Merge branch 'develop'

Author: hansenp

.github/workflows/deploy.yml

@@ -0,0 +1,55 @@
+name: Deploy to Sonatype Central
+
+on:
+  push:
+    tags:
+      - 'v*'  # Trigger the workflow when a tag starting with 'v' is pushed, like v1.0.0
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Set up JDK 21
+        uses: actions/setup-java@v5
+        with:
+          java-version: '21'
+          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>${{ secrets.SONATYPE_PASSWORD }}</password>
+              </server>
+            </servers>
+          </settings>
+          EOF
+
+      - name: Deploy to Sonatype Central
+        run: |
+          ./mvnw clean deploy --batch-mode -Prelease \
+            -Dgpg.keyname=${{ secrets.GPG_KEY_ID }}

.github/workflows/maven.yml

@@ -46,4 +46,4 @@ jobs:
     - name: Build with Maven
       run: ./mvnw -pl boqa-cli,boqa-core -am -B --quiet -Prelease --batch-mode package
     - name: Run CLI
-      run: java -jar boqa-cli/target/boqa-cli-0.1.0-SNAPSHOT.jar --help
+      run: java -jar boqa-cli/target/boqa-cli-0.1.0.jar --help

.gitignore

@@ -13,12 +13,14 @@ hs_err_pid*
 target/
 *.iml
 *.log
-data/
+boqa_info.*.gz
+/data/
 dev/
 results/
 dependency-reduced-pom.xml
 .settings
 .project
 .classpath
+boqacore.*.gz
 
 docs/_build/

LICENSE

@@ -1,35 +1,6 @@
 # BOQA
 
-Bayesian Ontology Query Analysis
-
-## Local setup
-
-The project uses Exomiser as a library. However, Exomiser is not available from Maven central repository.
-Therefore, we must install Exomiser locally to be able to build the code.
-
-The installation proceeds as follows:
-
-```shell
-# First, let's check out Exomiser source code
-git clone https://github.com/exomiser/Exomiser.git
-
-# Check out the version we use
-cd Exomiser
-git checkout 14.1.0
-
-# Make mvnw executable
-chmod u+x mvnw
-
-# Install Exomiser locally
-./mvnw install
-```
-
-This should install Exomiser into local Maven repository, and it should be possible to build the project.
-
-> **Note:** To only build the `boqa-cli` and `boqa-core` modules Exomiser is not needed. This can be done via
-```shell
-./mvnw -pl boqa-cli,boqa-core -am -Prelease package
-```
+Bayesian Ontology Query Algorithm
 
 ## Run tests
 
@@ -38,17 +9,6 @@ We use Maven Surefire plugin to run tests:
 ```shell
 ./mvnw test
 ```
-
-## Run CLI
-
-Run the following to run the CLI:
-
-```shell
-./mvnw -Prelease package
-
-java -jar boqa-cli/target/boqa-cli-0.1.0-SNAPSHOT.jar --help
-```
-
 ## Distribute CLI
 
 The compilation of JAR files, generation of sources and Javadoc, as well as packaging into distribution ZIP file
@@ -57,31 +17,29 @@ requires activation of the `release` profile:
 ```shell
 ./mvnw -Prelease package 
 ```
-
 ## Input data
 
 In BOQA analyses, observed phenotypic features of individuals are compared
 with annotated disease-phenotype associations.
-We use the following HPO data sources:
+We use the following [HPO resources](https://github.com/obophenotype/human-phenotype-ontology):
 
 **1. Disease-phenotype associations: `phenotype.hpoa`**
 
-```
-mkdir -p data
-wget -O data/phenotype.hpoa https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/phenotype.hpoa
-```
-
 **2. HPO: `hp.json`**
 
-```
-wget -O data/hp.json https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/hp.json
-```
-
-**3. Disease-gene associations: `phenotype.hpoa`**
+**3. Disease-gene associations: `genes_to_disease.txt`**
 
+Use the following command to download these files from the latest release:
+```shell
+java -jar boqa-cli/target/boqa-cli-0.1.0.jar download -d ./data 
 ```
-wget -O data/genes_to_disease.txt https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_disease.txt
+The files are downloaded to a subdirectory `./data/latest_<time_stamp>`.
+
+To download a specific release, use the following command;
+```shell
+java -jar boqa-cli/target/boqa-cli-0.1.0.jar download -d ./data -r v2025-05-06 
 ```
+The files are downloaded into a subdirectory of `./data` named after the release.
 
