org.lemsml.jlems.test.LemsExamplesReaderTest fails on display error

[rgerkin]

OSX 10.12.6
python getNeuroML.py development fails with:

Tests run: 37, Failures: 0, Errors: 1, Skipped: 0

stdout for the whole suite of tests is a bit hard to read (none of the \n or \r chars got correctly escaped in my terminal) but the error is in this test:

Richards-iMac:jNeuroML rgerkin$ more /Users/rgerkin/neuroml/jlems/target/surefire-reports/org.lemsml.jlems.test.LemsExamplesReaderTest.txt 
-------------------------------------------------------------------------------
Test set: org.lemsml.jlems.test.LemsExamplesReaderTest
-------------------------------------------------------------------------------
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.037 sec <<< FAILURE! - in org.lemsml.jlems.test.LemsExamplesReaderTest
testReadFromString(org.lemsml.jlems.test.LemsExamplesReaderTest)  Time elapsed: 0.036 sec  <<< ERROR!
org.lemsml.jlems.core.sim.ContentError: No display defined for recorder Recorder q=quantity, scale=scale, display=display, color=color
        at org.lemsml.jlems.core.type.simulation.Simulation.appendToBehavior(Simulation.java:100)
        at org.lemsml.jlems.core.type.ComponentType.makeStateType(ComponentType.java:991)
        at org.lemsml.jlems.core.type.Component.makeStateType(Component.java:759)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:814)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:793)
        at org.lemsml.jlems.core.type.ComponentType.makeStateType(ComponentType.java:970)
        at org.lemsml.jlems.core.type.Component.makeStateType(Component.java:759)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:814)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:793)
        at org.lemsml.jlems.core.type.ComponentType.makeStateType(ComponentType.java:970)
        at org.lemsml.jlems.core.type.Component.makeStateType(Component.java:759)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:814)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:793)
        at org.lemsml.jlems.core.type.ComponentType.makeStateType(ComponentType.java:970)
        at org.lemsml.jlems.core.type.Component.makeStateType(Component.java:759)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:814)
        at org.lemsml.jlems.core.type.Component.getStateType(Component.java:793)
        at org.lemsml.jlems.core.sim.Sim.build(Sim.java:87)
        at org.lemsml.jlems.test.LemsExamplesReaderTest.testReadFromString(LemsExamplesReaderTest.java:82)

There is some display variable issue.

I need to install this development version to get the changes you added a few weeks ago to allow include paths to be specified in the jnml command.

[pgleeson]

@rgerkin For errors like this when installing jNeuroML from source, I'd recommend going through each of jLEMS, org.neuroml.model, org.neuroml.export, org.neuroml.import, jNeuroML and

• make sure it's on development branch
• pull the latest
• make sure 'mvn clean install' works

Though it seems it's just jLEMS you have the problem with, which is simplest in terms of dependencies. Current development branch is passing fine: https://travis-ci.org/LEMS/jLEMS/branches

[rgerkin]

@pgleeson OK, thanks, that fixed that problem. Now how do I go about making this the jnml that ends up in pyneuroml/lib/jNeuroML-X-jar-with-dependencies.jar so I can use it from pyneuroml?

[pgleeson]

@rgerkin Best way for you to do that locally is just to copy the jar from jNeuroML/target/jNeuroML-0.8.3-jar-with-dependencies.jar to pyNeuroML/pyneuroml/lib/jNeuroML-0.8.3-jar-with-dependencies.jar and python setup.py install again.

I wanted to do a binary release with these, but have some more testing to complete before doing that. A week or so...

[rgerkin]

@pgleeson Thanks, everything works great now.