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

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

198
199
200
201
202
203
204
205
206
207
208
209
210
211
            } 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()));
            }
View Full Code Here
280
281
282
283
284
285
286
287
288
289
290
291
            // 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);
View Full Code Here
516
517
518
519
520
521
522
523
524
525
526
    private KamInfo getKamInfo(final KamStoreObjectRef kamElementRef,
            String errorMsg)
            throws KamStoreServiceException {

        final int kamInfoId = kamElementRef.getKamInfoId();
        KamInfo kamInfo = null;
        try {
            kamInfo = kamCatalogDao.getKamInfoById(kamInfoId);
        } catch (SQLException e) {
            throw new KamStoreServiceException(errorMsg, e);
        }
View Full Code Here
402
403
404
405
406
407
408
409
410
411
412
413
414
        } 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);
View Full Code Here
497
498
499
500
501
502
503
504
505
506
507
508
509
510
            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)
View Full Code Here
570
571
572
573
574
575
576
577
578
579
580
        List<org.openbel.framework.api.Kam.KamNode> nodes = findKamNodesByNamespacevalues(
                request.getNamespaceValues(), request.getFilter(), objKam,
                kAMStore, equivalencer);

        KamInfo kamInfo = objKam.getKamInfo();
        FindKamNodesByNamespaceValuesResponse response =
                OBJECT_FACTORY.createFindKamNodesByNamespaceValuesResponse();
        for (org.openbel.framework.api.Kam.KamNode node : nodes) {
            response.getKamNodes().add(convert(kamInfo, node));
        }
View Full Code Here
726
727
728
729
730
731
732
733
734
735
736
        return convert(objKam, edgeFilter);
    }

    private KamInfo getKamInfo(final KamStoreObjectRef kamElementRef,
            final String errorMsg) throws RequestException {
        KamInfo kamInfo = null;
        try {
            kamInfo = kamCatalogDao
                    .getKamInfoById(kamElementRef.getKamInfoId());
        } catch (SQLException e) {
            throw new RequestException(errorMsg, e);
View Full Code Here
130
131
132
133
134
135
136
137
138
139
140
        }
        if (kam.getName() == null) {
            throw new RequestException(KAM_REQUEST_NO_NAME);
        }

        KamInfo kamInfo = null;
        List<KamInfo> catalog;
        try {
            catalog = kamCatalogDao.getCatalog();
        } catch (SQLException e) {
            String msg = getFirstMessage(e);
View Full Code Here
249
250
251
252
253
254
255
256
257
258
259
     * Create a test KAM for testing path finds.
     *
     * @return {@link Kam} the test KAM
     */
    private Kam createTestKAM() {
        KamInfo testKAMInfo = null;
        try {
            testKAMInfo = KamInfoUtil.createKamInfo();
        } catch (Exception e) {
            fail(e.getMessage());
        }
View Full Code Here
335
336
337
338
339
340
341
342
343
344
345
        testKAM = createTestKAM();
        assertNotNull(testKAM);
    }

    private static Kam createTestKAM() {
        KamInfo testKAMInfo = null;
        try {
            testKAMInfo = KamInfoUtil.createKamInfo();
        } catch (Exception e) {
            e.printStackTrace();
            fail(e.getMessage());
View Full Code Here
TOP

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
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.