Merge branch 'develop' into update/scripted-plugin-1.10.5

.git-blame-ignore-revs

@@ -1,2 +1,5 @@
 # Scala Steward: Reformat with scalafmt 3.6.1
 0c093c52c09d7b12cdbd38008e0bbc58c9d110be
+
+# Scala Steward: Reformat with scalafmt 3.8.3
+fc6844bda9d3bdf0b5751381ed9e402fdeb577b8

.github/workflows/auto-approve-broadbot-prs.yml

@@ -5,9 +5,16 @@ permissions:
   pull-requests: write
 
 jobs:
-  dependabot:
+  getActor:
     runs-on: ubuntu-latest
-    if: github.actor == 'broadbot[bot]'
+    steps:
+    - name: "Echo github actor"
+      env:
+        GH_ACTOR: ${{ github.actor }}
+      run: echo "$GH_ACTOR"
+  broadbot:
+    runs-on: ubuntu-latest
+    if: github.actor == 'broadbot'
     steps:
       - name: Approve a PR
         run: gh pr review --approve "$PR_URL"

.scalafmt.conf

@@ -1,4 +1,4 @@
-version=3.6.1
+version=3.8.3
 style = default
 runner.dialect = scala213
 

automation/project/Dependencies.scala

@@ -34,8 +34,10 @@ object Dependencies {
       ExclusionRule("com.google.guava", "guava-jdk5"),
       ExclusionRule("org.apache.httpcomponents", "httpclient")
     ),
-    "com.google.api-client" % "google-api-client" % "1.22.0" excludeAll (ExclusionRule("com.google.guava", "guava-jdk5"),
-    ExclusionRule("org.apache.httpcomponents", "httpclient")),
+    "com.google.api-client" % "google-api-client" % "1.22.0" excludeAll (
+      ExclusionRule("com.google.guava", "guava-jdk5"),
+      ExclusionRule("org.apache.httpcomponents", "httpclient")
+    ),
     "com.typesafe.akka" %% "akka-http-core" % akkaHttpV,
     "com.typesafe.akka" %% "akka-stream-testkit" % akkaV,
     "com.typesafe.akka" %% "akka-http" % akkaHttpV,

