Merge pull request #3347 from yuvipanda/rstudio-shared

Make sure rstudio admins also get shared-readwrite mounted

config/clusters/2i2c-aws-us/showcase.values.yaml

@@ -120,17 +120,6 @@ basehub:
                     # Ensures container working dir is homedir
                     # https://github.com/2i2c-org/infrastructure/issues/2559
                     working_dir: /home/rstudio
-                    # Because this is a list, it will override our default volume mounts
-                    volume_mounts:
-                      # Mount the user home directory
-                      - name: home
-                        mountPath: /home/rstudio
-                        subPath: "{username}"
-                      # Mount the shared readonly directory
-                      - name: home
-                        mountPath: /home/rstudio/shared
-                        subPath: _shared
-                        readOnly: true
           kubespawner_override:
             mem_guarantee: 7.234G
             cpu_guarantee: 0.1

config/clusters/2i2c/imagebuilding-demo.values.yaml

@@ -59,17 +59,6 @@ jupyterhub:
                   # Ensures container working dir is homedir
                   # https://github.com/2i2c-org/infrastructure/issues/2559
                   working_dir: /home/rstudio
-                  # Because this is a list, it will override our default volume mounts
-                  volume_mounts:
-                    # Mount the user home directory
-                    - name: home
-                      mountPath: /home/rstudio
-                      subPath: "{username}"
-                    # Mount the shared readonly directory
-                    - name: home
-                      mountPath: /home/rstudio/shared
-                      subPath: _shared
-                      readOnly: true
               scipy:
                 display_name: Jupyter SciPy Notebook
                 slug: scipy

config/clusters/2i2c/ucmerced-staging.values.yaml

@@ -23,17 +23,6 @@ jupyterhub:
           # Ensures container working dir is homedir
           # https://github.com/2i2c-org/infrastructure/issues/2559
           working_dir: /home/rstudio
-          # Because this is a list, it will override our default volume mounts
-          volume_mounts:
-            # Mount the user home directory
-            - name: home
-              mountPath: /home/rstudio
-              subPath: "{username}"
-            # Mount the shared readonly directory
-            - name: home
-              mountPath: /home/rstudio/shared
-              subPath: _shared
-              readOnly: true
   hub:
     config:
       CILogonOAuthenticator:

config/clusters/2i2c/ucmerced.values.yaml

@@ -23,17 +23,6 @@ jupyterhub:
           # Ensures container working dir is homedir
           # https://github.com/2i2c-org/infrastructure/issues/2559
           working_dir: /home/rstudio
-          # Because this is a list, it will override our default volume mounts
-          volume_mounts:
-            # Mount the user home directory
-            - name: home
-              mountPath: /home/rstudio
-              subPath: "{username}"
-            # Mount the shared readonly directory
-            - name: home
-              mountPath: /home/rstudio/shared
-              subPath: _shared
-              readOnly: true
   hub:
     config:
       CILogonOAuthenticator:

config/clusters/catalystproject-africa/common.values.yaml

@@ -80,14 +80,6 @@ jupyterhub:
           mem_limit: null
           working_dir: /home/rstudio
           default_url: /rstudio
-          volume_mounts:
-            - name: home
-              mountPath: /home/rstudio
-              subPath: "{username}"
-            - name: home
-              mountPath: /home/rstudio/shared
-              subPath: _shared
-              readOnly: true
           node_selector:
             node.kubernetes.io/instance-type: r5.xlarge
       - display_name: "Medium: up to 16 CPU / 128 GB RAM"
@@ -145,14 +137,6 @@ jupyterhub:
           mem_limit: null
           working_dir: /home/rstudio
           default_url: /rstudio
-          volume_mounts:
-            - name: home
-              mountPath: /home/rstudio
-              subPath: "{username}"
-            - name: home
-              mountPath: /home/rstudio/shared
-              subPath: _shared
-              readOnly: true
           node_selector:
             node.kubernetes.io/instance-type: r5.4xlarge
       - display_name: "Large: up to 64 CPU / 512 GB RAM"
@@ -210,13 +194,5 @@ jupyterhub:
           mem_limit: null
           working_dir: /home/rstudio
           default_url: /rstudio
-          volume_mounts:
-            - name: home
-              mountPath: /home/rstudio
-              subPath: "{username}"
-            - name: home
-              mountPath: /home/rstudio/shared
-              subPath: _shared
-              readOnly: true
           node_selector:
             node.kubernetes.io/instance-type: r5.16xlarge

