Package org.openbel.framework.api.internal.KAMCatalogDao

Examples of org.openbel.framework.api.internal.KAMCatalogDao.KamInfo

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        testKAM = createTestKAM();
        assertNotNull(testKAM);
    }

    private static Kam createTestKAM() {
        KamInfo testKAMInfo = null;
        try {
            testKAMInfo = KamInfoUtil.createKamInfo();
        } catch (Exception e) {
            e.printStackTrace();
            fail(e.getMessage());
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     * {@inheritDoc}
     */
    @Override
    public boolean exists(final String name) {
        if (name == null) throw new InvalidArgument(DEFAULT_MSG);
        KamInfo ki = search(getCatalog(), new SearchFunction<KamInfo>() {

            @Override
            public boolean match(KamInfo t) {
                return name.equals(t.getName());
            }
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     * {@inheritDoc}
     */
    @Override
    public void close(Kam kam) {
        if (kam == null) throw new InvalidArgument(DEFAULT_MSG);
        final KamInfo ki = kam.getKamInfo();
        KAMStoreDao dao = daomap.get(ki);
        if (dao != null) {
            dao.terminate();
            daomap.remove(ki);
        }
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     */
    @Override
    public Kam getKam(String kamName) {
        if (kamName == null) throw new InvalidArgument(DEFAULT_MSG);
        if (!exists(kamName)) return null;
        final KamInfo ki = getKamInfo(kamName);
        return getKam(ki);
    }
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     */
    @Override
    public List<BelTerm> getSupportingTerms(KamNode kamNode,
            boolean removeDuplicates, NamespaceFilter fltr) {
        if (kamNode == null) throw new InvalidArgument("kamNode", kamNode);
        KamInfo ki = kamNode.getKam().getKamInfo();
        if (!exists(ki)) return null;
        List<BelTerm> terms;
        try {
            terms = kamStoreDao(ki).getSupportingTerms(kamNode, fltr);
        } catch (SQLException e) {
            final String fmt = "error getting supporting terms for %s";
            final String msg = format(fmt, ki.getName());
            throw new KAMStoreException(msg, e);
        }

        // Check for duplicates
        if (removeDuplicates) {
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     */
    @Override
    public KamNode getKamNode(final Kam kam, String belTermString) {
        if (noLength(belTermString))
            throw new InvalidArgument("belTermString", belTermString);
        KamInfo ki = kam.getKamInfo();
        if (!exists(ki)) return null;
        KamNode kamNode;
        Integer nodeID;
        try {
            nodeID = kamStoreDao(ki).getKamNodeId(belTermString);
            kamNode = kam.findNode(nodeID);
        } catch (SQLException e) {
            final String fmt = "error getting KAM node ID for %s";
            final String msg = format(fmt, ki.getName());
            throw new KAMStoreException(msg, e);
        }
        return kamNode;
    }
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    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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            throw new RequestException("Error mapping data", e);
        } catch (KAMStoreException e) {
            throw new RequestException("Error mapping data", e);
        }

        KamInfo kamInfo = kam.getKamInfo();
        final MapDataResponse res = OBJECT_FACTORY.createMapDataResponse();
        for (org.openbel.framework.api.Kam.KamNode kn : nodes) {
            res.getKamNodes().add(Converter.convert(kamInfo, kn));
        }
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            }

            org.openbel.framework.common.enums.CitationType citation;
            citation = convert(citationType);

            KamInfo ki = objKam.getKamInfo();
            List<org.openbel.framework.api.internal.KAMStoreDaoImpl.Citation> citations;
            if (belDocument != null) {
                BelDocumentInfo info;
                try {
                    info = convert(belDocument);
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                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()));
            }
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Related Classes of org.openbel.framework.api.internal.KAMCatalogDao.KamInfo

  • org.openbel.framework.api.BasicPathFinderTest
  • org.openbel.framework.api.DefaultKamCacheServiceTest
  • org.openbel.framework.api.EdgeFilterTest
  • org.openbel.framework.api.KAMStoreImpl
  • org.openbel.framework.api.NodeFilterTest
  • org.openbel.framework.test.TestKAMStoreDaoImpl
  • org.openbel.framework.tools.kamstore.KamComparator
  • org.openbel.framework.tools.kamstore.KamManager
  • org.openbel.framework.tools.OrthologizeTool
  • org.openbel.framework.tools.pkam.DefaultPKAMSerializationService
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