[WOR-1212] Update workbenchLibs version. #2503

cahrens · 2023-08-24T01:10:11Z

Ticket: https://broadworkbench.atlassian.net/browse/WOR-1212

My initial goal was just to update to the newest workbench libs version so it was using the Rawls model version specified in #2500, but this change became more complicated because a lot of 3rd party libraries were updated recently in workbench libs.

Given that we would eventually need to tackle this update, I figured it was worth sorting through the various issues now.

PR checklist

Include the JIRA issue number in the PR description and title
Make sure Swagger is updated if API changes
- ...and Orchestration's Swagger too!
If you changed anything in model/, then you should publish a new official rawls-model and update rawls-model in Orchestration's dependencies.
Get two thumbsworth of PR review
Verify all tests go green, including CI tests
Squash commits and merge to develop (branches are automatically deleted after merging)
Inform other teams of any substantial changes via Slack and/or email

cahrens · 2023-08-24T13:26:03Z

jenkins retest

cahrens · 2023-08-24T23:50:47Z

project/Merging.scala

@@ -15,8 +15,7 @@ object Merging {
    case PathList("javax", "ws", "rs", _ @_*)                  => MergeStrategy.first
    case "version.conf"                                        => MergeStrategy.concat
    case "logback.xml"                                         => MergeStrategy.first
-    case x if x.endsWith("kotlin-stdlib.kotlin_module")        => MergeStrategy.first
-    case x if x.endsWith("kotlin-stdlib-common.kotlin_module") => MergeStrategy.first
+    case x if x.endsWith("kotlin_module")                      => MergeStrategy.preferProject


I was getting the errors below in the automation build. I decided to just generalize the check, but please let me know if this is a bad approach… I really don't know much the merging strategy.

19:37:59 [info] Built: /working/google/target/scala-2.13/workbench-google-assembly-0.1-22c0a38-SNAP.jar 19:37:59 [info] Jar hash: e4ba67591bc5301b5203a65e2c6c9e3205e0c770 19:38:31 [info] done compiling 19:38:56 [error] 2 error(s) were encountered during the merge: 19:39:18 [error] 2 error(s) were encountered during the merge: 19:39:18 [error] java.lang.RuntimeException: 19:39:18 [error] Deduplicate found different file contents in the following: 19:39:18 [error] Jar name = auto-value-1.10.2.jar, jar org = com.google.auto.value, entry target = META-INF/kotlin-stdlib-jdk7.kotlin_module 19:39:18 [error] Jar name = kotlin-stdlib-jdk7-1.6.10.jar, jar org = org.jetbrains.kotlin, entry target = META-INF/kotlin-stdlib-jdk7.kotlin_module 19:39:18 [error] Deduplicate found different file contents in the following: 19:39:18 [error] Jar name = auto-value-1.10.2.jar, jar org = com.google.auto.value, entry target = META-INF/kotlin-stdlib-jdk8.kotlin_module 19:39:18 [error] Jar name = kotlin-stdlib-jdk8-1.6.10.jar, jar org = org.jetbrains.kotlin, entry target = META-INF/kotlin-stdlib-jdk8.kotlin_module

…ions.

cahrens · 2023-08-25T16:14:14Z

jenkins retest

cahrens · 2023-08-25T18:07:44Z

automation/project/Dependencies.scala

@@ -5,14 +5,14 @@ object Dependencies {

  val akkaV         = "2.6.8"
  val akkaHttpV     = "10.2.0"
-  val jacksonV      = "2.14.1"
+  val jacksonV      = "2.15.2"


Needed to update Jackson because workbenchLibs updated to this version, and we were getting mismatches in automation:

Caused by: com.fasterxml.jackson.databind.JsonMappingException: Scala module 2.14.1 requires Jackson Databind version >= 2.14.0 and < 2.15.0 - Found jackson-databind version 2.15.2

cahrens · 2023-08-25T18:08:44Z

automation/src/test/scala/org/broadinstitute/dsde/test/api/AuthDomainGroupRoleSpec.scala

@@ -61,7 +61,7 @@ class AuthDomainGroupRoleSpec extends AnyFreeSpec with WorkspaceFixtures with Gr
            AuthDomainMatcher.checkVisibleAndAccessible(projectName, workspaceName, List(groupName))(studentToken)

            // remove "student" from billing project
-            Rawls.billing.removeUserFromBillingProject(projectName, student.email, BillingProjectRole.Owner)(
+            Rawls.billingV2.removeUserFromBillingProject(projectName, student.email, BillingProjectRole.Owner)(


