From f965457553970bee7d60612bd2b423a30188b2eb Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 29 Jan 2024 13:45:42 -0800
Subject: [PATCH] modify to test ontobio code

---
 Jenkinsfile | 875 ++++------------------------------------------------
 1 file changed, 56 insertions(+), 819 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index f159d47..1c0b14a 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -17,7 +17,7 @@ pipeline {
 	///
 
 	// The branch of geneontology/go-site to use.
-	TARGET_GO_SITE_BRANCH = 'master'
+	TARGET_GO_SITE_BRANCH = 'mouse_upstream_from_silver_325_pipeline'
 	// The branch of geneontology/go-stats to use.
 	TARGET_GO_STATS_BRANCH = 'master'
 	// The branch of go-ontology to use.
@@ -32,31 +32,31 @@ pipeline {
 	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,debert@usc.edu,smoxon@lbl.gov'
-	TARGET_SUCCESS_EMAILS = 'sjcarbon@lbl.gov,debert@usc.edu,suzia@stanford.edu,smoxon@lbl.gov'
-	TARGET_RELEASE_HOLD_EMAILS = 'sjcarbon@lbl.gov,debert@usc.edu,pascale.gaudet@sib.swiss,pgaudet1@gmail.com,smoxon@lbl.gov'
-	// The file bucket(/folder) combination to use.
-	TARGET_BUCKET = 'go-data-product-experimental'
-	// 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'
-	// Sanity check for solr index being built--overall min count.
-	// See https://github.com/geneontology/pipeline/issues/315 .
-	// Only used on release attempts (as it saves QC time and
-	// getting the number for all branches would be a trick).
-	SANITY_SOLR_DOC_COUNT_MIN = 11000000
-	SANITY_SOLR_BIOENTITY_DOC_COUNT_MIN = 1400000
-	// 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'
+	TARGET_ADMIN_EMAILS = 'smoxon@lbl.gov'
+	TARGET_SUCCESS_EMAILS = 'smoxon@lbl.gov'
+	TARGET_RELEASE_HOLD_EMAILS = 'smoxon@lbl.gov'
+    // The file bucket(/folder) combination to use.
+    TARGET_BUCKET = null
+    // 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'
+    // Sanity check for solr index being built--overall min count.
+    // See https://github.com/geneontology/pipeline/issues/315 .
+    // Only used on release attempts (as it saves QC time and
+    // getting the number for all branches would be a trick).
+    SANITY_SOLR_DOC_COUNT_MIN = 11000000
+    SANITY_SOLR_BIOENTITY_DOC_COUNT_MIN = 1400000
+    // 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.
@@ -70,19 +70,19 @@ pipeline {
 
 	// The Zenodo concept ID to use for releases (and occasionally
 	// master testing).
-	ZENODO_ARCHIVE_CONCEPT = '1170314'
-	// 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 = 'E2CDVG5YT5R4K4'
-	AWS_CLOUDFRONT_RELEASE_DISTRIBUTION_ID = 'E2HF1DWYYDLTQP'
+    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/master/ontology/go.json"
+	VALIDATION_ONTOLOGY_URL="http://skyhook.berkeleybop.org/release/ontology/go.json"
 
 	///
 	/// Minerva input.
@@ -90,7 +90,7 @@ pipeline {
 
 	// Minerva operating profile.
 	MINERVA_INPUT_ONTOLOGIES = [
-	    "http://skyhook.berkeleybop.org/master/ontology/extensions/go-lego.owl"
+	    "http://skyhook.berkeleybop.org/release/ontology/extensions/go-lego.owl"
 	].join(" ")
 
 	///
@@ -101,19 +101,19 @@ pipeline {
 	GOLR_SOLR_MEMORY = "128G"
 	GOLR_LOADER_MEMORY = "192G"
 	GOLR_INPUT_ONTOLOGIES = [
-	    "http://skyhook.berkeleybop.org/master/ontology/extensions/go-amigo.owl"
+	    "http://skyhook.berkeleybop.org/release/ontology/extensions/go-amigo.owl"
 	].join(" ")
 	GOLR_INPUT_GAFS = [
-	    //"http://skyhook.berkeleybop.org/master/products/upstream_and_raw_data/paint_other.gaf.gz",
-	    "http://skyhook.berkeleybop.org/master/annotations/goa_chicken.gaf.gz",
-	    "http://skyhook.berkeleybop.org/master/annotations/goa_chicken_complex.gaf.gz",
-	    "http://skyhook.berkeleybop.org/master/annotations/goa_uniprot_all_noiea.gaf.gz",
-	    "http://skyhook.berkeleybop.org/master/annotations/mgi.gaf.gz",
-	    "http://skyhook.berkeleybop.org/master/annotations/pombase.gaf.gz",
-	    "http://skyhook.berkeleybop.org/master/annotations/wb.gaf.gz"
+	    //"http://skyhook.berkeleybop.org/full-issue-325-gopreprocess/products/upstream_and_raw_data/paint_other.gaf.gz",
+	    "http://skyhook.berkeleybop.org/release/annotations/goa_chicken.gaf.gz",
+	    "http://skyhook.berkeleybop.org/release/annotations/goa_chicken_complex.gaf.gz",
+	    "http://skyhook.berkeleybop.org/release/annotations/goa_uniprot_all_noiea.gaf.gz",
+	    "http://skyhook.berkeleybop.org/full-issue-325-gopreprocess/annotations/mgi.gaf.gz",
+	    "http://skyhook.berkeleybop.org/release/annotations/pombase.gaf.gz",
+	    "http://skyhook.berkeleybop.org/release/annotations/wb.gaf.gz"
 	].join(" ")
 	GOLR_INPUT_PANTHER_TREES = [
-	    "http://skyhook.berkeleybop.org/master/products/panther/arbre.tgz"
+	    "http://skyhook.berkeleybop.org/release/products/panther/arbre.tgz"
 	].join(" ")
 
 	///
@@ -134,15 +134,14 @@ pipeline {
 	// "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).
+    // 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"
-
+    // 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()
@@ -157,9 +156,6 @@ pipeline {
 		// Check to make sure we have coherent metadata so we
 		// don't clobber good products.
 		watchdog();
-
-		// Give us a minute to cancel if we want.
