[AN-551] Get minimal base image running on a BEE

core/src/main/scala/org/broadinstitute/dsde/workbench/leonardo/http/runtimeRoutesModels.scala

@@ -114,7 +114,6 @@ final case class GetRuntimeResponse(id: Long,
                                     defaultClientId: Option[String],
                                     clusterImages: Set[RuntimeImage],
                                     scopes: Set[String],
-                                    welderEnabled: Boolean,
                                     patchInProgress: Boolean,
                                     customClusterEnvironmentVariables: Map[String, String],
                                     diskConfig: Option[DiskConfig]
@@ -142,7 +141,6 @@ object GetRuntimeResponse {
     runtime.defaultClientId,
     runtime.runtimeImages,
     runtime.scopes,
-    runtime.welderEnabled,
     runtime.patchInProgress,
     runtime.customEnvironmentVariables,
     diskConfig

core/src/main/scala/org/broadinstitute/dsde/workbench/leonardo/runtimeModels.scala

@@ -41,7 +41,6 @@ final case class Runtime(id: Long,
                          allowStop: Boolean,
                          runtimeImages: Set[RuntimeImage],
                          scopes: Set[String],
-                         welderEnabled: Boolean,
                          customEnvironmentVariables: Map[String, String],
                          runtimeConfigId: RuntimeConfigId,
                          patchInProgress: Boolean

core/src/test/scala/org/broadinstitute/dsde/workbench/leonardo/http/RuntimeRoutesTestJsonCodec.scala

@@ -197,7 +197,6 @@ object RuntimeRoutesTestJsonCodec {
       defaultClientId,
       clusterImages,
       scopes,
-      true,
       false,
       Map.empty,
       None

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

@@ -31,7 +31,6 @@ export MEM_LIMIT=$(memLimit)
 export SHM_SIZE=$(shmSize)
 export WELDER_MEM_LIMIT=$(welderMemLimit)
 export PROXY_SERVER_HOST_NAME=$(proxyServerHostName)
-export WELDER_ENABLED=$(welderEnabled)
 export NOTEBOOKS_DIR=$(notebooksDir)
 
 START_USER_SCRIPT_URI=$(startUserScriptUri)
@@ -40,7 +39,8 @@ START_USER_SCRIPT_OUTPUT_URI=$(startUserScriptOutputUri)
 IS_GCE_FORMATTED=$(isGceFormatted)
 # Needs to be in sync with terra-docker container
 JUPYTER_HOME=/etc/jupyter
-JUPYTER_SCRIPTS=$JUPYTER_HOME/scripts
+JUPYTER_EXTENSIONS=$JUPYTER_HOME/extensions
+JUPYTER_SCRIPTS=$JUPYTER_EXTENSIONS/scripts
 JUPYTER_USER_HOME=$(jupyterHomeDirectory)
 RSTUDIO_SCRIPTS=/etc/rstudio/scripts
 SERVER_CRT=$(proxyServerCrt)
@@ -311,7 +311,7 @@ log 'Starting up the Jupyter...'
 # and wouldn't be remedied by retrying
 COMPOSE_FILES=(-f ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename ${PROXY_DOCKER_COMPOSE}`)
 cat ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename ${PROXY_DOCKER_COMPOSE}`
-if [ ! -z "$WELDER_DOCKER_IMAGE" ] && [ "$WELDER_ENABLED" == "true" ] ; then
+if [ ! -z "$WELDER_DOCKER_IMAGE" ]; then
   COMPOSE_FILES+=(-f ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename ${WELDER_DOCKER_COMPOSE}`)
   cat ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename ${WELDER_DOCKER_COMPOSE}`
 fi
@@ -351,7 +351,6 @@ JUPYTER_DOCKER_IMAGE=${JUPYTER_DOCKER_IMAGE}
 NOTEBOOKS_DIR=${NOTEBOOKS_DIR}
 OWNER_EMAIL=${OWNER_EMAIL}
 PET_SA_EMAIL=${PET_SA_EMAIL}
-WELDER_ENABLED=${WELDER_ENABLED}
 MEM_LIMIT=${MEM_LIMIT}
 SHM_SIZE=${SHM_SIZE}
 WELDER_SERVER_NAME=${WELDER_SERVER_NAME}
@@ -412,11 +411,9 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
   # See: https://github.com/DataBiosphere/leonardo/pull/4465/files
   if [ ! "$JUPYTER_USER_HOME" = "/home/jupyter" ] ; then
     # TODO: Remove once we stop supporting non AI notebooks based images
-    log 'Installing Jupyter kernelspecs...(Remove once we stop supporting non AI notebooks based images)'
-    KERNELSPEC_HOME=/usr/local/share/jupyter/kernels
-
+    log 'Installing Jupyter kernelspecs'
     # Install kernelspecs inside the Jupyter container
-    retry 3 docker exec -u root ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/kernel/kernelspec.sh ${JUPYTER_SCRIPTS}/kernel ${KERNELSPEC_HOME}
+    retry 3 docker exec -u root ${JUPYTER_SERVER_NAME} ${JUPYTER_HOME}/kernel/kernelspec.sh ${JUPYTER_SCRIPTS}/kernel ${KERNELSPEC_HOME}
   fi
 
