Jenkinsfile

pipeline {
    agent any
    // In additional to manual runs, trigger somewhere at midnight to
    // give us the max time in a day to get things right.
    triggers {
	// Master never runs--Feb 31st.
	cron('0 0 31 2 *')
	// Nightly @12am, for "snapshot", skip "release" night.
	//cron('0 0 2-31/2 * *')
	// First of the month @12am, for "release" (also "current").
	//cron('0 0 1 * *')
    }
    environment {
	///
	/// Automatic run variables.
	///

	// Pin dates and day to beginning of run.
	START_DATE = sh (
	    script: 'date +%Y-%m-%d',
	    returnStdout: true
	).trim()

	START_DAY = sh (
	    script: 'date +%A',
	    returnStdout: true
	).trim()

	///
	/// Internal run variables.
	///

	// The branch of geneontology/go-site to use.
	TARGET_GO_SITE_BRANCH = 'master'
	// The branch of geneontology/go-stats to use.
	TARGET_GO_STATS_BRANCH = 'master'
	// The branch of go-ontology to use.
	TARGET_GO_ONTOLOGY_BRANCH = 'master'
	// The branch of minerva to use.
	TARGET_MINERVA_BRANCH = 'master'
	// The branch of ROBOT to use in one silly section.
	// Necessary due to java version jump.
	// https://github.com/ontodev/robot/issues/997
	TARGET_ROBOT_BRANCH = 'master'
	// The branch of noctua-models to use.
	TARGET_NOCTUA_MODELS_BRANCH = 'master'
	// The people to call when things go bad. It is a comma-space
	// "separated" string.
	TARGET_ADMIN_EMAILS = 'sjcarbon@lbl.gov'
	TARGET_SUCCESS_EMAILS = 'sjcarbon@lbl.gov'
	TARGET_RELEASE_HOLD_EMAILS = 'sjcarbon@lbl.gov'
	// The file bucket(/folder) combination to use.
	TARGET_BUCKET = 'nope'
	// The URL prefix to use when creating site indices.
	TARGET_INDEXER_PREFIX = 'http://experimental.geneontology.io'
	// This variable should typically be 'TRUE', which will cause
	// some additional basic checks to be made. There are some
	// very exotic cases where these check may need to be skipped
	// for a run, in that case this variable is set to 'FALSE'.
	WE_ARE_BEING_SAFE_P = 'TRUE'
	// Variable to check if the "hard" ZENODO archive stage was passed.
	ZENODO_ARCHIVING_SUCCESSFUL = 'FALSE'
	// Control make to get through our loads faster if
	// possible. Assuming we're cpu bound for some of these...
	// wok has 48 "processors" over 12 "cores", so I have no idea;
	// let's go with conservative and see if we get an
	// improvement.
	MAKECMD = 'make --jobs 3 --max-load 10.0'
	//MAKECMD = 'make'

	///
	/// PANTHER/PAINT metadata.
	///

	PANTHER_VERSION = '15.0'
	// Currently unused, but see:
	// https://github.com/geneontology/pipeline/issues/86
	PAINT_RELEASE = 'XXXX-YY-ZZ'

	///
	/// Application tokens.
	///

	// The Zenodo concept ID to use for releases (and occasionally
	// master testing).
	ZENODO_REFERENCE_CONCEPT = 'null'
	ZENODO_ARCHIVE_CONCEPT = 'null'
	// Distribution ID for the AWS CloudFront for this branch,
	// used soley for invalidations. Versioned release does not
	// need this as it is always a new location and the index
	// upload already has an invalidation on it. For current,
	// snapshot, and experimental.
	AWS_CLOUDFRONT_DISTRIBUTION_ID = 'null'
	AWS_CLOUDFRONT_RELEASE_DISTRIBUTION_ID = 'null'

	///
	/// Ontobio Validation
	///
	VALIDATION_ONTOLOGY_URL="http://skyhook.berkeleybop.org/issue-265-go-cam-products/ontology/go.json"

	///
	/// Minerva input.
	///

	// Minerva operating profile.
	MINERVA_INPUT_ONTOLOGIES = [
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/ontology/extensions/go-lego.owl"
	].join(" ")

