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SolomonShorser-OICRSolomonShorser-OICR
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Merge pull request #148 from reactome/feature/post-step-tests-stid-history
Feature/post step tests stid history
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Diff for: ‎ortho-stable-id-history/Jenkinsfile

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// This Jenkinsfile is used by Jenkins to run the OrthoinferenceStableIdentifierHistory step of Reactome's release.
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// It requires that the Orthoinference step has been run successfully before it can be run.
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import org.reactome.release.jenkins.utilities.Utilities
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// Shared library maintained at 'release-jenkins-utils' repository.
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def utils = new Utilities()
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pipeline {
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agent any
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stages {
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// This stage checks that an upstream project, Orthoinference, was run successfully for its last build.
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stage('Check if Orthoinference build succeeded'){
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steps{
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script{
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utils.checkUpstreamBuildsSucceeded("Relational-Database-Updates/job/Orthoinference")
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}
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}
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}
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// Backs up the release_current and stable_identifiers databases.
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stage('Setup: Back up DBs'){
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steps{
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script{
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dir('ortho-stable-id-history'){
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withCredentials([usernamePassword(credentialsId: 'mySQLUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
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utils.takeDatabaseDumpAndGzip("${env.RELEASE_CURRENT_DB}", "ortho_stable_id_history", "before", "${env.RELEASE_SERVER}")
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utils.takeDatabaseDumpAndGzip("${env.STABLE_IDENTIFIERS_DB}", "ortho_stable_id_history", "before", "${env.RELEASE_SERVER}")
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}
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}
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}
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}
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}
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// Builds the jar file that will be used.
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stage('Setup: Build jar file'){
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steps{
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script{
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dir('ortho-stable-id-history'){
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utils.buildJarFile()
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}
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}
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}
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}
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// Runs the perl 'save_stable_id_history.pl' script.
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stage('Main: Save StableIdentifier History'){
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steps{
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script{
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dir('ortho-stable-id-history'){
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withCredentials([usernamePassword(credentialsId: 'mySQLUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
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def releaseVersion = utils.getReleaseVersion()
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sh "perl ${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/save_stable_id_history.pl -db ${env.RELEASE_CURRENT_DB} -sdb ${env.STABLE_IDENTIFIERS_DB} -host localhost -user $user -pass $pass -release ${releaseVersion}"
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}
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}
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}
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}
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}
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// Runs the perl 'old_stable_id_mapping.pl' script.
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stage('Main: Old StableIdentifier Mapping'){
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steps{
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script{
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dir('ortho-stable-id-history'){
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// Download 'stable_id_mapping.stored_data' from S3
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sh "aws s3 cp ${env.S3_RELEASE_DIRECTORY_URL}/supplementary_files/stable_id_mapping.stored_data.zip ."
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sh "unzip stable_id_mapping.stored_data.zip"
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// Ensure that the file is in the same location as the Perl script
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sh "cp ./stable_id_mapping.stored_data ${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/stable_id_mapping.stored_data"
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withCredentials([usernamePassword(credentialsId: 'mySQLUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
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sh "perl ${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/old_stable_id_mapping.pl -db ${env.RELEASE_CURRENT_DB} -host localhost"
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}
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sh "rm stable_id_mapping.stored_data*"
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}
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}
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}
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}
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// Runs the StableIdentifier QA.
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stage('Post: Run StableIdentifier QA'){
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steps{
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script{
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dir('ortho-stable-id-history') {
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withCredentials([file(credentialsId: 'Config', variable: 'ConfigFile')]) {
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sh "java -jar target/OrthoStableIdHistory-*-jar-with-dependencies.jar $ConfigFile"
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}
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}
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}
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}
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}
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// Backs up the 'release_current' and 'stable_identifier' databases after the step has run.
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stage('Post: Backup DBs'){
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steps{
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script{
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dir('ortho-stable-id-history'){
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// Download 'stable_id_mapping.stored_data' from S3
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def stableIdMappingStorFile = "stable_id_mapping.stored_data"
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sh "aws s3 --no-progress cp ${env.S3_RELEASE_DIRECTORY_URL}/supplementary_files/${stableIdMappingStorFile}.zip ."
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sh "unzip ${stableIdMappingStorFile}.zip"
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sh "mv ${stableIdMappingStorFile} ${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/"
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withCredentials([usernamePassword(credentialsId: 'mySQLUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
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sh "perl ${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/old_stable_id_mapping.pl -db ${env.RELEASE_CURRENT_DB} -host localhost"
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}
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sh "rm ${stableIdMappingStorFile}.zip"
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sh "rm ${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/${stableIdMappingStorFile}"
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}
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}
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}
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}
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// This stage archives all logs and database backups produced by OrthoinferenceStableIdentifierHistory.
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stage('Post: Archive Outputs'){
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steps{
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script{
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dir('ortho-stable-id-history'){
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def dataFiles = []
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def logFiles = ["${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/*log", "${env.ABS_RELEASE_PATH}/generate_stable_ids_orthoinference/*err"]
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def foldersToDelete = []
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utils.cleanUpAndArchiveBuildFiles("ortho_stable_id_history", dataFiles, logFiles, foldersToDelete)
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}
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}
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}
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}
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}
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}

