bug des volumes utilisateurs

.gitignore

@@ -4,5 +4,8 @@
 /jupyterhub_volumes/jupyterhub
 /jupyterhub_volumes/caddy
 /**/.DS_Store
-
+/web_src/**/*.RData
+/web_src/**/*.pdf
+/web_src/**/*_files
+/web_src/**/*_cache
 /.luarc.json

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
+      # Mount the parent volumes directory to access users/, shared/, course/
-      - users:/volumes
+      - ../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
+    # Personal volume - bind mount from REAL host path
-    'obijupyterhub_shared-{username}' : '/home/jovyan/work',
+    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

start-jupyterhub.sh

@@ -49,18 +49,27 @@ docker ps -aq --filter name=jupyter- | xargs -r docker rm -f 2>/dev/null || true
 # Build student image
 echo ""
 echo -e "${BLUE}🔨 Building student image...${NC}"
-docker build -t jupyterhub-student:latest -f Dockerfile .
+#docker build -t jupyterhub-student:latest -f Dockerfile .
 
 # Build hub image
 echo ""
 echo -e "${BLUE}🔨 Building JupyterHub image...${NC}"
-docker build -t jupyterhub-hub:latest -f Dockerfile.hub .
+#docker build -t jupyterhub-hub:latest -f Dockerfile.hub .
 
 # Compile the web site
 echo ""
 echo  -e "${BLUE}🔨 Building web site...${NC}"
 pushd ../web_src
 quarto render
+find . -name '*.pdf' -print \
+| while read pdfname ; do 
+    dest="../jupyterhub_volumes/web/pages/${pdfname}"
+	dirdest=$(dirname "$dest")
+	mkdir -p "$dirdest"
+    echo "cp '${pdfname}' '${dest}'"  
+  done \
+| bash
+python3 ../tools/generate_pdf_galleries.py
 python3 ../tools/generate_pages_json.py
 popd
 

tools/generate_pdf_galleries.py

@@ -0,0 +1,170 @@
+#!/usr/bin/env python3
+"""Generate lightweight HTML galleries for PDF files within PAGES_DIR."""
+from __future__ import annotations
+
+import html
+import os
+import re
+from pathlib import Path
+from typing import Iterable, List, Tuple
+from urllib.parse import quote
+
+SCRIPT_DIR = Path(__file__).resolve().parent
+PAGES_DIR = (SCRIPT_DIR / ".." / "jupyterhub_volumes" / "web" / "pages").resolve()
+
+GALLERY_TEMPLATE = """<!DOCTYPE html>
+<html lang="fr">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>{title}</title>
+  <style>
+    :root {{
+      font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif;
+      color: #222;
+      background: #f8f8f8;
+    }}
+    body {{
+      margin: 2rem;
+    }}
+    h1 {{
+      font-size: 1.4rem;
+      margin-bottom: 1rem;
+    }}
+    .gallery {{
+      display: grid;
+      grid-template-columns: repeat(auto-fit, minmax(180px, 1fr));
+      gap: 1rem;
+    }}
+    .pdf-card {{
+      background: #fff;
+      border-radius: 8px;
+      padding: 0.75rem;
+      text-decoration: none;
+      color: inherit;
+      box-shadow: 0 1px 4px rgb(15 15 15 / 12%);
+      display: flex;
+      flex-direction: column;
+      align-items: center;
+      gap: 0.5rem;
+    }}
+    .pdf-card:hover {{
+      box-shadow: 0 4px 12px rgb(15 15 15 / 18%);
+    }}
+    .pdf-card object {{
+      width: 150px;
+      height: 200px;
+      border: 1px solid #ddd;
+      border-radius: 4px;
+      background: #fafafa;
+      pointer-events: none;
+    }}
+    .pdf-fallback {{
+      width: 100%;
+      height: 100%;
+      font-size: 0.8rem;
+      color: #777;
+      display: flex;
+      flex-direction: column;
+      justify-content: center;
+      align-items: center;
+      padding: 0.5rem;
+      text-align: center;
+    }}
+    .pdf-label {{
+      font-weight: 500;
+      text-align: center;
+    }}
+  </style>
+</head>
+<body>
+  <h1>{title}</h1>
+  <div class="gallery">
+{cards}
+  </div>
+</body>
+</html>
+"""
+
+ITEM_TEMPLATE = """    <a class="pdf-card" href="{link_href}" target="_blank" rel="noopener">
+      <object data="{object_src}" type="application/pdf" aria-label="{label}">
+        <div class="pdf-fallback">
+          <span>{label}</span>
+          <small>Prévisualisation indisponible</small>
+        </div>
+      </object>
+      <span class="pdf-label">{label}</span>
+    </a>"""
+
+
+def clean_label(entry_name: str) -> str:
+    """Remove numeric prefixes and make a readable label."""
+    base = Path(entry_name).stem
+    base = re.sub(r"^\d+[_\-\s]*", "", base)
+    base = base.replace("_", " ").replace("-", " ")
+    base = re.sub(r"\s+", " ", base).strip()
+    return base.capitalize() if base else Path(entry_name).stem
+
+
+def should_skip_dir(dirname: str) -> bool:
+    """Return True if we should ignore the directory while walking."""
+    return dirname.startswith(".") or dirname.endswith("libs") or dirname == "__pycache__"
+
+
+def iter_pdf_directories(root: Path) -> Iterable[Tuple[Path, List[str]]]:
+    """Yield directories in root containing at least one PDF file."""
+    for current_dir, dirnames, filenames in os.walk(root):
+        dirnames[:] = [name for name in dirnames if not should_skip_dir(name)]
+        pdfs = sorted(name for name in filenames if name.lower().endswith(".pdf"))
+        if pdfs:
+            yield Path(current_dir), pdfs
+
+
+def directory_label(directory: Path) -> str:
+    """Return a human-readable label for the given directory."""
+    try:
+        relative = directory.relative_to(PAGES_DIR)
+    except ValueError:
+        relative = directory
+    if not relative.parts:
+        return "Documents"
+    return " / ".join(clean_label(part) for part in relative.parts)
+
+
+def build_gallery_html(directory: Path, pdf_files: List[str]) -> str:
+    """Create the HTML content for all PDFs in the directory."""
+    cards = []
+    for filename in pdf_files:
+        label = html.escape(clean_label(filename))
+        href = quote(filename)
+        object_src = f"{href}#page=1&view=Fit"
+        cards.append(
+            ITEM_TEMPLATE.format(
+                link_href=html.escape(href, quote=True),
+                object_src=html.escape(object_src, quote=True),
+                label=label,
+            )
+        )
+    title = html.escape(directory_label(directory))
+    return GALLERY_TEMPLATE.format(title=title, cards="\n".join(cards))
+
+
+def main() -> None:
+    if not PAGES_DIR.exists():
+        raise SystemExit(f"❌ PAGES_DIR inexistant: {PAGES_DIR}")
+
+    generated = 0
+    for directory, pdf_files in iter_pdf_directories(PAGES_DIR):
+        html_content = build_gallery_html(directory, pdf_files)
+        output_path = directory / "document.html"
+        output_path.write_text(html_content, encoding="utf-8")
+        rel_out = output_path.relative_to(PAGES_DIR)
+        print(f"✅ {rel_out} ({len(pdf_files)} PDF)")
+        generated += 1
+
+    if not generated:
+        print("ℹ️ Aucun PDF trouvé, aucun document.html généré.")
+
+
+if __name__ == "__main__":
+    main()