-		sleep time: 1, unit: 'MINUTES'
 		cleanWs deleteDirs: true, disableDeferredWipeout: true
 	    }
 	}
@@ -320,180 +316,6 @@ pipeline {
 		}
 	    }
 	}
-	// See https://github.com/geneontology/go-ontology for details
-	// on the ontology release pipeline. This ticket runs
-	// daily(TODO?) and creates all the files normally included in
-	// a release, and deploys to S3.
-	stage('Produce ontology (*)') {
-	    agent {
-		docker {
-		    // Upgrade test for: geneontology/go-ontology#25019, from v1.2.32
-    		    image 'obolibrary/odkfull:v1.4'
-		    // Reset Jenkins Docker agent default to original
-		    // root.
-		    args '-u root:root'
-		}
-	    }
-	    // CHECKPOINT: Recover key environmental variables.
-	    environment {
-		START_DOW = sh(script: 'curl http://skyhook.berkeleybop.org/$BRANCH_NAME/metadata/dow.txt', , returnStdout: true).trim()
-		START_DATE = sh(script: 'curl http://skyhook.berkeleybop.org/$BRANCH_NAME/metadata/date.txt', , returnStdout: true).trim()
-	    }
-	    steps {
-		// Create a relative working directory and setup our
-		// data environment.
-		dir('./go-ontology') {
-
-		    // We're starting to run into problems with
-		    // ontology download taking too long for the
-		    // default 10m, so try and get into the guts of
-		    // the git commands a little. Issues #248.
-		    // git branch: TARGET_GO_ONTOLOGY_BRANCH, url: 'https://github.com/geneontology/go-ontology.git'
-                    checkout changelog: false, poll: false, scm: [$class: 'GitSCM', branches: [[name: TARGET_GO_ONTOLOGY_BRANCH]], extensions: [[$class: 'CloneOption', depth: 1, noTags: true, reference: '', shallow: true, timeout: 120]], userRemoteConfigs: [[url: 'https://github.com/geneontology/go-ontology.git', refspec: "+refs/heads/${env.TARGET_GO_ONTOLOGY_BRANCH}:refs/remotes/origin/${env.TARGET_GO_ONTOLOGY_BRANCH}"]]]
-
-		    // Default namespace.
-		    sh 'env'
-
-		    dir('./src/ontology') {
-			retry(3){
-			    sh 'make RELEASEDATE=$START_DATE OBO=http://purl.obolibrary.org/obo ROBOT_ENV="ROBOT_JAVA_ARGS=-Xmx48G" all'
-			}
-			retry(3){
-			    sh 'make prepare_release'
-			}
-		    }
-
-		    // Make sure that we copy any files there,
-		    // including the core dump of produced.
-		    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-			//sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology'
-			sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology/'
-		    }
-
-		    // Now that the files are safely away onto skyhook for
-		    // debugging, test for the core dump.
-		    script {
-			if( WE_ARE_BEING_SAFE_P == 'TRUE' ){
-
-			    def found_core_dump_p = fileExists 'target/core_dump.owl'
-			    if( found_core_dump_p ){
-				error 'ROBOT core dump detected--bailing out.'
-			    }
-			}
-		    }
-
-		    // Try and force destruction of anything remaining
-		    // on disk after build as cleanup.
-		    sh 'git clean -fx || true'
-		}
-	    }
-	}
-	stage('Minerva generations') {
-	    steps {
-		parallel(
-		    "Make Noctua GPAD": {
-
-			// May be parallelized in the future, but may need to
-			// serve as input into into mega step.
-			script {
-
-			    // Create a relative working directory and setup our
-			    // data environment.
-			    dir('./noctua-models') {
-
-				// Attempt to trim/prune/speed up
-				// noctua-models as we do for
-				// go-ontology for
-				// https://github.com/geneontology/pipeline/issues/278
-				// .
-				checkout changelog: false, poll: false, scm: [$class: 'GitSCM', branches: [[name: TARGET_NOCTUA_MODELS_BRANCH]], extensions: [[$class: 'CloneOption', depth: 1, noTags: true, reference: '', shallow: true, timeout: 120]], userRemoteConfigs: [[url: 'https://github.com/geneontology/noctua-models.git', refspec: "+refs/heads/${env.TARGET_NOCTUA_MODELS_BRANCH}:refs/remotes/origin/${env.TARGET_NOCTUA_MODELS_BRANCH}"]]]
-
-				// Make all software products
-				// available in bin/ (and lib/).
-				sh 'mkdir -p bin/'
-				sh 'mkdir -p lib/'
-				withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-				    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/* ./bin/'
-				    // WARNING/BUG: needed for blazegraph-runner
-				    // to run at this point.
-				    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/lib/* ./lib/'
-				}
-				sh 'chmod +x bin/*'
-
-				// Compile models.
-				sh 'mkdir -p legacy/gpad'
-				withEnv(['MINERVA_CLI_MEMORY=128G']){
-				    // "Import" models.
-				    sh './bin/minerva-cli.sh --import-owl-models -f models -j blazegraph.jnl'
-				    // Convert GO-CAM to GPAD.
-				    sh './bin/minerva-cli.sh --lego-to-gpad-sparql --ontology $MINERVA_INPUT_ONTOLOGIES --ontojournal ontojournal.jnl -i blazegraph.jnl --gpad-output legacy/gpad'
-				}
-
-				// Collation.
-				// Hack for iterating quickly on
-				// https://github.com/geneontology/pipeline/issues/313 .
-				sh 'wget -N https://raw.githubusercontent.com/geneontology/go-site/$TARGET_GO_SITE_BRANCH/scripts/collate-gpads.pl'
-				sh 'perl ./collate-gpads.pl legacy/gpad/*.gpad'
-
-				// Rename, compress, and move to skyhook.
-				sh 'mcp "legacy/*.gpad" "legacy/noctua_#1-src.gpad"'
-				sh 'gzip -vk legacy/noctua_*.gpad'
-				withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-				    sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY legacy/noctua_*-src.gpad.gz skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/upstream_and_raw_data/'
-				}
-			    }
-			}
-		    },
-		    "JSON model generation": {
-
-			// May be parallelized in the future, but may need to
-			// serve as input into into mega step.
-			script {
-
-			    // Create a relative working directory and setup our
-			    // data environment.
-			    dir('./json-noctua-models') {
-
-				// Attempt to trim/prune/speed up
-				// noctua-models as we do for
-				// go-ontology for
-				// https://github.com/geneontology/pipeline/issues/278
-				// .
