Authors: Lucian Smith.
License: This code is licensed under the LGPL version 2.1. Please see the file LICENSE.txt for details.
Repository: https://github.com/sbmlteam/mathml-tests
Developers' discussion group: https://groups.google.com/forum/#!forum/libsbml-development
This repository contains tests for infix-to-mathML and mathML-to-infix for both libSBML and JSBML.
The files summary.txt and summary.xlsx are spreadsheets containing a summary of the tests. The first column is the infix input used; the second is the MathML output; the third is the infix ouput (after being round-tripped), and the fourth column contains alternate round-trip infix output if JSBML is used instead of libSBML.
The dev directory contains a C++ program to create these tests, which works with libSBML.
The tests directory contains all the individual tests themselves. Each test is an XML file containing MathML. The infix input used to create that MathML is included as a MathML <annotation> element with the encoding 'infix-input'::
<annotation encoding="infix-input">a</annotation>
If both libSBML and JSBML produce the same infix output from this MathML, this will be annotated with the encoding 'infix-output':
<annotation encoding="infix-output">a</annotation>
If libSBML and JSBML produce different (but correct) infix output from this MathML, each output will be included as a separate annotation, the first with the encoding 'infix-output-libsbml', and the second with the encoding 'infix-output-jsbml':
<annotation encoding="infix-output-libsbml">1.000000e+003</annotation>
<annotation encoding="infix-output-jsbml">1E3</annotation>
Note that libSBML contains options in its infix parser to change how it parses certain input. None of these options are tested here, and the defaults are used throughout. In particular, this means:
log(x)is always parsed as the natural log of x.- Unary minuses (
-5,--5, etc.) are not collapsed, and will always appear in the MathML with the<minus>element:
<apply>
<minus/>
<cn type="integer"> 3 </cn>
</apply>
instead of:
<cn type="integer"> -3 </cn>
- Numerical values followed by a string are parsed as that value, with units of the string (
"5 mL"). - The string
"avogadro"is parsed as the SMBL Level 3 csymbol 'avogadro'. - All parsing of built-in functions and constants is case-insensitive.
If you find an issue, please submit it in the GitHub issue tracker for this repository. Alternatively, you are welcome to contact the author or the SBML Team via email with questions.
These files are distributed freely under the terms of the LGPL. Please see the file LICENSE.txt for more copyright and license details.
Funding for this and other SBML work has come from the National Institute of General Medical Sciences via grant NIH R01 GM070923 (Principal Investigator: Michael Hucka).
