Adding jenkinsfile

Jenkinsfile

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+// This Jenkinsfile is used by Jenkins to run the 'SearchIndexer' step of Reactome's release.
+// It requires that the 'DiagramConverter' step has been run successfully before it can be run.
+
+import org.reactome.release.jenkins.utilities.Utilities
+
+// Shared library maintained at 'release-jenkins-utils' repository.
+def utils = new Utilities()
+
+pipeline{
+	agent any
+
+        environment {
+		ECR_URL = 'public.ecr.aws/reactome/search-indexer'
+	        CONT_NAME = 'search_indexer_container'
+        }
+
+	stages{
+		// This stage checks that the upstream project 'DiagramConverter' was run successfully.
+		stage('Check DiagramConverter build succeeded'){
+			steps{
+				script{
+                			utils.checkUpstreamBuildsSucceeded("File-Generation/job/DiagramConverter/")
+				}
+			}
+		}
+
+		stage('Pull diagram exporter Docker image') {
+			steps{
+				script {
+                			sh "docker pull ${ECR_URL}:latest"
+					sh """
+						if docker ps -a --format '{{.Names}}' | grep -Eq '${CONT_NAME}'; then
+							docker rm -f ${CONT_NAME}
+						fi
+					"""
+				}
+			}
+		}
+
+		// Execute the jar file, producing data-export files. This step uses a bash script, 'run-indexer.sh' that is found in the 'scripts' folder.
+		// This step requires both the neo4j and solr credentials.
+		stage('Main: Run Search-Indexer'){
+			steps{
+				script{
+					def releaseVersion = utils.getReleaseVersion()
+					withCredentials([usernamePassword(credentialsId: 'neo4jUsernamePassword', passwordVariable: 'neo4jPass', usernameVariable: 'neo4jUser')]){
+						withCredentials([usernamePassword(credentialsId: 'solrUsernamePassword', passwordVariable: 'solrPass', usernameVariable: 'solrUser')]){
+						sh "mkdir -p output && rm -rf output/*"
+						sh "mkdir -p output/icons"
+						sh """
+                                                      docker run \\
+						         -v scripts:/opt/search-indexer/scripts \\
+						         -v ${env.ICONS_ABS_PATH}:/data/icons:ro \\
+                                                         -v ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/ehld/:/data/ehld:ro \\
+							 -v output:/opt/search-indexer/output \\
+						         --net=host \\
+						         --name ${CONT_NAME} \\
+						         ${ECR_URL}:latest \\
+	                                                 /bin/bash -c \"
+                                                             ./scripts/run-indexer.sh solrpass=${solrPass} neo4jpass=${neo4jPass} iconsdir=/data/icons ehlddir=/data/ehld/ maildest=${env.RELEASE_DEVELOPER_EMAIL}
+                                                             if [ \\$? -ne 0 ]; then echo '❌ run-indexer.sh failed'; exit 1; fi
+
+                                                                  mv ebeye*gz ./output/
+                                                             if [ \\$? -ne 0 ]; then echo '❌ Moving .gz failed'; exit 2; fi
+
+                                                                  mv *txt output/icons/
+                                                             if [ \\$? -ne 0 ]; then echo '❌ Moving .txt failed'; exit 3; fi
+
+                                                                 mv sitemap* output/
+                                                             if [ \\$? -ne 0 ]; then echo '❌ Moving sitemap failed'; exit 4; fi
+                                                         \"
+						   """
+						}
+					}
+				}
+			}
+		}
+
+		// Optimise indexes to reduce memory usage and boost performance
+        stage('Main: Optimize SOLR cores'){
+            steps{
+                script{
+                    withCredentials([usernamePassword(credentialsId: 'solrUsernamePassword', passwordVariable: 'solrPass', usernameVariable: 'solrUser')]){
+                        sh "curl --user ${solrUser}:${solrPass} 'http://localhost:8983/solr/reactome/update?optimize=true&maxSegments=1'"
+                        sh "curl --user ${solrUser}:${solrPass} 'http://localhost:8983/solr/target/update?optimize=true&maxSegments=1'"
+                    }
+                }
+            }
+        }
+
+		// Gzips both ebeye.xml and ebeye-covid.xml files, and then moves them, along with Icons folder, to the downloads folder.
+		stage('Post: Move ebeye and Icons txt files to download'){
+		    steps{
+		        script{
+				def releaseVersion = utils.getReleaseVersion()
+				def iconsFolder = "icons/"
+				// Gzip ebeye.xml and ebeye-covid.xml files before moving them to download/XX.
+				dir("output") {
+				    sh "gzip ebeye*"
+				    sh "cp ebeye*gz ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/"
+				    sh "gunzip ebeye*gz"
+				}
+				// Archives Icons folder before moving to download/XX folder.
+				dir("output"){
+				    sh "tar -zcvf icons-v${releaseVersion}.tar ${iconsFolder}"
+				    sh "mv ${iconsFolder} ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/"
+				}
+		        }
+		    }
+		}
+		// Uses 'changeSiteMapFiles.sh' script to move site_map files to the proper location and set appropriate permissions.
+		stage('Post: Update sitemap files and restart Solr') {
+		    steps{
+		        script{
+			    dir("output") {
+				   try {
+                                       sh "sudo bash ../scripts/changeSiteMapFiles.sh"
+                                   } finally {
+                                       sh "sudo service solr restart"
+                                   }
+			    }
+		        }
+		    }
+		}
+		// Archive everything on S3.
+		stage('Post: Archive Outputs'){
+			steps{
+				script{
+					def releaseVersion = utils.getReleaseVersion()
+					def dataFiles = ["output/ebeye.xml", "output/ebeyecovid.xml", "output/icons-v${releaseVersion}.tar"]
+					def logFiles = []
+					def foldersToDelete = []
+					utils.cleanUpAndArchiveBuildFiles("search_indexer", dataFiles, logFiles, foldersToDelete)
+				}
+			}
+		}
+	}
+}