[AN-304] Point to latest rstudio bioconductor image with fix (3.20.1) (#4815)

Author: LizBaldo

.github/workflows/azure_automation_test.yml

@@ -162,7 +162,7 @@ jobs:
     outputs:
       project-name: ${{ steps.gen.outputs.project_name }}
     steps:
-      - uses: 'actions/checkout@v3'
+      - uses: 'actions/checkout@v4'
 
       - name: Generate a random billing project name
         id: 'gen'

.github/workflows/consumer_contract_tests.yml

@@ -94,7 +94,7 @@ jobs:
       fork: ${{ steps.extract-branch.outputs.fork }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Obtain branch properties
         id: extract-branch
@@ -137,7 +137,7 @@ jobs:
       pact-b64: ${{ steps.encode-pact.outputs.pact-b64 }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Run consumer tests
         run: |
           docker run --rm -v $PWD:/working \

.github/workflows/custom_image_generation.yml

@@ -34,7 +34,7 @@ jobs:
       OUTPUT_FILE_RELATIVE_PATH: jenkins/gce-custom-images/output.txt
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - id: 'auth'
       name: 'Authenticate to Google Cloud'
@@ -81,7 +81,7 @@ jobs:
       DATAPROC_IMAGE_BUCKET: gs://leo-dataproc-image-creation-logs
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - id: 'auth'
         name: 'Authenticate to Google Cloud'

.github/workflows/publish_java_client.yml

@@ -29,7 +29,8 @@ jobs:
       SBT_OPTS: -Xmx3g
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - uses: sbt/setup-sbt@v1
 
       # coursier cache action caches both coursier and sbt caches
       - name: coursier-cache-action

.github/workflows/tag.yml

@@ -46,7 +46,7 @@ jobs:
       new-tag: ${{ steps.tag.outputs.new_tag }}
     steps:
     - name: Checkout current code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: ${{ inputs.ref }}
         token: ${{ secrets.BROADBOT_TOKEN }} # this allows the push to succeed later

.github/workflows/trivy.yml

@@ -7,7 +7,7 @@ jobs:
     name: DSP AppSec Trivy check
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       # The Dockerfile copies this, so it needs
       # to exist for the build to succeed

.github/workflows/unit_test.yml

@@ -36,7 +36,8 @@ jobs:
           - 3307:3306
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+    - uses: sbt/setup-sbt@v1
 
     - name: Set up JDK 17
       uses: actions/setup-java@v3

.github/workflows/verify_consumer_contracts.yml

@@ -107,7 +107,7 @@ jobs:
 
     steps:
     - name: Checkout current code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 

automation/src/test/resources/reference.conf

@@ -7,7 +7,7 @@ leonardo {
     baseImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3"
     gcrWelderUri = "us.gcr.io/broad-dsp-gcr-public/welder-server"
     dockerHubWelderUri = "broadinstitute/welder-server"
-    rstudioBioconductorImageUrl = "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0"
+    rstudioBioconductorImageUrl = "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.20.1"
     //each fiab will have a unique topic name sourced from leonardo.conf, this is never published to in automation tests to ensure pub/sub components can auth properly, but never read from to avoid conflicts.
     topicName = "leonardo-pubsub-test"
     location = "us-central1-a"

http/src/main/resources/reference.conf

@@ -70,7 +70,7 @@ dataproc {
   }
 
   # Cached dataproc image used by Terra
-  customDataprocImage = "projects/broad-dsp-gcr-public/global/images/leo-dataproc-image-2-1-11-debian11-2024-12-11-20-54-48"
+  customDataprocImage = "projects/broad-dsp-gcr-public/global/images/leo-dataproc-image-2-1-11-debian11-2024-12-16-17-22-28"
 
   # The ratio of memory allocated to spark. 0.8 = 80%.
   # Hail/Spark users generally allocate 80% of the ram to the JVM.
@@ -111,7 +111,7 @@ dataproc {
 }
 
 gce {
-  customGceImage = "projects/broad-dsp-gcr-public/global/images/leo-gce-image-2024-12-11-20-55-03"
+  customGceImage = "projects/broad-dsp-gcr-public/global/images/leo-gce-image-2024-12-16-17-22-39"
   userDiskDeviceName = "user-disk"
   defaultScopes = [
     "https://www.googleapis.com/auth/userinfo.email",