revisions to make restarting Jupyter lab in container easier

Author: andrewdelman

Docker/Dockerfile

@@ -82,13 +82,17 @@ RUN echo "Installing Miniforge..." \
     && find ${CONDA_DIR} -follow -type f -name '*.a' -delete
 
 
-COPY --chown=${NB_USER}:${NB_USER} ./ECCO-v4-Python-Tutorial /home/${NB_USER}/ECCO-v4-Python-Tutorial
+COPY --chown=${NB_USER}:${NB_USER} ./ECCO-v4-Python-Tutorial ${HOME}/ECCO-v4-Python-Tutorial
 
 RUN echo "Using environment.yml to create conda environment ${CONDA_ENV}" & \
         mamba env create --name ${CONDA_ENV} \
-        -f ./ECCO-v4-Python-Tutorial/Docker/environment.yml
+        -f ${HOME}/ECCO-v4-Python-Tutorial/Docker/environment.yml
+
+# create symlink from home directory to jupyter_lab_start_docker.sh
+RUN ln -s ${HOME}/ECCO-v4-Python-Tutorial/Docker/jupyter_lab_start_docker.sh \
+            ${HOME}/jupyter_lab_start_docker.sh
 
 EXPOSE 8888
 
 # start jupyter lab inside the container
-ENTRYPOINT ["./ECCO-v4-Python-Tutorial/Docker/jupyter_lab_start_docker.sh"]
+ENTRYPOINT ["${HOME}/jupyter_lab_start_docker.sh"]

Docker/README.md

@@ -28,16 +28,32 @@ As Jupyter lab is launched, you will see a lot of output tagged `ServerApp` or `
 
 ## Open Jupyter lab in your browser
 
-Now you need to open a connection between your local machine and the EC2 instance with the correct port forwarding. This will look something like
+Now you need to open a connection between your local machine and the EC2 instance with the correct port forwarding. On your local machine you can use any unused port; note that if you are already running Jupyter lab/notebooks locally that port 8888 will likely already be in use. This example uses 9889 as the local port
 
 ```bash
 ssh -i ~/.ssh/aws_ec2.pem -L 9889:localhost:8888 ec2-user@100.104.70.127
 ```
 
-and then in a browser window on your local machine, access the port you specified before `localhost` above
+and in a browser window on your local machine, access the port you specified before `localhost` above
 
 ```bash
 http://localhost:9889
 ```
 
-You will see a screen that asks for a password, but if you didn't enter any before, you can just go ahead and click `Login`. Now you have access to the tutorial repository, and the tutorials are in the directory `Tutorials_as_Jupyter_Notebooks`. Enjoy!
+You will see a screen that asks for a password, but if you didn't enter any before, you can just go ahead and click `Login`. Now you have access to the tutorial repository, and the tutorials are in the directory `Tutorials_as_Jupyter_Notebooks`.
+
+## Re-connect to Jupyter lab in Docker container
+
+If the Docker container is stopped or exited, the Jupyter lab session will also exit. To restart a Docker container use `docker ps -a` to find the container name and ID, and then use
+
+```bash
+docker start <container-name or id>
+```
+
+to re-start the container. Then you may need to run the following on your instance to re-start Jupyter lab within the container:
+
+```bash
+docker exec -it <container-name or id> ~/jupyter_lab_start_docker.sh
+```
+
+and you should see the `ServerApp` and `LabApp` output appear indicating that the session has started. Then you can use `Ctrl-p` `Ctrl-q` to escape that window from the container.

Docker/jupyter_lab_start_docker.sh

@@ -9,7 +9,7 @@ nocolor_start='\033[0m'
 
 
 # Add Earthdata credentials to ~/.netrc if they are not already present
-sh ./ECCO-v4-Python-Tutorial/Docker/earthdata_auth_docker.sh
+sh ~/ECCO-v4-Python-Tutorial/Docker/earthdata_auth_docker.sh
 
 echo "Starting Jupyter lab session!"
 echo ""
@@ -29,7 +29,7 @@ PW="$(python3 -c 'from jupyter_server.auth import passwd; import getpass; print(
 # Start Jupyter lab
 source /srv/conda/bin/activate
 conda activate jupyter
-jupyter lab --no-browser --autoreload --port=${user_port} --ip='0.0.0.0' --NotebookApp.token='' --NotebookApp.password=\"$PW\" --notebook-dir=\"./ECCO-v4-Python-Tutorial\"
+jupyter lab --no-browser --autoreload --port=${user_port} --ip='0.0.0.0' --NotebookApp.token='' --NotebookApp.password=\"$PW\" --notebook-dir=\"~/ECCO-v4-Python-Tutorial\"
 
 # Print info about session
 echo -e "${red_start}Started Jupyter lab in Docker container"