Merge pull request #97 from tom-and-the-toothfairies/release-1

Release 1

README.md

@@ -0,0 +1,107 @@
+# Tom and the Toothfairies
+[![spacemacs badge]][spacemacs github] [![build status badge]][circle ci]
+
+*Note: this document is written Markdown. While it can be easily read in a text
+editor, we recommend viewing our documentation on
+Github [here](https://github.com/tom-and-the-toothfairies/pathways#readme) for
+maximum conveniece - the ability to click links for example.*
+
+This file contains instructions on how to install and run the project, as well
+as an overview of the project's design. The target platform is Ubuntu 16.04.
+
+At the time of writing the current release is `1.0`
+
+## Installing Dependencies
+
+This project uses Docker and Docker Compose. For Ubuntu 16.04, an installation
+script `install-docker.sh` is provided for convenience.
+
+```bash
+$ ./install-docker.sh
+```
+
+For platforms other than Ubuntu, follow the installation instructions on
+the [Docker Website][install docker ce]. Note - on other platforms, sudo is not
+required for docker commands.
+
+You can test your docker installation by running docker's built in hello-world:
+
+```bash
+$ sudo docker run hello-world
+```
+
+## Running
+
+The project can be run with `docker compose`
+
+```bash
+$ sudo docker-compose up -d
+```
+
+The system is then accessible at [localhost:4000](http://localhost:4000).
+
+To stop the project, run the following command
+
+```bash
+$ sudo docker-compose down
+```
+
+## Features
+
+The feature list for the project can be found [here](./doc/FEATURES.md)
+
+## Change Log
+
+The change log for the project can be found [here](./doc/CHANGELOG.md)
+
+
+## Architecture Overview
+
+The system is split into three distinct services; Panacea, Asclepius and Chiron.
+The auxiliary service, Athloi, is used for automated testing.
+They each run inside a docker container. The containers can be easily managed
+using `docker-compose` as mentioned earlier.
+
+### Panacea
+
+Panacea is responsible for the UI and PML analysis. It is a web application that
+serves the UI and exposes an API for uploading PML files for analysis.
+
+More information about Panacea can be found [here](./panacea/README.md).
+
+### Chiron
+
+Chiron houses the DINTO data. The data is compiled into a triple store. Chiron
+exposes a HTTP API for querying the triple store.
+
+More information about Chiron can be found [here](./chiron/README.md).
+
+### Asclepius
+
+Asclepius acts as an intermediary between Panacea and Chiron. It accepts
+requests to identify DDIs from Panacea, creates the necessary SPARQL query and
+passes it on to Chiron.
+
+More information about Asclepius can be found [here](./asclepius/README.md).
+
+### Athloi
+
+Athloi is the service that runs our end to end tests.
+
+More information about Athloi can be found [here](./athloi/README.md).
+
+## Building Manually
+
+Docker compose will pull down the required versions of each service from [Docker
+Hub] when you run the project. If for some reason you wish to build these
+services manually, instructions for doing so can be
+found [here](./doc/BUILDING_MANUALLY.md).
+
+
+
+[spacemacs badge]: https://cdn.rawgit.com/syl20bnr/spacemacs/442d025779da2f62fc86c2082703697714db6514/assets/spacemacs-badge.svg
+[spacemacs github]: https://github.com/syl20bnr/spacemacs
+[build status badge]: https://img.shields.io/circleci/project/github/tom-and-the-toothfairies/pathways/master.svg
+[circle ci]: https://circleci.com/gh/tom-and-the-toothfairies/pathways
+[install docker ce]: https://www.docker.com/community-edition#/download
+[docker hub]:  https://hub.docker.com/u/tomtoothfairies/

asclepius/Dockerfile

@@ -7,7 +7,7 @@ EXPOSE 5000
 ENV PYTHONPATH=asclepius
 ENV FLASK_CONFIGURATION=production
 
-RUN apk --no-cache add git gcc musl-dev
+RUN apk --no-cache add gcc musl-dev
 
 RUN mkdir -p /opt/app
 WORKDIR /opt/app