@Test @Transactional(propagation = Propagation.REQUIRES_NEW) public void testRegisterBed() throws IOException, FeatureFileReadingException { BedFile bedFile = testRegisterBed(GENES_SORTED_BED_PATH); Assert.assertTrue(testLoadBedRecords(bedFile)); }
public BedFile registerBed(final IndexedFileRegistrationRequest request) { final String requestPath = request.getPath(); Assert.isTrue(StringUtils.isNotBlank(requestPath), getMessage( MessagesConstants.ERROR_NULL_PARAM, "path")); Assert.notNull(request.getReferenceId(), getMessage(MessagesConstants.ERROR_NULL_PARAM, "referenceId")); if (request.getType() == null) { request.setType(BiologicalDataItemResourceType.FILE); } BedFile bedFile; try { bedFile = createBedFile(request); } catch (IOException | HistogramReadingException e) { throw new RegistrationException(e.getMessage(), e); } return bedFile; }
BedManager { public BedFile registerBed(final IndexedFileRegistrationRequest request) { final String requestPath = request.getPath(); Assert.isTrue(StringUtils.isNotBlank(requestPath), getMessage( MessagesConstants.ERROR_NULL_PARAM, "path")); Assert.notNull(request.getReferenceId(), getMessage(MessagesConstants.ERROR_NULL_PARAM, "referenceId")); if (request.getType() == null) { request.setType(BiologicalDataItemResourceType.FILE); } BedFile bedFile; try { bedFile = createBedFile(request); } catch (IOException | HistogramReadingException e) { throw new RegistrationException(e.getMessage(), e); } return bedFile; } }
BedManager { public BedFile registerBed(final IndexedFileRegistrationRequest request) { final String requestPath = request.getPath(); Assert.isTrue(StringUtils.isNotBlank(requestPath), getMessage( MessagesConstants.ERROR_NULL_PARAM, "path")); Assert.notNull(request.getReferenceId(), getMessage(MessagesConstants.ERROR_NULL_PARAM, "referenceId")); if (request.getType() == null) { request.setType(BiologicalDataItemResourceType.FILE); } BedFile bedFile; try { bedFile = createBedFile(request); } catch (IOException | HistogramReadingException e) { throw new RegistrationException(e.getMessage(), e); } return bedFile; }  }
BedManager { public BedFile registerBed(final IndexedFileRegistrationRequest request) { final String requestPath = request.getPath(); Assert.isTrue(StringUtils.isNotBlank(requestPath), getMessage( MessagesConstants.ERROR_NULL_PARAM, "path")); Assert.notNull(request.getReferenceId(), getMessage(MessagesConstants.ERROR_NULL_PARAM, "referenceId")); if (request.getType() == null) { request.setType(BiologicalDataItemResourceType.FILE); } BedFile bedFile; try { bedFile = createBedFile(request); } catch (IOException | HistogramReadingException e) { throw new RegistrationException(e.getMessage(), e); } return bedFile; }  BedFile registerBed(final IndexedFileRegistrationRequest request); Track<BedRecord> loadFeatures(final Track<BedRecord> track); Track<BedRecord> loadFeatures(final Track<BedRecord> track, String fileUrl, String indexUrl); Track<Wig> loadHistogram(final Track<Wig> track); BedFile unregisterBedFile(long bedFileId); BedFile reindexBedFile(long bedFileId); }
BedManager { public BedFile registerBed(final IndexedFileRegistrationRequest request) { final String requestPath = request.getPath(); Assert.isTrue(StringUtils.isNotBlank(requestPath), getMessage( MessagesConstants.ERROR_NULL_PARAM, "path")); Assert.notNull(request.getReferenceId(), getMessage(MessagesConstants.ERROR_NULL_PARAM, "referenceId")); if (request.getType() == null) { request.setType(BiologicalDataItemResourceType.FILE); } BedFile bedFile; try { bedFile = createBedFile(request); } catch (IOException | HistogramReadingException e) { throw new RegistrationException(e.getMessage(), e); } return bedFile; }  BedFile registerBed(final IndexedFileRegistrationRequest request); Track<BedRecord> loadFeatures(final Track<BedRecord> track); Track<BedRecord> loadFeatures(final Track<BedRecord> track, String fileUrl, String indexUrl); Track<Wig> loadHistogram(final Track<Wig> track); BedFile unregisterBedFile(long bedFileId); BedFile reindexBedFile(long bedFileId);  }