config/clusters/hhmi/common.values.yaml

@@ -69,17 +69,6 @@ basehub:
                     # Ensures container working dir is homedir
                     # https://github.com/2i2c-org/infrastructure/issues/2559
                     working_dir: /home/rstudio
-                    # Because this is a list, it will override our default volume mounts
-                    volume_mounts:
-                      # Mount the user home directory
-                      - name: home
-                        mountPath: /home/rstudio
-                        subPath: "{username}"
-                      # Mount the shared readonly directory
-                      - name: home
-                        mountPath: /home/rstudio/shared
-                        subPath: _shared
-                        readOnly: true
                 desktop:
                   display_name: Linux desktop
                   slug: desktop

config/clusters/nasa-ghg/common.values.yaml

@@ -85,17 +85,6 @@ basehub:
                     # Ensures container working dir is homedir
                     # https://github.com/2i2c-org/infrastructure/issues/2559
                     working_dir: /home/rstudio
-                    # Because this is a list, it will override our default volume mounts
-                    volume_mounts:
-                      # Mount the user home directory
-                      - name: home
-                        mountPath: /home/rstudio
-                        subPath: "{username}"
-                      # Mount the shared readonly directory
-                      - name: home
-                        mountPath: /home/rstudio/shared
-                        subPath: _shared
-                        readOnly: true
                 qgis:
                   display_name: QGIS on Linux Desktop
                   slug: qgis

config/clusters/nasa-veda/common.values.yaml

@@ -139,17 +139,6 @@ basehub:
                     # Ensures container working dir is homedir
                     # https://github.com/2i2c-org/infrastructure/issues/2559
                     working_dir: /home/rstudio
-                    # Because this is a list, it will override our default volume mounts
-                    volume_mounts:
-                      # Mount the user home directory
-                      - name: home
-                        mountPath: /home/rstudio
-                        subPath: "{username}"
-                      # Mount the shared readonly directory
-                      - name: home
-                        mountPath: /home/rstudio/shared
-                        subPath: _shared
-                        readOnly: true
                     init_containers:
                       # Need to explicitly fix ownership here, as otherwise these directories will be owned
                       # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid

config/clusters/smithsonian/common.values.yaml

@@ -87,14 +87,6 @@ basehub:
                     image: rocker/binder:4.3
                     working_dir: /home/rstudio
                     default_url: /rstudio
-                    volume_mounts:
-                      - name: home
-                        mountPath: /home/rstudio
-                        subPath: "{username}"
-                      - name: home
-                        mountPath: /home/rstudio/shared
-                        subPath: _shared
-                        readOnly: true
                 scipy:
                   display_name: Jupyter SciPy Notebook
                   slug: scipy

config/clusters/utoronto/r-common.values.yaml

@@ -11,9 +11,6 @@ jupyterhub:
         # https://github.com/2i2c-org/infrastructure/issues/2559
         working_dir: /home/rstudio
   singleuser:
-    storage:
-      # From https://jupyterhub-image.guide/rocker.html#step-7-setup-zero-to-jupyterhub-configuration-for-home-directory
-      homeMountPath: /home/rstudio
     defaultUrl: /rstudio
     image:
       name: quay.io/2i2c/utoronto-r-image

docs/howto/features/rocker.md

@@ -112,17 +112,6 @@ jupyterhub:
                 # Ensures container working dir is homedir
                 # https://github.com/2i2c-org/infrastructure/issues/2559
                 working_dir: /home/rstudio
-                # Because this is a list, it will override our default volume mounts
-                volume_mounts:
-                  # Mount the user home directory
-                  - name: home
-                    mountPath: /home/rstudio
-                    subPath: "{username}"
-                  # Mount the shared readonly directory
-                  - name: home
-                    mountPath: /home/rstudio/shared
-                    subPath: _shared
-                    readOnly: true
             scipy:
               display_name: Jupyter SciPy Notebook
               slug: scipy
@@ -137,6 +126,6 @@ is configured to automatically install packages from the [Posit Package Manager]
 which provides fast binary package installs.
 
