Fix broken documentation links

.github/workflows/main.yaml

@@ -21,9 +21,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Set up JDK 17
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v5.2.0
         with:
           java-version: '17'
           distribution: 'adopt'
       - name: Build with Maven
-        run: mvn --batch-mode --update-snapshots verify
+        run: ./mvnw --batch-mode --update-snapshots verify

.github/workflows/pages.yml

@@ -14,23 +14,23 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v6.0.2
       with:
         fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
         ref: main
 
     - name: Set up Python 3.
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6.2.0
       with:
-        python-version: 3.9
+        python-version: 3.12
 
     - name: Install Python dependencies
       run: |
         pip install sphinx
         pip install sphinx-rtd-theme
 
     - name: Set up JDK 17
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v5.2.0
       with:
         java-version: '17'
         distribution: 'adopt'
@@ -100,7 +100,7 @@ jobs:
 
     - name: Deploy documentation.
       if: ${{ github.event_name == 'push' }}
-      uses: JamesIves/github-pages-deploy-action@v4.4.1
+      uses: JamesIves/github-pages-deploy-action@v4.8.0
       with:
         branch: gh-pages
         force: true

.gitignore

@@ -75,3 +75,5 @@ families/*
 phenopackets/*
 cohorts/*
 
+# Python stuff
+venv/

.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
 

README.md

@@ -33,15 +33,15 @@ a *Library user guide*, and the *Javadoc API documentation*.
 
 The documentation is published in two documentation branches:
 - **stable**: corresponds to the latest published release, and generally also to the last commit of the `main` Git branch
-  - [Tutorial](http://phenopackets.org/phenopacket-tools/stable/tutorial.html)
-  - [CLI user guide](http://phenopackets.org/phenopacket-tools/stable/cli.html)
-  - [Library user guide](http://phenopackets.org/phenopacket-tools/stable)
-  - [Javadoc API documentation](http://phenopackets.org/phenopacket-tools/stable/apidocs)
+  - [Tutorial](https://phenopackets.github.io/phenopacket-tools/stable/tutorial.html)
+  - [CLI user guide](https://phenopackets.github.io/phenopacket-tools/stable/cli.html)
+  - [Library user guide](https://phenopackets.github.io/phenopacket-tools/stable)
+  - [Javadoc API documentation](https://phenopackets.github.io/phenopacket-tools/stable/apidocs)
 - **latest**: corresponds to the bleeding edge code that is on the `develop` Git branch
-  - [Tutorial](http://phenopackets.org/phenopacket-tools/latest/tutorial.html)
-  - [CLI user guide](http://phenopackets.org/phenopacket-tools/latest/cli.html)
-  - [Library user guide](http://phenopackets.org/phenopacket-tools/latest)
-  - [Javadoc API documentation](http://phenopackets.org/phenopacket-tools/latest/apidocs)  
+  - [Tutorial](https://phenopackets.github.io/phenopacket-tools/latest/tutorial.html)
+  - [CLI user guide](https://phenopackets.github.io/phenopacket-tools/latest/cli.html)
+  - [Library user guide](https://phenopackets.github.io/phenopacket-tools/latest)
+  - [Javadoc API documentation](https://phenopackets.github.io/phenopacket-tools/latest/apidocs)  
 
 ## Issues
 

docs/conf.py

@@ -6,22 +6,6 @@
 # -- 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'
 author = u'Daniel Danis, Peter Robinson'
@@ -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-RC4-SNAPSHOT'
 
 # -- 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/converting.rst

@@ -44,5 +44,5 @@ See also
 ^^^^^^^^
 
 The API documentation of the conversion functionality is located in the
-`org.phenopackets.phenopackettools.converter <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.converter/module-summary.html>`_
+`org.phenopackets.phenopackettools.converter <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.converter/module-summary.html>`_
 module.

docs/creating.rst

@@ -12,7 +12,7 @@ of the phenopacket framework will want to use a recommended set of ontology term
 the equivalent message.
 
 This section exemplifies usage of `PhenotypicFeatureBuilder`, one of many builders provided by the
-`org.phenopackets.phenopackettools.builder <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
+`org.phenopackets.phenopackettools.builder <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
 module.
 
 
@@ -89,12 +89,12 @@ See also
 ========
 
 See the API documentation of the
-`org.phenopackets.phenopackettools.builder <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
+`org.phenopackets.phenopackettools.builder <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
 module for a comprehensive list of ontology constants, convenience methods, and builders provided
 by the *phenopacket-tools* library.
 
 Several detailed examples are available in the ``phenopackets-tools-cli`` module in the
-`org.phenopackets.phenopackettools.cli.examples <https://github.com/phenopackets/phenopacket-tools/tree/main/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/examples>`_
+`org.phenopackets.phenopackettools.cli.examples <https://phenopackets.github.io/phenopacket-tools/tree/main/phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/examples>`_
 package.
 
 .. _Protocol Buffer (protobuf): https://developers.google.com/protocol-buffers

docs/validation.rst

@@ -185,7 +185,7 @@ and the discovered issues (if any):
 
 
 The API documentation of the core validation API can be found in the
-`org.phenopackets.phenopackettools.validator.core <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
+`org.phenopackets.phenopackettools.validator.core <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
 module.
 
 
@@ -327,7 +327,7 @@ because an annotation with a specific HPO term (e.g., a patient with perimembran
 
 In this section, we describe validators that use HPO file to perform several checks that can be useful in many contexts.
 The API documentation and the corresponding Java classes can be found in
-`org.phenopackets.phenopackettools.validator.core.phenotype <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/org/phenopackets/phenopackettools/validator/core/phenotype/package-summary.html>`_
+`org.phenopackets.phenopackettools.validator.core.phenotype <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/org/phenopackets/phenopackettools/validator/core/phenotype/package-summary.html>`_
 package.
 
 
@@ -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:
 
@@ -432,7 +446,7 @@ See also
 ^^^^^^^^
 
 Check out the
-`org.phenopackets.phenopackettools.validator.core <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
+`org.phenopackets.phenopackettools.validator.core <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
 and
-`org.phenopackets.phenopackettools.validator.jsonschema <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.jsonschema/module-summary.html>`_
+`org.phenopackets.phenopackettools.validator.jsonschema <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.jsonschema/module-summary.html>`_
 modules for more information regarding the public validation API.

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-RC4-SNAPSHOT</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-RC4-SNAPSHOT</version>
     </parent>
 
     <artifactId>phenopacket-tools-cli</artifactId>