From 2e7b714bea8d75b377d650e6bcd2fc7aa5c53d79 Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Thu, 13 Jun 2024 07:10:20 -0700
Subject: [PATCH 1/3] Removed commented out Jenkinsfile sections

---
 Jenkinsfile | 33 +++++++++++++++------------------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 03cae5ec..02e174da 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -45,19 +45,17 @@ pipeline {
             }
         }
         stage('transform') {
-            // TODO: turn --rdf back on as an argument to ingest transform 
             steps {
                 sh 'poetry run ingest transform --all --log --write-metadata'
                 sh '''
                    sed -i.bak 's@\r@@g' output/transform_output/*.tsv
                    rm output/transform_output/*.bak
                 '''
-// TODO: turn this back on
-//                sh '''
-//                   gunzip output/rdf/*.gz
-//                   sed -i.bak 's@\\r@@g' output/rdf/*.nt
-//                   rm output/rdf/*.bak
-//                   gzip output/rdf/*.nt
+               sh '''
+                  gunzip output/rdf/*.gz
+                  sed -i.bak 's@\\r@@g' output/rdf/*.nt
+                  rm output/rdf/*.bak
+                  gzip output/rdf/*.nt
                 '''
             }
         }
@@ -71,17 +69,16 @@ pipeline {
                 sh 'poetry run kgx graph-summary -i tsv -c "tar.gz" --node-facet-properties provided_by --edge-facet-properties provided_by output/monarch-kg.tar.gz -o output/merged_graph_stats.yaml'
             }
         }
-// TODO: this needs to be rewritten to use less memory
-//         stage('jsonl-conversion'){
-//             steps {
-//                 sh 'poetry run ingest jsonl'
-//             }
-//         }
-//        stage('kgx-transforms'){
-//            steps {
-//                sh './scripts/kgx_transforms.sh'
-//            }
-//        }
+        stage('jsonl-conversion'){
+            steps {
+                sh 'poetry run ingest jsonl'
+            }
+        }
+       stage('kgx-transforms'){
+           steps {
+               sh './scripts/kgx_transforms.sh'
+           }
+       }
         stage('denormalize') {
             steps {
                 sh 'poetry run ingest closure'

From 9e81321f17fcb8e486d81bfe0b4da46e69342c0a Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Thu, 13 Jun 2024 07:11:52 -0700
Subject: [PATCH 2/3] Comment out individual ingest rdf conversions for speed

---
 Jenkinsfile | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 02e174da..18d7b927 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -45,18 +45,19 @@ pipeline {
             }
         }
         stage('transform') {
+            //TODO: add --rdf flag back to produce individual rdf files
             steps {
                 sh 'poetry run ingest transform --all --log --write-metadata'
                 sh '''
                    sed -i.bak 's@\r@@g' output/transform_output/*.tsv
                    rm output/transform_output/*.bak
                 '''
-               sh '''
-                  gunzip output/rdf/*.gz
-                  sed -i.bak 's@\\r@@g' output/rdf/*.nt
-                  rm output/rdf/*.bak
-                  gzip output/rdf/*.nt
-                '''
+//                sh '''
+//                   gunzip output/rdf/*.gz
+//                   sed -i.bak 's@\\r@@g' output/rdf/*.nt
+//                   rm output/rdf/*.bak
+//                   gzip output/rdf/*.nt
+//                 '''
             }
         }
         stage('merge') {

From 543b64afeb237d3db22f27206af55b4794b32d8b Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Thu, 13 Jun 2024 08:42:05 -0700
Subject: [PATCH 3/3] switch to xlarge node

---
 Jenkinsfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 18d7b927..20ae2bc1 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -1,5 +1,5 @@
 pipeline {
-    agent { label 'monarch-agent-large' }
+    agent { label 'monarch-agent-xlarge' }
     environment {
         HOME = "${env.WORKSPACE}"
         RELEASE = sh(script: "echo `date +%Y-%m-%d`", returnStdout: true).trim()