Release 1.0.0

.github/workflows/deploy.yml

@@ -0,0 +1,57 @@
+name: Deploy to Sonatype Central
+
+on:
+  push:
+    tags:
+      - 'v*'  # Trigger the workflow when a tag starting with 'v' is pushed, like v1.0.0
+  workflow_dispatch:
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Set up JDK 17
+        uses: actions/setup-java@v5
+        with:
+          java-version: '17'
+          distribution: 'adopt'
+
+      - name: Cache Maven dependencies
+        uses: actions/cache@v4
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+
+      - name: Import GPG key
+        run: |
+          echo "${{ secrets.GPG_PRIVATE_KEY }}" | gpg --import --armor --batch --no-tty
+
+      - name: Setup Maven settings
+        run: |
+          rm ${HOME}/.m2/settings.xml
+
+          cat << EOF > ${HOME}/.m2/settings.xml
+          <settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
+            xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+            xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 https://maven.apache.org/xsd/settings-1.0.0.xsd">
+            <servers>
+              <server>
+                <id>central</id>
+                <username>${{ secrets.SONATYPE_USERNAME }}</username>
+                <password>${{ secrets.SONATYPE_PASSWORD }}</password>
+              </server>
+            </servers>
+          </settings>
+          EOF
+
+      - name: Deploy to Sonatype Central
+        run: |
+          ./mvnw clean deploy -Prelease \
+            --batch-mode \
+            -Dgpg.keyname=${{ secrets.GPG_KEY_ID }}

.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

.mvn/wrapper/maven-wrapper.properties

@@ -1 +1 @@
-distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.6.0/apache-maven-3.6.0-bin.zip
+distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.6.3/apache-maven-3.6.3-bin.zip

CHANGELOG.rst

@@ -9,7 +9,7 @@ Changelog
 * Improve user guide, tutorial, and documentation.
   * Introduce *latest* and *stable* documentation branches
   * Add showcase of apps that use phenopacket-tools to add more code examples
-* Run `MetaDataValidator` during base validation
+* Run `MetaDataValidator` and `HpoUniqueValidator` during base validation
 * Finalize JSON and YAML format sniffing
 * Fix example phenopackets
 

docs/conf.py

@@ -6,24 +6,8 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-#############
-# JR added:
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath('../../'))
-extensions = [
-   'sphinx.ext.autodoc',
-   'sphinx.ext.githubpages',
-   'sphinx_rtd_theme',
-   'recommonmark'
-]
-
-html_theme = 'sphinx_rtd_theme'
-##############
-
 project = 'phenopacket-tools'
-copyright = '2022, Daniel Danis, Peter Robinson'
+copyright = '2026, Daniel Danis, Peter Robinson'
 author = u'Daniel Danis, Peter Robinson'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -33,7 +17,7 @@
 # The short X.Y version.
 version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0-RC3'
+release = '1.0.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -48,7 +32,6 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'alabaster'
 html_static_path = ['_static']
 html_css_files = ['pxftools.css']
 

docs/validation.rst

@@ -353,6 +353,20 @@ library to parse the HPO JSON file. The `OntologyLoader` is part of
 `phenol-io <https://mvnrepository.com/artifact/org.monarchinitiative.phenol/phenol-io>`_ module, you may need to add
 an appropriate dependency into your build file.
 
+.. _rstuniquephenotypevalidation:
+
+Unique phenotypic features
+##########################
+
+The `HpoUniqueValidator` checks if the HPO terms used by a phenopacket are *unique* - present at most once.
+If a term is not unique, the validator points this out along with the term's occurrence count.
+
+In code, we add the corresponding validator into the validation workflow by running:
+
+.. code-block:: java
+
+  builder.addValidator(HpoPhenotypeValidators.Unique.phenopacketValidator(hpo));
+
 
 .. _rstancestryphenotypevalidation:
 

phenopacket-tools-builder/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.phenopackets.phenopackettools</groupId>
         <artifactId>phenopacket-tools</artifactId>
-        <version>1.0.0-RC3</version>
+        <version>1.0.0</version>
     </parent>
 
     <artifactId>phenopacket-tools-builder</artifactId>

phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VariationDescriptorBuilder.java

@@ -100,6 +100,10 @@ public VariationDescriptorBuilder transcript() {
         return this;
     }
 
+    public VariationDescriptorBuilder moleculeContext(MoleculeContext context) {
+        builder.setMoleculeContext(context);
+        return this;
+    }
 
     public VariationDescriptorBuilder structuralType(OntologyClass structuralType) {
         builder.setStructuralType(structuralType);

phenopacket-tools-builder/src/main/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilder.java

@@ -2,9 +2,14 @@
 
 import org.ga4gh.vrsatile.v1.VcfRecord;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class VcfRecordBuilder {
 
     private final VcfRecord.Builder builder;
+    private boolean passIsSet = false;
+    private List<String> filters = null;
 
     private VcfRecordBuilder(String assembly, String chromosome, int position, String ref, String alt) {
         builder = VcfRecord.newBuilder()
@@ -48,18 +53,46 @@ public VcfRecordBuilder qual(String qual) {
     }
 
