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Online SBML Validator Archive Support

This document summarizes support for archives containing more than one file in the Online SBML Validator.

Image:icon_exclaim.gif NOTE: Use of the COMBINE Archive is preferable.

Detecting the master file in a zip file may not be reliable.

Image:icon_exclaim.gif

Types of archive supported

  1. COMBINE Archive
  2. Archive with PKZip format

Determining the master file in a COMBINE archive

The validator will look at the manifest within the archive and using the following criteria in the order specified:

  • The first SBML file marked as master
  • The first file marked as SBML
  • An xml file with the same name as the archive
  • master.xml
  • main.xml
  • top.xml

If none of the above files is found, the validator will chose the first xml file in the archive.

Determining the master file in a zip archive

The validator will look within the archive and chose a file using the following criteria in the order specified:

  • An xml file with the same name as the archive
  • master.xml
  • main.xml
  • top.xml

If none of the above files is found, the validator will chose the first xml file in the archive.

Models using the SBML Level 3 Hierarchical Model Composition Package

  • All files referenced by a comp model must be present in the archive.
  • If the master model has been correctly identified the validator will
    • attempt to flatten the model
    • if not successful it will
      • report errors from the attempt to flatten
      • NOTE: The Document Listing and line numbers reported will be the original master model
    • if successful it will
      • validate the flat model and report results
      • NOTE: The Document Listing and line numbers reported will be the flat version of the model

Limitations

  1. Only one xml file is validated.
  2. Only PKZip format is supported.
  3. As yet the REST API has not been updated.

Retrieved from "http://sbml.org/Facilities/Validator/Online_SBML_Validator_Archive_Support"

This page was last modified 08:16, 10 July 2018.



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