link TermId}s.
          * <p>
-         * <b>NOTE:</b> the organ system {@link TermId} that is absent from the {@link Ontology} is disregarded
+         * <b>NOTE:</b> the organ system {@link TermId} that is absent from the {@link MinimalOntology} is disregarded
          * and not used for validation.
          *
          * @param hpo HPO ontology
          * @param organSystemTermIds a collection of HPO {@link TermId}s corresponding to organ systems.
          */
-        public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoOrganSystemValidator(Ontology hpo,
+        public static PhenopacketValidator<PhenopacketOrBuilder> phenopacketHpoOrganSystemValidator(MinimalOntology hpo,
                                                                                                     Collection<TermId> organSystemTermIds) {
             return new PhenopacketHpoOrganSystemValidator(hpo, organSystemTermIds);
         }
 
         /**
          * Get {@link PhenopacketValidator} to validate annotation of organ systems in a {@link Family}
-         * using provided {@link Ontology} and a collection of organ system {@link TermId}s.
+         * using provided {@link MinimalOntology} and a collection of organ system {@link TermId}s.
          * <p>
-         * <b>NOTE:</b> the organ system {@link TermId} that is absent from the {@link Ontology} is disregarded
+         * <b>NOTE:</b> the organ system {@link TermId} that is absent from the {@link MinimalOntology} is disregarded
          * and not used for validation.
          *
          * @param hpo HPO ontology
          * @param organSystemTermIds a collection of HPO {@link TermId}s corresponding to organ systems.
          */
-        public static PhenopacketValidator<FamilyOrBuilder> familyHpoOrganSystemValidator(Ontology hpo,
+        public static PhenopacketValidator<FamilyOrBuilder> familyHpoOrganSystemValidator(MinimalOntology hpo,
                                                                                           Collection<TermId> organSystemTermIds) {
             return new FamilyHpoOrganSystemValidator(hpo, organSystemTermIds);
         }
 
         /**
          * Get {@link PhenopacketValidator} to validate annotation of organ systems in a {@link Cohort}
-         * using provided {@link Ontology} and a collection of organ system {@link TermId}s.
+         * using provided {@link MinimalOntology} and a collection of organ system {@link TermId}s.
          * <p>
-         * <b>NOTE:</b> the organ system {@link TermId} that is absent from the {@link Ontology} is disregarded
+         * <b>NOTE:</b> the organ system {@link TermId} that is absent from the {@link MinimalOntology} is disregarded
          * and not used for validation.
          *
          * @param hpo HPO ontology
          * @param organSystemTermIds a collection of HPO {@link TermId}s corresponding to organ systems.
          */
-        public static PhenopacketValidator<CohortOrBuilder> cohortHpoOrganSystemValidator(Ontology hpo,
+        public static PhenopacketValidator<CohortOrBuilder> cohortHpoOrganSystemValidator(MinimalOntology hpo,
                                                                                           Collection<TermId> organSystemTermIds) {
             return new CohortHpoOrganSystemValidator(hpo, organSystemTermIds);
         }