NeuroMLImporter.cpp

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#include "NeuroMLImporter.h" 
#include <iostream>

NeuroMLImporter::NeuroMLImporter(std::string schema_location) :
    schema_location(schema_location)
{
    connect_parsers();
    this->env = new PCSIMParserEnvironment();
    setSimulationEnvironment();
}

NeuroMLImporter::~NeuroMLImporter()
{
    delete this->env;
}

void NeuroMLImporter::load(std::string filename, SimNetwork &net)
{

    ::xml_schema::document neuroml_doc_p(NeuroMLLevel3_p, "http://morphml.org/neuroml/schema", "neuroml");

    ::xml_schema::properties propneuro;
    propneuro.schema_location("http://morphml.org/neuroml/schema", schema_location);

    env->net = &net;

    try {
        NeuroMLLevel3_p.pre();
        neuroml_doc_p.parse(filename, 0, propneuro);
        NeuroMLLevel3_p.post_NeuroMLLevel3();
    }
    catch (::xml_schema::exception& xmle)
    {
        std::cerr << filename << ": XML parsing failure: " << xmle << std::endl;
        throw;
    }
    catch (std::ios_base::failure&)
    {
        std::cerr << filename << ": IO failure: " << std::endl;
        throw;
    }
}

void NeuroMLImporter::setSimulationEnvironment()
{
NeuroMLLevel3_p.setenv(env);
Notes_p.setenv(env);
Properties_p.setenv(env);
Property_p.setenv(env);
Annotation_p.setenv(env);
Group_p.setenv(env);
Authors_p.setenv(env);
Person_p.setenv(env);
Publication_p.setenv(env);
NeuronDBReference_p.setenv(env);
ModelDBReference_p.setenv(env);
Level3Cells_p.setenv(env);
Level3Cell_p.setenv(env);
cellBody_p.setenv(env);
Polygon_p.setenv(env);
Point_p.setenv(env);
Polyhedron_p.setenv(env);
polygons_p.setenv(env);
Sphere_p.setenv(env);
segments_p.setenv(env);
Segment_p.setenv(env);
SegmentIdInCell_p.setenv(env);
FreePoints_p.setenv(env);
spines_p.setenv(env);
Spine_p.setenv(env);
SpineShape_p.setenv(env);
cables_p.setenv(env);
Cable_p.setenv(env);
ZeroToOne_p.setenv(env);
CableGroup_p.setenv(env);
cable_p.setenv(env);
InhomogeneousParam_p.setenv(env);
metric_p.setenv(env);
proximal_p.setenv(env);
distal_p.setenv(env);
Level3Biophysics_p.setenv(env);
Mechanism_p.setenv(env);
NamedParameter_p.setenv(env);
VariableNamedParameter_p.setenv(env);
InhomogeneousValue_p.setenv(env);
MechanismType_p.setenv(env);
SpecCapacitance_p.setenv(env);
UnnamedParameter_p.setenv(env);
VariableParameter_p.setenv(env);
SpecAxialResistance_p.setenv(env);
InitialMembPotential_p.setenv(env);
IonProperties_p.setenv(env);
Units_p.setenv(env);
PotentialSynapticLocation_p.setenv(env);
SynapseDirection_p.setenv(env);
Level3Connectivity_p.setenv(env);
PotentialSynLoc_p.setenv(env);
ChannelML_p.setenv(env);
Ion_p.setenv(env);
VoltageValue_p.setenv(env);
IonRole_p.setenv(env);
ChannelType_p.setenv(env);
Status_p.setenv(env);
StatusValue_p.setenv(env);
CurrentVoltageRelation_p.setenv(env);
Ohmic_p.setenv(env);
conductance_p.setenv(env);
RateAdjustments_p.setenv(env);
q10_settings_p.setenv(env);
TemperatureValue_p.setenv(env);
offset_p.setenv(env);
Gate_p.setenv(env);
state_p.setenv(env);
ConductanceDensityValue_p.setenv(env);
IntegrateAndFire_p.setenv(env);
TimeValue_p.setenv(env);
ConductanceValue_p.setenv(env);
HHGate_p.setenv(env);
Transition_p.setenv(env);
VoltageGate_p.setenv(env);
RateConstantEqnChoice_p.setenv(env);
AkdEquation_p.setenv(env);
Parameter_p.setenv(env);
GenericEquation_p.setenv(env);
VoltageConcGate_p.setenv(env);
ConcDependence_p.setenv(env);
ConcentrationValue_p.setenv(env);
RateConstVoltConcDep_p.setenv(env);
KSGate_p.setenv(env);
KSState_p.setenv(env);
ImplementationPrefs_p.setenv(env);
table_settings_p.setenv(env);
YesNo_p.setenv(env);
SynapseType_p.setenv(env);
ElectricalSynapse_p.setenv(env);
DoubleExponentialSynapse_p.setenv(env);
TimeConstantValueIncZero_p.setenv(env);
TimeConstantValue_p.setenv(env);
BlockingSynapse_p.setenv(env);
Block_p.setenv(env);
MultiDecaySynapse_p.setenv(env);
FacDepSynapse_p.setenv(env);
FacDep_p.setenv(env);
IonConcentration_p.setenv(env);
IonSpecies_p.setenv(env);
DecayingPoolModel_p.setenv(env);
InvTimeConstantValue_p.setenv(env);
PoolVolumeInfo_p.setenv(env);
LengthValue_p.setenv(env);
FixedPoolInfo_p.setenv(env);
Populations_p.setenv(env);
Population_p.setenv(env);
Instances_p.setenv(env);
CellInstance_p.setenv(env);
Point3D_p.setenv(env);
PopulationLocation_p.setenv(env);
RandomArrangement_p.setenv(env);
RectangularBox_p.setenv(env);
size_p.setenv(env);
GridArrangement_p.setenv(env);
spacing_p.setenv(env);
NonSpatialGrid_p.setenv(env);
Projections_p.setenv(env);
Projection_p.setenv(env);
GlobalSynapticProperties_p.setenv(env);
SynapticDelayValue_p.setenv(env);
NonNegativeDouble_p.setenv(env);
SynapseInternalProperties_p.setenv(env);
Connections_p.setenv(env);
Connection_p.setenv(env);
SynapticLocation_p.setenv(env);
LocalSynapticProperties_p.setenv(env);
ConnectivityPattern_p.setenv(env);
all_to_all_p.setenv(env);
fixed_probability_p.setenv(env);
PerCellConnection_p.setenv(env);
direction_p.setenv(env);
PositiveDouble_p.setenv(env);
Inputs_p.setenv(env);
Input_p.setenv(env);
PulseInput_p.setenv(env);
CurrentValue_p.setenv(env);
RandomStim_p.setenv(env);
FrequencyValue_p.setenv(env);
InputTarget_p.setenv(env);
InputSites_p.setenv(env);
InputSite_p.setenv(env);
CellIdInNetwork_p.setenv(env);
InputSitePattern_p.setenv(env);
all_cells_p.setenv(env);
percentage_cells_p.setenv(env);
Percentage_p.setenv(env);
LengthUnits_p.setenv(env);
VolumeUnits_p.setenv(env);
}

