Reproducible data management with Maven
Open PHACTS combines pharmacological data in a single Linked Data cache, and provide RESTful APIs to query and examine the data in a uniform interface. Data is loaded from several data providers like EBI and Uniprot - some of it is loaded directly as RDF, other datasets are translated to RDF from more specific data formats. A series of VoID linksets are also loaded to provide identity equivalence across the different RDF graphs. These linksets are derived from existing references in the earlier loaded data sources, but can also be found computationally (e.g. by comparing chemical structures or protein sequences).
Building Open PHACTS showed a challenge in how to keep all these data sources up to date, particularly when changing our architecture to allow for a Docker-based installation of the Open PHACTS platform and data at customer sites.
Open PHACTS platform is a service oriented architecture with components like a mySQL database, Virtuoso RDF store, memcache and PHP, Tomcat and ElasticSearch. We found Docker to be a great tool for managing and deploying these components in isolation, and combined with Docker Compose, provide an easy way to link them together to form a uniform and installable platform.
The mechanism of
Dockerfile provides a reproducible way to build docker images, which can be created automatically by the Docker hub, typically based on a
GitHub repository. Changes pushed to the GitHub repository causes a new Docker image to be built. Instructions in the Dockerfile consists of commands like
The challenge in setting up the Open PHACTS platform is the data loading. Docker images are stored as a series of differential file system layers, which can be pushed and pull from registries like the Docker Hub and third-party installations of the Docker Registry. This mechanism works well for typical Docker applications, where each layer can have a size in the magnitude of 100 MB, and the full Docker image a size of the magnitude 1 GB. We found that using this mechanism breaks down when used with the Open PHACTS data, which can be in the magnitude of 100 GB as uncompressed RDF.
My open Gigascience review and re-review of Peter Cock's GigaScience article "NCBI BLAST+ integrated into Galaxy": (Cock 2015)
Open science - with Immediate response and impact:
Apache Maven is a build and dependency management system that is widely popular for the Java platform. While newer build systems like Apache Ivy and Gradle have evolved to counter Maven's apparent verbosity and lack of flexibility, they still derive their dependency resolution and metadata aspects from Maven.
A software project that is built using Maven defines its compile settings and metadata in a
Maven has an extensive list of official and third-party plugins to cater for customized build requirement, but also strongly encourage a fixed directory structure (e.g. main source code in
src/main/java and test resources in