fix PYTHONPATH and PATH

http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml

@@ -31,6 +31,10 @@ services:
       PIP_USER: "false"
       PIP_TARGET: "${NOTEBOOKS_DIR}/packages"
       R_LIBS: "${NOTEBOOKS_DIR}/packages"
+      # The next two lines aren't great. But they're for updating PYTHONPATH, PATH in older than (inclusive) us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2
+      # We should remove the two lines once we no longer support older images. In the meantime, we need to be careful updating Jupyter base images.
+      PYTHONPATH: "/etc/jupyter/custom:/usr/lib/spark/python:${NOTEBOOKS_DIR}/packages"
+      PATH: "/opt/conda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:${NOTEBOOKS_DIR}/.local/bin:${NOTEBOOKS_DIR}/packages/bin"
     env_file:
       - /var/google_application_credentials.env
       - /var/custom_env_vars.env

http/src/main/resources/init-resources/jupyter-docker-compose.yaml

@@ -45,6 +45,10 @@ services:
       WELDER_ENABLED: "${WELDER_ENABLED}"
       NOTEBOOKS_DIR: "${NOTEBOOKS_DIR}"
       MEM_LIMIT: "${MEM_LIMIT}"
+      # The next two lines aren't great. But they're for updating PYTHONPATH, PATH in older than (inclusive) us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2.
+      # We should remove the two lines once we no longer support older images
+      PYTHONPATH: "/etc/jupyter/custom:/usr/lib/spark/python:${NOTEBOOKS_DIR}/packages"
+      PATH: "/opt/conda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:${NOTEBOOKS_DIR}/.local/bin:${NOTEBOOKS_DIR}/packages/bin"
     env_file:
       - /var/google_application_credentials.env
       - /var/custom_env_vars.env

http/src/main/resources/init-resources/startup.sh

@@ -68,6 +68,7 @@ export START_USER_SCRIPT_URI=$(startUserScriptUri)
 export START_USER_SCRIPT_OUTPUT_URI=$(startUserScriptOutputUri)
 export WELDER_MEM_LIMIT=$(welderMemLimit)
 export MEM_LIMIT=$(memLimit)
+export INIT_BUCKET_NAME=$(initBucketName)
 export USE_GCE_STARTUP_SCRIPT=$(useGceStartupScript)
 GPU_ENABLED=$(gpuEnabled)
 export IS_RSTUDIO_RUNTIME="false" # TODO: update to commented out code once we release Rmd file syncing
@@ -107,6 +108,8 @@ then
     if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
         echo "Restarting Jupyter Container $GOOGLE_PROJECT / $CLUSTER_NAME..."
 
+        $GSUTIL_CMD cp gs://${INIT_BUCKET_NAME}/`basename ${JUPYTER_DOCKER_COMPOSE}` $JUPYTER_DOCKER_COMPOSE
+
         tee /var/variables.env << END
 JUPYTER_SERVER_NAME=${JUPYTER_SERVER_NAME}
 JUPYTER_DOCKER_IMAGE=${JUPYTER_DOCKER_IMAGE}
@@ -134,6 +137,7 @@ else
 
     if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
         echo "Restarting Jupyter Container $GOOGLE_PROJECT / $CLUSTER_NAME..."
+        $GSUTIL_CMD cp gs://${INIT_BUCKET_NAME}/`basename ${JUPYTER_DOCKER_COMPOSE}` $JUPYTER_DOCKER_COMPOSE
 
         ${DOCKER_COMPOSE} -f ${JUPYTER_DOCKER_COMPOSE} stop
         ${DOCKER_COMPOSE} -f ${JUPYTER_DOCKER_COMPOSE} rm -f
@@ -256,7 +260,7 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
     # kernel tries to connect to it.
     docker exec $JUPYTER_SERVER_NAME /bin/bash -c "R -e '1+1'" || true
 