 They are installed under `/usr/local`, and hence *cleared on server stop*. So installed
-packages will *not* persist across user sessions. 
+packages will *not* persist across user sessions.
 
 If users need to have persistent packages installed, we would need a custom image.

helm-charts/basehub/values.yaml

@@ -72,6 +72,9 @@ jupyterhub:
         - name: home
           mountPath: /home/jovyan/shared-readwrite
           subPath: _shared
+        - name: home
+          mountPath: /home/rstudio/shared-readwrite
+          subPath: _shared
     cloudResources:
       provider: ""
       gcp:
@@ -307,6 +310,24 @@ jupyterhub:
           mountPath: /home/jovyan/shared
           subPath: _shared
           readOnly: true
+
+        # For all pods, mount home in both /home/jovyan (done via singleuser.storage.static)
+        # as well as /home/rstudio. This allows rocker images (which use the
+        # rstudio user and put home ine /home/rstudio) to be first class citizens
+        # along with jupyter based images, regardless of how they are specified (
+        # via the configurator, or with unlisted_choice, or as a profile). For non-rocker
+        # images, this is just invisible in the UI and there is no performance overhead
+        # for these extra bind mounts. An additional positive here is that in case *students*
+        # end up accidentally hardcoding paths in their notebooks, it will continue to work
+        # regardless of wether they or on RStudio or JupyterLab (described to us as a serious
+        # problem by openscapes)
+        - name: home
+          mountPath: /home/rstudio
+          subPath: "{username}"
+        - name: home
+          mountPath: /home/rstudio/shared
+          subPath: _shared
+          readOnly: true
     memory:
       guarantee: 256M
       limit: 1G
@@ -621,18 +642,43 @@ jupyterhub:
         # adjusts the spawner to add config specific to admin users
 
         from z2jh import get_config
+        from kubespawner.utils import get_k8s_model
         from kubespawner import KubeSpawner
         from jupyterhub_configurator.mixins import ConfiguratorSpawnerMixin
+        from kubernetes_asyncio.client.models import V1VolumeMount
+
+
+        def modify_pod_hook(spawner, pod):
+            """
+            Modify the pod manifest for admins.
+
+            This is used to modify attributes of the pod that are *lists*,
+            as those are not merged but replaced by KubeSpawner. Everything
+            else is managed via the CustomSpawner's start method below.
+            """
+            custom_admin = get_config('custom.singleuserAdmin', {})
+            if not (spawner.user.admin and custom_admin):
+                return pod
+
+            for c in pod.spec.containers:
+                if c.name == "notebook":
+                  notebook_container = c
+                  break
+            else:
+                raise Exception("No container named 'notebook' found in pod definition")
+
+            admin_volume_mounts = custom_admin.get('extraVolumeMounts', [])
+            notebook_container.volume_mounts += [get_k8s_model(V1VolumeMount, obj) for obj in (admin_volume_mounts)]
+
+            return pod
+        c.KubeSpawner.modify_pod_hook = modify_pod_hook
 
         class CustomSpawner(ConfiguratorSpawnerMixin, KubeSpawner):
             def start(self, *args, **kwargs):
                 custom_admin = get_config('custom.singleuserAdmin', {})
                 if not (self.user.admin and custom_admin):
                     return super().start(*args, **kwargs)
 
-                admin_volume_mounts = custom_admin.get('extraVolumeMounts', [])
-                self.volume_mounts += [vm for vm in admin_volume_mounts if vm not in self.volume_mounts]
-
                 admin_environment = custom_admin.get('extraEnv', {})
                 self.environment.update(admin_environment)