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sbmlteam / jsbml

JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
https://sbml.org/software/jsbml/
GNU Lesser General Public License v2.1
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implement extended reaction class constraints - 20601 & 20602 #167

Closed bhavyejain closed 5 years ago

bhavyejain commented 5 years ago

The test files for 20601 and 20602 had to be created manually. 20602 is working perfectly. 20601 is working perfectly for catching unknown attributes, but the call to isSetIsLocal() faced some issue while testing for spatial:isLocal to be present necessarily. The tests showed that the function was accessed and worked fine when isLocal is present, even with a wrong value, but was not accessed at all when the attribute was missing altogether. This might be a test case related problem since I hand made it. Please have a look at the code, because I'm certain it should work for a proper test case.

niko-rodrigue commented 5 years ago

Can you attached the constraint files that you modified like this I can check them and add them to my set of test files so that the test work for me as well.

bhavyejain commented 5 years ago

@niko-rodrigue I'll just confirm the test files and attach them here after the meeting.

bhavyejain commented 5 years ago

@niko-rodrigue the link for new test files is: https://drive.google.com/drive/folders/1HwZP-O1JSS-5JUPyDVrBo-33_saRIa52?usp=sharing

Could you please have a look at 1220601-fail-01-01 result? I am not able to figure out why the control is not even entering the check() when the spatial:isLocal attribute is missing! Putting a line logger.warn("set local: "+srp.isSetIsLocal()); before the if() in check() chows that the control is not even reaching the if statement. There does not seem to be a problem with the parser, because the second test file does not show a similar behaviour. It enters the check and also validates the unknown attribute.

bhavyejain commented 5 years ago

https://github.com/sbmlteam/jsbml/blob/500be9dac9020b93a3848e67464bf06ada2bfbed/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java#L77-L79

The constructor Boolean(boolean) is deprecated too. I hope this is not problematic?