Diff for: ‎ortho-stable-id-history/pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.reactome.release</groupId>
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<artifactId>OrthoStableIdHistory</artifactId>
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<version>1.0-SNAPSHOT</version>
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<dependencies>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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<version>2.11.0</version>
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</dependency>
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<dependency>
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<groupId>org.reactome.release</groupId>
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<artifactId>release-common-lib</artifactId>
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<version>1.1.1-SNAPSHOT</version>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<source>8</source>
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<target>8</target>
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</configuration>
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</plugin>
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<plugin>
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<artifactId>maven-assembly-plugin</artifactId>
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<configuration>
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<archive>
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<manifest>
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<mainClass>org.reactome.release.orthoStableIdentifierHistory.Main</mainClass>
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</manifest>
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</archive>
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<descriptorRefs>
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<descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>

Diff for: ‎ortho-stable-id-history/src/main/java/org/reactome/release/orthoStableIdentifierHistory/Main.java

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package org.reactome.release.orthoStableIdentifierHistory;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.gk.persistence.MySQLAdaptor;
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import java.io.FileInputStream;
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import java.nio.file.Paths;
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import java.util.Properties;
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public class Main {
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private static final Logger logger = LogManager.getLogger();
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private static final String RESOURCES_DIR = Paths.get("src", "main", "resources").toString();
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public static void main(String[] args) throws Exception {
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String pathToConfig = args.length > 0 ? args[0] : Paths.get(RESOURCES_DIR ,"config.properties").toString();
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Properties props = new Properties();
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props.load(new FileInputStream(pathToConfig));
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//Set up DB adaptors
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String releaseUsername = props.getProperty("release.database.user");
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String releasePassword = props.getProperty("release.database.password");
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String releaseHost = props.getProperty("release.database.host");
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int releasePort = Integer.valueOf(props.getProperty("release.database.port"));
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String releaseCurrent = props.getProperty("release_current.name");
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String curatorUsername = props.getProperty("curator.database.user");
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String curatorPassword = props.getProperty("curator.database.password");
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String curatorHost = props.getProperty("curator.database.host");
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int curatorPort = Integer.valueOf(props.getProperty("curator.database.port"));
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String curatorDatabase = props.getProperty("curator.database.name");
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MySQLAdaptor dbAdaptor = new MySQLAdaptor(releaseHost, releaseCurrent, releaseUsername, releasePassword, releasePort);
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MySQLAdaptor dbAdaptorCurator = new MySQLAdaptor(curatorHost, curatorDatabase, curatorUsername, curatorPassword, curatorPort);
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logger.info("Executing post-step checks");
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PostStepChecks.performStableIdentifierHistoryQA(dbAdaptor, dbAdaptorCurator);
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logger.info("Finished post-step checks");
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}
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}

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