From 73648ebe3113b98733c130c254ef28fda07944c0 Mon Sep 17 00:00:00 2001
From: Florez Ospina Juan Felipe <juan.florez-ospina@psi.ch>
Date: Wed, 2 Apr 2025 14:09:44 +0200
Subject: [PATCH] Update Dockerfile and docker-compose.yaml. By default,
 container can use cifs to map network drives so no need to install, and added
 bash command to docker compose file to run both jupyterlab and dash board
 simultanously

---
 Dockerfile          | 96 +++++++++++++++++++++++----------------------
 docker-compose.yaml |  8 +++-
 2 files changed, 56 insertions(+), 48 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 615e4af..1b637a0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,46 +1,50 @@
-# Get additional info about the Dockerfile at https://docs.docker.com/reference/dockerfile/ 
-
-FROM continuumio/miniconda3:latest
-
-# Define the name of the environment
-ARG ENV_NAME=apog_penv
-ENV ENV_NAME=apog_penv
-
-# Set the working directory
-WORKDIR /acsmdc
-
-# Use mamba if available for faster installation
-RUN conda install -y -n base -c conda-forge mamba && \
-    mamba create -y -n $ENV_NAME -c conda-forge -c defaults python=3.11 \
-    jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip && \
-    conda clean --all -y && rm -rf /root/.cache/pip
-
-# Activate the environment and install additional pip packages
-RUN conda run -n $ENV_NAME pip install pybis==1.35 igor2 ipykernel sphinx dash dash-bootstrap-components
-
-# Set the default environment when the container starts
-ENV CONDA_DEFAULT_ENV=$ENV_NAME
-ENV PATH=/opt/conda/envs/$ENV_NAME/bin:$PATH
-
-# Create necessary directories for VOLUME
-RUN mkdir -p /acsmdc/data /acsmdc/figures /acsmdc/pipelines/params
-
-# Copy project files, excluding certain directories (handled via .dockerignore)
-COPY . /acsmdc
-
-# Copy and install dependencies from requirements.txt
-COPY requirements.txt /acsmdc/requirements.txt
-RUN conda run -n $ENV_NAME pip install -r /acsmdc/requirements.txt
-
-# Define volumes for excluded directories
-VOLUME ["/acsmdc/data", "/acsmdc/figures", "/acsmdc/pipelines/params"]
-
-# Add JupyterLab
-RUN pip install --no-cache-dir jupyterlab
-#RUN pip install pipx
-#RUN pipx install renku
-# Add any other packages needed for JupyterLab
-#RUN pip install --no-cache-dir matplotlib scikit-learn
-
-# If you want to set JupyterLab as the default command
-CMD ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token='my-token'"]
+# Get additional info about the Dockerfile at https://docs.docker.com/reference/dockerfile/ 
+
+FROM continuumio/miniconda3:latest
+
+# Define the name of the environment
+ARG ENV_NAME=apog_penv
+ENV ENV_NAME=apog_penv
+
+# Set the working directory
+WORKDIR /acsmdc
+
+#RUN apt-get update && apt-get install -y cifs-utils
+
+# Use mamba if available for faster installation
+RUN conda install -y -n base -c conda-forge mamba && \
+    mamba create -y -n $ENV_NAME -c conda-forge -c defaults python=3.11 \
+    jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip && \
+    conda clean --all -y && rm -rf /root/.cache/pip
+
+# Activate the environment and install additional pip packages
+RUN conda run -n $ENV_NAME pip install pybis==1.35 igor2 ipykernel sphinx dash dash-bootstrap-components
+
+# Set the default environment when the container starts
+ENV CONDA_DEFAULT_ENV=$ENV_NAME
+ENV PATH=/opt/conda/envs/$ENV_NAME/bin:$PATH
+
+# Create necessary directories for VOLUME
+RUN mkdir -p /acsmdc/data /acsmdc/figures /acsmdc/pipelines/params
+#RUN mkdir -p /mnt/lac_ord
+
+# Copy project files, excluding certain directories (handled via .dockerignore)
+COPY . /acsmdc
+
+# Copy and install dependencies from requirements.txt
+COPY requirements.txt /acsmdc/requirements.txt
+RUN conda run -n $ENV_NAME pip install -r /acsmdc/requirements.txt
+
+# Define volumes for excluded directories
+VOLUME ["/acsmdc/data", "/acsmdc/figures", "/acsmdc/pipelines/params"]
+
+# Add JupyterLab
+RUN pip install --no-cache-dir jupyterlab
+#RUN pip install pipx
+#RUN pipx install renku
+# Add any other packages needed for JupyterLab
+#RUN pip install --no-cache-dir matplotlib scikit-learn
+
+# If you want to set JupyterLab as the default command
+#CMD ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token='my-token'"]
+CMD ["/bin/bash"]
\ No newline at end of file
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 834edf7..d6e2beb 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -1,5 +1,5 @@
 services:
-  data_processor:
+  datachain_processor:
     image: datachain_processor
     container_name: datachain_processor
     restart: unless-stopped
@@ -13,7 +13,11 @@ services:
       - ./figures:/acsmdc/figures
       - ./pipelines/params:/acsmdc/pipelines/params
       - lac_ord:/mnt/network/lac_ord:rw
-    command: ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token='my-token'"]
+    command: >
+      bash -c "
+      jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='my-token' & 
+      python /acsmdc/app/data_flagging_app.py
+      " 
 
 volumes:
   lac_ord: