Merge branch 'develop' into update/reactor-netty-1.0.48

broadinstitute · Nov 13, 2024 · 128f7e8 · 128f7e8
2 parents d39de4c + c6b7df4
commit 128f7e8
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diff --git a/.git-blame-ignore-revs b/.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
diff --git a/.github/workflows/auto-approve-broadbot-prs.yml b/.github/workflows/auto-approve-broadbot-prs.yml
@@ -0,0 +1,23 @@
+name: Broadbot auto-approve
+on: pull_request
+
+permissions:
+  pull-requests: write
+
+jobs:
+  getActor:
+    runs-on: ubuntu-latest
+    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"
+        env:
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.BROADBOT_TOKEN }}
diff --git a/.scalafmt.conf b/.scalafmt.conf
@@ -1,4 +1,4 @@
-version=3.6.1
+version=3.8.3
 style = default
 runner.dialect = scala213
 

diff --git a/automation/project/Dependencies.scala b/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,

diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/sam/MockTestSupport.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/sam/MockTestSupport.scala
@@ -158,7 +158,7 @@ object MockTestSupport extends MockTestSupport {
       policyDAO,
       googleExt,
       FakeOpenIDConnectConfiguration,
-      azureService:Option[AzureService]
+      azureService: Option[AzureService]
     )
   }
 

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
@@ -8,7 +8,7 @@ object Dependencies {
   val scalaTestV = "3.2.19"
   val scalaCheckV = "1.18.1"
   val scalikejdbcVersion = "3.4.2"
-  val postgresDriverVersion = "42.7.2"
+  val postgresDriverVersion = "42.7.4"
   val sentryVersion = "6.15.0"
 
   val workbenchLibV = "fa46370" // If updating this, make sure googleStorageLocal in test dependencies is up-to-date
@@ -47,13 +47,13 @@ object Dependencies {
   val jacksonCore: ModuleID = "com.fasterxml.jackson.core" % "jackson-core" % jacksonV
 
   val logstashLogback: ModuleID = "net.logstash.logback" % "logstash-logback-encoder" % "6.6"
-  val logbackClassic: ModuleID = "ch.qos.logback" % "logback-classic" % "1.4.14"
+  val logbackClassic: ModuleID = "ch.qos.logback" % "logback-classic" % "1.5.12"
   val ravenLogback: ModuleID = "com.getsentry.raven" % "raven-logback" % "7.8.6"
   val scalaLogging: ModuleID = "com.typesafe.scala-logging" %% "scala-logging" % scalaLoggingV
   val ficus: ModuleID = "com.iheart" %% "ficus" % "1.5.2"
 //  val stackdriverLogging: ModuleID = "org.springframework.cloud" % "spring-cloud-gcp-logging" % "1.2.8.RELEASE" excludeAll(excludeSpring, excludeSpringBoot)
   val stackdriverLogging: ModuleID = "com.google.cloud" % "google-cloud-logging-logback" % "0.127.11-alpha"
-  val janino: ModuleID = "org.codehaus.janino" % "janino" % "3.1.7" // For if-else logic in logging config
+  val janino: ModuleID = "org.codehaus.janino" % "janino" % "3.1.12" // For if-else logic in logging config
 
   val akkaActor: ModuleID = "com.typesafe.akka" %% "akka-actor" % akkaV
   val akkaSlf4j: ModuleID = "com.typesafe.akka" %% "akka-slf4j" % akkaV
@@ -71,7 +71,7 @@ object Dependencies {
   val ioGrpc: ModuleID = "io.grpc" % "grpc-core" % "1.34.1"
 
   val googleOAuth2: ModuleID = "com.google.auth" % "google-auth-library-oauth2-http" % "0.18.0" excludeAll excludIoGrpc
-  val googleStorage: ModuleID = "com.google.apis" % "google-api-services-storage" % "v1-rev20220401-1.32.1" excludeAll excludIoGrpc // force this version
+  val googleStorage: ModuleID = "com.google.apis" % "google-api-services-storage" % "v1-rev20241008-2.0.0" excludeAll excludIoGrpc // force this version
 
   val monocle: ModuleID = "com.github.julien-truffaut" %% "monocle-core" % monocleVersion
   val monocleMacro: ModuleID = "com.github.julien-truffaut" %% "monocle-macro" % monocleVersion
@@ -95,19 +95,30 @@ 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"
 