 **4. Phenopackets containing phenotypic features observed in individuals: `phenopacket-store`**
 
@@ -90,6 +48,12 @@ wget -O data/all_phenopackets.zip https://github.com/monarch-initiative/phenopac
 unzip data/all_phenopackets.zip -d data
 ```
 
-## TODO
+## Run CLI
+
+Run the following to run the CLI:
 
-Add more information at some point. 
+```shell
+./mvnw -Prelease package
+
+java -jar boqa-cli/target/boqa-cli-0.1.0.jar --help
+```

README.md

@@ -4,16 +4,16 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
-        <groupId>com.github.p2gx.boqa</groupId>
+        <groupId>io.github.p2gx.boqa</groupId>
         <artifactId>BOQA</artifactId>
-        <version>0.1.0-SNAPSHOT</version>
+        <version>0.1.0</version>
     </parent>
 
     <artifactId>boqa-cli</artifactId>
 
     <dependencies>
         <dependency>
-            <groupId>com.github.p2gx.boqa</groupId>
+            <groupId>io.github.p2gx.boqa</groupId>
             <artifactId>boqa-core</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
@@ -22,6 +22,20 @@
             <groupId>info.picocli</groupId>
             <artifactId>picocli</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.monarchinitiative.biodownload</groupId>
+            <artifactId>biodownload</artifactId>
+            <version>1.0.1</version>
+        </dependency>
+        <dependency>
+            <groupId>net.lingala.zip4j</groupId>
+            <artifactId>zip4j</artifactId>
+            <version>2.11.5</version>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+        </dependency>
     </dependencies>
 
 
@@ -49,7 +63,7 @@
                                     <addClasspath>true</addClasspath>
                                     <classpathPrefix>lib/</classpathPrefix>
                                     <useUniqueVersions>false</useUniqueVersions>
-                                    <mainClass>com.github.p2gx.boqa.cli.Main</mainClass>
+                                    <mainClass>org.p2gx.boqa.cli.Main</mainClass>
                                     <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                                 </manifest>
                             </archive>
@@ -98,4 +112,4 @@
         </profile>
     </profiles>
 
-</project>
+</project>

boqa-cli/pom.xml

@@ -1,11 +1,28 @@
-package com.github.p2gx.boqa.cli;
+package org.p2gx.boqa.cli;
 
-import com.github.p2gx.boqa.cli.cmd.BoqaCommand;
-import com.github.p2gx.boqa.cli.cmd.BlendedCommand;
+import org.p2gx.boqa.cli.cmd.BoqaBenchmarkCommand;
+import org.p2gx.boqa.cli.cmd.BlendedBenchmarkCommand;
+import org.p2gx.boqa.cli.cmd.DownloadCommand;
 import picocli.CommandLine;
 import java.util.concurrent.Callable;
 import static picocli.CommandLine.Help.Ansi.Style.*;
 
+/**
+ * Main entry point for the BOQA (Bayesian Ontology Query Analysis) command-line application.
+ * <p>
+ * This class configures and executes the CLI using PicoCLI framework. It sets up the main command
+ * with three subcommands:
+ * <ul>
+ *   <li>{@code download} - Downloads disease and phenotype data</li>
+ *   <li>{@code plain} - Runs BOQA benchmark analysis using plain scoring</li>
+ *   <li>{@code blended} - Runs BOQA benchmark analysis using blended scoring (work in progress)</li>
+ * </ul>
+ * The application matches phenotypic features observed in patients with annotated 
+ * disease-phenotype associations.
+ * </p>
+ *
+ * @version v0.1.0
+ */
 @CommandLine.Command(name = "boqa",
         header = "Bayesian Ontology Query Analysis (BOQA)\n",
         mixinStandardHelpOptions = true,
@@ -14,7 +31,7 @@
         footer = Main.FOOTER)
 public class Main implements Callable<Integer> {
 
-    public static final String VERSION = "v0.1.0-SNAPSHOT";
+    public static final String VERSION = "v0.1.0";
     public static final int WIDTH = 120;
     public static final String FOOTER = "The BOQA algorithm matches phenotypic features observed in patients " +
             "with annotated disease-phenotype associations.";
@@ -34,8 +51,9 @@ public static void main(String[] args) {
 
         CommandLine cline = new CommandLine(new Main())
                 .setColorScheme(COLOR_SCHEME)
-                .addSubcommand("plain", new BoqaCommand())
-                .addSubcommand("blended", new BlendedCommand());
+                .addSubcommand("download", new DownloadCommand())
+                .addSubcommand("plain", new BoqaBenchmarkCommand())
+                .addSubcommand("blended", new BlendedBenchmarkCommand());
         cline.setToggleBooleanFlags(false);
         System.exit(cline.execute(args));
     }