   # Install notebook.json which is used to populate Jupyter.notebook.config in JavaScript extensions.
@@ -447,14 +444,14 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
         $GSUTIL_CMD cp $ext /var
         JUPYTER_EXTENSION_ARCHIVE=`basename $ext`
         docker cp /var/${JUPYTER_EXTENSION_ARCHIVE} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
-        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_notebook_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
+        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_install_notebook_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
       elif [[ $ext == 'http://'* || $ext == 'https://'* ]]; then
         JUPYTER_EXTENSION_FILE=`basename $ext`
         curl $ext -o /var/${JUPYTER_EXTENSION_FILE}
         docker cp /var/${JUPYTER_EXTENSION_FILE} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/${JUPYTER_EXTENSION_FILE}
-        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_notebook_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_FILE}
+        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_install_notebook_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_FILE}
       else
-        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_pip_install_notebook_extension.sh $ext
+        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_pip_install_notebook_extension.sh $ext
       fi
     done
   fi
@@ -468,9 +465,9 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
         $GSUTIL_CMD cp $ext /var
         JUPYTER_EXTENSION_ARCHIVE=`basename $ext`
         docker cp /var/${JUPYTER_EXTENSION_ARCHIVE} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
-        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_server_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
+        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_install_server_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
       else
-        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_pip_install_server_extension.sh $ext
+        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_pip_install_server_extension.sh $ext
       fi
     done
   fi
@@ -485,9 +482,9 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
         $GSUTIL_CMD cp $ext /var
         JUPYTER_EXTENSION_ARCHIVE=`basename $ext`
         docker cp /var/${JUPYTER_EXTENSION_ARCHIVE} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
-        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_combined_extension.sh ${JUPYTER_EXTENSION_ARCHIVE}
+        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_install_combined_extension.sh ${JUPYTER_EXTENSION_ARCHIVE}
       else
-        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_pip_install_combined_extension.sh $ext
+        retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_pip_install_combined_extension.sh $ext
       fi
     done
   fi
@@ -503,14 +500,14 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
         $GSUTIL_CMD cp -r $ext /var
         JUPYTER_EXTENSION_ARCHIVE=`basename $ext`
         docker cp /var/${JUPYTER_EXTENSION_ARCHIVE} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
-        retry 3 docker exec -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_lab_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
+        retry 3 docker exec -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_install_lab_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
       elif [[ $ext == 'http://'* || $ext == 'https://'* ]]; then
         JUPYTER_EXTENSION_FILE=`basename $ext`
         curl $ext -o /var/${JUPYTER_EXTENSION_FILE}
         docker cp /var/${JUPYTER_EXTENSION_FILE} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/${JUPYTER_EXTENSION_FILE}
-        retry 3 docker exec -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_lab_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_FILE}
+        retry 3 docker exec -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_install_lab_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_FILE}
       else
-        retry 3 docker exec -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_lab_extension.sh $ext
+        retry 3 docker exec -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/jupyter_install_lab_extension.sh $ext
       fi
     done
   fi
@@ -524,24 +521,26 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
   docker exec $JUPYTER_SERVER_NAME /bin/bash -c "R -e '1+1'" || true
 
