Update Dockerfile and scripts for v1 layout compatibility, enhancing directory structure and credential handling. Adjust paths for executable and storage, and improve README documentation to reflect changes.

Dockerfile

@@ -29,12 +29,12 @@ RUN make
 # Stage 2: Runtime stage - Create minimal application container
 FROM ubuntu:latest
 
-# Build arguments for configurable credentials and paths
+# Build arguments for configurable credentials and paths (v1 VM layout)
 ARG SSH_USERNAME=piscaladmin
 ARG SSH_PASSWORD=piscaladmin
 ARG SSH_GROUP=piscaladmin
 ARG STORAGE_PATH=/home/piscaladmin/LeafWeb_storage
-ARG PISCAL_EXECUTABLE=/srv/piscal
+ARG PISCAL_EXECUTABLE=/home/piscaladmin/piscal_executable/piscal
 
 # Install runtime dependencies only
 RUN set -xe \
@@ -67,12 +67,13 @@ RUN set -xe \
 RUN set -xe \
 	&& mkdir /run/sshd
 
-# Ensure the job/workspace base under /srv is writable.
+# v1 VM layout: LeafWeb contains scripts + project directories
-# The client uses `/srv/${PiscalDirectoryName}/input` and `PiscalDirectoryName`
+# Create LeafWeb (scripts and job dirs), piscal_executable, and storage
-# can itself be prefixed with `LeafWeb/...`.
 RUN set -xe \
-	&& mkdir -p /srv/LeafWeb \
+	&& mkdir -p /home/${SSH_USERNAME}/LeafWeb \
-	&& chown -R ${SSH_USERNAME}:${SSH_GROUP} /srv/LeafWeb
+	&& mkdir -p /home/${SSH_USERNAME}/piscal_executable \
+	&& chown -R ${SSH_USERNAME}:${SSH_GROUP} /home/${SSH_USERNAME}/LeafWeb \
+	&& chown -R ${SSH_USERNAME}:${SSH_GROUP} /home/${SSH_USERNAME}/piscal_executable
 
 # Create storage directory structure with proper ownership
 RUN set -xe \
@@ -80,25 +81,23 @@ RUN set -xe \
 	&& mkdir -p ${STORAGE_PATH}/output \
 	&& chown -R ${SSH_USERNAME}:${SSH_GROUP} ${STORAGE_PATH}
 
-# Copy compiled executable from builder stage
+# Copy compiled executable and scripts to staging dir (COPY can't use ARG in dest)
-COPY --from=builder /build/leafres/testrun/piscal /srv/piscal
+COPY --from=builder /build/leafres/testrun/piscal /tmp/piscal
+COPY piscal-manager/piscal_launcher.sh piscal-manager/piscal_manager.sh piscal-manager/subdir_year.sh piscal-manager/README.txt /tmp/leafweb/
 
-# Copy piscal-manager scripts (excluding .cfg, we'll generate it)
+# Install to user's home (supports custom SSH_USERNAME)
-COPY piscal-manager/*.sh /srv/
-COPY piscal-manager/README.txt /srv/
-
-# Generate piscal_launcher.cfg with build-time parameters
 RUN set -xe \
-	&& echo "piscal_executable=\"${PISCAL_EXECUTABLE}\"" > /srv/piscal_launcher.cfg \
+	&& cp /tmp/piscal /home/${SSH_USERNAME}/piscal_executable/piscal \
-	&& echo "storage_directory=\"${STORAGE_PATH}\"" >> /srv/piscal_launcher.cfg \
+	&& chown ${SSH_USERNAME}:${SSH_GROUP} /home/${SSH_USERNAME}/piscal_executable/piscal \
-	&& chown ${SSH_USERNAME}:${SSH_GROUP} /srv/piscal_launcher.cfg
+	&& cp /tmp/leafweb/* /home/${SSH_USERNAME}/LeafWeb/ \
+	&& echo "piscal_executable=\"${PISCAL_EXECUTABLE}\"" > /home/${SSH_USERNAME}/LeafWeb/piscal_launcher.cfg \
+	&& echo "storage_directory=\"${STORAGE_PATH}\"" >> /home/${SSH_USERNAME}/LeafWeb/piscal_launcher.cfg \
+	&& chown ${SSH_USERNAME}:${SSH_GROUP} /home/${SSH_USERNAME}/LeafWeb/* \
+	&& find /home/${SSH_USERNAME}/LeafWeb -name "*.sh" -type f -exec sed -i 's/\r$//' {} \; \
+	&& chmod +x /home/${SSH_USERNAME}/LeafWeb/*.sh || true \
+	&& rm -rf /tmp/piscal /tmp/leafweb
 