-				checkout changelog: false, poll: false, scm: [$class: 'GitSCM', branches: [[name: TARGET_NOCTUA_MODELS_BRANCH]], extensions: [[$class: 'CloneOption', depth: 1, noTags: true, reference: '', shallow: true, timeout: 120]], userRemoteConfigs: [[url: 'https://github.com/geneontology/noctua-models.git', refspec: "+refs/heads/${env.TARGET_NOCTUA_MODELS_BRANCH}:refs/remotes/origin/${env.TARGET_NOCTUA_MODELS_BRANCH}"]]]
-
-				// Make all software products
-				// available in bin/ (and lib/).
-				sh 'mkdir -p bin/'
-				sh 'mkdir -p lib/'
-				withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-				    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/bin/* ./bin/'
-				    // WARNING/BUG: needed for blazegraph-runner
-				    // to run at this point.
-				    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/lib/* ./lib/'
-				}
-				sh 'chmod +x bin/*'
-
-				// Compile models.
-				sh 'mkdir -p jsonout'
-				withEnv(['MINERVA_CLI_MEMORY=128G']){
-				    // "Import" models.
-				    sh './bin/minerva-cli.sh --import-owl-models -f models -j blazegraph.jnl'
-				    // JSON out to directory.
-				    sh './bin/minerva-cli.sh --dump-owl-json --journal blazegraph.jnl --ontojournal blazegraph-go-lego-reacto-neo.jnl --folder jsonout'
-				}
-
-				// Compress and out.
-				sh 'tar --use-compress-program=pigz -cvf noctua-models-json.tgz -C jsonout .'
-				withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-				    sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY noctua-models-json.tgz skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/json/'
-				}
-			    }
-			}
-		    }
-		)
-	    }
-	}
-
 	stage('Produce GAFs, TTLs, and journal (*)') {
 	    agent {
 		docker {
@@ -526,7 +348,7 @@ pipeline {
 		    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/lib/* /opt/lib/'
 		    // Copy the sources we downloaded earlier to local.
 		    // We're grabbing anything that's gaf, zipped or unzipped. This leaves gpad or anything else behind since currently we only expect gafs
-		    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/upstream_and_raw_data/*.gaf*  /opt/go-site/sources/'
+		    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/release/products/upstream_and_raw_data/*.gaf*  /opt/go-site/sources/'
 		}
 		sh "chmod +x /opt/bin/*"
 
@@ -582,7 +404,7 @@ pipeline {
 		    //  - all irregular gaffy files + anything paint-y
 		    //  - but not uniprot_all anything (elsewhere)
 		    //  - and not any of the ttls
-		    sh 'find /opt/go-site/pipeline/target/groups -type f -regex "^.*\\(\\-src.gaf\\|\\-src.gpi\\|\\_noiea.gaf\\|\\_valid.gaf\\|paint\\_.*\\).gz$" -not -regex "^.*.ttl.gz$" -not -regex "^.*goa_uniprot_all_noiea.gaf.gz$" -not -regex "^.*.ttl.gz$" -exec scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY {} skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/upstream_and_raw_data \\;'
+		    sh 'find /opt/go-site/pipeline/target/groups -type f -regex "^.*\\(\\-src.gaf\\|\\-src.gpi\\|\\_noiea.gaf\\|\\_valid.gaf\\|paint\\_.*\\).gz$" -not -regex "^.*.ttl.gz$" -not -regex "^.*goa_uniprot_all_noiea.gaf.gz$" -not -regex "^.*.ttl.gz$" -exec scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY {} skyhook@skyhook.berkeleybop.org:/home/skyhook/release/products/upstream_and_raw_data \\;'
 		    // No longer copy goa uniprot all source to products:
 		    // https://github.com/geneontology/pipeline/issues/207
 		    // // Now copy over the (single) uniprot
@@ -596,13 +418,13 @@ pipeline {
 		    // 	}
 		    // }
 		    // Finally, the non-zipped prediction files.
-		    sh 'find /opt/go-site/pipeline/target/groups -type f -regex "^.*\\-prediction.gaf$" -exec scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY {} skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/upstream_and_raw_data \\;'
+		    sh 'find /opt/go-site/pipeline/target/groups -type f -regex "^.*\\-prediction.gaf$" -exec scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY {} skyhook@skyhook.berkeleybop.org:/home/skyhook/release/products/upstream_and_raw_data \\;'
 		    // Flatten all GAFs and GAF-like products
 		    // onto skyhook. Basically:
 		    //  - all product-y files
 		    //  - but not uniprot_all anything (elsewhere)
 		    //  - and not anything "irregular", like src
-		    sh 'find /opt/go-site/pipeline/target/groups -type f -regex "^.*.\\(gaf\\|gpad\\|gpi\\).gz$" -not -regex "^.*\\(\\-src.gaf\\|\\-src.gpi\\|\\_noiea.gaf\\|\\_valid.gaf\\|noctua_.*\\|paint_.*\\).gz$" -exec scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY {} skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/annotations \\;'
+		    sh 'find /opt/go-site/pipeline/target/groups -type f -regex "^.*.\\(gaf\\|gpad\\|gpi\\).gz$" -not -regex "^.*\\(\\-src.gaf\\|\\-src.gpi\\|\\_noiea.gaf\\|\\_valid.gaf\\|noctua_.*\\|paint_.*\\).gz$" -exec scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY {} skyhook@skyhook.berkeleybop.org:/home/skyhook/release/annotations \\;'
 		    // Now copy over the four uniprot core
 		    // files, if they are in our run set
 		    // (e.g. may not be there on speed runs
@@ -892,591 +714,6 @@ pipeline {
 		}
 	    }
 	}
-	stage('Sanity I') {
-	    steps {
-		// Prep a copyover point, as the overhead for doing
-		// large i/o over sshfs seems /really/ high.
-		sh 'mkdir -p $WORKSPACE/copyover/ || true'
-		// Mount the remote filesystem.
-		sh 'mkdir -p $WORKSPACE/mnt/ || true'
-		withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-		    sh 'sshfs -oStrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -o idmap=user skyhook@skyhook.berkeleybop.org:/home/skyhook $WORKSPACE/mnt/'
-		}
-		// Copy over the files that we want to work on--both
-		// annotations/ and reports/ (which we separated
-		// earlier).