   # For older jupyter images, jupyter_delocalize.py is using 127.0.0.1 as welder's url, which won't work now that we're no longer using `network_mode: host` for GCE VMs
-  docker exec $JUPYTER_SERVER_NAME /bin/bash -c "sed -i 's/127.0.0.1/welder/g' /etc/jupyter/custom/jupyter_delocalize.py"
+  docker exec $JUPYTER_SERVER_NAME /bin/bash -c "sed -i 's/127.0.0.1/welder/g' $JUPYTER_EXTENSIONS/jupyter_delocalize.py"
+
+  log 'Wget the gitignore_global file, set gitignore in Git Config'
 
   # Copy gitignore into jupyter container (ask AOU?)
-  docker exec $JUPYTER_SERVER_NAME /bin/bash -c "wget -N https://raw.githubusercontent.com/DataBiosphere/terra-docker/045a139dbac19fbf2b8c4080b8bc7fff7fc8b177/terra-jupyter-aou/gitignore_global"
+  docker exec $JUPYTER_SERVER_NAME /bin/bash -c "wget -N https://raw.githubusercontent.com/DataBiosphere/terra-docker/045a139dbac19fbf2b8c4080b8bc7fff7fc8b177/terra-jupyter-aou/gitignore_global \
+  && git config --global core.excludesfile $JUPYTER_USER_HOME/gitignore_global"
+
+  docker exec $JUPYTER_SERVER_NAME /bin/bash -c "whoami"
 
-  # Install nbstripout and set gitignore in Git Config (ask AOU?)
-  docker exec $JUPYTER_SERVER_NAME /bin/bash -c "pip install nbstripout \
-        && nbstripout --install --global \
-        && git config --global core.excludesfile $JUPYTER_USER_HOME/gitignore_global"
+  docker exec $JUPYTER_SERVER_NAME /bin/bash -c "ls -l $JUPYTER_EXTENSIONS"
 
   # Starts the locking logic (used for AOU). google_sign_in.js  is likely not used anymore
-  docker exec -u 0 $JUPYTER_SERVER_NAME /bin/bash -c "$JUPYTER_HOME/scripts/extension/install_jupyter_contrib_nbextensions.sh \
+  docker exec -u 0 $JUPYTER_SERVER_NAME /bin/bash -c "$JUPYTER_SCRIPTS/install_jupyter_contrib_nbextensions.sh \
        && mkdir -p $JUPYTER_USER_HOME/.jupyter/custom/ \
-       && cp $JUPYTER_HOME/custom/google_sign_in.js $JUPYTER_USER_HOME/.jupyter/custom/ \
-       && ls -la $JUPYTER_HOME/custom/extension_entry_jupyter.js \
-       && cp $JUPYTER_HOME/custom/extension_entry_jupyter.js $JUPYTER_USER_HOME/.jupyter/custom/custom.js \
-       && cp $JUPYTER_HOME/custom/safe-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
-       && cp $JUPYTER_HOME/custom/edit-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
+       && cp $JUPYTER_EXTENSIONS/google_sign_in.js $JUPYTER_USER_HOME/.jupyter/custom/ \
+       && ls -la $JUPYTER_EXTENSIONS/extension_entry_jupyter.js \
+       && cp $JUPYTER_EXTENSIONS/extension_entry_jupyter.js $JUPYTER_USER_HOME/.jupyter/custom/custom.js \
+       && cp $JUPYTER_EXTENSIONS/safe-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
+       && cp $JUPYTER_EXTENSIONS/edit-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
        && mkdir -p $JUPYTER_HOME/nbconfig"
 
   # In new jupyter images, we should update jupyter_notebook_config.py in terra-docker.
@@ -566,7 +565,7 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
    STEP_TIMINGS+=($(date +%s))
 
   log 'Starting Jupyter Notebook...'
-  retry 3 docker exec -d $JUPYTER_SERVER_NAME /bin/bash -c "${JUPYTER_SCRIPTS}/run-jupyter.sh ${NOTEBOOKS_DIR}"
+  retry 3 docker exec -d $JUPYTER_SERVER_NAME /bin/bash -c "${JUPYTER_HOME}/run-jupyter.sh ${NOTEBOOKS_DIR}"
 
