Examples of KamNode

org.openbel.framework.api.Kam.KamNode
org.openbel.framework.ws.model.KamNode
amework.org/ws/schemas}Node"> </extension> </complexContent> </complexType>

Examples of org.openbel.framework.api.Kam.KamNode

        kam = kam(kamName);
        info = kam.getKamInfo();
        Map<KamNode, KamNode> collapsed = orthokam.getCollapsedNodes();
        Set<Entry<KamNode, KamNode>> set = collapsed.entrySet();
        for (Entry<KamNode, KamNode> e : set) {
            KamNode collapsing = e.getKey();
            KamNode collapseTo = e.getValue();


            collapsing = kam.findNode(collapsing.getId());
            collapseTo = kam.findNode(collapseTo.getId());
            kamstore.collapseKamNode(info, collapsing, collapseTo);
        }


        // remove orthologous edges/statements
        kamstore.removeKamEdges(info, ORTHOLOGOUS);

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Examples of org.openbel.framework.api.Kam.KamNode

        Map<Integer, Resource> termResources = new HashMap<Integer, Resource>();


        // handle kam nodes first
        Iterator<KamNode> kamNodes = kam.getNodes().iterator();
        while (kamNodes.hasNext()) {
            KamNode kamNode = kamNodes.next();


            // TODO: This is a sanity check that should be removed as LIST is not a KAM function type
            if (FunctionEnum.LIST == kamNode.getFunctionType()) {
                System.err.println("Invalid KAM node type found: "
                        + kamNode.getFunctionType().getDisplayValue());
                continue;
            }


            Resource functionResource = model.getResource(KAMVocabulary
                    .resourceForFunction(kamNode.getFunctionType()).getURI());


            // Retrieve seen KAMNode Resource or create a new Blank Node for it.
            Resource kamNodeResource;
            if (kamNodeResources.containsKey(kamNode)) {
                kamNodeResource = kamNodeResources.get(kamNode);
            } else {
                kamNodeResource = model.createResource(new AnonId(UUID
                        .randomUUID().toString()));


                // associate kam node with kam resource
                kamResource.addProperty(composedOf, kamNodeResource);
            }


            // node type KAMNode
            kamNodeResource.addProperty(RDF.type, KAMNode);


            // node hasFunction Function
            kamNodeResource.addProperty(hasFunction, functionResource);


            // node hasId "1"^^xsd:int
            kamNodeResource.addLiteral(hasId,
                    model.createTypedLiteral(kamNode.getId()));


            // node hasLabel "p(EG:207)"^^xsd:string
            kamNodeResource.addLiteral(hasLabel,
                    model.createTypedLiteral(kamNode.getLabel()));


            // hold on to kam node resources
            kamNodeResources.put(kamNode, kamNodeResource);


            // handle terms for this KAMNode
            // TODO Support nested terms instead of just Parameters!
            List<BelTerm> terms = kAMStore.getSupportingTerms(kamNode);
            for (BelTerm term : terms) {
                Resource termResource = model.createResource(new AnonId(UUID
                        .randomUUID().toString()));


                termResource.addProperty(RDF.type, Term);
                termResource.addProperty(hasId,
                        model.createTypedLiteral(term.getId()));
                termResource.addProperty(hasLabel,
                        model.createTypedLiteral(term.getLabel()));
                termResource.addProperty(hasFunction,
                        resourceForFunction(kamNode.getFunctionType()));


                RDFList argumentres = model.createList();


                List<TermParameter> termParameters =
                        kAMStore.getTermParameters(kamInfo, term);

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Examples of org.openbel.framework.ws.model.KamNode

        final Kam.KamNode[] nodes =
                new Kam.KamNode[wsn
                        .size()];


        for (int i = 0; i < wsn.size(); i++) {
            final KamNode wsKamNode = wsn.get(i);


            KamStoreObjectRef kamElementRef;
            try {
                kamElementRef = Converter.decodeNode(wsKamNode);
            } catch (InvalidIdException e) {
                throw new PathFindServiceException(
                        "Error retreving KAM associated with node", e);
            }


            int kamNodeId = kamElementRef.getKamStoreObjectId();
            Kam.KamNode kamNode = kam.findNode(kamNodeId);


            if (kamNode == null) {
                throw new PathFindServiceException("KamNode with id '"
                        + wsKamNode.getId()
                        + "' does not exist in KAM '"
                        + kam.getKamInfo().getName() + "'.");
            }


            nodes[i] = kamNode;