void NeuroMLImporter::connect_parsers()
{
    // Connect the parsers together.
    //
    NeuroMLLevel3_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Authors_p, Publication_p, NeuronDBReference_p, ModelDBReference_p, Level3Cells_p,
            ChannelML_p, Populations_p, Projections_p, Inputs_p, string_p, LengthUnits_p, VolumeUnits_p);

    Properties_p.parsers(Property_p);

    Property_p.parsers(string_p, string_p, string_p, string_p);

    Authors_p.parsers(Person_p, Person_p);

    Person_p.parsers(string_p, string_p, string_p, string_p);

    Publication_p.parsers(string_p, string_p);

    NeuronDBReference_p.parsers(string_p, string_p);

    ModelDBReference_p.parsers(string_p, string_p);

    Level3Cells_p.parsers(Level3Cell_p);

    Level3Cell_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Authors_p, Publication_p, NeuronDBReference_p, ModelDBReference_p, cellBody_p,
            segments_p, FreePoints_p, spines_p, cables_p, string_p, Level3Biophysics_p, Level3Connectivity_p);

    cellBody_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Polygon_p, Polyhedron_p, Sphere_p);

    Point_p.parsers(double_p, double_p, double_p, double_p);

    Polyhedron_p.parsers(polygons_p);

    polygons_p.parsers(Polygon_p);

    Sphere_p.parsers(Point_p, string_p);

    segments_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Segment_p, string_p);

    Segment_p.parsers(Point_p, Point_p, Properties_p, SegmentIdInCell_p, string_p, SegmentIdInCell_p, non_negative_integer_p);

    spines_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Spine_p);

    Spine_p.parsers(Point_p, Point_p, SegmentIdInCell_p, double_p, double_p, SpineShape_p);

    cables_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Cable_p, CableGroup_p);

    Cable_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, non_negative_integer_p, string_p, non_negative_integer_p, ZeroToOne_p, ZeroToOne_p);

    CableGroup_p.parsers(cable_p, InhomogeneousParam_p, string_p);

    cable_p.parsers(non_negative_integer_p);

    InhomogeneousParam_p.parsers(metric_p, proximal_p, distal_p, string_p, string_p);

    proximal_p.parsers(double_p);

    distal_p.parsers(double_p);