	///
	/// GOlr/AmiGO input.
	///

	// GOlr load profile.
	GOLR_SOLR_MEMORY = "128G"
	GOLR_LOADER_MEMORY = "192G"
	GOLR_INPUT_ONTOLOGIES = [
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/ontology/extensions/go-gaf.owl",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/ontology/extensions/gorel.owl",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/ontology/extensions/go-modules-annotations.owl",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/ontology/extensions/go-taxon-subsets.owl",
	    "http://purl.obolibrary.org/obo/eco/eco-basic.owl",
	    "http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl",
	    "http://purl.obolibrary.org/obo/cl/cl-basic.owl",
	    "http://purl.obolibrary.org/obo/pato.owl",
	    "http://purl.obolibrary.org/obo/po.owl",
	    "http://purl.obolibrary.org/obo/chebi.owl",
	    "http://purl.obolibrary.org/obo/uberon/basic.owl",
	    "http://purl.obolibrary.org/obo/wbbt.owl"
	].join(" ")
	GOLR_INPUT_GAFS = [
	    //"http://skyhook.berkeleybop.org/issue-265-go-cam-products/products/annotations/paint_other.gaf.gz",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/annotations/goa_chicken.gaf.gz",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/annotations/goa_chicken_complex.gaf.gz",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/annotations/goa_uniprot_all_noiea.gaf.gz",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/annotations/mgi.gaf.gz",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/annotations/pombase.gaf.gz",
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/annotations/wb.gaf.gz"
	].join(" ")
	GOLR_INPUT_PANTHER_TREES = [
	    "http://skyhook.berkeleybop.org/issue-265-go-cam-products/products/panther/arbre.tgz"
	].join(" ")

	///
	/// Groups to run and tests to avoid running during the current
	/// mega-make.
	///

	// The gorule tag is used to identify which rules to suppress
	// reports from during the megastep and during templating the
	// reports after the megastep. The tags are currently
	// respected at two times in the pipeline: the gorules report
	// take the flag as a CLI argument, supressing it; ontobio
	// takes it during the same stage as the JSON
	// generation/parsing step, to supress the .md output. At this
	// time, this variable can be either nothing or empty string
	// for no rule suppression (default behavior everything), or a
	// single value (practically speaking pretty much always
	// "silent")
	//GORULE_TAGS_TO_SUPPRESS="silent"

	// Optional. Groups to run.
	RESOURCE_GROUPS="ecocyc goa mgi paint pseudocap wb"
	// Optional. Datasets to skip within the resources that we
	// will run (defined in the line above).
	DATASET_EXCLUDES="goa_uniprot_gcrp goa_pdb goa_chicken_isoform goa_chicken_rna goa_cow goa_cow_complex goa_cow_isoform goa_cow_rna goa_dog goa_dog_complex goa_dog_isoform goa_dog_rna goa_human goa_human goa_human_complex goa_human_rna paint_cgd paint_dictybase paint_fb paint_goa_chicken paint_goa_human paint_other paint_rgd paint_sgd paint_tair paint_zfin"
	// Optional. This acts as an override, /if/ it's grabbed (as
	// defined above).
	GOA_UNIPROT_ALL_URL="http://skyhook.berkeleybop.org/goa_uniprot_short.gaf.gz"

    }
    options{
	timestamps()
	buildDiscarder(logRotator(numToKeepStr: '14'))
    }
    stages {
	// Very first: pause for a few minutes to give a chance to
	// cancel and clean the workspace before use.
	stage('Ready and clean') {
	    steps {

		// Check that we do not affect public targets on
		// non-mainline runs.
		script {
		    if( BRANCH_NAME != 'master' && TARGET_BUCKET == 'go-data-product-experimental'){
			echo 'Only master can touch that target.'
			sh '`exit -1`'
		    }else if( BRANCH_NAME != 'snapshot' && TARGET_BUCKET == 'go-data-product-snapshot'){
			echo 'Only master can touch that target.'
			sh '`exit -1`'
		    }else if( BRANCH_NAME != 'release' && TARGET_BUCKET == 'go-data-product-release'){
			echo 'Only master can touch that target.'
			sh '`exit -1`'
		    }
		}

