OpenClinica’s Extract Data architecture lets you develop data extract formats that meet your precise requirements. It does this by:
- Specifying available formats, their associated stylesheets, and associated properties (like filename, archival settings, and whether to compress the file) in a properties file (the extract.properties file)
- Using XSL stylesheet transformations to read native CDISC ODM XML and output the data in a transformed format.
- Optionally, enabling postprocessing of the transformed data to output to certain non-text file formats and destinations.
Add an extract format to your OpenClinica environment
- Locate XSL files for the format you want to add. You can find packages on the OpenClinica Extensions site and in Lindsay Steven’s Github repository.
- Add your files to the xslt directory in your OC environment, normally your_OC_data_directory/xslt
- Edit your extract.properties and add a new extract form.
- Restart OpenClinica and test it out!
Create a new extract format
You can add your own transformations to get data into a wide variety of formats using the XSLT language.
- Familiarize yourself with OpenClinica’s implementation of CDISC ODM.
- Create your XSL file. While you can start from scratch, you’ll save time if you work off one of the existing OpenClinica extract files, from the Extensions site, github, or CDISC’s Define.xsl.
- If your requirements include outputting several files at once (such as a data file and load script), look at the SPSS format in extract.properties to see how you can include multiple XSL files and have them produce multiple output files.
- Postprocessing: To do things that XSLT cannot do by itself, like produce PDF files or load the data into external relational databases for ad-hoc reporting, a postprocessor framework is available to generate binary output formats or send data to a target destination. Two postprocessors are included: output to a database using JDBC connectivity and generate PDF files using XSL-FO. The postprocessing step is transparent to end-users; they simply get their files for download or alternatively receive a message that the data has been loaded into the database. Instructions for use are provided in the extract.properties.
- Add the XSL to your OpenClinica environment as described above.
Use your extract format
Initiate an extract for your study from the Download Data screen or via a job and select your new output format. Execution follows a five step process:
- OpenClinica generates CDISC ODM XML version 1.3 with OpenClinica Extensions
- OpenClinica applies the XSL transformation and generates output file(s) according to the settings in extract.properties for the specified format
- Optionally, if postprocessing is enabled for the requested format, OpenClinica runs the post processing action according to the settings in extract.properties.
- OpenClinica provides user notification with success or failure message.
- The data is available for download.
- A framework exists in the code to add additional postprocessors via the addition of Java classes with references to those class names in the extract.properties file.
- Do not replace the extract XSLs that come with OpenClinica. If you do, your changes will be overwritten with the original contents every time OpenClinica is restarted.
- The Java code in the OpenClinica Extract Data module outputs study metadata and clinical data in only one format: CDISC ODM (version 1.3, with OpenClinica Extensions). OpenClinica’s vendor extensions in the ODM file ensure that we can extract all possible data related to a study and its clinical data, even if not supported by the core ODM standard. This includes audit trail, discrepancy, and electronic signature information.
- Transformations are powered by the Saxon XSLT and XQuery processor.
If you improve an existing extract format, create your own, or add a new postprocessor, please share it with the community!