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

Example 26 with MNode

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

the class ImportJob method spikingSynapse.

/**
 *        Create a spike generator, which may be associated with its intended synapse.
 */
public void spikingSynapse(Node node) {
    String id = getAttribute(node, "id");
    String synapse = getAttribute(node, "synapse");
    // "spikeTarget" appears to be redundant with "synapse". Probably exists due to some oddity in LEMS.
    MNode part = models.childOrCreate(modelName, id);
    String inherit = node.getNodeName();
    NameMap nameMap = partMap.importMap(inherit);
    inherit = nameMap.internal;
    if (!inherit.isEmpty()) {
        part.set("$inherit", inherit);
        addDependency(part, inherit);
    }
    // "spikeArray" does not have an associated synapse.
    if (!synapse.isEmpty())
        part.set("$metadata", "backend.lems.synapse", synapse);
    addAttributes(node, part, nameMap, "id", "synapse", "spikeTarget");
    Map<Double, String> sorted = new TreeMap<Double, String>();
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() == Node.ELEMENT_NODE && child.getNodeName().equals("spike")) {
            String time = biophysicalUnits(getAttribute(child, "time"));
            sorted.put(Scalar.convert(time), time);
        }
    }
    if (// generate spikeArray-like code
    sorted.size() > 0) {
        String times = "";
        for (String s : sorted.values()) times += ";" + s;
        // This shuts down spiking after last specified time.
        times += ";∞";
        times = "[" + times.substring(1) + "]";
        part.set("times", times);
    }
}

Example 27 with MNode

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

the class ImportJob method typeFor.

/**
 *        Converts an element name to an internal part name, if one is available.
 */
public String typeFor(String nodeName, List<MNode> parents) {
    String query = "backend.lems.children." + nodeName;
    for (MNode parent : parents) {
        // TODO: for lookup of direct child, may need to map node name in context of parent.
        // This is only necessary if the subpart has a different internal name.
        // Assumes single inheritance
        String type = parent.get(nodeName, "$inherit").replace("\"", "");
        if (!type.isEmpty())
            return type;
        MNode c = parent.child("$metadata", query);
        if (c != null)
            return c.getOrDefault(nodeName);
    }
    return "";
}

Example 28 with MNode

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

the class ImportJob method resolve.

