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jLEMS does not appear to like multi-line XML tags #127

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sanjayankur31 opened this issue Aug 14, 2024 · 0 comments
Open

jLEMS does not appear to like multi-line XML tags #127

sanjayankur31 opened this issue Aug 14, 2024 · 0 comments
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@sanjayankur31
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<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
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