    Level3Biophysics_p.parsers(Mechanism_p, SpecCapacitance_p, SpecCapacitance_p, SpecAxialResistance_p, SpecAxialResistance_p, InitialMembPotential_p,
            InitialMembPotential_p, IonProperties_p, IonProperties_p, Units_p, PotentialSynapticLocation_p);

    Mechanism_p.parsers(NamedParameter_p, VariableNamedParameter_p, string_p, MechanismType_p, boolean_p, boolean_p);

    NamedParameter_p.parsers(string_p, string_p, double_p);

    VariableNamedParameter_p.parsers(string_p, InhomogeneousValue_p, string_p);

    InhomogeneousValue_p.parsers(string_p, string_p);

    SpecCapacitance_p.parsers(UnnamedParameter_p, VariableParameter_p);

    UnnamedParameter_p.parsers(string_p, double_p);

    VariableParameter_p.parsers(string_p, InhomogeneousValue_p, string_p);

    SpecAxialResistance_p.parsers(UnnamedParameter_p, VariableParameter_p);

    InitialMembPotential_p.parsers(UnnamedParameter_p, VariableParameter_p);

    IonProperties_p.parsers(NamedParameter_p, string_p);

    PotentialSynapticLocation_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, string_p, SynapseDirection_p, string_p);

    Level3Connectivity_p.parsers(PotentialSynLoc_p);

    PotentialSynLoc_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, string_p, string_p, SynapseDirection_p);

    ChannelML_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Ion_p, ChannelType_p, SynapseType_p, IonConcentration_p, Units_p);

    Ion_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, string_p, VoltageValue_p, positive_integer_p, IonRole_p);

    ChannelType_p.parsers(Status_p, Notes_p, Properties_p, Annotation_p, Group_p, Authors_p, Publication_p, NeuronDBReference_p, ModelDBReference_p,
            CurrentVoltageRelation_p, HHGate_p, KSGate_p, ImplementationPrefs_p, string_p, YesNo_p);

    Status_p.parsers(string_p, string_p, Person_p, StatusValue_p);

    CurrentVoltageRelation_p.parsers(Ohmic_p, IntegrateAndFire_p, string_p);

    Ohmic_p.parsers(conductance_p, string_p);

    conductance_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, RateAdjustments_p, Gate_p, ConductanceDensityValue_p);

    RateAdjustments_p.parsers(q10_settings_p, offset_p);

    q10_settings_p.parsers(string_p, double_p, double_p, TemperatureValue_p);

    offset_p.parsers(VoltageValue_p);

    Gate_p.parsers(state_p, non_negative_integer_p);

    state_p.parsers(string_p, ZeroToOne_p);

    IntegrateAndFire_p.parsers(VoltageValue_p, TimeValue_p, VoltageValue_p, ConductanceValue_p);

    HHGate_p.parsers(Transition_p, string_p);

    Transition_p.parsers(VoltageGate_p, VoltageConcGate_p, string_p, string_p);

    VoltageGate_p.parsers(RateConstantEqnChoice_p, RateConstantEqnChoice_p, RateConstantEqnChoice_p, RateConstantEqnChoice_p, RateConstantEqnChoice_p,
            RateConstantEqnChoice_p);

    RateConstantEqnChoice_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, AkdEquation_p, GenericEquation_p);

    AkdEquation_p.parsers(Parameter_p, string_p, string_p);

    Parameter_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, string_p, double_p);

    GenericEquation_p.parsers(string_p);

    VoltageConcGate_p.parsers(ConcDependence_p, RateConstVoltConcDep_p, RateConstVoltConcDep_p, RateConstantEqnChoice_p, RateConstantEqnChoice_p,
            RateConstVoltConcDep_p, RateConstVoltConcDep_p);

    ConcDependence_p.parsers(string_p, string_p, string_p, ConcentrationValue_p, ConcentrationValue_p);

    RateConstVoltConcDep_p.parsers(GenericEquation_p);

    KSGate_p.parsers(KSState_p, Transition_p);

    KSState_p.parsers(string_p);

    ImplementationPrefs_p.parsers(string_p, table_settings_p);

    table_settings_p.parsers(double_p, double_p, positive_integer_p);

    SynapseType_p.parsers(Status_p, Notes_p, Properties_p, Annotation_p, Group_p, Authors_p, Publication_p, NeuronDBReference_p, ModelDBReference_p,
            ElectricalSynapse_p, DoubleExponentialSynapse_p, BlockingSynapse_p, MultiDecaySynapse_p, FacDepSynapse_p, string_p);

    ElectricalSynapse_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, ConductanceValue_p);

    DoubleExponentialSynapse_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, ConductanceValue_p, TimeConstantValueIncZero_p, TimeConstantValue_p,
            VoltageValue_p);

    BlockingSynapse_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, ConductanceValue_p, TimeConstantValueIncZero_p, TimeConstantValue_p,
            VoltageValue_p, Block_p);