-# Fix Windows line endings (CRLF -> LF) for scripts and make scripts executable
+WORKDIR /home/${SSH_USERNAME}/LeafWeb
-RUN set -xe \
-	&& find /srv -name "*.sh" -type f -exec sed -i 's/\r$//' {} \; \
-	&& chmod +x /srv/*.sh || true
-
-WORKDIR /srv
 
 EXPOSE 22
 CMD ["/usr/sbin/sshd", "-D"]

README-Docker.md

@@ -64,16 +64,26 @@ The Dockerfile accepts these build arguments if you need to customize:
 | `SSH_PASSWORD` | `piscaladmin` | SSH password for container access |
 | `SSH_GROUP` | `piscaladmin` | Primary group for SSH user |
 | `STORAGE_PATH` | `/home/piscaladmin/LeafWeb_storage` | Storage directory for PISCAL data |
-| `PISCAL_EXECUTABLE` | `/srv/piscal` | Path to PISCAL executable |
+| `PISCAL_EXECUTABLE` | `/home/piscaladmin/piscal_executable/piscal` | Path to PISCAL executable |
 
-### Storage Directory Structure
+### v1 Directory Layout (VM-compatible)
 
-The storage directory is automatically created with:
+The image uses the v1 layout expected by the LeafWeb client:
 
 ```
-/home/piscaladmin/LeafWeb_storage/
+/home/piscaladmin/
-├── input/       # Input files for processing
+├── LeafWeb/                      # Scripts + project directories
-└── output/      # Results from PISCAL processing
+│   ├── piscal_launcher.cfg
+│   ├── piscal_launcher.sh
+│   ├── piscal_manager.sh
+│   ├── subdir_year.sh
+│   ├── README.txt
+│   └── <project_name>/            # Job dirs (e.g. 280_CinnamomumbodinieriLévl)
+├── LeafWeb_storage/
+│   ├── input/
+│   └── output/
+└── piscal_executable/
+    └── piscal
 ```
 
 ### Port Mapping

README-V1.md

@@ -0,0 +1,59 @@
+# v1 VM Deployment (LeafWeb Layout)
+
+This branch configures PISCAL for deployment on a VM matching the layout used by `piscal.eastus.cloudapp.azure.com`, so the LeafWeb client can access jobs and storage at the expected paths.
+
+## Directory Layout
+
+```
+/home/piscaladmin/
+├── LeafWeb/                      # Scripts + project directories
+│   ├── piscal_launcher.cfg       # Config (piscal_executable, storage paths)
+│   ├── piscal_launcher.sh
+│   ├── piscal_manager.sh
+│   ├── subdir_year.sh
+│   ├── README.txt
+│   ├── 280_CinnamomumbodinieriLévl/   # Project dirs (input/, output/, run/, etc.)
+│   ├── 311_AnnaAsaday3high/
+│   └── ...
+├── LeafWeb_storage/              # Shared storage for client
+│   ├── input/
+│   └── output/
+├── piscal/                       # Source (optional)
+└── piscal_executable/            # Compiled binary
+    └── piscal
+```
+
+## Deployment
+
+**Docker (recommended):** The Docker image uses this layout by default. See [README-Docker.md](README-Docker.md).
+
+**Manual VM deployment:** Copy scripts to LeafWeb and the compiled `piscal` binary to `piscal_executable/`:
+
+```bash
+ssh piscaladmin@host 'mkdir -p ~/LeafWeb ~/piscal_executable ~/LeafWeb_storage/input ~/LeafWeb_storage/output'
+scp piscal-manager/*.cfg piscal-manager/*.sh piscal-manager/README.txt piscaladmin@host:~/LeafWeb/
+scp leafres/testrun/piscal piscaladmin@host:~/piscal_executable/
+ssh piscaladmin@host 'chmod +x ~/LeafWeb/*.sh'
+```
+
+## Configuration
+
+`piscal_launcher.cfg` uses VM paths:
+
+- `piscal_executable="/home/piscaladmin/piscal_executable/piscal"`
+- `storage_directory="/home/piscaladmin/LeafWeb_storage"`
+
+Adjust if your VM uses different locations.
+
+## Running Jobs
+
+From `~/LeafWeb`:
+
+```bash
+cd ~/LeafWeb
+./piscal_manager.sh -d 280_CinnamomumbodinieriLévl -s -p C3_photosynthesis_leafweb
+./piscal_manager.sh -d 280_CinnamomumbodinieriLévl   # status
+./piscal_manager.sh -d 280_CinnamomumbodinieriLévl -c   # cleanup
+```
+
+The `-d` argument is the project directory name (a subdir of LeafWeb).

