oXygen XML Editor

It is recommended to use oXygen XML Editor for general work with JATS XML files. XML and JATS are open standards and there are many software programs that can be used to work with JATS XML files, including software that is specialized for particular tasks such as typesetting. oXygen XML Editor is recommended for general use because of its excellent support for XML standards and for JATS, and because of its extensive set of useful features. oXygen’s user interface is easy and intuitive for beginners and it has many capabilities that can be learned over time as they are needed.

On this page:

oXygen Add-On

Taylor & Francis has created a custom add-on for oXygen that provides configuration presets for the XML formats that are frequently used in the Digital Production team. This add-on includes:

  • JATS XML files are validated using the DTD and Schematron phase Current by default when the Validate button is pressed and automatically while typing.
  • TF JATS XML files are validated using the DTD and Schematron phase Final by default when the Validate button is pressed and automatically while typing.
  • TFJA XML files are validated using the DTD when the Validate button is pressed and automatically while typing.
  • XML Catalog with other frequently used DTDs.
  • Templates to help with creating new files.

This add-on contains two parts:

  1. Frameworks for JATS, TF JATS, and TFJA
  2. Project file template that provides configuration settings

Installing the add-on

oXygen XML Editor version 25.0 or higher is required to install the add-on. To install the add-on:

  1. Open oXygen XML Editor if it is not already open.
  2. Go to the Help menu, then “Install new add-ons”
  3. In the “Show add-ons from” box enter this URL: https://jats.taylorandfrancis.com/oxygen/addon.xml
  4. A list of add-ons will be displayed.
    1. Check the box next to “Taylor & Francis JATS”
    2. Alternatively, if you are doing user acceptance testing and want the oXygen to use the latest UAT version of the Schematron by default, check the box next to “Taylor & Francis JATS UAT”. The two options differ only in which version of the JATS Schematron is the default.
    3. If nothing appears in the list or if oXygen displays an message about a certificate error, you can resolve this problem by:
      1. Close the “Install new add-ons” window.
      2. Go to the Options menu, then Preferences.
      3. Go to “Network Connection Settings” then “HTTP(S)/WebDAV”
      4. Check the box next to “Automatically accept a security certificate, even if invalid”
      5. Click the OK button, and then start again from step 2.
  5. Click the Next button, then check the box to accept the license, and then click the Install button. A warning will be displayed about a missing signature. Click the “Continue anyway” button. Then click the Ok button.
  6. Go to the File menu, then “Exit” to exit out of oXygen.
  7. Open oXygen XML Editor

If oXygen gives a security prompt about connecting to https://jats-dev.taylorandfrancis.com or https://jats.taylorandfrancis.com click the “Allow and Remember” button.

Next, you will use the template provided by the add-on to create a project file.

Project File Template

The project file template contains essential configuration settings. Follow these steps to create a new project file for yourself using the project file template.

  1. In oXygen, go to the Project menu, then “New project”
  2. From the list of templates, choose “JATS Project” which is under “Framework templates” > “JATS Taylor & Francis”
  3. In the “Project directory” box, choose a folder on your computer where the project file will be saved.
  4. In the “Project file name” box, you can change the change the name of the project file if you wish or you can use the default name “JATS Project”.
  5. Click the “Create” button.

oXygen uses project files to remember configuration settings and open files. If you frequently switch between working on different sets of files in oXygen you might find it useful to create more than one project file. Using a project file for each different activity, and opening the relevant project file when switching tasks, can be helpful.

Using the add-on

When working in oXygen, make sure that oXygen is using the correct project file that you created using the add-on. There are several ways to do this.

  1. The “Project” sidebar panel displays the name of the current project file. If you need to open a different project, click on the current project name and then select a different project from the list or select “Open project”
  2. Alternatively, go to the Project menu, then “Open project” or “Reopen project”, and then select the project file to open.

When editing a JATS XML file in oXygen, the file will be automatically validated using the JATS DTD and Schematron phase Current. oXygen will also automatically validate TF JATS XML and TFJA XML.

If you want a different automatic validation to be applied to a particular file (for example, to choose a different Schematron phase) you can: click the arrow next to the “Validate” button, then “Configure Validation Scenario(s)", check the boxes for the validation scenarios that you want to use, and then click the “Apply associated” button. This association will be saved in the project file.

Updating the add-on

When oXygen is first started, if a new version of the add-on is available oXygen will display an alert about Updates Available.

  1. On the “Updates Available” alert, click the “Review updates” button.
  2. The “Manage add-ons” window will open with the available updates selected.
  3. Click the “Update” button.
  4. Check the box to accept the license, and then click the “Finish” button. A warning will be displayed about a missing signature. Click the “Continue anyway” button. Then click the Ok button.
  5. Go to the File menu, then “Exit” to exit out of oXygen.
  6. Open oXygen XML Editor

After updating the addon, create a new project file using the JATS Project template as you did after installing the add-on. The old project file that was created using the previous version of the add-on can be deleted.

Removing the add-on

If you need to switch to the UAT add-on, or switch from the UAT add-on, you will need to first uninstall the current add-on and then install the version that you need. To uninstall the current addon:

  1. In oXygen, go to the Help menu, then “Manage add-ons”.
  2. Check the box next to “Taylor & Francis JATS” or “Taylor & Francis JATS UAT”.
  3. Click the “Uninstall” button.
  4. When prompted to confirm click the Yes button, then click the OK button.
  5. Go to the File menu, then “Exit” to exit out of oXygen.
  6. Open oXygen XML Editor

oXygen tips and tricks

Go directly to an XPath location

To quickly go to an XPath location in the document that you currently have open for editing in oXygen:

  1. In the “XPath” input box in the top-left toolbar, type in the XPath that you want to find, and then press the enter key.
    • For example: //abstract will find all <abstract> elements.
  2. The “Results” panel will display a list of the locations in the document that match the XPath. If there is no match, a message will be displayed letting you know that there were no results.
  3. Click on any line in the Results panel to go to that location in the document.

Find/Replace using XPath

The Find/Replace function can be instructed to Find/Replace text within elements that match an XPath. This feature can be used to make find/replace actions very specific.

  1. Go to the Edit menu, then Find/Replace.
  2. Enter the text to Find.
  3. Optionally, enter replacement text.
  4. In the XPath box, enter an XPath.
    • For example, to Find/Replace an article DOI enter the XPath //article-id[@pub-id-type="doi"].
  5. Click one of the buttons to Find or Replace.

NVDA and oXygen

Using the NVDA screen reader automatically activates accessibility features in oXygen. This can be disruptive if you do not want to use these accessibility features and may prevent normal typing in oXygen. To restore normal behavior in oXygen perform the following steps.

  1. Exit out of oXygen
  2. Locate the directory where oXygen is installed. For example “C:\Users\user\AppData\Local\Programs\Oxygen XML Editor 25”
  3. Open a Command Prompt or PowerShell in this directory.
  4. Enter this command and then press the enter key jre\bin\jabswitch -disable.
  5. A message should be displayed “The Java Access Bridge has been disabled.”
  6. Close the Command Prompt or Powershell window.
  7. Open oXygen