Implement Dockerization

MANIFEST.in

@@ -3,6 +3,7 @@ graft tests
 prune docs
 prune scripts
 prune docs/_data
+prune docker
 
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
 

docker/Dockerfile

@@ -0,0 +1,11 @@
+FROM python:3.9
+
+# Note: you can only clone HTTP anonymously so we clone using HTTPs
+# and then use sed to rewrite the remote to be SSH-based
+RUN git clone https://github.com/biopragmatics/biomappings.git && \
+    cd biomappings && \
+    sed -i 's/https:\/\/github.com\//[email protected]:/g' .git/config && \
+    pip install -e .[web]
+
+COPY startup.sh /startup.sh
+ENTRYPOINT ["/startup.sh"]

docker/README.md

@@ -0,0 +1,59 @@
+# Running Biomappings via Docker for curation
+
+## 1. Fork the Biomappings repository
+
+To preform curations using the Biomappings web interface, and contribute these
+back through GitHub, you first have to fork the Biomappings repository as
+follows:
+
+1. Go to https://github.com/biopragmatics/biomappings
+2. Click on the Fork button in the right upper corner of the page. Assuming your
+   username is `GITHUBUSER`, this will create a forked repository at
+   https://github.com/GITHUBUSER/biomappings.
+
+See also the
+GitHub [Fork a Repo](https://docs.github.com/en/get-started/quickstart/fork-a-repo)
+tutorial.
+
+## 2. Run the Biomappings Docker
+
+Since contributions are pushed to GitHub, when running the Docker locally, the
+Docker needs to have (read only) access to:
+
+- The host machine's git configuration (which contains the name and email of the
+  contributor) and is typically stored in `~/.gitconfig`
+- The host machine's SSH key which provides push access to GITHUBUSER's fork of
+  the Biomappings repo. This is typically stored in the `~/.ssh` folder. If you
+  don't have one already, follow GitHub's guide
+  to [making an SSH key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account)
+
+In the run command below, these two paths are mounted into the container.
+Further, the `GITHUBUSER` value described above has to be provided as an
+environment variable.
+
+```shell
+docker run -it -p 5000:5000 -v ~/.ssh:/root/.ssh:ro -v ~/.gitconfig:/root/.gitconfig:ro -e GITHUBUSER=<GITHUBUSER> biomappings:latest
+```
+
+Add `-d` to detach.
+
+## 3. Launch the website and curate
+
+Once the Docker container is running, you can open a browser and go to
+http://localhost:5000, and start curating. Once done with a batch of curations,
+click on the Commit button to have these committed and pushed to the `curation`
+branch of https://github.com/GITHUBUSER/biomappings.
+
+## 4. Submit a pull request
+
+To contribute curations back to the main Biomappings repository, go
+to https://github.com/biopragmatics/biomappings, and open a pull request from
+the GITHUBUSER/curation branch.
+
+# Building the docker image
+
+To build the image, run the following
+
+```shell
+docker build --tag biomappings:latest .
+```

docker/startup.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+cd /biomappings
+git remote set-url origin [email protected]:$GITHUBUSER/biomappings.git
+git checkout -b curation
+biomappings --version
+biomappings web --host "0.0.0.0"

src/biomappings/wsgi.py

@@ -357,4 +357,4 @@ def _go_home():
 
 
 if __name__ == "__main__":
-    app.run()
+    app.run(host="0.0.0.0")