tarelli

import os
import sys
from subprocess import check_output as co
from distutils.core import run_setup

class working_dir(object):
    """Context manager for changing the current working directory"""
    def __init__(self, newPath):
        self.newPath = newPath

tarelli

org.geppetto/utilities/source_setup/python gitall.py pull //make sure everything is updated
org.geppetto/mvn install //this will download all the new libraries required (if any)
org.geppetto/utilities/source_setup/python update_server.py eclipse //this will copy everything to virgo

tarelli

server-3.6.3.RELEASE/geppettoTmp/RUN/projects/17/NEURONModel_18012016_101203/BackgroundRandomIClamps.mod at:  
[2016-01-18 10:12:04.851] ERROR Thread-67                    System.err                                                        java.lang.NumberFormatException: For input string: "null" 
[2016-01-18 10:12:04.851] ERROR Thread-67                    System.err                                                        	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) 
[2016-01-18 10:12:04.851] ERROR Thread-67                    System.err                                                        	at java.lang.Integer.parseInt(Integer.java:492) 
[2016-01-18 10:12:04.851] ERROR Thread-67                    System.err                                                        	at java.lang.Integer.parseInt(Integer.java:527) 
[2016-01-18 10:12:04.851] ERROR Thread-67                    System.err                                                        	at org.neuroml.export.utils.LEMSQua

tarelli

Valid paths

acnet2.pyramidals_48[4].soma.v (acnet2.pyramidals_48[4].soma.v might not always be possible because the name is optional)
acnet2.pyramidals_48[4].soma.spiking
acnet2.pyramidals_48[4].apical2.spiking

(Not for now, short/medium term) //acnet2.pyramidals_48[4].soma.bioPhys1.membraneProperties.Kdr_bask_soma_group.iDensity

acnet2.pyramidals_48[4].bioPhys1.membraneProperties.Kdr_bask_soma_group.erev (It's valid without the morphology because it's a parameter)

tarelli

WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].biophys(biophys).membraneProperties(membraneProperties).ca_boyle_all(ca_boyle_all).iDensity(StateVariable) 0
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].caConc(StateVariable) 1
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].biophys(biophys).membraneProperties(membraneProperties).k_fast_all(k_fast_all).iDensity(StateVariable) 2
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable time(StateVariable) 3
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).neuron(generic_iaf_cell)[0].v(StateVariable) 4
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].biophys(biophys).membraneProperties(membraneProp

tarelli

<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2  https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="network_t3">
    <notes>
Network structure (NeuroML 2beta4) for project: t3 saved with neuroConstruct v1.7.1 on: 19:48:05, 22-Oct-15
Cell Group: CG_C04_RS_sm contains 20 cells
Cell Group: CG_C04_AxAx_sm contains 10 cells
Cell Group: CG_C04_Bask_sm contains 10 cells
Cell Group: CG_C04_LTS_sm contains 10 cells
Cell Group: CG_C04_FRB_sm contains 6 cells
Network connection: RS_RS_gap_sm contains 24 individual synaptic connections
Network connection: AxAx_AxAx_gap_sm contains 20 individual synaptic connections

tarelli

    window.EMBEDDED = true;
    window.EMBEDDEDURL = "http://0.0.0.0:3000/";

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osgi> ss ckson
"Framework is launched."


id	State       Bundle
82	ACTIVE      com.fasterxml.jackson.core.jackson-core_2.8.5
89	ACTIVE      jackson-core-asl_1.9.13
90	ACTIVE      jackson-mapper-asl_1.9.13
145	ACTIVE      com.fasterxml.jackson.core.jackson-annotations_2.8.5
146	ACTIVE      com.fasterxml.jackson.core.jackson-databind_2.8.5

tarelli

<?xml version="1.0" encoding="ASCII"?>
<gep:GeppettoModel xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:gep="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore" xmlns:gep_1="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore#//types" xmlns:gep_2="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore#//values">
  <libraries>
    <types xsi:type="gep_1:CompositeType" id="hd__vhalflmin73" name="hd__vhalflmin73" superType="//@libraries.0/@types.1">
      <variables id="conductance" name="Conductance" types="//@libraries.1/@types.0" static="true">
        <initialValues key="//@libraries.1/@types.0">
          <value xsi:type="gep_2:PhysicalQuantity" value="10.0">
            <unit unit="pS"/>
          </value>
        </initialValues>

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        window.plotIV = function(protocolName, e){

            e.preventDefault();
            // figure out if we have any protocol and organize into a map
            var experiments = Project.getExperiments();
            var protocolExperimentsMap = {};
            for(var i=0; i<experiments.length; i++){
                if(experiments[i].getName().startsWith('[P]')){
                    // parse protocol pattern
                    var experimentName = experiments[i].getName();