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draeger-lab / 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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Travis tests are currently failing #34

Closed matthiaskoenig closed 4 years ago

matthiaskoenig commented 4 years ago

Currently the tests are failing https://github.com/draeger-lab/SBSCL/commits/master https://travis-ci.com/github/draeger-lab/SBSCL/builds/154929373

hemilpanchiwala commented 4 years ago

@matthiaskoenig, I updated the JDK in my forked repo of SBSCL and the build still fails and that is due to some issues in the CompSimulatorTest files which have to be resolved.

My forked repo Travis build results: https://travis-ci.com/github/hemilpanchiwala/SBSCL/builds/165539283

The updated code in the forked repo (develop branch): https://github.com/hemilpanchiwala/SBSCL/tree/develop

matthiaskoenig commented 4 years ago

Did you get the tests locally to run and see the same issue? You should fix the underlying cause in the CompTests. This is a good chance to get to know the test structures and how the comp simulations work currently.

I.e. get the tests running locally and fix the CompIssues. If you tests pass on your travis make a pull request with the changes so we can review it.

hemilpanchiwala commented 4 years ago

Yes, I see the same issues while running the tests locally. Okay, I will fix the comp issues, and once the test pass, I will make a pull request with the changes.

hemilpanchiwala commented 4 years ago

@matthiaskoenig, this error occurs when two or more parameters or compartments are specified in the SBML files with comp, i.e., from test6.xml to test10.xml. The error is returned when the flatten method is called on the SBML document in CompSimulator.java.

I don't understand that is this error in the CompFlatteningConverter.java of JSBML?

Error while running test on src/test/resources/comp/test6.xml:- ERROR (Model.java:4687) - An element of type parameter with the id "Mod1subparam2" is already present in this model. The new element of type parameter will not have it's id set. In some cases, the new element will not be added to the model.

matthiaskoenig commented 4 years ago

A lot happend in the CompFlatteningConverter in JSBML. We probably have to update JSBML first to the latest version to see if the error still exists in the latest version. I.e. fix https://github.com/draeger-lab/SBSCL/issues/32. You should update JSBML first and see it does not break any other tests. Then see if the Comp errors exist still with the latest JSBML version.

hemilpanchiwala commented 4 years ago

@matthiaskoenig, I had updated to JSBML 1.5 in pom.xml before doing this. Only the comp tests are failing while other tests are working as before.

Commit Link: https://github.com/hemilpanchiwala/SBSCL/commit/ae34768d22aa722fcd48b41550589e2ac9eadaff

matthiaskoenig commented 4 years ago

@hemilpanchiwala Trying to get this running locally to figure out what is going on.

matthiaskoenig commented 4 years ago

I could reproduce the issue and checked that

This seems to be an issue with the flattening routine and is reported here: sbmlteam/jsbml#213

Please ignore the CompTests for now, which are tracked in #36. The main issue here is resolved and can be closed.