Quickly download, clean up, and install ecological datasets into a database management system
Python Inno Setup Shell
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README.md

Retriever logo

Build Status Build Status (windows) Research software impact codecov.io Documentation Status License Join the chat at https://gitter.im/weecology/retriever

Finding data is one thing. Getting it ready for analysis is another. Acquiring, cleaning, standardizing and importing publicly available data is time consuming because many datasets lack machine readable metadata and do not conform to established data structures and formats. The Data Retriever automates the first steps in the data analysis pipeline by downloading, cleaning, and standardizing datasets, and importing them into relational databases, flat files, or programming languages. The automation of this process reduces the time for a user to get most large datasets up and running by hours, and in some cases days.

Installing the Current Release

If you have Python installed you can install the current release using pip:

pip install retriever

Depending on your system configuration this may require sudo:

sudo pip install retriever

Precompiled binary installers are also available for Windows, OS X, and Ubuntu/Debian on the releases page. These do not require a Python installation. Download the installer for your operating system and follow the instructions at on the download page.

Installing From Source

To install the Data Retriever from source, you'll need Python 2.7+ or 3.3+ with the following packages installed:

  • xlrd

The following packages are optionally needed to interact with associated database management systems:

  • PyMySQL (for MySQL)
  • sqlite3 (for SQLite)
  • psycopg2 (for PostgreSQL)
  • pyodbc (for MS Access - this option is only available on Windows)

To install from source

Either use pip to install directly from GitHub:

pip install git+https://git@github.com/weecology/retriever.git

or:

  1. Clone the repository
  2. From the directory containing setup.py, run the following command: pip install .. You may need to include sudo at the beginning of the command depending on your system (i.e., sudo pip install .).

More extensive documentation for those that are interested in developing can be found here

Using the Command Line

After installing, run retriever update to download all of the available dataset scripts. To see the full list of command line options and datasets run retriever --help. The output will look like this:

usage: retriever [-h] [-v] [-q] {install,update,new,ls,citation,help} ...

positional arguments:
  {install,update,new,ls,citation,help}
                        sub-command help
    install             download and install dataset
    update              download updated versions of scripts
    new                 create a new sample retriever script
    ls                  display a list all available dataset scripts
    citation            view citation
    help

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -q, --quiet           suppress command-line output

To install datasets, use retriever install:

usage: retriever install [-h] [--compile] [--debug]
                         {mysql,postgres,sqlite,msaccess,csv} ...

positional arguments:
  {mysql,postgres,sqlite,msaccess,csv}
                        engine-specific help
    mysql               MySQL
    postgres            PostgreSQL
    sqlite              SQLite
    msaccess            Microsoft Access
    csv                 CSV

optional arguments:
  -h, --help            show this help message and exit
  --compile             force re-compile of script before downloading
  --debug               run in debug mode

Examples

These examples are using Breeding Bird Survey data (BBS)

Using Install

  retriever install -h   (gives install options)

Using specific database engine, retriever install {Engine}

  retriever install mysql -h     (gives install mysql options)
  retriever install mysql --user myuser --password ******** --host localhost --port 8888 --database_name testdbase BBS

install data into an sqlite database named mydatabase.db you would use:

  retriever install sqlite BBS -f mydatabase.db

Using download

  retriever download -h    (gives you help options)
  retriever download BBS"
  retriever download BBS --path C:\Users\Documents

Using citation
  retriever citation   (citation of the retriever engine)
  retriever citation BBS   (citation of BBS data)

Website

For more information see the Data Retriever website.

Acknowledgments

Development of this software was funded by the Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative through Grant GBMF4563 to Ethan White and the National Science Foundation as part of a CAREER award to Ethan White.