build-docker.ps1

@@ -26,10 +26,12 @@ if ($LASTEXITCODE -eq 0) {
     Write-Host "  - piscal:latest" -ForegroundColor Green
     Write-Host "  - piscal:dev" -ForegroundColor Green
     Write-Host ""
-    Write-Host "Default credentials:" -ForegroundColor Cyan
+    Write-Host "Default credentials (v1 layout):" -ForegroundColor Cyan
     Write-Host "  Username: piscaladmin" -ForegroundColor Cyan
     Write-Host "  Password: piscaladmin" -ForegroundColor Cyan
+    Write-Host "  LeafWeb:  /home/piscaladmin/LeafWeb (scripts + project dirs)" -ForegroundColor Cyan
     Write-Host "  Storage:  /home/piscaladmin/LeafWeb_storage" -ForegroundColor Cyan
+    Write-Host "  Executable: /home/piscaladmin/piscal_executable/piscal" -ForegroundColor Cyan
     Write-Host ""
     Write-Host "To run: docker run -d -p 2222:22 --name piscal-server piscal:latest" -ForegroundColor Yellow
     Write-Host "To SSH: ssh -p 2222 piscaladmin@localhost (password: piscaladmin)" -ForegroundColor Yellow

build-docker.sh

@@ -25,10 +25,12 @@ echo "  - piscal:${VERSION}"
 echo "  - piscal:latest"
 echo "  - piscal:dev"
 echo ""
-echo "Default credentials:"
+echo "Default credentials (v1 layout):"
 echo "  Username: piscaladmin"
 echo "  Password: piscaladmin"
+echo "  LeafWeb:  /home/piscaladmin/LeafWeb (scripts + project dirs)"
 echo "  Storage:  /home/piscaladmin/LeafWeb_storage"
+echo "  Executable: /home/piscaladmin/piscal_executable/piscal"
 echo ""
 echo "To run: docker run -d -p 2222:22 --name piscal-server piscal:latest"
 echo "To SSH: ssh -p 2222 piscaladmin@localhost (password: piscaladmin)"

piscal-manager/piscal_launcher.cfg

@@ -1,7 +1,10 @@
-# NOTE: This file is for reference only when using non-Docker deployments.
+# v1 VM-compatible configuration
-# For Docker builds, this file is generated dynamically at build time from
+# Deploy this file to /home/piscaladmin/LeafWeb/ alongside piscal_launcher.sh,
-# Dockerfile ARG values (see Dockerfile). The Docker-generated version will
+# piscal_manager.sh, and subdir_year.sh. Project directories (e.g. 280_*,
-# use the configured SSH_USERNAME and STORAGE_PATH build arguments.
+# 311_*) live as subdirs of LeafWeb.
+#
+# For Docker builds, this file is NOT used; the Dockerfile generates
+# Docker builds generate this file in LeafWeb at build time.
 
-piscal_executable="/srv/piscal"
+piscal_executable="/home/piscaladmin/piscal_executable/piscal"
 storage_directory="/home/piscaladmin/LeafWeb_storage"