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Initial commit of service
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@matthewhorridge
matthewhorridge committed May 10, 2024
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17 changes: 17 additions & 0 deletions .github/workflows/ci.yaml
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name: Java CI

on: [push]

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- name: Set up JDK 17
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'temurin'
- name: Build with Maven
run: mvn --batch-mode --update-snapshots package
29 changes: 29 additions & 0 deletions .github/workflows/pub-docker-hub.yaml
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name: Publish Docker image to Docker Hub
on:
release:
types:
- published

jobs:
publish:
runs-on: ubuntu-latest
steps:
- name: Login to Docker Hub
uses: docker/login-action@v2
with:
username: ${{secrets.DOCKER_USERNAME}}
password: ${{secrets.DOCKER_PASSWORD}}
- uses: actions/checkout@v3
- name: Set up Maven Central Repository
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'adopt'
server-id: docker.io
server-username: DOCKER_USERNAME
server-password: DOCKER_PASSWORD
- name: Publish package
run: mvn --batch-mode -Prelease package dockerfile:push
env:
DOCKER_USERNAME: ${{secrets.DOCKER_USERNAME}}
DOCKER_TOKEN: ${{secrets.DOCKER_PASSWORD}}
26 changes: 26 additions & 0 deletions .github/workflows/pub.yaml
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name: Publish package to the Maven Central Repository
on:
release:
types: [released]

jobs:
publish:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Maven Central Repository
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'adopt'
server-id: ossrh
server-username: OSSRH_USERNAME
server-password: OSSRH_TOKEN
gpg-private-key: ${{secrets.GPG_PRIVATE_KEY}}
gpg-passphrase: GPG_PASSPHRASE
- name: Publish package
run: mvn --batch-mode -Prelease deploy
env:
GPG_PASSPHRASE: ${{secrets.GPG_PASSPHRASE}}
OSSRH_USERNAME: ${{secrets.OSSRH_USERNAME}}
OSSRH_TOKEN: ${{secrets.OSSRH_TOKEN}}
33 changes: 33 additions & 0 deletions .gitignore
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HELP.md
target/
!.mvn/wrapper/maven-wrapper.jar
!**/src/main/**/target/
!**/src/test/**/target/

### STS ###
.apt_generated
.classpath
.factorypath
.project
.settings
.springBeans
.sts4-cache

### IntelliJ IDEA ###
.idea
*.iws
*.iml
*.ipr

### NetBeans ###
/nbproject/private/
/nbbuild/
/dist/
/nbdist/
/.nb-gradle/
build/
!**/src/main/**/build/
!**/src/test/**/build/

### VS Code ###
.vscode/
6 changes: 6 additions & 0 deletions Dockerfile
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FROM openjdk:17
MAINTAINER protege.stanford.edu

ARG JAR_FILE
COPY target/${JAR_FILE} webprotege-initial-revision-history-service.jar
ENTRYPOINT ["java","-jar","/webprotege-initial-revision-history-service.jar"]
214 changes: 214 additions & 0 deletions pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.2.5</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<groupId>edu.stanford.protege</groupId>
<artifactId>webprotege-initial-revision-history-service</artifactId>
<version>0.0.1</version>
<name>webprotege-initial-revision-history-service</name>
<description>This service reads Binary OWL ontology documents from cloud storage (using MinIO) and, from these, generates WebProtégé
revision history document that contains a single revision to create these ontologies.</description>
<properties>
<java.version>17</java.version>
</properties>


<distributionManagement>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
<snapshotRepository>
<id>nexus-snapshots</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
</distributionManagement>

<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>

<dependency>
<groupId>edu.stanford.protege</groupId>
<artifactId>webprotege-ipc</artifactId>
<version>1.0.1</version>
</dependency>

<dependency>
<groupId>edu.stanford.protege</groupId>
<artifactId>webprotege-jackson</artifactId>
<version>0.9.2</version>
</dependency>

<dependency>
<groupId>io.minio</groupId>
<artifactId>minio</artifactId>
<version>8.5.10</version>
</dependency>

<dependency>
<groupId>edu.stanford.protege</groupId>
<artifactId>webprotege-revision-manager</artifactId>
<version>0.9.2</version>
</dependency>

<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>minio</artifactId>
<version>1.19.7</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>com.github.dasniko</groupId>
<artifactId>testcontainers-keycloak</artifactId>
<version>3.3.0</version>
<scope>test</scope>
</dependency>


<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>binaryowl</artifactId>
<version>2.0.1</version>
</dependency>

<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>rabbitmq</artifactId>
<version>1.19.7</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>com.spotify</groupId>
<artifactId>dockerfile-maven-plugin</artifactId>
<version>1.4.13</version>
<executions>
<execution>
<id>default</id>
<goals>
<goal>build</goal>
</goals>
</execution>
</executions>
<configuration>
<repository>protegeproject/${project.artifactId}</repository>
<tag>${project.version}</tag>
<buildArgs>
<JAR_FILE>${project.build.finalName}.jar</JAR_FILE>
</buildArgs>
</configuration>
</plugin>
</plugins>
</build>

<profiles>
<profile>
<id>release</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<doclint>none</doclint>
<release>16</release>
</configuration>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<gpgArguments>
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
</configuration>
</execution>
</executions>
</plugin>

<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.7</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
<dependencies>
<!--
TODO:
Remove after OSSRH-66257, NEXUS-26993 are fixed,
possibly via https://github.com/sonatype/nexus-maven-plugins/pull/91
-->
<dependency>
<groupId>com.thoughtworks.xstream</groupId>
<artifactId>xstream</artifactId>
<version>1.4.15</version>
</dependency>
</dependencies>
</plugin>

</plugins>
</build>
</profile>
</profiles>

</project>
42 changes: 42 additions & 0 deletions .../webprotege/initialrevisionhistoryservice/CreateInitialRevisionHistoryCommandHandler.java
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package edu.stanford.protege.webprotege.initialrevisionhistoryservice;

import edu.stanford.protege.webprotege.ipc.CommandHandler;
import edu.stanford.protege.webprotege.ipc.ExecutionContext;
import edu.stanford.protege.webprotege.ipc.WebProtegeHandler;
import org.jetbrains.annotations.NotNull;
import reactor.core.publisher.Mono;

/**
* Matthew Horridge
* Stanford Center for Biomedical Informatics Research
* 2024-05-03
*/
@WebProtegeHandler
public class CreateInitialRevisionHistoryCommandHandler implements CommandHandler<CreateInitialRevisionHistoryRequest, CreateInitialRevisionHistoryResponse> {

private final InitialRevisionGenerator initialRevisionGenerator;

public CreateInitialRevisionHistoryCommandHandler(InitialRevisionGenerator initialRevisionGenerator) {
this.initialRevisionGenerator = initialRevisionGenerator;
}

@NotNull
@Override
public String getChannelName() {
return CreateInitialRevisionHistoryRequest.CHANNEL;
}

@Override
public Class<CreateInitialRevisionHistoryRequest> getRequestClass() {
return CreateInitialRevisionHistoryRequest.class;
}

@Override
public Mono<CreateInitialRevisionHistoryResponse> handleRequest(CreateInitialRevisionHistoryRequest request,
ExecutionContext executionContext) {
var changeDocumentLocation = initialRevisionGenerator.writeRevisionHistoryFromOntologies(executionContext.userId(),
request.documentLocations(),
"Initial import");
return Mono.just(new CreateInitialRevisionHistoryResponse(changeDocumentLocation));
}
}
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