extract expressions failing for some models about neuroml2modellite

[borismarin]

changing defs to ionchannelhh doesn't seem to fix the problem. 2018-04-05 13:13 GMT-03:00 Matt Earnshaw <[email protected]>:

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for example with https://gist.github.com/mattearnshaw/3f0f3f3cf591e7390815fd82280da87a, no channels available for plotting in model desc. however https://gist.github.com/mattearnshaw/ c6f964739f647bfc8d7589eebc8c57b3 works likely difference that makes a difference: <ionChannelHH> vs <ionChannel type="ionChannelHH"/> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADSvb8OG3-9zyXY4nuhaUDkUqNwIcpnFks5tlkK7gaJpZM4TIv6o> .

[pgleeson]

The issue is down to org.lemsml.model support for the gap junction comp type. See
https://github.com/NeuroML/neuroml2model/compare/development?expand=1
The dev branch is failing due to inclusion of gap junction:
https://travis-ci.org/NeuroML/neuroml2model/jobs/363091513

I've fixed this in the lite version, making sure gap junctions are ignored.
Latest geppetto builds fine with this and can plot rate vars..

[pgleeson]

@borismarin you may want to look at support for gap junctions (down to InstanceRequirement?) in org.lemsml.model, but it's not a bottleneck here...

[borismarin]

org.lemsml.models predates tunnels and gapjunctions, I guess. The construct that breaks things is the path at https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Synapses.xml#L472 which makes sense as we have not implemented semantics for InstanceRequirements. Thus, things break when trying to resolve the path at https://github.com/LEMS/org.lemsml.model/blob/development/src/main/java/org/lemsml/model/extended/PathQDParser.java#L96 2018-04-06 11:30 GMT-03:00 Padraig Gleeson <[email protected]>:

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@borismarin <https://github.com/borismarin> you may want to look at support for gap junctions (down to InstanceRequirement?) in org.lemsml.model, but it's not a bottleneck here... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADSvb0zOo8KCo6KsT1KtYQLjCxq7ws_tks5tl3whgaJpZM4TIv6o> .

[pgleeson]

Well, it doesn't prevent your rates from being displayed anymore:

Will be on live OSB by the end of next week hopefully...