jLEMS does not appear to like multi-line XML tags #127
Description
<neuroml
xmlns="http://www.neuroml.org/schema/neuroml2"
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="kd3">
<ionChannelHH id="kd3" species="K" conductance="10 pS">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:foaf="http://xmlns.com/foaf/0.1/">
<rdf:Description rdf:about="kd3">
<dc:title>Potassium channel</dc:title>
<dc:description>Potassium channel with Hodgkin-Huxley style kinetics</dc:description>
<dc:source>
<rdf:Bag>
<rdf:li rdf:resource="https://modeldb.science/8210"/>
</rdf:Bag>
</dc:source>
<dc:creator>
<rdf:Bag>
<rdf:li rdf:resource="#Zack_Mainen"/>
</rdf:Bag>
</dc:creator>
<dc:contributor>
<rdf:Bag>
<rdf:li rdf:resource="#Volker_Steuber"/>
<rdf:li rdf:resource="#Padraig_Gleeson"/>
<rdf:li rdf:resource="#Ankur_Sinha"/>
</rdf:Bag>
</dc:contributor>
</rdf:Description>
<rdf:Description rdf:about="#Zack_Mainen">
<foaf:name>Zack Mainen</foaf:name>
</rdf:Description>
<rdf:Description rdf:about="#Padraig_Gleeson">
<foaf:name>Padraig Gleeson</foaf:name>
</rdf:Description>
<rdf:Description rdf:about="#Ankur_Sinha">
<foaf:name>Ankur Sinha</foaf:name>
</rdf:Description>
<rdf:Description rdf:about="#Volker_Steuber">
<foaf:name>Volker Steuber</foaf:name>
</rdf:Description>
</rdf:RDF>
</annotation>
<gate id="n" instances="1" type="gateHHrates">
<q10Settings type="q10ExpTemp" q10Factor="3" experimentalTemp="16 degC"/>
<forwardRate type="HHNearlyExpLinearRate" rate="0.02 per_ms" midpoint="20 mV" scale="9 mV"/>
<reverseRate type="HHNearlyExpLinearRate" rate="-0.002 per_ms" midpoint="20 mV" scale="-9 mV"/>
</gate>
</ionChannelHH>
<ComponentType name="HHNearlyExpLinearRate" extends="baseHHRate" description="A HHExpLinearRate, but not quite">
<Parameter name="scale" dimension="voltage"/>
<Parameter name="midpoint" dimension="voltage"/>
<Parameter name="rate" dimension="per_time"/>
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Dynamics>
<DerivedVariable name="x" dimension="voltage" value="(v - midpoint)"/>
<DerivedVariable name="xnodim" dimension="none" value="x / VOLT_SCALE"/>
<ConditionalDerivedVariable name="r" dimension="per_time" exposure="r">
<Case condition="xnodim .neq. 0" value="rate * xnodim/(1 - exp(0 - x/scale))"/>
<Case value="rate"/>
</ConditionalDerivedVariable>
</Dynamics>
</ComponentType>
</neuroml>
Just having the top neuroml tag in multiple lines makes jLEMS fail, e.g.:
pynml-channelanalysis Kd3.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: Kd3.channel.nml
pyNeuroML >>> INFO -
Analysing channels from files: ['Kd3.channel.nml']
pyNeuroML >>> INFO - Loading NeuroML2 file: Kd3.channel.nml
pyNeuroML >>> INFO - Generating LEMS file to investigate kd3 in Kd3.channel.nml, -100mV->100mV, 6.3degC
pyNeuroML >>> INFO - Loading NeuroML2 file: Kd3.channel.nml
pyNeuroML >>> INFO - Loading LEMS file: /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml and running with jNeuroML
pyNeuroML >>> INFO - Executing: (java -Xmx400M -Djava.awt.headless=true -jar "/home/asinha/Documents/02_Code/00_mine/NeuroML/software/pyNeuroML/pyneuroml/utils/./../lib/jNeuroML-0.13.2-jar-with-dependencies.jar" /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml -nogui -I '') in directory: .
pyNeuroML >>> CRITICAL - *** Problem running command:
Command 'java -Xmx400M -Djava.awt.headless=true -jar "/home/asinha/Documents/02_Code/00_mine/NeuroML/software/pyNeuroML/pyneuroml/utils/./../lib/jNeuroML-0.13.2-jar-with-dependencies.jar" /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml -nogui -I ''' returned non-zero exit status 1.
pyNeuroML >>> CRITICAL - jNeuroML >> jNeuroML v0.13.2
jNeuroML >> Loading: /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml with jLEMS, NO GUI mode...