-    docker exec -d $JUPYTER_SERVER_NAME /bin/bash -c "export WELDER_ENABLED=$WELDER_ENABLED && export NOTEBOOKS_DIR=$NOTEBOOKS_DIR && export PYTHONPATH=${PYTHONPATH:+$PYTHONPATH:}${NOTEBOOKS_DIR}/packages && export PATH=${PATH:+$PATH:}${NOTEBOOKS_DIR}/packages/bin && (/etc/jupyter/scripts/run-jupyter.sh $NOTEBOOKS_DIR || /opt/conda/bin/jupyter notebook)"
+    docker exec -d $JUPYTER_SERVER_NAME /bin/bash -c "export WELDER_ENABLED=$WELDER_ENABLED && export NOTEBOOKS_DIR=$NOTEBOOKS_DIR && (/etc/jupyter/scripts/run-jupyter.sh $NOTEBOOKS_DIR || /opt/conda/bin/jupyter notebook)"
 
     if [ "$WELDER_ENABLED" == "true" ] ; then
         # fix for https://broadworkbench.atlassian.net/browse/IA-1453

http/src/main/scala/org/broadinstitute/dsde/workbench/leonardo/util/BaseRuntimeInterpreter.scala

@@ -22,7 +22,8 @@ import scala.util.Try
 
 abstract private[util] class BaseRuntimeInterpreter[F[_]](
   config: RuntimeInterpreterConfig,
-  welderDao: WelderDAO[F]
+  welderDao: WelderDAO[F],
+  bucketHelper: BucketHelper[F]
 )(implicit F: Async[F],
   dbRef: DbReference[F],
   metrics: OpenTelemetryMetrics[F],
@@ -83,6 +84,9 @@ abstract private[util] class BaseRuntimeInterpreter[F[_]](
         }
         .map(_.getOrElse(params.runtimeAndRuntimeConfig.runtime))
 
+      // Re-upload Jupyter Docker Compose file to init bucket for updating environment variables in Jupyter
+      _ <- bucketHelper.uploadFileToInitBucket(params.initBucket, config.clusterResourcesConfig.jupyterDockerCompose)
+
       startGoogleRuntimeReq = StartGoogleRuntime(params.runtimeAndRuntimeConfig.copy(runtime = updatedRuntime),
                                                  params.initBucket,
                                                  welderAction)

http/src/main/scala/org/broadinstitute/dsde/workbench/leonardo/util/BucketHelper.scala

@@ -90,6 +90,13 @@ class BucketHelper[F[_]](
         .drain
     } yield ()
 
+  def uploadFileToInitBucket(initBucketName: GcsBucketName, runtimeResource: RuntimeResource): F[Unit] =
+    (TemplateHelper.resourceStream[F](runtimeResource) through google2StorageDAO
+      .streamUploadBlob(
+        initBucketName,
+        GcsBlobName(runtimeResource.asString)
+      )).compile.drain
+
   def initializeBucketObjects(
     initBucketName: GcsBucketName,
     serviceAccountKey: Option[ServiceAccountKey],

http/src/main/scala/org/broadinstitute/dsde/workbench/leonardo/util/DataprocInterpreter.scala

@@ -105,7 +105,7 @@ class DataprocInterpreter[F[_]: Parallel](
   metrics: OpenTelemetryMetrics[F],
   logger: StructuredLogger[F],
   dbRef: DbReference[F])
-    extends BaseRuntimeInterpreter[F](config, welderDao)
+    extends BaseRuntimeInterpreter[F](config, welderDao, bucketHelper)
     with RuntimeAlgebra[F]
     with LazyLogging {
 

http/src/main/scala/org/broadinstitute/dsde/workbench/leonardo/util/GceInterpreter.scala

@@ -52,7 +52,7 @@ class GceInterpreter[F[_]](
   dbRef: DbReference[F],
   F: Async[F],
   logger: StructuredLogger[F])
-    extends BaseRuntimeInterpreter[F](config, welderDao)
+    extends BaseRuntimeInterpreter[F](config, welderDao, bucketHelper)
     with RuntimeAlgebra[F] {
   override def createRuntime(
     params: CreateRuntimeParams