bug des volumes utilisateurs

obijupyterhub/Dockerfile

@@ -30,6 +30,7 @@ RUN apt-get update && apt-get install -y \
     r-base \
     libcurl4-openssl-dev libssl-dev libxml2-dev \
     curl \
+    git \
     texlive-xetex texlive-fonts-recommended texlive-plain-generic \
     ruby ruby-dev \
     vim nano \
@@ -37,9 +38,16 @@ RUN apt-get update && apt-get install -y \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Installer R et packages
-RUN R -e "install.packages(c('IRkernel','tidyverse','vegan','ade4','BiocManager','remotes'), repos='http://cran.rstudio.com/')" && \
+RUN R -e "install.packages(c('IRkernel','tidyverse','vegan','ade4','BiocManager','remotes','igraph'), \
+                             dependencies=TRUE, \
+                             repos='http://cran.rstudio.com/')" && \
     R -e "BiocManager::install('biomformat')" && \
     R -e "remotes::install_github('metabaRfactory/metabaR')" && \
+    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBIUtils.git')" && \
+    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBITaxonomy.git')" && \
+    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBITools.git')" && \
+    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBITaxonomy.git')" && \
+    R -e "remotes::install_git('https://forge.metabarcoding.org/MetabarcodingSchool/biodiversity-metrics.git')" && \
     R -e "IRkernel::installspec(user = FALSE)" && \
     rm -rf /tmp/Rtmp*
 

obijupyterhub/docker-compose.yml

@@ -13,8 +13,8 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock
       # JupyterHub database persistence
       - data:/srv/jupyterhub
-      # The Jupyter user volumes
-      - users:/volumes
+      # Mount the parent volumes directory to access users/, shared/, course/
+      - ../jupyterhub_volumes:/volumes
       # Mount config file directly (for easy modifications)
       - ./jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py:ro
     networks:
@@ -27,6 +27,8 @@ services:
       JUPYTERHUB_ADMIN_PASSWORD: admin2025
       # Optional environment variables
       DOCKER_NOTEBOOK_DIR: /home/jovyan/work
+      # Use PWD to get absolute path relative to docker-compose.yml location
+      HOST_VOLUMES_PATH: ${PWD}/../jupyterhub_volumes
 
   # ---------- Nginx ----------
 

obijupyterhub/jupyterhub_config.py

@@ -10,7 +10,8 @@ c.JupyterHub.spawner_class = 'dockerspawner.DockerSpawner'
 c.JupyterHub.log_level = 'DEBUG'
 c.Spawner.debug = True
 
-VOLUMES_BASE_PATH = '/volumes'
+VOLUMES_BASE_PATH = '/volumes/users'  # Path as seen from JupyterHub container (for user dirs)
+HOST_VOLUMES_PATH = os.environ.get('HOST_VOLUMES_PATH', '/volumes')  # Real path on host machine (parent dir)
 
 # Docker image to use for student containers
 c.DockerSpawner.image = 'jupyterhub-student:latest'
@@ -52,31 +53,28 @@ c.DockerSpawner.notebook_dir = notebook_dir
 async def create_user_dir(spawner):
     """Create user directory if it doesn't exist"""
     user_dir = os.path.join(VOLUMES_BASE_PATH, spawner.user.name)
-    spawner.log.info(f"Ensured user directory exists: {user_dir}")
     Path(user_dir).mkdir(parents=True, exist_ok=True)
+
+    # Change owner to jovyan user (UID 1000, GID 100 in Jupyter images)
+    os.chown(user_dir, 1000, 100)
     os.chmod(user_dir, 0o755)
 
+    spawner.log.info(f"Created user directory with correct permissions: {user_dir}")
+
 c.Spawner.pre_spawn_hook = create_user_dir
 
 c.DockerSpawner.volumes = {
-    # Personal volume (persistent) - root directory
-    'obijupyterhub_shared-{username}' : '/home/jovyan/work',
+    # Personal volume - bind mount from REAL host path
+    f'{HOST_VOLUMES_PATH}/users/{{username}}': '/home/jovyan/work',
     # Shared volume between all students - under work/
-    'obijupyterhub_shared': '/home/jovyan/work/shared',
+    f'{HOST_VOLUMES_PATH}/shared': '/home/jovyan/work/shared',
     # Shared read-only volume for course files - under work/
-    'obijupyterhub_course': {
+    f'{HOST_VOLUMES_PATH}/course': {
         'bind': '/home/jovyan/work/course',
         'mode': 'ro'  # read-only
     }
 }
 
-c.DockerSpawner.volume_driver = 'local'
-c.DockerSpawner.volume_driver_opts = {
-    'type': 'none',
-    'device': '/volumes',
-    'o': 'bind'
-}
-
 # Memory and CPU configuration (adjust according to your needs)
 c.DockerSpawner.mem_limit = '2G'
 c.DockerSpawner.cpu_limit = 1.0