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Examples of org.openbel.framework.ws.model.KamNode

            node = objKam.findNode(elemid, filter);


            if (node == null) {
                kamNodes.add(null);
            } else {
                final KamNode kamNode = convert(objKam.getKamInfo(), node);
                kamNodes.add(kamNode);
            }
        }


        FindKamNodesByIdsResponse response = OBJECT_FACTORY

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Examples of org.openbel.framework.ws.model.KamNode

                            .findNode(label, filter);
            if (ksKamNode == null) {
                // add null for array symmetry
                kamNodes.add(null);
            } else {
                final KamNode kamNode = convert(objKam.getKamInfo(), ksKamNode);
                kamNodes.add(kamNode);
            }
        }


        FindKamNodesByLabelsResponse response =

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Examples of org.openbel.framework.ws.model.KamNode


            final Set<org.openbel.framework.api.Kam.KamNode> nodes =
                    objKam
                            .findNode(javaPattern, filter);
            for (org.openbel.framework.api.Kam.KamNode node : nodes) {
                final KamNode kamNode = convert(objKam.getKamInfo(), node);
                kamNodes.add(kamNode);
            }
        }


        final FindKamNodesByPatternsResponse response =

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Examples of org.openbel.framework.ws.model.KamNode

        if (request == null) {
            throw new MissingRequest(GET_ADJACENT_KAM_NODES_REQUEST);
        }


        // Make sure a KamNode was specified
        KamNode kamNode = request.getKamNode();
        if (null == kamNode) {
            throw new RequestException("KamNode payload is missing");
        }


        // See if we got a DirectionType to use
        org.openbel.framework.api.EdgeDirectionType direction =
                null;
        EdgeDirectionType edgeDirectionType = request.getDirection();
        if (null != edgeDirectionType) {
            direction = convert(edgeDirectionType);
        }


        // Get the real Kam from the KamCache
        KamStoreObjectRef kamElementRef;
        try {
            kamElementRef = Converter.decodeNode(kamNode);
        } catch (InvalidIdException e) {
            throw new RequestException("Error processing KAM node", e);
        }


        org.openbel.framework.api.Kam objKam;
        final KamInfo kamInfo = getKamInfo(kamElementRef,
                "Error processing KAM node");
        objKam = kamCacheService.getKam(kamInfo.getName());


        // Get the Dialect (may be null)
        final Dialect dialect = getDialect(request.getDialect());
        if (dialect != null) {
            objKam = new KamDialect(objKam, dialect);
        }


        if (objKam == null) {
            throw new RequestException("Error processing KAM node",
                    new InvalidIdException(kamElementRef.getEncodedString()));
        }


        final org.openbel.framework.api.NodeFilter nodes =
                convertNodeFilterInRequest(
                        request.getNodeFilter(), objKam);


        final org.openbel.framework.api.EdgeFilter edges =
                convertEdgeFilterInRequest(
                        request.getEdgeFilter(), objKam);


        // Get the real KamNode from the Kam
        Integer elemid = kamElementRef.getKamStoreObjectId();
        org.openbel.framework.api.Kam.KamNode objKamNode;
        objKamNode = objKam.findNode(elemid);


        // Process the request
        GetAdjacentKamNodesResponse response =
                OBJECT_FACTORY.createGetAdjacentKamNodesResponse();


        // Get the adjacent nodes
        Set<org.openbel.framework.api.Kam.KamNode> adjnodes;
        if (direction == null) {
            adjnodes = objKam.getAdjacentNodes(objKamNode, edges, nodes);
        } else {
            adjnodes = objKam.getAdjacentNodes(objKamNode, direction, edges,
                    nodes);
        }
        for (org.openbel.framework.api.Kam.KamNode node : adjnodes) {
            KamNode kn = convert(kamInfo, node);
            response.getKamNodes().add(kn);
        }


        return response;
    }

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Examples of org.openbel.framework.ws.model.KamNode

        if (request == null) {
            throw new MissingRequest(GET_ADJACENT_KAM_EDGES_REQUEST);
        }


        // Make sure a KamNode was specified
        KamNode kamNode = request.getKamNode();
        if (kamNode == null) {
            throw new RequestException("KamNode payload is missing");
        }


        if (kamNode.getFunction() == null) {
            final String msg = "KAM node is missing function";
            throw new RequestException(msg);
        }
        if (noLength(kamNode.getId())) {
            final String msg = "KAM node is missing id";
            throw new RequestException(msg);
        }
        if (noLength(kamNode.getLabel())) {
            final String msg = "KAM node is missing label";
            throw new RequestException(msg);
        }


        // See if we got a DirectionType to use

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