This is because the newer version of workbenchLibs no longer has the v1 code. The revert of the v1 API deletion reintroduced Rawls.billing calls in this file.

cahrens · 2023-08-25T18:09:20Z

.../src/main/scala/org/broadinstitute/dsde/rawls/monitor/BillingAccountChangeSynchronizer.scala

@@ -7,7 +7,7 @@ import cats.effect.unsafe.implicits.global
 import cats.effect.{IO, LiftIO}
 import cats.implicits.{
  catsSyntaxApplicativeError,
-  catsSyntaxApply,
+  catsSyntaxApplyOps,


cats changes required by workbenchLibs updates

cahrens · 2023-08-25T18:10:05Z

project/Merging.scala

@@ -15,8 +15,7 @@ object Merging {
    case PathList("javax", "ws", "rs", _ @_*)                  => MergeStrategy.first
    case "version.conf"                                        => MergeStrategy.concat
    case "logback.xml"                                         => MergeStrategy.first
-    case x if x.endsWith("kotlin-stdlib.kotlin_module")        => MergeStrategy.first
-    case x if x.endsWith("kotlin-stdlib-common.kotlin_module") => MergeStrategy.first
+    case x if x.endsWith("kotlin_module")                      => MergeStrategy.first


I was getting the errors below in the automation build. I decided to just generalize the check, but please let me know if this is a bad approach… I really don't know much the merging strategy.

19:37:59 [info] Built: /working/google/target/scala-2.13/workbench-google-assembly-0.1-22c0a38-SNAP.jar 19:37:59 [info] Jar hash: e4ba67591bc5301b5203a65e2c6c9e3205e0c770 19:38:31 [info] done compiling 19:38:56 [error] 2 error(s) were encountered during the merge: 19:39:18 [error] 2 error(s) were encountered during the merge: 19:39:18 [error] java.lang.RuntimeException: 19:39:18 [error] Deduplicate found different file contents in the following: 19:39:18 [error] Jar name = auto-value-1.10.2.jar, jar org = com.google.auto.value, entry target = META-INF/kotlin-stdlib-jdk7.kotlin_module 19:39:18 [error] Jar name = kotlin-stdlib-jdk7-1.6.10.jar, jar org = org.jetbrains.kotlin, entry target = META-INF/kotlin-stdlib-jdk7.kotlin_module 19:39:18 [error] Deduplicate found different file contents in the following: 19:39:18 [error] Jar name = auto-value-1.10.2.jar, jar org = com.google.auto.value, entry target = META-INF/kotlin-stdlib-jdk8.kotlin_module 19:39:18 [error] Jar name = kotlin-stdlib-jdk8-1.6.10.jar, jar org = org.jetbrains.kotlin, entry target = META-INF/kotlin-stdlib-jdk8.kotlin_module

blakery

Looks like this was a headache to go through.
Thank you for taking it on.

cahrens changed the title ~~Try updating workbenchLibs versions (WOR-1212).~~ [WOR-1212] Try updating workbenchLibs versions. Aug 24, 2023

cahrens commented Aug 24, 2023

View reviewed changes

cahrens added 8 commits August 25, 2023 09:59

Try updating workbenchLibs versions (WOR-1212).

e8365f0

cats updates

707c685

Try removing merge strategy.

a5d60f3

Try discard.

631f6e9

preferProject

486820e

another attempt

b887c1b

another attempt

5e11421

Try updating Jackson version to be compatible work workbenchLibs vers…

0d1f9f1

…ions.

cahrens force-pushed the WOR-1188 branch from 80597e3 to 0d1f9f1 Compare August 25, 2023 13:59

Update billing endpoint.

f137256

cahrens commented Aug 25, 2023

View reviewed changes

cahrens changed the title ~~[WOR-1212] Try updating workbenchLibs versions.~~ [WOR-1212] Update workbenchLibs version. Aug 25, 2023

cahrens requested review from blakery and marctalbott August 25, 2023 18:15

cahrens marked this pull request as ready for review August 25, 2023 18:16

blakery approved these changes Aug 25, 2023

View reviewed changes

marctalbott approved these changes Aug 25, 2023

View reviewed changes

cahrens merged commit 0bdfcad into develop Aug 25, 2023
12 checks passed

cahrens deleted the WOR-1188 branch August 25, 2023 18:48

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[WOR-1212] Update workbenchLibs version. #2503

[WOR-1212] Update workbenchLibs version. #2503

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[WOR-1212] Update workbenchLibs version. #2503

[WOR-1212] Update workbenchLibs version. #2503

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