-		sh 'cp $WORKSPACE/mnt/$BRANCH_NAME/annotations/* $WORKSPACE/copyover/'
-		sh 'cp $WORKSPACE/mnt/$BRANCH_NAME/products/upstream_and_raw_data/* $WORKSPACE/copyover/'
-		sh 'cp $WORKSPACE/mnt/$BRANCH_NAME/reports/* $WORKSPACE/copyover/'
-		// Ready...
-		dir('./go-site') {
-		    git branch: TARGET_GO_SITE_BRANCH, url: 'https://github.com/geneontology/go-site.git'
-
-		    // Run sanity checks.
-		    sh 'python3 ./scripts/sanity-check-ann-report.py -v -d $WORKSPACE/copyover/ --ignore_noctua'
-		    // Make sure that the SPARTA report has nothing
-		    // nasty in it.
-		    // Note: Used to be pipes (|), but Jenkins Pipeline shell
-		    // commands do not apparently respect that.
-		    sh 'jq \'.build\' $WORKSPACE/copyover/sparta-report.json > $WORKSPACE/build-status.txt'
-		    sh 'grep -v \'fail\' $WORKSPACE/build-status.txt'
-		}
-	    }
-	    // WARNING: Extra safety as I expect this to sometimes fail.
-	    post {
-		always {
-		    // Bail on the remote filesystem.
-		    sh 'fusermount -u $WORKSPACE/mnt/ || true'
-		    // Purge the copyover point.
-		    sh 'rm -r -f $WORKSPACE/copyover || true'
-		}
-	    }
-	}
-	//...
-	stage('Produce derivatives (*)') {
-	    agent {
-		docker {
-		    image 'geneontology/golr-autoindex:28a693d28b37196d3f79acdea8c0406c9930c818_2022-03-17T171930_master'
-		    // Reset Jenkins Docker agent default to original
-		    // root.
-		    args '-u root:root --mount type=tmpfs,destination=/srv/solr/data'
-		}
-	    }
-	    // CHECKPOINT: Recover key environmental variables.
-	    environment {
-		START_DOW = sh(script: 'curl http://skyhook.berkeleybop.org/$BRANCH_NAME/metadata/dow.txt', , returnStdout: true).trim()
-		START_DATE = sh(script: 'curl http://skyhook.berkeleybop.org/$BRANCH_NAME/metadata/date.txt', , returnStdout: true).trim()
-	    }
-
-	    steps {
-
-		// Build index into tmpfs.
-		sh 'bash /tmp/run-indexer.sh'
-
-		// Immediately check to see if it looks like we have
-		// enough docs when trying a
-		// release. SANITY_SOLR_DOC_COUNT_MIN must be greater
-		// than what we seen in the index.
-		script {
-		    if( env.BRANCH_NAME == 'release' ){
-
-			// Test overall.
-			echo "SANITY_SOLR_DOC_COUNT_MIN:${env.SANITY_SOLR_DOC_COUNT_MIN}"
-			sh 'curl "http://localhost:8080/solr/select?q=*:*&rows=0&wt=json"'
-			sh 'if [ $SANITY_SOLR_DOC_COUNT_MIN -gt $(curl "http://localhost:8080/solr/select?q=*:*&rows=0&wt=json" | grep -oh \'"numFound":[[:digit:]]*\' | grep -oh [[:digit:]]*) ]; then exit 1; else echo "We seem to be clear wrt doc count"; fi'
-
-			// Test bioentity.
-			echo "SANITY_SOLR_BIOENTITY_DOC_COUNT_MIN:${env.SANITY_SOLR_BIOENTITY_DOC_COUNT_MIN}"
-			sh 'curl "http://localhost:8080/solr/select?q=*:*&rows=0&wt=json&fq=document_category:bioentity"'
-			sh 'if [ $SANITY_SOLR_BIOENTITY_DOC_COUNT_MIN -gt $(curl "http://localhost:8080/solr/select?q=*:*&rows=0&wt=json&fq=document_category:bioentity" | grep -oh \'"numFound":[[:digit:]]*\' | grep -oh [[:digit:]]*) ]; then exit 1; else echo "We seem to be clear wrt doc count"; fi'
-		    }
-		}
-
-		// Copy tmpfs Solr contents onto skyhook.
-		sh 'tar --use-compress-program=pigz -cvf /tmp/golr-index-contents.tgz -C /srv/solr/data/index .'
-		withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-		    // Copy over index.
-		    // Copy over log.
-		    //sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" /tmp/golr-index-contents.tgz skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/solr/'
-		    //sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" /tmp/golr_timestamp.log skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/solr/'
-		    sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY /tmp/golr-index-contents.tgz skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/solr/'
-		    sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY /tmp/golr_timestamp.log skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/solr/'
-		}
-
-		// Solr should still be running in the background here
-		// from indexing--create stats products from running
-		// GOlr.
-		// Prepare a working directory based around go-site.
-		dir('./go-stats') {
-		    git branch: TARGET_GO_STATS_BRANCH, url: 'https://github.com/geneontology/go-stats.git'
-
-		    // Not much want or need here--simple
-		    // python3. However, using the information hidden
-		    // in run-indexer.sh to know where the Solr
-		    // instance is hiding.
-		    sh 'mkdir -p /tmp/stats/ || true'
-		    sh 'cp ./libraries/go-stats/*.py /tmp'
-		    // Needed as extra library.
-		    sh 'pip3 install --force-reinstall requests==2.19.1'
-		    sh 'pip3 install --force-reinstall networkx==2.2'
-
-		    // Final command, sealed into docker work
-		    // environment.
-		    echo "Check that results have been stored properly"
-		    sh "curl 'http://localhost:8080/solr/select?q=*:*&rows=0'"
-		    echo "End of results"
-		    retry(3){
-			sh 'python3 /tmp/go_reports.py -g http://localhost:8080/solr/ -s http://current.geneontology.org/release_stats/go-stats.json -n http://current.geneontology.org/release_stats/go-stats-no-pb.json -c http://skyhook.berkeleybop.org/$BRANCH_NAME/ontology/go.obo -p http://current.geneontology.org/ontology/go.obo -r http://current.geneontology.org/release_stats/go-references.tsv -o /tmp/stats/ -d $START_DATE'
-		    }
-		    retry(3) {
-		    	sh 'wget -N http://current.geneontology.org/release_stats/aggregated-go-stats-summaries.json'
-		    }
-
-		    // Roll the stats forward.