public void resolve(MNode dependent) {
    dependents.remove(dependent);
    boolean isChildrenType = dependent.key().startsWith("backend.lems.children");
    boolean isConnect = dependent.get().contains("$connect");
    String dependentInherit = dependent.get("$inherit");
    // For connections, the part name might be a direct value.
    if (dependentInherit.isEmpty())
        dependentInherit = dependent.get();
    if (dependentInherit.startsWith("$connect")) {
        dependentInherit = dependentInherit.replace("$connect(", "");
        dependentInherit = dependentInherit.replace(")", "");
    }
    String[] sourceNames = dependentInherit.split(",");
    for (int sourceIndex = 0; sourceIndex < sourceNames.length; sourceIndex++) {
        String sourceName = sourceNames[sourceIndex].replace("\"", "");
        MNode source = models.child(modelName, sourceName);
        if (source == null)
            continue;
        // Ensure that the source part has no unresolved dependencies of its own before using it.
        resolveChildren(source);
        boolean proxy;
        if (source.child("$proxy") == null) {
            proxy = true;
            String inherit = source.key();
            for (MNode c : source) {
                String key = c.key();
                if (key.equals("$count"))
                    continue;
                if (key.equals("$connected"))
                    continue;
                if (key.equals("$lems"))
                    continue;
                if (key.equals("$lemsUses"))
                    continue;
                // Inheriting our own name is characteristic of being a proxy.
                if (key.equals("$inherit") && c.get().replace("\"", "").equals(inherit))
                    continue;
                // key is something other than our temporary special keys, so not shallow
                proxy = false;
                break;
            }
            if (proxy) {
                // proxies only have single inheritance
                source.set("$inherit", "\"" + inherit + "\"");
                MNode parent = AppData.models.child(inherit);
                if (parent == null) {
                    source.set("$proxy", "1");
                } else {
                    source.set("$proxy", "found");
                    String id = parent.get("$metadata", "id");
                    if (!id.isEmpty())
                        source.set("$inherit", "0", id);
                }
            } else {
                source.set("$proxy", "0");
            }
        } else {
            proxy = !source.get("$proxy").equals("0");
        }
        // Triage
        // -1 == source has exactly one user. Merge and delete immediately.
        // -2 == source is lightweight, but has multiple users. Merge and wait to delete.
        // -3 == source is heavyweight. Keep reference and move out to independent model.
        // -4 == source is the endpoint of a connection. Leave in place.
        // Note that a "lightweight" part could also be a proxy, in which case it is an external reference.
        // A proxy is configured (above) to inherit the external model, so when the part is merged,
        // the dependent will end up referring directly to the external model.
        int count = source.getInt("$count");
        boolean connected = source.child("$connected") != null;
        boolean lemsUses = source.child("$lemsUses") != null;
        if (// triage is necessary
        count > 0) {
            if (lemsUses && !proxy) {
                // Anything a LEMS component depends on must be even more abstract, and thus should be an independent model.
                count = -3;
            } else if (connected) {
                if (// One dependent, with only one connection target, so OK to embed.
                dependent.getOrDefaultInt("$n", "1") == 1 && count == 1)
                    // One dependent, with only one connection target, so OK to embed.
                    count = -1;
                else
                    // Otherwise, the source should be separate from the connection part.
                    count = -4;
            } else if (count == 1) {
                count = -1;
            } else // count > 1 and not connected, so could be moved out to independent model
            {
                // Criterion: If a part has subparts, then it is heavy-weight and should be moved out.
                // A part that merely sets some parameters on an inherited model is lightweight, and should simply be merged everywhere it is used.
                boolean heavy = false;
                for (MNode s : source) {
                    if (MPart.isPart(s)) {
                        heavy = true;
                        break;
                    }
                }
                if (heavy)
                    count = -3;
                else
                    count = -2;
            }
            source.set("$count", count);
            if (count == -3) {
                MNode id = source.childOrCreate("$metadata", "id");
                if (id.get().isEmpty())
                    id.set(AddDoc.generateID());
            }
        }
        if (count == -1 || count == -2) {
            if (// Those two node types don't receive part injection, and don't change the name they use to reference the part.
            !isChildrenType && !isConnect) {
                dependent.set("");
                sourceNames[sourceIndex] = source.get("$inherit");
                String inherit = "";
                for (int i = 0; i < sourceNames.length; i++) inherit += "," + sourceNames[i];
                inherit = inherit.substring(1);
                if (// This can happen if source is a Cell, which currently lacks a base class since it is merely a container for segments.
                inherit.isEmpty()) {
                    dependent.clear("$inherit");
                } else {
                    dependent.set("$inherit", inherit);
                    // Assume single-inheritance in sources
                    dependent.set("$inherit", sourceIndex, source.get("$inherit", "0"));
                }
                for (MNode n : source) {
                    String key = n.key();
                    if (key.equals("$count"))
                        continue;
                    if (key.equals("$connected"))
                        continue;
                    if (key.equals("$lems"))
                        continue;
                    if (key.equals("$lemsUses"))
                        continue;
                    if (key.equals("$proxy"))
                        continue;
                    // already handled above
                    if (key.equals("$inherit"))
                        continue;
                    MNode c = dependent.child(key);
                    if (c == null)
                        dependent.set(key, n);
                    else
                        c.mergeUnder(n);
                }
                if (!proxy)
                    dependent.set("$metadata", "backend.lems.id", sourceName);
            }
            if (count == -1)
                models.clear(modelName, sourceName);
        } else if (count == -3) {
            String inherit = modelName + " " + sourceName;
            String id = source.get("$metadata", "id");
            if (isChildrenType) {
                // TODO: Can't store ID under metadata node, but could tack it on the end as a comma-separated value.
                dependent.set(inherit);
            } else if (isConnect) {
                dependent.set("$connect(\"" + inherit + "\")");
            // dependent.set ("0", id);  // TODO: Store ID with $connect() ?
            } else {
                sourceNames[sourceIndex] = "\"" + inherit + "\"";
                inherit = "";
                for (int i = 0; i < sourceNames.length; i++) inherit += "," + sourceNames[i];
                dependent.set("$inherit", inherit.substring(1));
                dependent.set("$inherit", sourceIndex, id);
            }
        }
    }
}

Example 29 with MNode

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

the class ImportJob method simulation.

public void simulation(Node node) {
    String id = getAttribute(node, "id");
    String length = getAttribute(node, "length");
    String step = getAttribute(node, "step");
    String target = getAttribute(node, "target");
    // redirect, since "Simulation" itself is not a proper object.
    if (primaryModel.equals(id))
        primaryModel = target;
    MNode part = models.childOrCreate(modelName, target);
    part.set("$t'", step);
    part.set("$p", "$t<" + length);
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() == Node.ELEMENT_NODE)
            output(child, part);
    }
}

Example 30 with MNode

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

the class ImportJob method collectParents.

/**
 *        Locates all the accessible parents of the given node and lists them in ascending
 *        order by distance from child. That is, most direct ancestor comes first in the list.
 *        In addition to terminating at the root parent, also terminates when a parent can't
 *        be found, so the list may be incomplete.
 */
public List<MNode> collectParents(MNode child) {
    List<MNode> result = new ArrayList<MNode>();
    String childInherit = child.get("$inherit");
    String[] inherits = childInherit.split(",");
    for (String inherit : inherits) {
        inherit = inherit.replace("\"", "");
        if (inherit.isEmpty())
            continue;
        MNode parent = models.child(modelName, inherit);
        // Prevent infinite loop on proxies.
        if (parent == child)
            parent = null;
        if (parent == null)
            parent = AppData.models.child(inherit);
        if (parent == null)
            continue;
        result.add(parent);
        result.addAll(collectParents(parent));
    }
    return result;
}