From fb253157977cc2e6f592a8a18167f9533f0d9ca4 Mon Sep 17 00:00:00 2001
From: Vincent Emonet <vincent.emonet@gmail.com>
Date: Wed, 22 Apr 2020 11:31:43 +0200
Subject: [PATCH] Now deploy JupyterLab to enable access to the terminal
 through the Jupyter web UI and improve the user experience when running
 Docket. Documentation to define a secure password for the jupyter notebook
 has been added to the README also

---
 README.md          | 99 ++++++++++++++++++++++++++++++++--------------
 docker-compose.yml |  3 ++
 requirements.txt   |  3 +-
 3 files changed, 75 insertions(+), 30 deletions(-)

diff --git a/README.md b/README.md
index 95a828c..159d23c 100644
--- a/README.md
+++ b/README.md
@@ -8,50 +8,57 @@ Run these commands from the root DOCKET directory that contains the docker-compo
 
 To build the DOCKET docker image:
 
+```bash
 docker-compose build
+```
 
-This docker container is built off the jupyter/scipy-notebook
-base image and installs java 8, nextflow and specific perl
-and python libraries used by DOCKET
+This docker container is built off the jupyter/scipy-notebook base image and installs java 8, nextflow and specific perl and python libraries used by DOCKET
 
  https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-scipy-notebook
 
-jupyter/scipy-notebook comes installed with gcc
- pandas, matplotlib, scipy, seaborn, scikit-learn, cython, Click
- uses apt-get to install system packages
- uses conda to install python libraries
+jupyter/scipy-notebook comes installed with gcc, pandas, matplotlib, scipy, seaborn, scikit-learn, cython, Click, uses apt-get to install system packages, uses conda to install python libraries
 
 ## Run
 
 To run the DOCKET docker container:
 
+```bash
 docker-compose up
+```
 
 ## Connect
 
 To connect to the DOCKET docker container:
 
-  docker-compose exec docket bash
+```bash
+docker-compose exec docket bash
+```
 
 
 ## Nextflow
 
 Connect to the container and run:
 
-  nextflow run docket_study --infile test/dataset1.txt --docket test/ds1_test
+```bash
+nextflow run docket_study --infile test/dataset1.txt --docket test/ds1_test
+```
 
 ## Python sample
 
 Connect to the container and run:
 
-  python scripts/hello_docket.py --files test/hello_docket.txt
+```bash
+python scripts/hello_docket.py --files test/hello_docket.txt
+```
 
 ## Tests
 
 Connect to the container and run:
 
-  pip install -r common/tests/requirements.txt
-  python -m pytest common/tests
+```bash
+pip install -r common/tests/requirements.txt
+python -m pytest common/tests
+```
 
 ## Jupyter notebook
 
@@ -59,7 +66,9 @@ Jupyter notebook runs on port 8888.
 To see the token, either start the container without the detached flag
 or check the logs using:
 
-  docker-compose logs -f docket
+```bash
+docker-compose logs -f docket
+```
 
 ## Data
 
@@ -84,19 +93,51 @@ If this is the configuration you wanted, you would add this line to the docker-c
 
 /Data/datasets:/datasets
 
-An example docker-compose.yml
-
-    version: "2.1"
-    services:
-      docket:
-        build: "."
-        image: "docket-dev"
-        environment:
-          DEBUG: 1
-          PYTHONUNBUFFERED: 1
-          PYTHONPATH: '/app'
-        ports:
-          - 8888:8888
-        volumes:
-          - ./:/app
-          - /Data/datasets:/datasets
\ No newline at end of file
+An example `docker-compose.yml` 
+
+```yaml
+version: "2.1"
+services:
+  docket:
+    build: "."
+    image: "docket-dev"
+    environment:
+      DEBUG: 1
+      PYTHONUNBUFFERED: 1
+      PYTHONPATH: '/app'
+      JUPYTER_ENABLE_LAB: 'yes'
+    ports:
+      - 8888:8888
+    volumes:
+      - ./:/app
+      - /Data/datasets:/datasets
+```
+## Password
+
+Generate a hash to safely define your password by executing the following 2 lines in a Jupyter Notebook:
+
+```python
+from notebook.auth import passwd
+passwd()
+```
+
+Use this hash to define the password in the command run when the container is started:
+
+```yaml
+version: "2.1"
+services:
+  docket:
+    build: "."
+    image: "docket-dev"
+    command: start-notebook.sh  --NotebookApp.password='sha1:9316432938f9:93985dffbb854d31308dfe0602a51db947fb7d80'
+    environment:
+      DEBUG: 1
+      PYTHONUNBUFFERED: 1
+      PYTHONPATH: '/app'
+      JUPYTER_ENABLE_LAB: 'yes'
+    ports:
+      - 8888:8888
+    volumes:
+      - ./:/app
+```
+
diff --git a/docker-compose.yml b/docker-compose.yml
index 8d43862..975128d 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -3,10 +3,13 @@ services:
   docket:
     build: "."
     image: "docket-dev"
+    # sha1 hash used to define password ("test" here)
+    command: start-notebook.sh  --NotebookApp.password='sha1:9316432938f9:93985dffbb854d31308dfe0602a51db947fb7d80'
     environment:
       DEBUG: 1
       PYTHONUNBUFFERED: 1
       PYTHONPATH: '/app'
+      JUPYTER_ENABLE_LAB: 'yes'
     ports:
       - 8888:8888
     volumes:
diff --git a/requirements.txt b/requirements.txt
index 9258a76..d6fcfd6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,5 @@
 annoy==1.16.3
 cyjupyter==0.2.0
 plotly==4.5.2
-git+git://github.com/gglusman/data-fingerprints#egg=datafingerprint
\ No newline at end of file
+git+git://github.com/gglusman/data-fingerprints#egg=datafingerprint
+jupyterlab