   # done start Jupyter
   STEP_TIMINGS+=($(date +%s))

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

@@ -159,7 +159,8 @@ if [[ "${ROLE}" == 'Master' ]]; then
     bash add-google-cloud-ops-agent-repo.sh --also-install
 
     JUPYTER_HOME=/etc/jupyter
-    JUPYTER_SCRIPTS=${JUPYTER_HOME}/scripts
+    JUPYTER_EXTENSIONS=$JUPYTER_HOME/extensions
+    JUPYTER_SCRIPTS=$JUPYTER_EXTENSIONS/scripts
     KERNELSPEC_HOME=/usr/local/share/jupyter/kernels
 
     # Set variables
@@ -185,7 +186,6 @@ if [[ "${ROLE}" == 'Master' ]]; then
     export PROXY_DOCKER_IMAGE=$(proxyDockerImage)
     export WELDER_DOCKER_IMAGE=$(welderDockerImage)
     export CRYPTO_DETECTOR_DOCKER_IMAGE=$(cryptoDetectorDockerImage)
-    export WELDER_ENABLED=$(welderEnabled)
     export NOTEBOOKS_DIR=$(notebooksDir)
     export MEM_LIMIT=$(memLimit)
     export SHM_SIZE=$(shmSize)
@@ -291,7 +291,7 @@ EOF
 
     cat /etc/`basename ${PROXY_DOCKER_COMPOSE}`
 
-    if [ ! -z ${WELDER_DOCKER_IMAGE} ] && [ "${WELDER_ENABLED}" == "true" ] ; then
+    if [ ! -z ${WELDER_DOCKER_IMAGE} ]; then
       COMPOSE_FILES+=(-f /etc/`basename ${WELDER_DOCKER_COMPOSE}`)
       cat /etc/`basename ${WELDER_DOCKER_COMPOSE}`
     fi
@@ -360,7 +360,7 @@ EOF
             gsutil cp $ext /etc
             JUPYTER_EXTENSION_ARCHIVE=`basename $ext`
             docker cp /etc/${JUPYTER_EXTENSION_ARCHIVE} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
-            retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/jupyter_install_notebook_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
+            retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_EXTENSIONS}/jupyter_install_notebook_extension.sh ${JUPYTER_HOME}/${JUPYTER_EXTENSION_ARCHIVE}
           elif [[ $ext == 'http://'* || $ext == 'https://'* ]]; then
             JUPYTER_EXTENSION_FILE=`basename $ext`
             curl $ext -o /etc/${JUPYTER_EXTENSION_FILE}
@@ -459,7 +459,7 @@ EOF
 
       # jupyter_delocalize.py now assumes welder's url is `http://welder:8080`, but on dataproc, we're still using host network
       # A better to do this might be to take welder host as an argument to the script
-      docker exec $JUPYTER_SERVER_NAME /bin/bash -c "sed -i 's/http:\/\/welder/http:\/\/127.0.0.1/g' /etc/jupyter/custom/jupyter_delocalize.py"
+      docker exec $JUPYTER_SERVER_NAME /bin/bash -c "sed -i 's/http:\/\/welder/http:\/\/127.0.0.1/g' ${JUPYTER_EXTENSIONS}/jupyter_delocalize.py"
 
       # In new jupyter images, we should update jupyter_notebook_config.py in terra-docker.
       # This is to make it so that older images will still work after we change notebooks location to home dir
@@ -474,17 +474,17 @@ EOF
             && git config --global core.excludesfile $JUPYTER_USER_HOME/gitignore_global"
 