-		    sh 'python3 /tmp/aggregate-stats.py -a aggregated-go-stats-summaries.json -b /tmp/stats/go-stats-summary.json -o /tmp/stats/aggregated-go-stats-summaries.json'
-
-		    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-		    	retry(3) {
-			    // Copy over stats files.
-			    //sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" /tmp/stats/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/release_stats/'
-			    sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY /tmp/stats/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/release_stats/'
-			}
-		    }
-		}
-	    }
-	}
-	//...
-	stage('Sanity II') {
-	    when { anyOf { branch 'release' } }
-	    steps {
-
-		//
-		echo 'Push pre-release to http://amigo-staging.geneontology.io for testing.'
-
-		// Ninja in our file credentials from Jenkins.
-		withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY'), file(credentialsId: 'go-svn-private-key', variable: 'GO_SVN_IDENTITY'), file(credentialsId: 'ansible-bbop-local-slave', variable: 'DEPLOY_LOCAL_IDENTITY'), file(credentialsId: 'go-aws-ec2-ansible-slave', variable: 'DEPLOY_REMOTE_IDENTITY')]) {
-
-		    // Get our operations code and decend into ansible
-		    // working directory.
-		    dir('./operations') {
-
-			git([branch: 'master',
-			     credentialsId: 'bbop-agent-github-user-pass',
-			     url: 'https://github.com/geneontology/operations.git'])
-			dir('./ansible') {
-
-			    retry(3){
-				sh 'ansible-playbook update-golr-w-skyhook-forced.yaml --inventory=hosts.amigo --private-key="$DEPLOY_LOCAL_IDENTITY" -e skyhook_branch=release -e target_host=amigo-golr-staging'
-			    }
-
-			    // Pause on user input.
-			    echo 'Sanity II: Awaiting user input before proceeding.'
-			    emailext to: "${TARGET_RELEASE_HOLD_EMAILS}",
-				subject: "GO Pipeline waiting on input for ${env.BRANCH_NAME}",
-				body: "The ${env.BRANCH_NAME} pipeline is waiting on user input. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
-			    lock(resource: 'release-run', inversePrecedence: true) {
-				echo "Sanity II: A release run holds the lock."
-				timeout(time:7, unit:'DAYS') {
-				    input message:'Approve release products?'
-				}
-			    }
-			    echo 'Sanity II: Positive user input input given.'
-			}
-		    }
-		}
-	    }
-	}
-
-	stage('Archive (*)') {
-	    // CHECKPOINT: Recover key environmental variables.
-	    environment {
-		START_DOW = sh(script: 'curl http://skyhook.berkeleybop.org/$BRANCH_NAME/metadata/dow.txt', , returnStdout: true).trim()
-		START_DATE = sh(script: 'curl http://skyhook.berkeleybop.org/$BRANCH_NAME/metadata/date.txt', , returnStdout: true).trim()
-	    }
-
-	    when { anyOf { branch 'release'; branch 'snapshot'; branch 'master' } }
-	    steps {
-		// Experimental stanza to support mounting the sshfs
-		// using the "hidden" skyhook identity.
-		sh 'mkdir -p $WORKSPACE/mnt/ || true'
-		withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-		    sh 'sshfs -oStrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -o idmap=user skyhook@skyhook.berkeleybop.org:/home/skyhook $WORKSPACE/mnt/'
-
-		    // Try to catch and prevent goa_uniprot_all-src
-		    // from getting into zenodo archive, etc. Re:
-		    // #207.
-		    sh 'pwd'
-		    sh 'ls -AlF $WORKSPACE/mnt/$BRANCH_NAME/products/upstream_and_raw_data/ || true'
-		    sh 'rm -f $WORKSPACE/mnt/$BRANCH_NAME/products/upstream_and_raw_data/goa_uniprot_all-src.gaf.gz || true'
-		    sh 'ls -AlF $WORKSPACE/mnt/$BRANCH_NAME/products/upstream_and_raw_data/ || true'
-
-		    // Redo goa_uniprot_all names for publication. From:
-		    // https://github.com/geneontology/go-site/issues/1984
-		    sh 'mv $WORKSPACE/mnt/$BRANCH_NAME/annotations/goa_uniprot_all.gaf.gz $WORKSPACE/mnt/$BRANCH_NAME/annotations/filtered_goa_uniprot_all.gaf.gz || true'
-		    sh 'mv $WORKSPACE/mnt/$BRANCH_NAME/annotations/goa_uniprot_all_noiea.gaf.gz $WORKSPACE/mnt/$BRANCH_NAME/annotations/filtered_goa_uniprot_all_noiea.gaf.gz || true'
-		    sh 'mv $WORKSPACE/mnt/$BRANCH_NAME/annotations/goa_uniprot_all_noiea.gpad.gz $WORKSPACE/mnt/$BRANCH_NAME/annotations/filtered_goa_uniprot_all_noiea.gpad.gz || true'
-		    sh 'mv $WORKSPACE/mnt/$BRANCH_NAME/annotations/goa_uniprot_all_noiea.gpi.gz $WORKSPACE/mnt/$BRANCH_NAME/annotations/filtered_goa_uniprot_all_noiea.gpi.gz || true'
-
-		    // Get annotation download directory prepped. From:
-		    // https://github.com/geneontology/go-site/issues/1971
-		    sh 'rm -f README-annotation-downloads.txt || true'
-		    sh 'wget -N https://raw.githubusercontent.com/geneontology/go-site/$TARGET_GO_SITE_BRANCH/static/pages/README-annotation-downloads.txt'
-		    sh 'mv README-annotation-downloads.txt $WORKSPACE/mnt/$BRANCH_NAME/annotations/README.txt || true'
-
-		    // Try and remove /lib and /bin from getting into
-		    // the archives by removing them now that we're
-		    // done using them for product builds. Re: #268.
-		    sh 'ls -AlF $WORKSPACE/mnt/$BRANCH_NAME/'
-		    sh 'rm -r -f $WORKSPACE/mnt/$BRANCH_NAME/bin || true'
-		    sh 'rm -r -f $WORKSPACE/mnt/$BRANCH_NAME/lib || true'
-		    sh 'ls -AlF $WORKSPACE/mnt/$BRANCH_NAME/'
-		}
-		// Copy the product to the right location. As well,
-		// archive.