    Block_p.parsers(string_p, ConcentrationValue_p, double_p, double_p);

    MultiDecaySynapse_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, ConductanceValue_p, TimeConstantValueIncZero_p, TimeConstantValue_p,
            VoltageValue_p, ConductanceValue_p, TimeConstantValue_p, ConductanceValue_p, TimeConstantValue_p);

    FacDepSynapse_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, ConductanceValue_p, TimeConstantValueIncZero_p, TimeConstantValue_p, VoltageValue_p,
            ConductanceValue_p, TimeConstantValue_p, ConductanceValue_p, TimeConstantValue_p, FacDep_p);

    FacDep_p.parsers(double_p, TimeConstantValue_p, TimeConstantValue_p);

    IonConcentration_p.parsers(Status_p, Notes_p, Properties_p, Annotation_p, Group_p, Authors_p, Publication_p, NeuronDBReference_p, ModelDBReference_p,
            IonSpecies_p, DecayingPoolModel_p, string_p);

    IonSpecies_p.parsers(string_p);

    DecayingPoolModel_p.parsers(ConcentrationValue_p, TimeConstantValue_p, InvTimeConstantValue_p, ConcentrationValue_p, PoolVolumeInfo_p, FixedPoolInfo_p,
            ConcentrationValue_p, TimeConstantValue_p, InvTimeConstantValue_p, ConcentrationValue_p);

    PoolVolumeInfo_p.parsers(LengthValue_p, LengthValue_p);

    FixedPoolInfo_p.parsers(double_p);

    Populations_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Population_p);

    Population_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, string_p, Instances_p, PopulationLocation_p, string_p, string_p);

    Instances_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, CellInstance_p, non_negative_integer_p);

    CellInstance_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Point3D_p, non_negative_integer_p, non_negative_integer_p);

    Point3D_p.parsers(double_p, double_p, double_p);

    PopulationLocation_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, RandomArrangement_p, GridArrangement_p, string_p);

    RandomArrangement_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, non_negative_integer_p, Sphere_p, RectangularBox_p);

    RectangularBox_p.parsers(Point_p, size_p, string_p);

    size_p.parsers(double_p, double_p, double_p);

    GridArrangement_p.parsers(RectangularBox_p, spacing_p, Notes_p, Properties_p, Annotation_p, Group_p, NonSpatialGrid_p);

    spacing_p.parsers(double_p, double_p, double_p);

    NonSpatialGrid_p.parsers(positive_integer_p, positive_integer_p, positive_integer_p);

    Projections_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Projection_p, Units_p);

    Projection_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, string_p, string_p, GlobalSynapticProperties_p, Connections_p, ConnectivityPattern_p,
            string_p, string_p, string_p);

    GlobalSynapticProperties_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, SynapticDelayValue_p, SynapticDelayValue_p, SynapticDelayValue_p,
            SynapticDelayValue_p, NonNegativeDouble_p, VoltageValue_p, string_p, SynapseInternalProperties_p, string_p);

    SynapseInternalProperties_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, SynapticDelayValue_p, SynapticDelayValue_p, SynapticDelayValue_p,
            SynapticDelayValue_p, NonNegativeDouble_p, VoltageValue_p);

    Connections_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Connection_p);

    Connection_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, SynapticLocation_p, SynapticLocation_p, LocalSynapticProperties_p, integer_p, integer_p,
            integer_p, ZeroToOne_p, integer_p, integer_p, ZeroToOne_p);

    SynapticLocation_p.parsers(integer_p, integer_p, ZeroToOne_p);

    LocalSynapticProperties_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, SynapticDelayValue_p, SynapticDelayValue_p, SynapticDelayValue_p,
            SynapticDelayValue_p, NonNegativeDouble_p, VoltageValue_p, string_p);

    ConnectivityPattern_p.parsers(all_to_all_p, fixed_probability_p, PerCellConnection_p);

    fixed_probability_p.parsers(ZeroToOne_p);

    PerCellConnection_p.parsers(direction_p, PositiveDouble_p, positive_integer_p);

    Inputs_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, Input_p, Units_p);

    Input_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, PulseInput_p, RandomStim_p, InputTarget_p, string_p);

    PulseInput_p.parsers(TimeValue_p, TimeValue_p, CurrentValue_p);

    RandomStim_p.parsers(FrequencyValue_p, string_p);

    InputTarget_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, InputSites_p, InputSitePattern_p, string_p);

    InputSites_p.parsers(Notes_p, Properties_p, Annotation_p, Group_p, InputSite_p);

    InputSite_p.parsers(CellIdInNetwork_p, SegmentIdInCell_p, ZeroToOne_p);

    InputSitePattern_p.parsers(all_cells_p, percentage_cells_p);

    percentage_cells_p.parsers(Percentage_p);
}

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