We are very exited to announce a major new release of the Data Retriever, our software for making it quick and easy to get clean, ready to analyze, versions of publicly available data.
The Data Retriever, automates the downloading, cleaning, and installing of ecological and environmental data into your choice of databases and flat file formats. Instead of hours tracking down the data on the web, downloading it, trying to import it, running into issues (e.g, non-standard nulls, problematic column names, encoding issues), fixing one problem, and then encountering the next, all you need to do is run a single command from the command line:
$ retriever install csv iris $ retriever install sqlite breed-bird-survey -f bbs.sqlite
or from R:
>>> rdataretriever::install('postgres', 'wine-quality') >>> portal_data <- rdataretriever::fetch('portal')
The Data Retriever uses information in Frictionless Data datapackage.json files to automatically handle all of the complexities of “simple” data for you. For more complicated complicated datasets, with dozens of components or major data structure issues, the Retriever uses Python scripts as plugins to handle the major data cleaning work and then automatically handles the rest.
Expanded focus and name change
For those of you familiar with the EcoData Retriever, this is the same software with a new name. Challenges with the data end of the analysis pipeline occur across disciplines and our tools work just as well for non-ecological data, so we’ve started adding non-ecological data and changed our name to reflect that. We’d love to hear from anyone interested in leading a push to add data from another discipline or just interested in adding a single favorite dataset.
As part of this we’ve changed the name of the R package from
The 2.0 release includes a number of major changes including:
- Python 3 support (a single code base runs on both Python 2 and 3)
- Adoption of the frictionless data datapackage.json standard (replacing our old YAML like metadata system), including a command line interface for creating and editing datapackage.json files
- Add json and xml as available output formats
- Major expansion of the documentation and hosting of the documentation at Read the Docs
- Remove the graphical user interface (to allow us to focus that development time on wrappers for other languages)
- Lots of work under the hood and major improvements in testing
- Broaden scope to include non-ecological data
We are also in the process of releasing version 1.0 of the R package. This version adds the new features in the Data Retriever and also includes major stability improvements, in particular in RStudio and on Windows.
We also have a brand new website.
Upgrading to the new version (UPDATED)
To ensure the smoothest upgrade to the new version we recommend:
retriever reset scriptsfrom the command line
- Uninstall the old version of the EcoData Retriever
- Install the new version
retriever updatefrom the command line
Henry Senyondo is the lead developer for the Data Retriever and has done an amazing job over the past year developing new features and shoring up the fundamentals for the software. He lead the work on 2.0 start to finish.
Akash Goel was a Google Summer of Code student with the project last summer and was responsible for the majority of the work adding Python 3 support and switching the project over to the
Dan McGlinn, the creator of the R package, has continued his excellent leadership of the development of this package. Shawn Taylor, a new contributor, was instrumental in solving the stability issues on Windows/RStudio.
In addition to these core folks our growing group of contributors to both projects have been invaluable for adding new functionality, fixing bugs, and testing new changes. We are super excited to have contributions from 30 different people and will keep working hard to make sure that everyone feels welcome and supported in contributing to the project.
The level of work done to get these releases out the door was only possible due to generous support of the Gordon and Betty Moore Foundation’s Data Driven Discovery Initiative. This support allowed my group to employ Henry as a full time software engineer to work on these and other projects. This kind of active support for the development and maintenance of research oriented software makes sustainable software development at universities possible.