Converter

The converter for JATS 1.2 can convert XML within zip packages from TF JATS 1.0 format to JATS 1.2 format.

The converter also includes a validation tool. The validation tool runs the DTD and Schematron on JATS 1.2 files in zip packages and produces reports in Excel and XML formats.

Getting started

The current version of the converter can be downloaded from the Download page. Download the current release and extract the .zip package to a convenient folder on your computer.

You will also need to have Java available on your computer. The minimum requirement is Java 8 JRE and 64-bit. If you do not already have Java, you can download Java 11 JRE 64-bit for Windows or select and download a Java that works on your machine. Also, check the environment variables on your computer to ensure that PATH includes the folder where java.exe is located.

The converter has been tested on Windows 10, but it can also run on Linux or MacOS.

Convert TF JATS 1.0 to JATS 1.2

The converter tool upgrades the format of Article XML and Issue XML within a .zip package from TF JATS to JATS 1.2, and as part of this process it makes certain improvements to the XML tagging. Please note, however, that the converter is only able to fix certain types of problems appearing in the source TF JATS files as part of the conversion. The JATS 1.2 files that are output from the converter might pass validation, as do the majority of converted files, or might fail validation. For example, there have been files converted to JATS 1.2 that fail validation due to incorrectly tagged references (e.g. missing author or missing fpage). These kinds of problems due to errors in the source file need to be corrected either by making the correction in the TF JATS file and converting again or by making the correction in the JATS 1.2 file after conversion.

Simple usage:

  1. Copy TF JATS files into the files\in folder. The files should be issue or article .zip files.
  2. Go to the bin folder and run ConvertFiles.cmd.
  3. The converter will run and show the file names of each file that it converts.
  4. The converted JATS 1.2 files will appear in the files\out folder.

Alternate usage:

  1. Locate a TF JATS article zip file, a TF JATS issue zip file, or a folder containing TF JATS issue and/or article zip files.
  2. Drag and drop the file or folder onto ConvertFiles.cmd.
  3. The converter will run and show the file names of each file that it converts.
  4. The converted JATS 1.2 files will appear in the files\out folder.

Command line usage:

  1. Open a Command Prompt or PowerShell window.
  2. Run ConvertFiles.cmd. The two parameters allowed are as follows:
    1. Path to a TF JATS article zip file, a TF JATS issue zip file, or a folder containing TF JATS issue and/or article zip files.
    2. Path to a folder where the converted JATS 1.2 files should be saved.

Validate JATS 1.2 files

The validation tool has three options that correspond to the Schematron phases. The instructions below mention ValidateCurrent.cmd because this is the most common scenario, but you can substitute any of the three options.

  • ValidateCurrent.cmd - Use for current journal content in production.
  • ValidateScanned.cmd - Use for retrodigitization projects where XML is created from PDF or hard copy source materials.
  • ValidateConverted.cmd - Use for content that has been converted to JATS 1.2 from pre-existing digital files in a different format.

The validation tool saves a report in Excel format, which is named validation-summary.xlsx. An XML version of the same report is also created, which is named validation-summary.xml.

Simple usage:

  1. Copy JATS 1.2 files into the files\out folder. The files should be issue or article .zip files. Note: If you have just run the converter there may already be JATS 1.2 files in the files\out folder.
  2. Go to the bin folder and run ValidateCurrent.cmd.
  3. The validation tool will run and show the file names of each file that it validates.
  4. The validation report validation-summary.xlsx will appear in the files\out folder and can be opened in Excel.

Alternate usage:

  1. Locate a JATS 1.2 article zip file, a JATS 1.2 issue zip file, or a folder containing JATS 1.2 issue and/or article zip files.
  2. Drag and drop the file or folder onto ValidateCurrent.cmd.
  3. The validation tool will run and show the file names of each file that it validates.
  4. The validation report validation-summary.xlsx will appear in the same folder and can be opened in Excel.

Command line usage:

  1. Open a Command Prompt or PowerShell window.
  2. Run ValidateCurrent.cmd. A parameter may be provided for the path to a TF JATS article zip file, a TF JATS issue zip file, or a folder containing TF JATS issue and/or article zip files.
  3. The validation report validation-summary.xlsx will appear in the same folder and can be opened in Excel.

The Command Prompt window might freeze if you click the mouse within the Command Prompt window. If this happens, the window will appear to be frozen and you may notice that the timer stops. To recover, right-click in the Command Prompt window. This behavior is due to the Windows Command Prompt.

This validation tool performs Schematron and DTD validation. The benefit of this validation tool is that it can be run locally. Please note that this is a subset of the validation rules that are applied by the online validation service when files are delivered to Taylor & Francis via S3. The online validation service performs Schematron and DTD validation, and also performs validation on file naming and validation that compares XML metadata with the content management system.

Linux and MacOS

The converter can also be used on Linux-based operating systems, including MacOS. The conversion and validation tools work the same, but the commands for running the tools are different on Linux than on Windows.

First, check to see if Java is available by running java -version. If Java is available this command will display information about the Java version that is installed, including the version number. If Java is not available, you will need to install Java using the method that works for your operating system. For example on Ubuntu Linux, Java can be installed using this command, sudo apt update && sudo apt install default-jre.

Next, download the current version of the converter from the Download page and extract the zip package to a convenient folder on your computer. After extracting the zip package, ensure that the gradlew script is executable by entering the command chmod +x gradlew.

Use the commands below to convert files or validate files. To convert files, can place TF JATS 1.0 files into the “files/in” folder or change “files/in” to the location of a folder or file to convert. Similarly, to validate files you can place JATS 1.2 files into the “files/out” folder or change “files/out” to the location of a folder or file to validate.

Action Command
Convert Files ./gradlew convert -Pi="files/in" -Po="files/out"
Validate Current ./gradlew validate validate -Pp=current_content -Pv="files/out"
Validate Scanned ./gradlew validate validate -Pp=scanned_content -Pv="files/out"
Validate Converted ./gradlew validate validate -Pp=converted_content -Pv="files/out"

Java memory

If you encounter an “Out of Main Memory.” error there are a few things you can do.

  1. Check to see if Java you have a 64-bit version of Java by entering the command java -version. If the version message does not mention “64-Bit” you probably have a 32 bit version that has limited ability to access memory. To remedy this, install a 64 bit version of Java.
  2. If you are running the tool on a folder that contains a large number of files try reducing the number of files in the folder.