       # Install the custom jupyter extensions needed to lock notebooks into edit or safe modes (required by AOU)
-      docker exec -u 0 $JUPYTER_SERVER_NAME /bin/bash -c "$JUPYTER_HOME/scripts/extension/install_jupyter_contrib_nbextensions.sh \
-           && mkdir -p $JUPYTER_USER_HOME/.jupyter/custom/ \
-           && cp $JUPYTER_HOME/custom/google_sign_in.js $JUPYTER_USER_HOME/.jupyter/custom/ \
-           && ls -la $JUPYTER_HOME/custom/extension_entry_jupyter.js \
-           && cp $JUPYTER_HOME/custom/extension_entry_jupyter.js $JUPYTER_USER_HOME/.jupyter/custom/custom.js \
-           && cp $JUPYTER_HOME/custom/safe-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
-           && cp $JUPYTER_HOME/custom/edit-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
-           && mkdir -p $JUPYTER_HOME/nbconfig"
+#      docker exec -u 0 $JUPYTER_SERVER_NAME /bin/bash -c "$JUPYTER_SCRIPTS/install_jupyter_contrib_nbextensions.sh \
+#           && mkdir -p $JUPYTER_USER_HOME/.jupyter/custom/ \
+#           && cp $JUPYTER_EXTENSIONS/google_sign_in.js $JUPYTER_USER_HOME/.jupyter/custom/ \
+#           && ls -la $JUPYTER_EXTENSIONS/extension_entry_jupyter.js \
+#           && cp $JUPYTER_EXTENSIONS/extension_entry_jupyter.js $JUPYTER_USER_HOME/.jupyter/custom/custom.js \
+#           && cp $JUPYTER_EXTENSIONS/safe-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
+#           && cp $JUPYTER_EXTENSIONS/edit-mode.js $JUPYTER_USER_HOME/.jupyter/custom/ \
+#           && mkdir -p $JUPYTER_HOME/nbconfig"
 
       log 'Starting Jupyter Notebook...'
-      retry 3 docker exec -d ${JUPYTER_SERVER_NAME} /bin/bash -c "${JUPYTER_SCRIPTS}/run-jupyter.sh ${NOTEBOOKS_DIR}"
+      retry 3 docker exec -d ${JUPYTER_SERVER_NAME} /bin/bash -c "${JUPYTER_HOME}/custom/run-jupyter.sh ${NOTEBOOKS_DIR}"
 
       STEP_TIMINGS+=($(date +%s))
     fi

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

@@ -27,14 +27,13 @@ services:
       OWNER_EMAIL: "${OWNER_EMAIL}"
       PET_SA_EMAIL: "${PET_SA_EMAIL}"
       # Value must be the string "true" to enable.
-      WELDER_ENABLED: "${WELDER_ENABLED}"
       NOTEBOOKS_DIR: "${NOTEBOOKS_DIR}"
       PIP_USER: "true"
       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"
+      PATH: "/opt/conda/bin:/opt/uv/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/custom_env_vars.env
     # See https://docs.docker.com/engine/reference/run/#user-memory-constraints

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

@@ -44,15 +44,14 @@ services:
       OWNER_EMAIL: "${OWNER_EMAIL}"
       PET_SA_EMAIL: "${PET_SA_EMAIL}"
       # Value must be the string "true" to enable.
-      WELDER_ENABLED: "${WELDER_ENABLED}"
       NOTEBOOKS_DIR: "${NOTEBOOKS_DIR}"
       MEM_LIMIT: "${MEM_LIMIT}"
       # (1/6/2022) When it's a year from now, consider removing the next two lines.
       # The next two lines aren't great. But they're for updating PYTHONPATH, PATH in older than (inclusive) us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2.
       # We should remove the two lines once we no longer support older images.
       # When we update base image in terra-docker next time, we should verify the paths are still valid
       PYTHONPATH: "/etc/jupyter/custom:/usr/lib/spark/python:${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:${HOME}/.local/bin:${NOTEBOOKS_DIR}/packages/bin"
+      PATH: "/opt/conda/bin:/opt/uv/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:${HOME}/.local/bin:${NOTEBOOKS_DIR}/packages/bin"
     env_file:
       - /var/custom_env_vars.env
     # See https://docs.docker.com/engine/reference/run/#user-memory-constraints

http/src/main/resources/init-resources/notebook.json

@@ -3,5 +3,4 @@
   "clusterName": $(clusterName),
   "loginHint": $(loginHint),
   "googleClientId": $(googleClientId),
-  "welderEnabled": $(welderEnabled)
 }