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OpenSourceBrain / AllenInstituteNeuroML

Example files to test interaction between models developed at the Allen Brain Institute and NeuroML
http://www.opensourcebrain.org/projects/alleninstituteneuroml
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Support for all active celltype #27

Closed anujanegi closed 2 years ago

anujanegi commented 2 years ago

Trying to make sense of this error message. What am I missing? @sanjayankur31 @pgleeson

When I try to validate the generated .cell.nml:

jNeuroML >>  Validating: /home/anujanegi/tj/AllenInstituteNeuroML/CellTypesDatabase/models/NeuroML2/Cell_497233223.cell.nml
 jNeuroML >>  Valid against schema
 jNeuroML >>    Test: 10005 (Segment Group used in the include element of segmentGroup should exist) failed! ... SegmentGroup: soma_group, includes: soma
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: pas_soma specifies: soma which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: pas_apic specifies: apic which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: NaV_soma specifies: soma which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: SK_soma specifies: soma which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: Kv3_1_soma specifies: soma which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: Ih_soma specifies: soma which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: NaV_apic specifies: apic which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: Kv3_1_apic specifies: apic which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: Im_v2_apic specifies: apic which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: Ih_apic specifies: apic which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: Ca_HVA_soma specifies: soma which doesn't exist
 jNeuroML >>    Test: 10006 (Segment Groups used in biophysicalProperties should exist) failed! ... ChannelDensity: Ca_LVA_soma specifies: soma which doesn't exist
pgleeson commented 2 years ago

@anujanegi Testing this out in my branch here:https://github.com/OpenSourceBrain/AllenInstituteNeuroML/tree/pg_test. I've just realised that the script can't handle both all active and perisomatic in the one run... If you run with one type the other will fail...

pgleeson commented 2 years ago

@anujanegi The issue with generating the soma segment group is fixed in https://github.com/OpenSourceBrain/AllenInstituteNeuroML/commit/af1a0baeeee029a09bca7d5f9cd809eda55adaf8#diff-ea7fc52438018fb455633304804ded95b1bfbd3d88bb46345a6c4aaa7885c609 I believe...

Looking at another issue now with the group apic...

pgleeson commented 2 years ago

@anujanegi I've tested the latest changes with another all active cell on here: https://github.com/OpenSourceBrain/AllenInstituteNeuroML/tree/pg_another_all_active and it seems to work now. Let's discuss tomorrow.

pgleeson commented 2 years ago

Closing this @anujanegi as I assume all relevant changes are on the master branch now..?