Feature/verifier

Dockerfile

@@ -63,6 +63,7 @@ FROM eclipse-temurin:11-jre-focal
 WORKDIR /opt/release-download-directory
 
 COPY --from=build-download-directory /gitroot/reactome-release-directory/target/download-directory.jar target/
+COPY --from=build-download-directory /gitroot/reactome-release-directory/target/download-directory-verifier.jar target/
 
 COPY --from=build-download-directory /gitroot/reactome-release-directory/src/main/resources/ src/main/resources/
 

Jenkinsfile

@@ -7,13 +7,13 @@ import org.reactome.release.jenkins.utilities.Utilities
 def utils = new Utilities()
 
 pipeline {
-    agent any
+	agent any
 
-    environment {
-        ECR_URL = 'public.ecr.aws/reactome/release-download-directory'
-        CONT_NAME = 'release_download_directory_container'
-        CONT_ROOT = '/opt/release-download-directory'
-    }
+	environment {
+		ECR_URL = 'public.ecr.aws/reactome/release-download-directory'
+		CONT_NAME = 'release_download_directory_container'
+		CONT_ROOT = '/opt/release-download-directory'
+	}
 
 	stages {
 		// This stage checks that an upstream project 'BioModels' was run successfully for its last build.
@@ -47,7 +47,17 @@ pipeline {
 						sh "sudo service neo4j stop"
 						sh "mkdir -p config"
 						sh "sudo cp $ConfigFile config/auth.properties"
-						sh "docker run -v /var/run/mysqld/mysqld.sock:/var/run/mysqld/mysqld.sock  -v \$(pwd)/config:/config -v \$(pwd)/${releaseVersion}:/opt/release-download-directory/${releaseVersion} --net=host  ${ECR_URL}:latest /bin/bash -c \'java -Xmx${env.JAVA_MEM_MAX}m -javaagent:src/main/resources/spring-instrument-4.2.4.RELEASE.jar -jar target/download-directory.jar -g /config/auth.properties\'"
+						sh """
+							docker run \\
+							--rm \\
+							-v /var/run/mysqld/mysqld.sock:/var/run/mysqld/mysqld.sock \\
+							-v ${pwd()}/config:/config \\
+							-v ${pwd()}/${releaseVersion}:${CONT_ROOT}/${releaseVersion} \\
+							--net=host \\
+							--name ${CONT_NAME} \\
+							 ${ECR_URL}:latest \\
+							 /bin/bash -c "java -Xmx${env.JAVA_MEM_MAX}m -javaagent:src/main/resources/spring-instrument-4.2.4.RELEASE.jar -jar target/download-directory.jar -g /config/auth.properties"
+						"""
 						sh "sudo service neo4j start"
 						sh "sudo service tomcat9 start"
 						sh "sudo mv ${releaseVersion}/* ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/"
@@ -56,45 +66,80 @@ pipeline {
 				}
 			}
 		}
-
+
+		// Execute the verifier jar file checking for the existence and proper file sizes of the download_directory output
+		stage('Post: Verify DownloadDirectory ran correctly') {
+			steps {
+				script {
+					def releaseVersion = utils.getReleaseVersion()
+
+					sh """
+						docker run \\
+						--rm \\
+						-v ${pwd()}/${releaseVersion}:${CONT_ROOT}/${releaseVersion}/ \\
+						-v \$HOME/.aws:/root/.aws:ro \\
+						-e AWS_REGION=us-east-1 \\
+						--net=host \\
+						--name ${CONT_NAME}_verifier \\
+						${ECR_URL}:latest \\
+						/bin/bash -c "java -jar target/data-export-verifier.jar --releaseNumber ${releaseVersion} --output ${CONT_ROOT}/${releaseVersion}"
+					"""
+				}
+			}
+		}
+
+		// Creates a list of files and their sizes to use for comparison baseline during next release
+		stage('Post: Create files and sizes list to upload for next release\'s verifier') {
+			steps {
+				script {
+					def fileSizeList = "files_and_sizes.txt"
+					def releaseVersion = utils.getReleaseVersion()
+
+					sh "find ${releaseNumber} -type f -printf \"%s\t%P\n\" > ${fileSizeList}"
+					sh "aws s3 --no-progress cp ${fileSizeList} s3://reactome/private/releases/${releaseVersion}/download_directory/data/"
+					sh "rm ${fileSizeList}"
+				}
+			}
+		}
+
 		stage('Post: Validate Release Number in BioPax Files') {
-		    steps {
-		        script {
-		            def biopaxSandboxDir = 'biopax/'
-		            def releaseVersion = utils.getReleaseVersion()
+			steps {
+				script {
+					def biopaxSandboxDir = 'biopax/'
+					def releaseVersion = utils.getReleaseVersion()
 
-		            sh """
-		                set -e
+					sh """
+						set -e
 
-		                mkdir -p ${biopaxSandboxDir}
-		                cp ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/biopax* ${biopaxSandboxDir}
+						mkdir -p ${biopaxSandboxDir}
+						cp ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/biopax* ${biopaxSandboxDir}
 