-		withCredentials([file(credentialsId: 'aws_go_push_json', variable: 'S3_PUSH_JSON'), file(credentialsId: 's3cmd_go_push_configuration', variable: 'S3CMD_JSON'), string(credentialsId: 'zenodo_go_production_token', variable: 'ZENODO_PRODUCTION_TOKEN'), string(credentialsId: 'zenodo_go_sandbox_token', variable: 'ZENODO_SANDBOX_TOKEN')]) {
-		    // Ready...
-		    dir('./go-site') {
-			git branch: TARGET_GO_SITE_BRANCH, url: 'https://github.com/geneontology/go-site.git'
-
-			// WARNING: Caveats and reasons as same
-			// pattern above. We need this as some clients
-			// are not standard and it turns out there are
-			// some subtle incompatibilities with urllib3
-			// and boto in some versions, so we will use a
-			// virtual env to paper that over.  See:
-			// https://github.com/geneontology/pipeline/issues/8#issuecomment-356762604
-			sh 'python3 -m venv mypyenv'
-			withEnv(["PATH+EXTRA=${WORKSPACE}/go-site/bin:${WORKSPACE}/go-site/mypyenv/bin", 'PYTHONHOME=', "VIRTUAL_ENV=${WORKSPACE}/go-site/mypyenv", 'PY_ENV=mypyenv', 'PY_BIN=mypyenv/bin']){
-
-			    // Extra package for the indexer.
-			    sh 'python3 ./mypyenv/bin/pip3 install --force-reinstall pystache==0.5.4'
-
-			    // Correct for (possibly) bad boto3,
-			    // as mentioned above.
-			    sh 'python3 ./mypyenv/bin/pip3 install boto3==1.18.52'
-			    sh 'python3 ./mypyenv/bin/pip3 install botocore==1.21.52'
-
-			    // Needed to work around new incompatibility:
-			    // https://github.com/geneontology/pipeline/issues/286
-			    sh 'python3 ./mypyenv/bin/pip3 install --force-reinstall certifi==2021.10.8'
-
-			    // Extra package for the uploader.
-			    sh 'python3 ./mypyenv/bin/pip3 install filechunkio'
-
-			    // Grab BDBag.
-			    sh 'python3 ./mypyenv/bin/pip3 install bdbag'
-
-			    // Need for large uploads in requests.
-			    sh 'python3 ./mypyenv/bin/pip3 install requests-toolbelt'
-
-			    // Need as replacement for awful requests lib.
-			    sh 'python3 ./mypyenv/bin/pip3 install pycurl'
-
-			    // Apparently something wrong with default
-			    // version; error like
-			    // https://stackoverflow.com/questions/45821085/awshttpsconnection-object-has-no-attribute-ssl-context
-			    sh 'python3 ./mypyenv/bin/pip3 install awscli'
-
-			    // A temporary workaround for
-			    // https://github.com/geneontology/pipeline/issues/247,
-			    // forcing requests used by bdbags to a
-			    // verion that is usable by python 3.5
-			    // (our current raw machine default
-			    // version of python3).
-			    sh 'python3 ./mypyenv/bin/pip3 install --force-reinstall requests==2.25.1'
-
-			    // Well, we need to do a couple of things here in
-			    // a structured way, so we'll go ahead and drop
-			    // into the scripting mode.
-			    script {
-
-				// Build either a release or testing
-				// version of a generic BDBag/DOI
-				// workflow, keeping special bucket
-				// mappings in mind.
-				if( env.BRANCH_NAME == 'release' ){
-				    sh 'python3 ./scripts/create-bdbag-remote-file-manifest.py -v --walk $WORKSPACE/mnt/$BRANCH_NAME/ --remote http://release.geneontology.org/$START_DATE --output manifest.json'
-				}else if( env.BRANCH_NAME == 'snapshot' || env.BRANCH_NAME == 'master' ){
-				    sh 'python3 ./scripts/create-bdbag-remote-file-manifest.py -v --walk $WORKSPACE/mnt/$BRANCH_NAME/ --remote $TARGET_INDEXER_PREFIX --output manifest.json'
-				}
-
-				// To make a full BDBag, we first need
-				// a copy of the data as BDBags change
-				// directory layout (e.g. data/).
-				sh 'mkdir -p $WORKSPACE/copyover/ || true'
-				sh 'cp -r $WORKSPACE/mnt/$BRANCH_NAME/* $WORKSPACE/copyover/'
-				// Make the BDBag in the copyover/
-				// (unarchived, as we want to leave it
-				// to pigz).
-				sh 'python3 ./mypyenv/bin/bdbag $WORKSPACE/copyover'
-				// Tarball the whole directory for
-				// "deep" archive (handmade BDBag).
-				sh 'tar --use-compress-program=pigz -cvf go-release-archive.tgz -C $WORKSPACE/copyover .'
-
-				// We have the archives, now let's try
-				// and get them into position--this is
-				// fail-y, so we are going to try and
-				// buffer failure here for the time
-				// being until we work it all out. We
-				// are going to do the "hard"/large
-				// one first, then skip the
-				// "easy"/small one if we fail, so
-				// that we can retry this whole stage
-				// again on failure.
-				try {
-				    // Archive full archive.
-				    if( env.BRANCH_NAME == 'release' ){
-					sh 'python3 ./scripts/zenodo-version-update.py --verbose --key $ZENODO_PRODUCTION_TOKEN --concept $ZENODO_ARCHIVE_CONCEPT --file go-release-archive.tgz --output ./release-archive-doi.json --revision $START_DATE'
-				    }else if( env.BRANCH_NAME == 'snapshot' ){
-					// WARNING: to save Zenodo 1TB
-					// a month, for snapshot,
-					// we'll lie about the DOI
-					// that we get (not a big lie
-					// as they don't resolve on
-					// sandbox anyways).
