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Setup

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Data

Download the data file Portal_rodents_19772002_simplified.csv, which is a csv file that will open in a new browser tab. Be sure to right click or control click in order to save the file (NOTE: In Safari, right click and select Download linked file; in Chrome and Firefox, right-click and select Save link as...). Make a note of the location (i.e. the folder, your Desktop) to which you save the file.

About the data

The data for this lesson is a part of the Data Carpentry Ecology workshop. It is a teaching version of the Portal Database. The data in this lesson is a subset of the teaching version that has been intentionally 'messed up' for this lesson.

The data for this lesson and the workshop are in the Portal Project Teaching Database available on FigShare, with a CC-BY license available for reuse.

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Software

For this lesson you will need OpenRefine version 3.7.2 and a web browser.

Note: OpenRefine is a Java program that runs on your machine (not in the cloud). It runs inside your browser, but no web connection is needed.

Download OpenRefine version 3.7.2 from https://openrefine.org/download.

  • Do not download beta versions or the release candidates. These are only for development and testing of the software.
  • If you are on Windows and do not have Java installed, download the version Windows (including Java).
  • Unzip the downloaded file into a directory and name that directory something like OpenRefine.
  • Check below for further instructions depending on your operating system.

Windows

  1. Go to your newly created OpenRefine directory.
  2. Launch OpenRefine by double clicking on openrefine.exe (this will launch a black command prompt window first; ignore this window, and wait for OpenRefine to launch in the web browser, which is where you will interact with the program).
  • If Windows displays a blue notification titled Microsoft Defender SmartScreen prevented an unrecognized app from starting, click on More info and then click on Run anyway.
  1. If you are using a different browser, or OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to launch the program.

Mac

  1. Go to your newly created OpenRefine directory.
  2. Drag the OpenRefine icon into Applications folder, and Ctrl-click/Open… it.
  • If Mac shows a notification when you try to run the program that it cannot verify the developer, click Cancel. Then, Right-click or Ctrl-click the icon and select Open. The notification will now have an Open button. If it does not allow to open the program, repeat the process and there will be an Open button the second time. For additional details, consult the OpenRefine installation guide.
  1. If you are using a different browser, or OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to launch the program.

Linux

  1. Navigate to your newly created OpenRefine directory using the command line.
  2. Type ./refine into the terminal within the OpenRefine directory
  3. If you are using a different browser, or OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to launch the program.

Web Browser

OpenRefine requires one of these web browsers installed in your computer:

  • Google Chrome
  • Chromium
  • Safari
  • Opera
  • Microsoft Edge

OpenRefine has some issues with Firefox. Internet Explorer is not supported.

Note: Other versions of OpenRefine should work, but the results might be different due to changes in the software or default settings.

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