Merge branch 'develop' into update/google-cloud-nio-0.127.1

broadinstitute · Aug 15, 2023 · 8969db6 · 8969db6
2 parents 4d27564 + 85d2bcf
commit 8969db6
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Showing 5 changed files with 16 additions and 9 deletions.
diff --git a/automation/project/Dependencies.scala b/automation/project/Dependencies.scala
@@ -34,7 +34,7 @@ object Dependencies {
   val rootDependencies: Seq[ModuleID] = Seq(
     "com.fasterxml.jackson.module" %% "jackson-module-scala" % jacksonV,
     "net.virtual-void" %% "json-lenses" % "0.6.2" % "test",
-    "ch.qos.logback" % "logback-classic" % "1.4.9",
+    "ch.qos.logback" % "logback-classic" % "1.4.11",
     "com.typesafe.akka"   %%  "akka-http-core"     % akkaHttpV,
     "com.typesafe.akka"   %%  "akka-stream-testkit" % akkaV,
     "com.typesafe.akka"   %%  "akka-http"           % akkaHttpV,

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
@@ -39,7 +39,7 @@ object Dependencies {
 
     // elasticsearch requires log4j, but we redirect log4j to logback
     "org.apache.logging.log4j"       % "log4j-to-slf4j"      % "2.20.0",
-    "ch.qos.logback"                 % "logback-classic"     % "1.4.9",
+    "ch.qos.logback"                 % "logback-classic"     % "1.4.11",
     "com.getsentry.raven"            % "raven-logback"       % "8.0.3", // TODO: this should be io.sentry / sentry-logback instead
     "com.typesafe.scala-logging"    %% "scala-logging"       % "3.9.5",
 
@@ -79,8 +79,8 @@ object Dependencies {
       exclude("org.apache.logging.log4j", "log4j-core"),
 
 
-    excludeGuava("com.google.apis"     % "google-api-services-pubsub"       % "v1-rev20230529-2.0.0"),
-    excludeGuava("com.google.apis"     % "google-api-services-admin-directory"  % "directory_v1-rev20230516-2.0.0"),
+    excludeGuava("com.google.apis"     % "google-api-services-pubsub"       % "v1-rev20230801-2.0.0"),
+    excludeGuava("com.google.apis"     % "google-api-services-admin-directory"  % "directory_v1-rev20230802-2.0.0"),
 
 
     "com.github.jwt-scala"          %% "jwt-core"            % "9.4.3",

diff --git a/src/main/scala/org/broadinstitute/dsde/firecloud/service/TSVFileSupport.scala b/src/main/scala/org/broadinstitute/dsde/firecloud/service/TSVFileSupport.scala
@@ -126,7 +126,7 @@ trait TSVFileSupport {
       if (value.equals("__DELETE__"))
         RemoveAttribute(AttributeName.fromDelimitedName(name))
       else {
-        AddUpdateAttribute(AttributeName.fromDelimitedName(name), AttributeString(StringContext.processEscapes(value)))
+        AddUpdateAttribute(AttributeName.fromDelimitedName(name), checkForJson(StringContext.processEscapes(value)))
       }
     }
   }
@@ -165,12 +165,18 @@ trait TSVFileSupport {
               case Success(ref) => ref
               case Failure(_) => AttributeString(value)
             }
-
         }
       }
     }
   }
 
+  def checkForJson(value: String): Attribute = {
+    Try(value.parseJson) match {
+        case Success(_: JsObject) => AttributeValueRawJson(value)
+        case _ => AttributeString(value)
+      }
+  }
+
   def matchesLiteral(value: String): Boolean = {
     value.toLowerCase().endsWith("d") || value.toLowerCase().endsWith("f")
   }

diff --git a/src/test/scala/org/broadinstitute/dsde/firecloud/mock/MockTSV.scala b/src/test/scala/org/broadinstitute/dsde/firecloud/mock/MockTSV.scala
@@ -3,7 +3,6 @@ package org.broadinstitute.dsde.firecloud.mock
 import akka.http.scaladsl.model.Multipart
 import akka.http.scaladsl.model.Multipart.FormData.BodyPart
 import org.broadinstitute.dsde.firecloud.utils.TSVLoadFile
-
 object MockTSVStrings {
 
   /*
@@ -309,7 +308,7 @@ object MockTSVLoadFiles {
     Seq("foo", "bar", "baz"),
     Seq(Seq("woop", "", "doo")))
 
-  val validWorkspaceAttributes = TSVLoadFile("workspace", Seq("a1", "a2", "a3"), Seq(Seq("v1", "2", "[1,2,3]")))
+  val validWorkspaceAttributes = TSVLoadFile("workspace", Seq("a1", "a2", "a3", "a4"), Seq(Seq("v1", "2", "[1,2,3]","""{"tables":{"sample":{"save":["participant",false,"sample",true]}}}""")))
   val validOneWorkspaceAttribute = TSVLoadFile("workspace", Seq("a1"), Seq(Seq("v1")))
   val validEmptyStrWSAttribute = TSVLoadFile("workspace", Seq("a1"), Seq(Seq("")))
   val validRemoveWSAttribute = TSVLoadFile("workspace", Seq("a1"), Seq(Seq("__DELETE__")))

diff --git a/src/test/scala/org/broadinstitute/dsde/firecloud/service/TSVFileSupportSpec.scala b/src/test/scala/org/broadinstitute/dsde/firecloud/service/TSVFileSupportSpec.scala
@@ -24,7 +24,9 @@ class TSVFileSupportSpec extends AnyFreeSpec with TSVFileSupport {
       assertResult(attributes) {
         List(AddUpdateAttribute(AttributeName("default", "a1"), AttributeString("v1")),
           AddUpdateAttribute(AttributeName("default", "a2"), AttributeString("2")),
-          AddUpdateAttribute(AttributeName("default", "a3"), AttributeString("[1,2,3]")))
+          AddUpdateAttribute(AttributeName("default", "a3"), AttributeString("[1,2,3]")),
+        AddUpdateAttribute(AttributeName("default", "a4"), AttributeValueRawJson("""{"tables":{"sample":{"save":["participant",false,"sample",true]}}}""")
+        ))
       }
     }