Examples of KamStoreObjectRef

org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

     */
    private Kam lookupKam(KamNode kamNode, Dialect dialect,
            final String errorMsg)
            throws KamCacheServiceException, InvalidIdException,
            RequestException {
        KamStoreObjectRef kamNodeRef = Converter.decodeNode(kamNode);
        KamInfo kamInfo = null;
        try {
            kamInfo = kamCatalogDao.getKamInfoById(kamNodeRef.getKamInfoId());
        } catch (SQLException e) {
            throw new RequestException(errorMsg, e);
        }
        if (kamInfo == null) {
            throw new InvalidIdException(kamNodeRef.getEncodedString());
        }
        final Kam kam = kamCacheService.getKam(kamInfo.getName());
        if (kam == null) {
            throw new InvalidIdException(kamNodeRef.getEncodedString());
        }
        return kam;
    }

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

            throws KamStoreServiceException {
        List<BelTerm> list = new ArrayList<BelTerm>();


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


            final KamInfo kamInfo =
                    getKamInfo(kamElementRef, "Error processing KAM node");
            final org.openbel.framework.api.Kam objKam =
                    kamCacheService.getKam(kamInfo.getName());
            if (objKam == null) {
                throw new KamStoreServiceException(
                        new InvalidIdException(kamElementRef.getEncodedString()));
            }


            // Get the real KamNode from the Kam
            org.openbel.framework.api.Kam.KamNode objKamNode =
                    objKam.findNode(kamElementRef.getKamStoreObjectId());
            // Get the supporting terms for the node
            for (org.openbel.framework.api.internal.KAMStoreDaoImpl.BelTerm objBelTerm : kAMStore
                    .getSupportingTerms(objKamNode)) {
                list.add(convert(objBelTerm, kamInfo));
            }

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

            KamFilter kamFilter) throws KamStoreServiceException {
        List<BelStatement> list = new ArrayList<BelStatement>();


        try {
            // Get the real Kam from the KamCache
            KamStoreObjectRef kamElementRef;
            try {
                kamElementRef = Converter.decodeEdge(kamEdge);
            } catch (InvalidIdException e) {
                throw new KamStoreServiceException("Error processing KAM edge",
                        e);
            }


            final KamInfo kamInfo =
                    getKamInfo(kamElementRef, "Error processing KAM edge");
            final org.openbel.framework.api.Kam objKam =
                    kamCacheService.getKam(kamInfo.getName());
            if (objKam == null) {
                throw new KamStoreServiceException(
                        new InvalidIdException(kamElementRef.getEncodedString()));
            }


            // Get the real KamEdge from the Kam
            org.openbel.framework.api.Kam.KamEdge objKamEdge =
                    objKam.findEdge(kamElementRef.getKamStoreObjectId());


            // Get the supporting evidence for the edge
            final List<org.openbel.framework.api.internal.KAMStoreDaoImpl.BelStatement> evidence;
            if (kamFilter != null) {
                // including edge and filter

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

            KamEdge first = kamEdges.iterator().next();


            // Get the real Kam from the KamCache
            org.openbel.framework.api.Kam kam;
            try {
                KamStoreObjectRef ref = Converter.decodeEdge(first);
                final KamInfo info = getKamInfo(ref, "Error processing KAM edge");
                kam = kamCacheService.getKam(info.getName());
                if (kam == null) {
                    throw new KamStoreServiceException(new InvalidIdException(ref.getEncodedString()));
                }
            } catch (InvalidIdException e) {
                throw new KamStoreServiceException("Error processing KAM edge", e);
            }


            // Convert kam edges
            for (KamEdge kamEdge : kamEdges) {
                // Get the real KamEdge from the Kam
                try {
                    KamStoreObjectRef ref = Converter.decodeEdge(kamEdge);
                    edges.add(kam.findEdge(ref.getKamStoreObjectId()));
                } catch (InvalidIdException e) {
                    throw new KamStoreServiceException("Error processing KAM edge", e);
                }
            }

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

                                .invoke(type);


                final String encoded =
                        (String) encode.invoke(null, kamInfoId, id, prefix);


                final KamStoreObjectRef objRef =
                        (KamStoreObjectRef) decode.invoke(
                                null, encoded, type);


                assertTrue(kamInfoId == objRef.getKamInfoId());
                assertTrue(id == objRef.getKamStoreObjectId());
                assertTrue(typeClass.equals(objRef.getKamStoreObjectClass()));
            }
        } catch (InvocationTargetException e) {
            throw e.getCause();
        }
    }

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

                        .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()

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

                convertNodeFilterInRequest(
                        request.getFilter(), objKam);


        List<KamNode> kamNodes = new ArrayList<KamNode>();
        for (String id : ids) {
            KamStoreObjectRef kamElementRef;
            try {
                kamElementRef = KamStoreObjectRef.decode(id);
            } catch (InvalidIdException e) {
                throw new RequestException("Error with KAM node ids", e);
            }


            Integer elemid = kamElementRef.getKamStoreObjectId();
            org.openbel.framework.api.Kam.KamNode node;
            node = objKam.findNode(elemid, filter);


            if (node == null) {
                kamNodes.add(null);

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

        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 =

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Examples of org.openbel.framework.ws.utils.Converter.KamStoreObjectRef

        if (edgeDirectionType != null) {
            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);
        }


        final KamInfo kamInfo = getKamInfo(kamElementRef,
                "Error processing KAM node");
        org.openbel.framework.api.Kam objKam;
        objKam = kamCacheService.getKam(kamInfo.getName());
        if (objKam == null) {
            throw new RequestException("Error processing KAM node",
                    new InvalidIdException(kamElementRef.getEncodedString()));
        }
        // Get the Dialect (may be null)
        final Dialect dialect = getDialect(request.getDialect());
        if (dialect != null) {
            objKam = new KamDialect(objKam, dialect);
        }


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


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


        GetAdjacentKamEdgesResponse response =
                OBJECT_FACTORY.createGetAdjacentKamEdgesResponse();


        // Get the adjacent edges

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