Examples with MNode gov.sandia.n2a.db.MNode used on opensource projects

Example 21 with MNode

use of gov.sandia.n2a.db.MNode in project n2a by frothga.

the class ImportJob method ionChannel.

public void ionChannel(Node node) {
    String id = getAttribute(node, "id");
    String type = getAttribute(node, "type");
    String species = getAttribute(node, "species");
    String inherit;
    if (type.isEmpty())
        inherit = node.getNodeName();
    else
        inherit = type;
    NameMap nameMap = partMap.importMap(inherit);
    inherit = nameMap.internal;
    // Expect to always create this part rather than fetch an existing child.
    MNode part = models.childOrCreate(modelName, id);
    part.set("$inherit", "\"" + inherit + "\"");
    addDependency(part, inherit);
    if (!species.isEmpty())
        part.set("$metadata", "species", species);
    addAttributes(node, part, nameMap, "id", "type", "species");
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() != Node.ELEMENT_NODE)
            continue;
        String name = child.getNodeName();
        if (name.startsWith("q10"))
            q10(child, part);
        else if (name.startsWith("gate"))
            gate(child, part);
        else
            genericPart(child, part);
    }
}

Example 22 with MNode

use of gov.sandia.n2a.db.MNode in project n2a by frothga.

the class ImportJob method transition.

public void transition(Node node, MNode container) {
    String id = getAttribute(node, "id");
    MNode part = container.set(id, "");
    NameMap nameMap = partMap.importMap(node.getNodeName());
    part.set("$inherit", "\"" + nameMap.internal + "\"");
    addAttributes(node, part, nameMap, "id");
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() == Node.ELEMENT_NODE)
            rate(child, part, true, false);
    }
}

Example 23 with MNode

use of gov.sandia.n2a.db.MNode in project n2a by frothga.

the class ImportJob method removeDependency.

public void removeDependency(MNode part, String inherit) {
    dependents.remove(part);
    MNode component = models.child(modelName, inherit);
    if (component == null)
        return;
    int count = component.getInt("$count") - 1;
    if (count > 0) {
        component.set("$count", count);
    } else {
        component.clear("$count");
        component.clear("$connected");
        component.clear("$lemsUses");
        // This is a proxy part created because a model is missing from the repo.
        if (component.size() == 0)
            models.clear(modelName, inherit);
    }
}

Example 24 with MNode

use of gov.sandia.n2a.db.MNode in project n2a by frothga.

the class ImportJob method remap.

public void remap(MNode part, NameMap nameMap) {
    MNode temp = new MVolatile();
    temp.merge(part);
    part.clear();
    for (MNode v : temp) {
        String key = nameMap.importName(v.key());
        part.set(key, v);
    }
}

Example 25 with MNode

use of gov.sandia.n2a.db.MNode in project n2a by frothga.

the class ImportJob method neuroml.

public void neuroml(Node node) {
    File source = sources.getLast();
    if (modelName.isEmpty()) {
        modelName = getAttribute(node, "id");
        if (// then get it from the filename
        modelName.isEmpty()) {
            modelName = source.getName();
            int index = modelName.lastIndexOf('.');
            if (index > 0)
                modelName = modelName.substring(0, index);
        }
        modelName = NodePart.validIdentifierFrom(modelName);
        // Preemptively scan for unique name, so our references to any sibling parts remain valid.
        // IE: a name collision in the main part implies that sibling parts will also have name collisions.
        modelName = AddDoc.uniqueName(modelName);
    }
    MNode model = models.childOrCreate(modelName);
    String description = getAttribute(node, "description");
    if (!description.isEmpty())
        model.set("$metadata", "description", description);
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() != Node.ELEMENT_NODE)
            continue;
        switch(child.getNodeName()) {
            case // NeuroML include
            "include":
                // TODO: what if href actually references a web document?
                File nextSource = new File(source.getParentFile(), getAttribute(child, "href"));
                process(nextSource);
                break;
            case // LEMS include
            "Include":
                nextSource = new File(source.getParentFile(), getAttribute(child, "file"));
                process(nextSource);
                break;
            // NeuroML ---------------------------------------------------
            case "intracellularProperties":
            case "extracellularProperties":
                properties.put(getAttribute(child, "id"), child);
                break;
            case "morphology":
                morphologies.put(getAttribute(child, "id"), child);
                break;
            case "ionChannel":
            case "ionChannelHH":
            case "ionChannelKS":
                ionChannel(child);
                break;
            case "decayingPoolConcentrationModel":
            case "fixedFactorConcentrationModel":
            case // This tag appears in Cells.xml, but not in NeuroML_v2beta4.xsd
            "fixedFactorConcentrationModelTraub":
                concentrationModel(child);
                break;
            case "blockingPlasticSynapse":
                blockingPlasticSynapse(child);
                break;
            case "biophysicalProperties":
                biophysics.put(getAttribute(child, "id"), child);
                break;
            case "cell":
                Cell cell = new Cell(child);
                cells.put(cell.id, cell);
                break;
            case "fitzHughNagumoCell":
                MNode FN = genericPart(child, model);
                // Force time-scale to match the hard-coded value in LEMS definitions.
                FN.set("TS", "1s");
                break;
            case "poissonFiringSynapse":
            case "transientPoissonFiringSynapse":
            case "spikeArray":
            case "timedSynapticInput":
                spikingSynapse(child);
                break;
            case "compoundInput":
                compoundInput(child);
                break;
            case "network":
                Network network = new Network(child);
                networks.put(network.id, network);
                break;
            // LEMS ------------------------------------------------------
            case "Target":
                target(child);
                break;
            case "Dimension":
                dimension(child);
                break;
            case "Unit":
                unit(child);
                break;
            case "Constant":
                // Create a bogus component to wrap the top level, so we can add a LEMS constant to it.
                new ComponentType(model).genericVariable(child, "");
                break;
            case "ComponentType":
                ComponentType component = new ComponentType(child);
                components.put(component.part.key(), component);
                break;
            case "Simulation":
                simulation(child);
                break;
            case "Component":
            default:
                // Any NeuroML part not specifically processed above will fall through to here.
                genericPart(child, model);
                break;
        }
    }
}