		// Give us a minute to cancel if we want.
		//sleep time: 1, unit: 'MINUTES'
		cleanWs deleteDirs: true, disableDeferredWipeout: true
	    }
	}
	stage('Initialize') {
	    steps {
		// Start preparing environment.
		parallel(
		    "Report": {
			sh 'env > env.txt'
			sh 'echo $BRANCH_NAME > branch.txt'
			sh 'echo "$BRANCH_NAME"'
			sh 'cat env.txt'
			sh 'cat branch.txt'
			sh 'echo $START_DAY > dow.txt'
			sh 'echo "$START_DAY"'
		    },
		    "Reset base": {
			// Get a mount point ready
			sh 'mkdir -p $WORKSPACE/mnt || true'
			// Ninja in our file credentials from Jenkins.
			withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
			    // Try and ssh fuse skyhook onto our local system.
			    sh 'sshfs -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -o idmap=user skyhook@skyhook.berkeleybop.org:/home/skyhook $WORKSPACE/mnt/'
			}
			// Remove anything we might have left around from
			// times past.
			sh 'rm -r -f $WORKSPACE/mnt/$BRANCH_NAME || true'
			// Rebuild directory structure.
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/bin || true'
			// WARNING/BUG: needed for arachne to run at
			// this point.
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/lib || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/api-static-files || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/ttl || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/blazegraph || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/annotations || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/pages || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/solr || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/panther || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/gaferencer || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/metadata || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/annotations || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/ontology || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/reports || true'
			sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/release_stats || true'
			// Tag the top to let the world know I was at least
			// here.
			sh 'echo "Runtime summary." > $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'date >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "Release notes: https://github.com/geneontology/go-site/tree/master/releases" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "Branch: $BRANCH_NAME" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "Start day: $START_DAY" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "Start date: $START_DATE" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'

			sh 'echo "Official release date: metadata/release-date.json" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "Official Zenodo archive DOI: metadata/release-archive-doi.json" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "Official Zenodo archive DOI: metadata/release-reference-doi.json" >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			sh 'echo "TODO: Note software versions." >> $WORKSPACE/mnt/$BRANCH_NAME/summary.txt'
			// TODO: This should be wrapped in exception
			// handling. In fact, this whole thing should be.
			sh 'fusermount -u $WORKSPACE/mnt/ || true'
		    }
		)
	    }
	}
	// Build owltools and get it into the shared filesystem.
	stage('Ready production software') {
	    steps {
		parallel(
		    "Ready owltools": {
			// Legacy: build 'owltools-build'
			dir('./owltools') {
			    // Remember that git lays out into CWD.
			    git 'https://github.com/owlcollab/owltools.git'
			    sh 'mvn -f OWLTools-Parent/pom.xml -U clean install -DskipTests -Dmaven.javadoc.skip=true -Dsource.skip=true'
			    // Attempt to rsync produced into bin/.
			    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-Runner/target/owltools skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-Oort/bin/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-NCBI/bin/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
				sh 'rsync -vhac -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" --exclude ".git" OWLTools-Oort/reporting/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
				sh 'rsync -vhac -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" --exclude ".git" OWLTools-Runner/contrib/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
			    }
			}
		    },
		    "Ready minerva": {
			dir('./minerva') {
			    // Remember that git lays out into CWD.
			    git branch: TARGET_MINERVA_BRANCH, url: 'https://github.com/geneontology/minerva.git'
			    sh './build-cli.sh'
			    // Attempt to rsync produced into bin/.
			    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" minerva-cli/bin/minerva-cli.* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
			    }
			}
		    },
		    "Ready robot": {
			// Legacy: build 'robot-build'
			dir('./robot') {
			    // Remember that git lays out into CWD.
			    git branch: TARGET_ROBOT_BRANCH, url:'https://github.com/kltm/robot-old.git'