jNeuroML >> Aug 14, 2024 5:56:38 PM org.lemsml.jlems.io.logging.DefaultLogger msg
jNeuroML >> SEVERE: (ERROR) non matching XML close in include: open tag=neuroml
jNeuroML >> end= ...ype>
jNeuroML >> </neuroml>
jNeuroML >> org.lemsml.jlems.core.sim.ContentError: No component found: kd3. Existing components:
jNeuroML >> - Component(id=holderCell_min100 type=vClampedCell)
jNeuroML >> - Component(id=holderCell_min80 type=null)
jNeuroML >> - Component(id=holderCell_min60 type=null)
jNeuroML >> - Component(id=holderCell_min40 type=null)
jNeuroML >> - Component(id=holderCell_min20 type=null)
jNeuroML >> - Component(id=holderCell_0 type=null)
jNeuroML >> - Component(id=holderCell_20 type=null)
jNeuroML >> - Component(id=holderCell_40 type=null)
jNeuroML >> - Component(id=holderCell_60 type=null)
jNeuroML >> - Component(id=holderCell_80 type=null)
jNeuroML >> - Component(id=holderCell_100 type=null)
jNeuroML >> - Component(id=rampCell0 type=null)
jNeuroML >> - Component(id=net1 type=networkWithTemperature)
jNeuroML >> - Component(id=sim1 type=null)
jNeuroML >>
jNeuroML >> at org.lemsml.jlems.core.type.Lems.getComponent(Lems.java:290)
jNeuroML >> at org.lemsml.jlems.core.type.Component.resolve(Component.java:424)
jNeuroML >> at org.lemsml.jlems.core.type.Component.resolve(Component.java:251)
jNeuroML >> at org.lemsml.jlems.core.type.Component.resolve(Component.java:238)
jNeuroML >> at org.lemsml.jlems.core.type.Component.checkResolve(Component.java:215)
jNeuroML >> at org.lemsml.jlems.core.type.Component.resolve(Component.java:471)
jNeuroML >> at org.lemsml.jlems.core.type.Component.resolve(Component.java:251)
jNeuroML >> at org.lemsml.jlems.core.type.Component.resolve(Component.java:238)
jNeuroML >> at org.lemsml.jlems.core.type.Component.checkResolve(Component.java:215)
jNeuroML >> at org.lemsml.jlems.core.type.Lems.resolve(Lems.java:163)
jNeuroML >> at org.lemsml.jlems.core.sim.LemsProcess.readModel(LemsProcess.java:82)
jNeuroML >> at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:263)
jNeuroML >> at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:247)
jNeuroML >> at org.neuroml.export.utils.Utils$1.importFile(Utils.java:538)
jNeuroML >> at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
jNeuroML >> at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:549)
jNeuroML >> at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:526)
jNeuroML >> at org.neuroml.JNeuroML.main(JNeuroML.java:622)
jNeuroML >> INFO Aug 14,2024 17:56 (INFO) Loading LEMS file from: /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml
jNeuroML >> INFO Aug 14,2024 17:56 (INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.logging.E.multiError(E.java:251)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.logging.E.error(E.java:217)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.trimOuterElement(AbstractInclusionReader.java:109)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:43)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:261)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:247)
jNeuroML >> INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.Utils$1.importFile(Utils.java:538)
jNeuroML >>
pyNeuroML >>> ERROR - execute_command_in_dir returned with output: jNeuroML v0.13.2
Loading: /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml with jLEMS, NO GUI mode...
Aug 14, 2024 5:56:38 PM org.lemsml.jlems.io.logging.DefaultLogger msg
SEVERE: (ERROR) non matching XML close in include: open tag=neuroml
end= ...ype>
</neuroml>
org.lemsml.jlems.core.sim.ContentError: No component found: kd3. Existing components:
- Component(id=holderCell_min100 type=vClampedCell)
- Component(id=holderCell_min80 type=null)
- Component(id=holderCell_min60 type=null)
- Component(id=holderCell_min40 type=null)
- Component(id=holderCell_min20 type=null)
- Component(id=holderCell_0 type=null)
- Component(id=holderCell_20 type=null)
- Component(id=holderCell_40 type=null)
- Component(id=holderCell_60 type=null)
- Component(id=holderCell_80 type=null)
- Component(id=holderCell_100 type=null)
- Component(id=rampCell0 type=null)
- Component(id=net1 type=networkWithTemperature)
- Component(id=sim1 type=null)
at org.lemsml.jlems.core.type.Lems.getComponent(Lems.java:290)
at org.lemsml.jlems.core.type.Component.resolve(Component.java:424)
at org.lemsml.jlems.core.type.Component.resolve(Component.java:251)
at org.lemsml.jlems.core.type.Component.resolve(Component.java:238)
at org.lemsml.jlems.core.type.Component.checkResolve(Component.java:215)
at org.lemsml.jlems.core.type.Component.resolve(Component.java:471)
at org.lemsml.jlems.core.type.Component.resolve(Component.java:251)
at org.lemsml.jlems.core.type.Component.resolve(Component.java:238)
at org.lemsml.jlems.core.type.Component.checkResolve(Component.java:215)
at org.lemsml.jlems.core.type.Lems.resolve(Lems.java:163)
at org.lemsml.jlems.core.sim.LemsProcess.readModel(LemsProcess.java:82)
at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:263)
at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:247)
at org.neuroml.export.utils.Utils$1.importFile(Utils.java:538)
at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:549)
at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:526)
at org.neuroml.JNeuroML.main(JNeuroML.java:622)
INFO Aug 14,2024 17:56 (INFO) Loading LEMS file from: /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml
INFO Aug 14,2024 17:56 (INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/UCL_PHOL0009/NeuroML/tutorial2/channels/LEMS_Test_kd3.xml
INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.logging.E.multiError(E.java:251)
INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.logging.E.error(E.java:217)
INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.trimOuterElement(AbstractInclusionReader.java:109)
INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:43)
INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
INFO Aug 14,2024 17:56 (LOG) at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:261)
INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:247)
INFO Aug 14,2024 17:56 (LOG) at org.neuroml.export.utils.Utils$1.importFile(Utils.java:538)
Needs to be tested with a simple LEMS file to confirm if the issue is in LEMS or the NeuroML export stack, though