From cc7394f509bb4ea0cbea5a58052e4989f40d50ad Mon Sep 17 00:00:00 2001
From: Seth Carbon <github.com@genkisugi.net>
Date: Tue, 1 Oct 2024 22:12:17 -0700
Subject: [PATCH] re-add initialize() code; for #388

---
 Jenkinsfile | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/Jenkinsfile b/Jenkinsfile
index 3c0d3c7..4253996 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -813,3 +813,63 @@ void watchdog() {
 	sh '`exit -1`'
     }
 }
+
+// Reset and initialize skyhook base.
+void initialize() {
+
+    // Possibly protect against issues like #350 by making sure
+    // $BRANCH_NAME is there and vaguely sane.
+    if(BRANCH_NAME instanceof String && BRANCH_NAME.size() >= 3 ) {
+
+	// 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/ttl || true'
+	sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/json || true'
+	sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/blazegraph || true'
+	sh 'mkdir -p $WORKSPACE/mnt/$BRANCH_NAME/products/upstream_and_raw_data || 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 "$START_DAY" > $WORKSPACE/mnt/$BRANCH_NAME/metadata/dow.txt'
+	sh 'echo "$START_DATE" > $WORKSPACE/mnt/$BRANCH_NAME/metadata/date.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 "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'
+    }else{
+	sh 'echo "HOW DID THIS EVEN HAPPEN?"'
+    }
+}