			    // Update the POMs by replacing "SNAPSHOT"
			    // with the current Git hash. First make
			    // sure maven-help-plugin is installed
			    sh 'mvn org.apache.maven.plugins:maven-help-plugin:2.1.1:evaluate -Dexpression=project.version'
			    // Now get and set the version.
			    // Originally: sh 'VERSION=`mvn org.apache.maven.plugins:maven-help-plugin:2.1.1:evaluate -Dexpression=project.version | grep -v '\[' | sed 's/-SNAPSHOT//'`'
			    sh 'VERSION=`mvn org.apache.maven.plugins:maven-help-plugin:2.1.1:evaluate -Dexpression=project.version | grep -v \'\\[\' | sed \'s/-SNAPSHOT//\'`'
			    sh 'BUILD=`git rev-parse --short HEAD`'
			    sh 'mvn versions:set -DnewVersion=$VERSION+$BUILD'
			    sh 'mvn -U clean install -DskipTests'
			    // Attempt to rsync produced into bin/.
			    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" bin/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
			    }
			}
		    },
		    "Ready arachne": {
			dir('./arachne') {
			    sh 'wget -N https://github.com/balhoff/arachne/releases/download/v1.0.2/arachne-1.0.2.tgz'
			    sh 'tar -xvf arachne-1.0.2.tgz'
			    // Attempt to rsync produced into bin/.
			    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" arachne-1.0.2/bin/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
				// WARNING/BUG: needed for arachne to
				// run at this point.
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" arachne-1.0.2/lib/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/lib/'
			    }
			}
		    },
		    "Ready blazegraph-runner": {
			dir('./blazegraph-runner') {
			    sh 'wget -N https://github.com/balhoff/blazegraph-runner/releases/download/v1.4/blazegraph-runner-1.4.tgz'
			    sh 'tar -xvf blazegraph-runner-1.4.tgz'
			    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
				// Attempt to rsync bin into bin/.
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" blazegraph-runner-1.4/bin/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
				// Attempt to rsync libs into lib/.
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" blazegraph-runner-1.4/lib/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/lib/'
			    }
			}
		    },
		    "Ready Gaferencer": {
			dir('./gaferencer') {
			    sh 'wget -N https://github.com/geneontology/gaferencer/releases/download/v0.5/gaferencer-0.5.tgz'
			    sh 'tar -xvf gaferencer-0.5.tgz'
			    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
				// Attempt to rsync bin into bin/.
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" gaferencer-0.5/bin/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/'
				// Attempt to rsync libs into lib/.
				sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" gaferencer-0.5/lib/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/lib/'
			    }
			}
		    }
		)
	    }
	}
	// Download GAFs from datasets.yaml in go-site and then upload
	// to skyhook in their appropriate locations.
	stage("Create GO-CAM JSON products") {
	    agent {
		docker {
		    image 'maven:3.6.3-openjdk-8'
		    args "-u root:root --tmpfs /opt:exec -w /opt"
		}
	    }

	    steps {
		dir("./go-graphstore") {
		    // Note: I currently cannot imagine a reason not
		    // to have this pinned to master.
		    git branch: 'master', url: 'https://github.com/geneontology/go-graphstore.git'

		    // Build/ready blazegraph (from go-graphstore
		    // pom.xml).
		    sh 'ls -AlF'
		    sh 'mvn package'

		    // Setup for future use as we need tools.
		    sh 'apt-get update'
		    sh 'apt-get -y install pigz'

		    // WARNING/TEMP: Get a blazegraph journal, get it
		    // setup in the right spot.
		    sh 'rm -f blazegraph-production.jnl.gz || true'
		    sh 'rm -f blazegraph-production.jnl || true'
		    sh 'rm -f blazegraph.jnl || true'
		    retry(3) {
		    	sh 'wget -N http://current.geneontology.org/products/blazegraph/blazegraph-production.jnl.gz'
		    	//sh 'wget -N http://skyhook.berkeleybop.org/master/products/blazegraph/blazegraph-production.jnl.gz'
		    }
		    sh 'pigz -d blazegraph-production.jnl.gz'
		    sh 'mv blazegraph-production.jnl blazegraph.jnl'

		    // Setup runtime.
		    sh 'echo \'#!/bin/bash\' > run.sh'
		    sh 'echo \'set -x\' >> run.sh'
		    sh 'echo \'java -server -Djetty.port=9876 -Xmx32G -Djetty.overrideWebXml=./conf/readonly_cors.xml -Dbigdata.propertyFile=./conf/blazegraph.properties -cp jars/blazegraph-jar.jar:jars/jetty-servlets.jar com.bigdata.rdf.sail.webapp.StandaloneNanoSparqlServer &\' >> run.sh'

		    // Check runtime.
		    sh 'ls -AlF ./run.sh'
		    sh 'cat ./run.sh'

		    // Create local config for runtime.
		    sh 'cp -f ./conf/readonly_cors.xml ./conf/readonly_cors.xml.bak'
		    sh 'cat ./conf/readonly_cors.xml.bak | sed \'s:30000:1200000:g\' > ./conf/readonly_cors.xml'
		    sh 'cat ./conf/readonly_cors.xml'

		    // Run runtime, sleep to give it a chance.
		    sh 'bash ./run.sh'
		    sh 'sleep 10'

		    // Check runtime.
		    sh 'curl -I http://localhost:9876/blazegraph/'

		    // Setup environmant to run npm.
		    sh 'curl -fsSL https://deb.nodesource.com/setup_17.x | bash -'
		    sh 'apt-get install -y nodejs'
		    dir("./go-graphstore/api-gorest-2021") {
			// Note: I currently cannot imagine a reason not
			// to have this pinned to master.
			git branch: 'master', url: 'https://github.com/geneontology/api-gorest-2021.git'
			sh 'npm install'