pact4s/README.md

@@ -13,8 +13,8 @@ On the command line, you can try the following:
 source env/local.env
 source src/main/resources/rendered/secrets.env
 export PACT_BROKER_URL="https://pact-broker.dsp-eng-tools.broadinstitute.org/"
-export PACT_BROKER_USERNAME="$(gcloud secrets versions access latest --project 'broad-dsp-eng-tools' --secret 'pact-broker-users-read-only' | jq -r '.basic_auth_read_only_username')"
-export PACT_BROKER_PASSWORD="$(gcloud secrets versions access latest --project 'broad-dsp-eng-tools' --secret 'pact-broker-users-read-only' | jq -r '.basic_auth_read_only_password')"
+export PACT_BROKER_USERNAME=$(vault read -field=basic_auth_read_only_username secret/dsp/pact-broker/users/read-only)
+export PACT_BROKER_PASSWORD=$(vault read -field=basic_auth_read_only_password secret/dsp/pact-broker/users/read-only)
 ```
 
 In IntelliJ, you can create a Run Configuration for `SamProviderSpec.scala` and save `Environment Variables` for:

project/Dependencies.scala

@@ -95,15 +95,26 @@ object Dependencies {
   val excludeGoogleAutoValue = ExclusionRule(organization = "com.google.auto.value", name = "auto-value")
   val excludeBouncyCastle = ExclusionRule("org.bouncycastle")
   val workbenchGoogle2: ModuleID =
-    "org.broadinstitute.dsde.workbench" %% "workbench-google2" % workbenchGoogle2V excludeAll (excludeWorkbenchModel, excludeWorkbenchUtil, excludeGoogleAutoValue, excludeBouncyCastle)
+    "org.broadinstitute.dsde.workbench" %% "workbench-google2" % workbenchGoogle2V excludeAll (
+      excludeWorkbenchModel,
+      excludeWorkbenchUtil,
+      excludeGoogleAutoValue,
+      excludeBouncyCastle
+    )
   val workbenchNotifications: ModuleID =
     "org.broadinstitute.dsde.workbench" %% "workbench-notifications" % workbenchNotificationsV excludeAll (excludeWorkbenchGoogle, excludeWorkbenchModel)
   val workbenchGoogleTests: ModuleID =
-    "org.broadinstitute.dsde.workbench" %% "workbench-google" % workbenchGoogleV % "test" classifier "tests" excludeAll (excludeWorkbenchUtil, excludeWorkbenchModel)
+    "org.broadinstitute.dsde.workbench" %% "workbench-google" % workbenchGoogleV % "test" classifier "tests" excludeAll (
+      excludeWorkbenchUtil,
+      excludeWorkbenchModel
+    )
   val workbenchGoogle2Tests: ModuleID =
-    "org.broadinstitute.dsde.workbench" %% "workbench-google2" % workbenchGoogle2V % "test" classifier "tests" excludeAll (excludeWorkbenchUtil, excludeWorkbenchModel)
+    "org.broadinstitute.dsde.workbench" %% "workbench-google2" % workbenchGoogle2V % "test" classifier "tests" excludeAll (
+      excludeWorkbenchUtil,
+      excludeWorkbenchModel
+    )
   val googleStorageLocal: ModuleID =
-    "com.google.cloud" % "google-cloud-nio" % "0.127.25" % "test" // needed for mocking google cloud storage. Should use same version as wb-libs
+    "com.google.cloud" % "google-cloud-nio" % "0.127.26" % "test" // needed for mocking google cloud storage. Should use same version as wb-libs
 
   val liquibaseCore: ModuleID = "org.liquibase" % "liquibase-core" % "4.2.2"
 
@@ -135,7 +146,14 @@ object Dependencies {
   )
 
   val cloudResourceLib: ModuleID =
-    "bio.terra" % "terra-cloud-resource-lib" % crlVersion excludeAll (excludeGoogleServiceUsage, excludeGoogleCloudResourceManager, excludeJerseyCore, excludeJerseyMedia, excludeSLF4J, excludeAwsSdk)
+    "bio.terra" % "terra-cloud-resource-lib" % crlVersion excludeAll (
+      excludeGoogleServiceUsage,
+      excludeGoogleCloudResourceManager,
+      excludeJerseyCore,
+      excludeJerseyMedia,
+      excludeSLF4J,
+      excludeAwsSdk
+    )
   val azureManagedApplications: ModuleID =
     "com.azure.resourcemanager" % "azure-resourcemanager-managedapplications" % "1.0.0-beta.4"
 
@@ -171,8 +189,6 @@ object Dependencies {
   // was included transitively before, now explicit
   val commonsCodec: ModuleID = "commons-codec" % "commons-codec" % "1.17.1"
 
-  val caffeine: ModuleID = "com.github.ben-manes.caffeine" % "caffeine" % "3.1.8"
-
   val rootDependencies = Seq(
     // proactively pull in latest versions of Jackson libs, instead of relying on the versions
     // specified as transitive dependencies, due to OWASP DependencyCheck warnings for earlier versions.
@@ -224,12 +240,11 @@ object Dependencies {
     sentry,
     sentryLogback,
     okio,
-    terraCommonLib,
-    caffeine
+    terraCommonLib
   )
 
   // Needed because it looks like the dependency overrides of wb-libs doesn't propagate to the importing project...
   val rootDependencyOverrides = Seq(
-    "org.apache.commons" % "commons-compress" % "1.26.0"
+    "org.apache.commons" % "commons-compress" % "1.26.2"
   )
 }

src/main/scala/org/broadinstitute/dsde/workbench/sam/dataAccess/AccessPolicyDAO.scala

@@ -125,6 +125,7 @@ trait AccessPolicyDAO {
       resourceTypeNames: Set[ResourceTypeName],
       policies: Set[AccessPolicyName],
       roles: Set[ResourceRoleName],
+      actions: Set[ResourceAction],
       includePublic: Boolean,
       samRequestContext: SamRequestContext
   ): IO[Seq[FilterResourcesResult]]