-					//sh 'python3 ./scripts/zenodo-version-update.py --verbose --sandbox --key $ZENODO_SANDBOX_TOKEN --concept $ZENODO_ARCHIVE_CONCEPT --file go-release-archive.tgz --output ./release-archive-doi.json --revision $START_DATE'
-					sh 'echo \'{\' > ./release-archive-doi.json'
-					sh 'echo \'    "doi": "10.5072/zenodo.000000"\' >> ./release-archive-doi.json'
-					sh 'echo \'}\' >> ./release-archive-doi.json'
-
-				    }else if( env.BRANCH_NAME == 'master' ){
-					sh 'python3 ./scripts/zenodo-version-update.py --verbose --sandbox --key $ZENODO_SANDBOX_TOKEN --concept $ZENODO_ARCHIVE_CONCEPT --file go-release-archive.tgz --output ./release-archive-doi.json --revision $START_DATE'
-				    }
-
-				    // Get the DOI to skyhook for
-				    // publishing, but don't bother
-				    // with the full thing--too much
-				    // space and already in Zenodo.
-				    sh 'cp release-archive-doi.json $WORKSPACE/mnt/$BRANCH_NAME/metadata/release-archive-doi.json'
-
-				} catch (exception) {
-				    // Something went bad with the
-				    // Zenodo archive upload.
-				    echo "There has been a failure in the archive upload to Zenodo."
-				    emailext to: "${TARGET_ADMIN_EMAILS}",
-					subject: "GO Pipeline Zenodo archive upload fail for ${env.BRANCH_NAME}",
-					body: "There has been a failure in the archive upload to Zenodo, in ${env.BRANCH_NAME}. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
-				    // Hard die if this is a release.
-				    if( env.BRANCH_NAME == 'release' ){
-					error 'Zenodo archive upload error on release--no recovery.'
-				    }
-				}
-			    }
-			}
-		    }
-		}
-	    }
-	    // WARNING: Extra safety as I expect this to sometimes fail.
-	    post {
-		always {
-		    // Bail on the remote filesystem.
-		    sh 'fusermount -u $WORKSPACE/mnt/ || true'
-		    // Purge the copyover point.
-		    sh 'rm -r -f $WORKSPACE/copyover || true'
-		}
-	    }
-	}
-	stage('Publish') {
-	    when { anyOf { branch 'release'; branch 'snapshot'; branch 'master' } }
-	    steps {
-		// Experimental stanza to support mounting the sshfs
-		// using the "hidden" skyhook identity.
-		sh 'mkdir -p $WORKSPACE/mnt/ || true'
-		withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-		    sh 'sshfs -oStrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -o idmap=user skyhook@skyhook.berkeleybop.org:/home/skyhook $WORKSPACE/mnt/'
-		}
-		// Copy the product to the right location. As well,
-		// archive.
-		withCredentials([file(credentialsId: 'aws_go_push_json', variable: 'S3_PUSH_JSON'), file(credentialsId: 's3cmd_go_push_configuration', variable: 'S3CMD_JSON'), string(credentialsId: 'aws_go_access_key', variable: 'AWS_ACCESS_KEY_ID'), string(credentialsId: 'aws_go_secret_key', variable: 'AWS_SECRET_ACCESS_KEY')]) {
-		    // Ready...
-		    dir('./go-site') {
-			git branch: TARGET_GO_SITE_BRANCH, url: 'https://github.com/geneontology/go-site.git'
-
-			// TODO: Special handling still needed w/o OSF.io?
-			// WARNING: Caveats and reasons as same
-			// pattern above. We need this as some clients
-			// are not standard and it turns out there are
-			// some subtle incompatibilities with urllib3
-			// and boto in some versions, so we will use a
-			// virtual env to paper that over.  See:
-			// https://github.com/geneontology/pipeline/issues/8#issuecomment-356762604
-			sh 'python3 -m venv mypyenv'
-			withEnv(["PATH+EXTRA=${WORKSPACE}/go-site/bin:${WORKSPACE}/go-site/mypyenv/bin", 'PYTHONHOME=', "VIRTUAL_ENV=${WORKSPACE}/go-site/mypyenv", 'PY_ENV=mypyenv', 'PY_BIN=mypyenv/bin']){
-
-			    // Extra package for the indexer.
-			    sh 'python3 ./mypyenv/bin/pip3 install --force-reinstall pystache==0.5.4'
-
-			    // Extra package for the uploader.
-			    sh 'python3 ./mypyenv/bin/pip3 install filechunkio'
-
-			    // Let's be explicit here as well, as there were recent issues.
-			    //
-			    sh 'python3 ./mypyenv/bin/pip3 install rsa'
-			    sh 'python3 ./mypyenv/bin/pip3 install awscli'
-
-			    // Version locking for boto3 / botocore
-			    // upgrade that is incompatible with
-			    // python3.5. See issues #250 and #271.
-			    sh 'python3 ./mypyenv/bin/pip3 install boto3==1.18.52'
-			    sh 'python3 ./mypyenv/bin/pip3 install botocore==1.21.52'
-			    sh 'python3 ./mypyenv/bin/pip3 install s3transfer==0.5.0'
-
-			    // Well, we need to do a couple of things here in
-			    // a structured way, so we'll go ahead and drop
-			    // into the scripting mode.
-			    script {
-
-				// Create working index off of
-				// skyhook. For "release", this will
-				// be "current". For "snapshot", this
-				// will be "snapshot".
-				sh 'python3 ./scripts/directory_indexer.py -v --inject ./scripts/directory-index-template.html --directory $WORKSPACE/mnt/$BRANCH_NAME --prefix $TARGET_INDEXER_PREFIX -x'
-
-				// Push into S3 buckets. Simple
-				// overall case: copy tree directly
-				// over. For "release", this will be
-				// "current". For "snapshot", this
-				// will be "snapshot".
-				sh 'python3 ./scripts/s3-uploader.py -v --credentials $S3_PUSH_JSON --directory $WORKSPACE/mnt/$BRANCH_NAME/ --bucket $TARGET_BUCKET --number $BUILD_ID --pipeline $BRANCH_NAME'
-
-				// Also, some runs have special maps
-				// to buckets...
-				if( env.BRANCH_NAME == 'release' ){
-
-				    // "release" -> dated path for
-				    // indexing (clobbering
-				    // "current"'s index.
-				    sh 'python3 ./scripts/directory_indexer.py -v --inject ./scripts/directory-index-template.html --directory $WORKSPACE/mnt/$BRANCH_NAME --prefix http://release.geneontology.org/$START_DATE -x -u'
-				    // "release" -> dated path for S3.