     /**
-     * If this method is called, "PASS" is added to the FILTER column
+     * If this method is called, the FILTER column is set to "PASS" and any other previously added filters are cleared.
+     * Calling {@code pass()} is equivalent to calling <code>filter("PASS")</code>.
      */
-    public VcfRecordBuilder pass() {
-        builder.setFilter("PASS");
+    public synchronized VcfRecordBuilder pass() {
+        passIsSet = true;
+        if (filters != null)
+            filters.clear();
+
         return this;
     }
 
     /**
-     * @param filter FILTER field of VCF. calling {@link #pass()} is equivant to calling filter("PASS)
+     * Add a VCF filter field.
+     * <p>
+     * The field can be a single value (e.g. <code>q50</code>) or several values joined by <code>;</code> (e.g. <code>q10;q50</code>).
+     * <p>
+     * Calling <code>filter("PASS")</code> is equivalent to calling {@link #pass()}. As a side effect,
+     * all previously added filter values are removed.
+     *
+     * @param filter add a FILTER field.
+     * @see #pass()
      */
-    public VcfRecordBuilder filter(String filter) {
-        builder.setFilter(filter);
+    public synchronized VcfRecordBuilder filter(String filter) {
+        passIsSet = false;
+        if (filters == null)
+            filters = new ArrayList<>();
+
+        if ("PASS".equalsIgnoreCase(filter))
+            return pass();
+        else {
+            if (filter.contains(";")) {
+                for (String field : filter.split(";")) {
+                    String trimmed = field.trim();
+                    if (!trimmed.isEmpty())
+                        this.filter(field);
+                }
+            } else
+                filters.add(filter);
+        }
+
         return this;
     }
 
@@ -71,7 +104,13 @@ public VcfRecordBuilder info(String info) {
         return this;
     }
 
-    public VcfRecord build() {
+    public synchronized VcfRecord build() {
+        if (passIsSet)
+            builder.setFilter("PASS");
+
+        else if (filters != null && !filters.isEmpty())
+            builder.setFilter(String.join(";", filters));
+
         return builder.build();
     }
 }

phenopacket-tools-builder/src/test/java/org/phenopackets/phenopackettools/builder/builders/VcfRecordBuilderTest.java

@@ -0,0 +1,30 @@
+package org.phenopackets.phenopackettools.builder.builders;
+
+import org.ga4gh.vrsatile.v1.VcfRecord;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.hamcrest.MatcherAssert.*;
+import static org.hamcrest.Matchers.*;
+
+public class VcfRecordBuilderTest {
+
+    @ParameterizedTest
+    @CsvSource({
+            "PASS,      PASS",
+            "pass,      PASS",
+            "q50,       q50",
+            "q50;q10,   q50;q10",
+            "q50;pass,  PASS",
+            "pass;q50,  q50",
+    })
+    public void addFilter(String filter, String expected) {
+        VcfRecord record = VcfRecordBuilder.builder("GRCh37", "chr1", 123_456, "C", "G")
+                .filter(filter)
+                .build();
+
+        assertThat(record.getFilter(), equalTo(expected));
+    }
+}

phenopacket-tools-cli/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.phenopackets.phenopackettools</groupId>
         <artifactId>phenopacket-tools</artifactId>
-        <version>1.0.0-RC3</version>
+        <version>1.0.0</version>
     </parent>
 
     <artifactId>phenopacket-tools-cli</artifactId>

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

@@ -15,7 +15,7 @@
                 "phenopacket-tools (pxf)",
                 "An application and library for building, conversion, and validation of GA4GH Phenopackets.\n"
         },
-        version = "v1.0.0-RC3",
+        version = "v1.0.0",
         mixinStandardHelpOptions = true,
         subcommands = {
                 // see https://picocli.info/autocomplete.html

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.
@@ -163,18 +163,24 @@ private <T extends MessageOrBuilder> List<PhenopacketValidator<T>> configureSema
                     //noinspection unchecked
                     validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(hpo));
                     //noinspection unchecked
+                    validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Unique.phenopacketValidator(hpo));
+                    //noinspection unchecked
                     validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Ancestry.phenopacketHpoAncestryValidator(hpo));
                 }
                 case FAMILY -> {
                     //noinspection unchecked
                     validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(hpo));
                     //noinspection unchecked
+                    validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Unique.familyValidator(hpo));
+                    //noinspection unchecked
                     validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Ancestry.familyHpoAncestryValidator(hpo));
                 }
                 case COHORT -> {
                     //noinspection unchecked
                     validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(hpo));
                     //noinspection unchecked
+                    validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Unique.cohortValidator(hpo));
+                    //noinspection unchecked
                     validators.add((PhenopacketValidator<T>) HpoPhenotypeValidators.Ancestry.cohortHpoAncestryValidator(hpo));
                 }
             }
@@ -191,7 +197,7 @@ 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);
     }