Merge pull request #6 from mtholyoke/fix-data-volume-location

Fix `data/` directory mapping

Author: abbydrury

README.md

@@ -19,3 +19,7 @@ Data to be shared between docker container and local machine.
 ### `environment/`
 
 Docker related files and package lists for Python and R as well as JupyterLab plug-ins.
+
+### `jupyterlab/`
+
+This is the root directory for the JupyterLab UI. By default, it will include the `analysis/` and `data/` directories via a symlink. This keeps the JupyterLab UI clean – `environment/` and other top-level files will not appear in the left rail.

environment/Dockerfile

@@ -4,9 +4,17 @@
 FROM jupyter/datascience-notebook:9e63909e0317
 
 # Volumes aren't in place yet 
-COPY --chown=${NB_UID}:${NB_GID} environment/ .
+WORKDIR /home/jovyan/
+COPY --chown=${NB_UID}:${NB_GID} . .
+
+# Set up jupyterlab/ for UI to use
+RUN mkdir jupyterlab
+WORKDIR /home/jovyan/jupyterlab
+RUN ln -s ../analysis analysis
+RUN ln -s ../data data
 
 # Install Python packages from requirements.txt file
+WORKDIR /home/jovyan/environment
 RUN pip install --quiet --no-cache-dir --requirement ./requirements.txt && \
   fix-permissions "${CONDA_DIR}" && \
   fix-permissions "/home/${NB_USER}"
@@ -16,3 +24,6 @@ RUN ./r-packages.R
 
 # Install JupyterLab extensions 
 RUN ./install-jupyter-extensions.sh
+
+
+WORKDIR /home/jovyan/

environment/README.md

@@ -87,6 +87,6 @@ This script installs the JupyterLab extensions, and is run by the `Dockerfile`.
 
 ### `jupyter_server_config.py`
 
-This is where you can make changes to the Jupyter server configuration. By default, it sets the JupyterLab UI to launch in the `analysis` folder of the main project and removes server authentication since this project is only meant to be run on a researcher's computer and not in a shared or production environment.
+This is where you can make changes to the Jupyter server configuration. By default, it sets the JupyterLab UI to launch in the `jupyterlab` folder of the main project and removes server authentication since this project is only meant to be run on a researcher's computer and not in a shared or production environment.
 
 

environment/compose.yml

@@ -13,10 +13,8 @@ services:
     # This connects the Jupyter notebook directory to the host machine so
     # that can all be checked into version control.
     volumes:
-      # Link the analysis directory into the container
+      # Link the analysis and data directories into the container
       - '../analysis:/home/jovyan/analysis'
-      # Link the data directory into the container so it can be made visible in
-      # the JupyterLab UI
       - '../data:/home/jovyan/data'
       # Make the server config file available in the correct place
       - '../environment/jupyter_server_config.py:/home/jovyan/.jupyter/jupyter_server_config.py'

environment/jupyter_server_config.py

@@ -492,7 +492,7 @@
 
 ## The directory to use for notebooks and kernels.
 #  Default: ''
-c.ServerApp.root_dir = 'analysis'
+c.ServerApp.root_dir = 'jupyterlab'
 
 ## The session manager class to use.
 #  Default: 'builtins.object'