-  val circeYAML: ModuleID = "io.circe" %% "circe-yaml" % "0.14.2"
+  val circeYAML: ModuleID = "io.circe" %% "circe-yaml" % "0.16.0"
   val snakeYAML: ModuleID = "org.yaml" % "snakeyaml" % "2.3"
 
   val scalikeCore = "org.scalikejdbc" %% "scalikejdbc" % scalikejdbcVersion
@@ -135,9 +146,16 @@ 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.1"
+    "com.azure.resourcemanager" % "azure-resourcemanager-managedapplications" % "1.0.0-beta.4"
 
   def excludeSpringBoot = ExclusionRule("org.springframework.boot")
   def excludeSpringAop = ExclusionRule("org.springframework.spring-aop")
@@ -169,7 +187,7 @@ object Dependencies {
   val terraCommonLib = tclExclusions("bio.terra" % "terra-common-lib" % tclVersion classifier "plain")
 
   // was included transitively before, now explicit
-  val commonsCodec: ModuleID = "commons-codec" % "commons-codec" % "1.15"
+  val commonsCodec: ModuleID = "commons-codec" % "commons-codec" % "1.17.1"
 
   val rootDependencies = Seq(
     // proactively pull in latest versions of Jackson libs, instead of relying on the versions
@@ -227,6 +245,6 @@ object Dependencies {
 
   // 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"
   )
 }
diff --git a/src/main/scala/org/broadinstitute/dsde/workbench/sam/dataAccess/PostgresGroupDAO.scala b/src/main/scala/org/broadinstitute/dsde/workbench/sam/dataAccess/PostgresGroupDAO.scala
@@ -28,8 +28,8 @@ import scala.util.{Failure, Try}
   *
   * Example database records: group(7795) contains user(userid) group(7798) contains user(userid) group(7801) contains group(7798) and group(7799)
   *
-  * testdb=# select * from sam_group_member; id | group_id | member_group_id | member_user_id
-  * -------+----------+-----------------+---------------- 15636 | 7795 | | userid 15637 | 7798 | | userid 15638 | 7801 | 7798 | 15639 | 7801 | 7799 |
+  * testdb=# select * from sam_group_member; id | group_id | member_group_id | member_user_id -------+----------+-----------------+---------------- 15636 | 7795
+  * \| | userid 15637 | 7798 | | userid 15638 | 7801 | 7798 | 15639 | 7801 | 7799 |
   *
   * testdb=# select * from sam_group_member_flat; id | group_id | member_group_id | member_user_id | group_membership_path | last_group_membership_element
   * --------+----------+-----------------+----------------+-----------------------+------------------------------ 345985 | 7795 | | userid | {7795} | 7795
@@ -115,19 +115,16 @@ trait PostgresGroupDAO {
     * the head path + tail path
     *
     * Example: Insert group T into group H. H starts empty but is already a member of groups A and B. T already has member groups X and Y which are empty. The
-    * flat group model starts containing: Group | Member Group | Path
-    * ------|--------------|------ A | H | {A} B | H | {B} T | X | {T} T | Y | {T}
+    * flat group model starts containing: Group | Member Group | Path ------|--------------|------ A | H | {A} B | H | {B} T | X | {T} T | Y | {T}
     *
-    * step 1 inserts direct membership of T in H Group | Member Group | Path
-    * ------|--------------|------ H | T | {H}
+    * step 1 inserts direct membership of T in H Group | Member Group | Path ------|--------------|------ H | T | {H}
     *
-    * step 2 inserts indirect memberships T in A and B Group | Member Group | Path
-    * ------|--------------|------ A | T | {A,H} B | T | {B,H}
+    * step 2 inserts indirect memberships T in A and B Group | Member Group | Path ------|--------------|------ A | T | {A,H} B | T | {B,H}
     *
     * step 3 inserts T's lower group hierarchy so that X and Y are members of H, A and B. The tail records are all of the records above where Group is T: ((T,
     * X, {T}), (T, Y, {T}) The head records are all of the records above where Member Group is T and the last path element is H: ((H, T, {H}), (A, T, {A,H}),
-    * (B, T, {B,H})) Group | Member Group | Path
-    * ------|--------------|------ H | X | {H,T} H | Y | {H,T} A | X | {A,H,T} A | Y | {A,H,T} B | X | {B,H,T} B | Y | {B,H,T}
+    * (B, T, {B,H})) Group | Member Group | Path ------|--------------|------ H | X | {H,T} H | Y | {H,T} A | X | {A,H,T} A | Y | {A,H,T} B | X | {B,H,T} B | Y
+    * \| {B,H,T}
     *
     * @param groupId
     *   group being added to