-		                cd ${biopaxSandboxDir}
+						cd ${biopaxSandboxDir}
 
-		                unzip -o biopax.zip
+						unzip -o biopax.zip
 
-		                numOfOwlFiles=\$(ls -1 *.owl | wc -l)
-		                numOfCorrectOwlFiles=\$(grep -l "xml:base=\\"http://www.reactome.org/biopax/${releaseVersion}" *.owl | wc -l)
+						numOfOwlFiles=\$(ls -1 *.owl | wc -l)
+						numOfCorrectOwlFiles=\$(grep -l "xml:base=\\"http://www.reactome.org/biopax/${releaseVersion}" *.owl | wc -l)
 
-		                echo "Found \$numOfOwlFiles OWL files, \$numOfCorrectOwlFiles have correct version"
+						echo "Found \$numOfOwlFiles OWL files, \$numOfCorrectOwlFiles have correct version"
 
-		                if [ "\$numOfOwlFiles" -eq "\$numOfCorrectOwlFiles" ]; then
-		                    echo "BioPax 3 files have correct Reactome version"
-		                else
-		                    echo "Not all BioPax 3 files have correct Reactome version."
-		                    exit 1
-		                fi
-		            """
-		        }
-		    }
+						if [ "\$numOfOwlFiles" -eq "\$numOfCorrectOwlFiles" ]; then
+							echo "BioPax 3 files have correct Reactome version"
+						else
+							echo "Not all BioPax 3 files have correct Reactome version."
+							exit 1
+						fi
+					"""
+				}
+			}
 
-		    post {
-		        always {
-		            sh "rm -rf biopax/"
-		        }
-		    }
+			post {
+				always {
+					sh "rm -rf biopax/"
+				}
+			}
 		}
-		
+
 		// This stage archives all logs and other outputs produced by DownloadDirectory on S3.
 		stage('Post: Archive logs and validation files'){
 			steps{

pom.xml

@@ -182,6 +182,11 @@
 			<version>${spring.version}</version>
 		</dependency>
 		-->
+		<dependency>
+			<groupId>org.reactome.release.verifier</groupId>
+			<artifactId>verifier-lib</artifactId>
+			<version>1.0-SNAPSHOT</version>
+		</dependency>
 
 		<!-- Test dependencies -->
 		<dependency>
@@ -260,39 +265,65 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-shade-plugin</artifactId>
 				<version>3.1.0</version>
+				<!-- Shared configuration -->
+				<configuration>
+					<filters>
+						<filter>
+							<artifact>*:*</artifact>
+							<excludes>
+								<exclude>META-INF/*.SF</exclude>
+								<exclude>META-INF/*.DSA</exclude>
+								<exclude>META-INF/*.RSA</exclude>
+							</excludes>
+						</filter>
+					</filters>
+
+					<transformers>
+						<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+							<resource>META-INF/spring.handlers</resource>
+						</transformer>
+						<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+							<resource>META-INF/spring.schemas</resource>
+						</transformer>
+					</transformers>
+				</configuration>
+
 				<executions>
 					<execution>
+						<id>download-directory</id>
 						<phase>package</phase>
 						<goals>
 							<goal>shade</goal>
 						</goals>
 						<configuration>
-							<filters>
-								<filter>
-									<artifact>*:*</artifact>
-									<excludes>
-										<exclude>META-INF/*.SF</exclude>
-										<exclude>META-INF/*.DSA</exclude>
-										<exclude>META-INF/*.RSA</exclude>
-									</excludes>
-								</filter>
-							</filters>
-							<transformers>
-								<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
-									<resource>META-INF/spring.handlers</resource>
-								</transformer>
-								<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
-									<resource>META-INF/spring.schemas</resource>
-								</transformer>
+							<finalName>download-directory</finalName>
+							<transformers combine.children="append">
 								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
 									<manifestEntries>
 										<Main-Class>org.reactome.release.downloaddirectory.Main</Main-Class>
 										<Multi-Release>true</Multi-Release>
 									</manifestEntries>
 								</transformer>
 							</transformers>
-							<finalName>download-directory</finalName>
+						</configuration>
+					</execution>
 
+					<!-- Verifier executable jar -->
+					<execution>
+						<id>download-directory-verifier</id>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+						<configuration>
+							<finalName>download-directory-verifier</finalName>
+							<transformers combine.children="append">
+								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+									<manifestEntries>
+										<Main-Class>org.reactome.release.downloaddirectory.verifier.DownloadDirectoryVerifier</Main-Class>
+									</manifestEntries>
+								</transformer>
+							</transformers>
 						</configuration>
 					</execution>
 				</executions>

src/main/java/org/reactome/release/downloaddirectory/verifier/DownloadDirectoryVerifier.java

@@ -0,0 +1,19 @@
+package org.reactome.release.downloaddirectory.verifier;
+
+import org.reactome.release.verifier.DefaultVerifier;
+import org.reactome.release.verifier.Verifier;
+
+import java.io.IOException;
+
+/**
+ * @author Joel Weiser (joel.weiser@oicr.on.ca)
+ * Created 12/20/2025
+ */
+public class DownloadDirectoryVerifier {
+
+	public static void main(String[] args) throws IOException {
+		Verifier verifier = new DefaultVerifier("download_directory");
+		verifier.parseCommandLineArgs(args);
+		verifier.run();
+	}
+}