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shalinshah1993 / SBSCL

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
https://draeger-lab.github.io/SBSCL/
GNU Lesser General Public License v3.0
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CompExample misses model files #15

Closed matthiaskoenig closed 6 years ago

matthiaskoenig commented 6 years ago

Test model for CompExample missing from repository.

Exception in thread "main" java.io.FileNotFoundException: files/comp/test58.xml (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:295)
    at org.sbml.jsbml.SBMLReader.readSBML(SBMLReader.java:116)
    at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:105)
    at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:92)
    at org.simulator.CompExample.main(CompExample.java:92)

Please add the test/example files to the repo.

draeger commented 6 years ago

Should we really do this? It will add a large number of redundant files. Wouldn't it be a better approach to use an environment variable that specifies the location of the files?

shalinshah1993 commented 6 years ago

I agree with @draeger when I am finished with this feature instead of taking the hard-coded path as input, I can just use command line args otherwise it will add a lot of files. However, we can add one example if you like.

You can download example files from this jsbml commit https://github.com/sbmlteam/jsbml/commit/46ca561edbca85a1f05f14dcc6e08acd65b2e235

matthiaskoenig commented 6 years ago

I would add a minimal set of test models in the repository which allows to run the core set of unit tests on the project. These tests would be very specific. There should be a way to test the core functionality without the need to run 10000 tests (i.e. all testsuite cases).

In addition there would be a large set of generic test, i.e. running test suite, running BiGG models.