-				    sh 'python3 ./scripts/s3-uploader.py -v --credentials $S3_PUSH_JSON --directory $WORKSPACE/mnt/$BRANCH_NAME/ --bucket go-data-product-release/$START_DATE --number $BUILD_ID --pipeline $BRANCH_NAME'
-
-				    // Build the capper index.html...
-				    sh 'python3 ./scripts/bucket-indexer.py --credentials $S3_PUSH_JSON --bucket go-data-product-release --inject ./scripts/directory-index-template.html --prefix http://release.geneontology.org > top-level-index.html'
-				    // ...and push it up to S3.
-				    sh 's3cmd -c $S3CMD_JSON --acl-public --mime-type=text/html --cf-invalidate put top-level-index.html s3://go-data-product-release/index.html'
-
-				}else if( env.BRANCH_NAME == 'snapshot' ){
-
-				    // Currently, the "daily"
-				    // debugging buckets are intended
-				    // to be RO directly in S3 for
-				    // debugging.
-				    sh 'python3 ./scripts/s3-uploader.py -v --credentials $S3_PUSH_JSON --directory $WORKSPACE/mnt/$BRANCH_NAME/ --bucket go-data-product-daily/$START_DAY --number $BUILD_ID --pipeline $BRANCH_NAME'
-
-				}else if( env.BRANCH_NAME == 'master' ){
-				    // Pass.
-				}
-
-				// Invalidate the CDN now that the new
-				// files are up.
-				sh 'echo "[preview]" > ./awscli_config.txt && echo "cloudfront=true" >> ./awscli_config.txt'
-				sh 'AWS_CONFIG_FILE=./awscli_config.txt python3 ./mypyenv/bin/aws cloudfront create-invalidation --distribution-id $AWS_CLOUDFRONT_DISTRIBUTION_ID --paths "/*"'
-				// The release branch also needs to
-				// deal with the second location.
-				if( env.BRANCH_NAME == 'release' ){
-				    sh 'AWS_CONFIG_FILE=./awscli_config.txt python3 ./mypyenv/bin/aws cloudfront create-invalidation --distribution-id $AWS_CLOUDFRONT_RELEASE_DISTRIBUTION_ID --paths "/*"'
-				}
-			    }
-			}
-		    }
-		}
-	    }
-	    // WARNING: Extra safety as I expect this to sometimes fail.
-	    post {
-		always {
-		    // Bail on the remote filesystem.
-		    sh 'fusermount -u $WORKSPACE/mnt/ || true'
-		}
-	    }
-	}
-	// Big things to do on major branches.
-	stage('Deploy') {
-	    // For exploration of #204, we'll hold back attempts to push out to AmiGO for master and snapshot
-	    // so we don't keep clobbering #204 trials out.
-	    //when { anyOf { branch 'release'; branch 'snapshot'; branch 'master' } }
-	    when { anyOf { branch 'release' } }
-	    steps {
-		parallel(
-		    "AmiGO": {
-
-			// Ninja in our file credentials from Jenkins.
-			withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY'), file(credentialsId: 'go-svn-private-key', variable: 'GO_SVN_IDENTITY'), file(credentialsId: 'ansible-bbop-local-slave', variable: 'DEPLOY_LOCAL_IDENTITY'), file(credentialsId: 'go-aws-ec2-ansible-slave', variable: 'DEPLOY_REMOTE_IDENTITY')]) {
-
-			    // Get our operations code and decend into ansible
-			    // working directory.
-			    dir('./operations') {
-
-				git([branch: 'master',
-				     credentialsId: 'bbop-agent-github-user-pass',
-				     url: 'https://github.com/geneontology/operations.git'])
-				dir('./ansible') {
-				    ///
-				    /// Push out to an AmiGO.
-				    ///
-				    script {
-					if( env.BRANCH_NAME == 'release' ){
-
-					    echo 'No current public push on release to Blazegraph.'
-					    // retry(3){
-					    //	sh 'ansible-playbook update-endpoint.yaml --inventory=hosts.local-rdf-endpoint --private-key="$DEPLOY_LOCAL_IDENTITY" -e target_user=bbop --extra-vars="pipeline=current build=production endpoint=production"'
-					    // }
-
-					    echo 'No current public push on release to GOlr.'
-					    // retry(3){
-					    //	sh 'ansible-playbook ./update-golr.yaml --inventory=hosts.amigo --private-key="$DEPLOY_LOCAL_IDENTITY" -e target_host=amigo-golr-aux -e target_user=bbop'
-					    // }
-					    // retry(3){
-					    //	sh 'ansible-playbook ./update-golr.yaml --inventory=hosts.amigo --private-key="$DEPLOY_LOCAL_IDENTITY" -e target_host=amigo-golr-production -e target_user=bbop'
-					    // }
-
-					}else if( env.BRANCH_NAME == 'snapshot' ){
-
-					    echo 'Push snapshot out internal Blazegraph'
-					    retry(3){
-						sh 'ansible-playbook update-endpoint.yaml --inventory=hosts.local-rdf-endpoint --private-key="$DEPLOY_LOCAL_IDENTITY" -e target_user=bbop --extra-vars="pipeline=current build=internal endpoint=internal"'
-					    }
-
-					    echo 'Push snapshot out to experimental AmiGO'
-					    retry(3){
-						sh 'ansible-playbook ./update-golr-w-snap.yaml --inventory=hosts.amigo --private-key="$DEPLOY_REMOTE_IDENTITY" -e target_host=amigo-golr-exp -e target_user=ubuntu'
-					    }
-
-					}else if( env.BRANCH_NAME == 'master' ){
-
-					    echo 'Push master out to experimental AmiGO'
-					    retry(3){
-						sh 'ansible-playbook ./update-golr-w-exp.yaml --inventory=hosts.amigo --private-key="$DEPLOY_REMOTE_IDENTITY" -e target_host=amigo-golr-exp -e target_user=ubuntu'
-					    }
-
-					}
-				    }
-				}
-			    }
-			}
-		    }
-		)
-	    }
-	    // WARNING: Extra safety as I expect this to sometimes fail.
-	    post {
-		always {
-		    // Bail on the remote filesystem.
-		    sh 'fusermount -u $WORKSPACE/mnt/ || true'
-		}
-	    }
-	}
-	// stage('TODO: Final status') {
-	//     steps {
-	//	echo 'TODO: final'
-	//     }
-	// }
-    }
-    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}"
-	}
-    }
 }
 
 // Check that we do not affect public targets on non-mainline runs.