			// Uncomment the last four lines of the app.js
			// file into a new runtime js.
			sh 'cat app.js > newapp.js'
			sh 'echo >> newapp.js'
			sh 'cat app.js | tail -4 | sed \'s:\\/::g\' >> newapp.js'
			sh 'echo >> newapp.js'
			sh 'cat newapp.js'

			// Create runner for newapp.
			sh 'echo \'#!/bin/bash\' > newapp.sh'
			sh 'echo \'set -x\' >> newapp.sh'
			sh 'echo \'node newapp.js &\' >> newapp.sh'
			sh 'cat ./newapp.sh'

			// Create local config for newapp.
			sh 'cp -f config.json config.json.bak'
			sh 'cat config.json.bak | sed \'s:rdf.geneontology.org:localhost\\:9876:g\' > config.json'
			sh 'cat config.json'

			// Increase utility timeout for newapp.
			sh 'cp -f utils.js utils.js.bak'
			sh 'cat utils.js.bak | sed \'s:60000:1200000:g\' > utils.js'
			sh 'cat utils.js'

			// Run newapp.
			sh 'bash newapp.sh'
			sh 'sleep 10'

			// Revert config.json now that it's running.
			sh 'cp -f config.json.bak config.json'

			// A little cleaning.
			sh 'rm -f gocam-*.json || true'
			sh 'rm -f gocam-*.json.gz || true'

			// Run commands.
			sh 'wget http://localhost:8888/models/go -O gocam-goterms.json'
			sh 'wget http://localhost:8888/models/gp -O gocam-gps.json'
			sh 'wget http://localhost:8888/models -O gocam-models.json'
			sh 'wget http://localhost:8888/models/pmid -O gocam-pmids.json'

			// Upload to skyhook to the expected location.
			withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
			    sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY ./gocam*.json skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/api-static-files/'
			}

			// WARNING/TEMP: Upload to a temporary working
			// location in S3. Grab tools needed.
			withCredentials([file(credentialsId: 'aws_go_push_json', variable: 'S3_PUSH_JSON'), file(credentialsId: 's3cmd_go_push_configuration', variable: 'S3CMD_JSON'), string(credentialsId: 'aws_go_access_key', variable: 'AWS_ACCESS_KEY_ID'), string(credentialsId: 'aws_go_secret_key', variable: 'AWS_SECRET_ACCESS_KEY')]) {
			    // Setup s3cmd.
			    sh 'apt-get install -y python-pip'
			    sh 'pip install s3cmd'

			    // Standard.
			    sh 's3cmd -c $S3CMD_JSON --acl-public --mime-type=application/json put gocam-goterms.json s3://go-public/files/gocam-goterms.json'
			    sh 's3cmd -c $S3CMD_JSON --acl-public --mime-type=application/json put gocam-gps.json s3://go-public/files/gocam-gps.json'
			    sh 's3cmd -c $S3CMD_JSON --acl-public --mime-type=application/json put gocam-models.json s3://go-public/files/gocam-models.json'
			    sh 's3cmd -c $S3CMD_JSON --acl-public --mime-type=application/json put gocam-pmids.json s3://go-public/files/gocam-pmids.json'
			}
		    }
		}
	    }
	}
    }
    post {
	// Let's let our people know if things go well.
	success {
	    script {
		if( env.BRANCH_NAME == 'release' ){
		    echo "There has been a successful run of the ${env.BRANCH_NAME} pipeline."
		    emailext to: "${TARGET_SUCCESS_EMAILS}",
			subject: "GO Pipeline success for ${env.BRANCH_NAME}",
			body: "There has been successful run of the ${env.BRANCH_NAME} pipeline. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
		}
	    }
	}
	// Let's let our internal people know if things change.
	changed {
	    echo "There has been a change in the ${env.BRANCH_NAME} pipeline."
	    emailext to: "${TARGET_ADMIN_EMAILS}",
		subject: "GO Pipeline change for ${env.BRANCH_NAME}",
		body: "There has been a pipeline status change in ${env.BRANCH_NAME}. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
	}
	// Let's let our internal people know if things go badly.
	failure {
	    echo "There has been a failure in the ${env.BRANCH_NAME} pipeline."
	    emailext to: "${TARGET_ADMIN_EMAILS}",
		subject: "GO Pipeline FAIL for ${env.BRANCH_NAME}",
		body: "There has been a pipeline failure in ${env.BRANCH_NAME}. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
	}
    }
}