@Test(expected = IllegalArgumentException.class) @Transactional(propagation = Propagation.REQUIRES_NEW, rollbackFor = Exception.class) public void testFindBlatReadSequenceEmptySpecies() throws IOException, ExternalDbUnavailableException { referenceGenomeManager.updateSpecies(testReference.getId(), "hg19"); String readSequence = "CAGTATCGTCCTTACTATTACATAGTGTGGTAGCGATGCAGTCCCAGTGAAAAAAAAAAAAAAAAAAAC"; blatSearchManager.findBlatReadSequence(testReference.getId(), readSequence); }
public List<PSLRecord> findBlatReadSequence(Long referenceId, String readSequence) throws ExternalDbUnavailableException, IOException { Assert.isTrue(referenceId != null && StringUtils.isNotBlank(readSequence), MessagesConstants.ERROR_NULL_PARAM); Reference reference = referenceGenomeManager.load(referenceId); Assert.notNull(reference.getSpecies(), getMessage(MessagesConstants.NULL_SPECIES_FOR_GENOME, reference.getName())); return find(readSequence, reference.getSpecies()); }
BlatSearchManager { public List<PSLRecord> findBlatReadSequence(Long referenceId, String readSequence) throws ExternalDbUnavailableException, IOException { Assert.isTrue(referenceId != null && StringUtils.isNotBlank(readSequence), MessagesConstants.ERROR_NULL_PARAM); Reference reference = referenceGenomeManager.load(referenceId); Assert.notNull(reference.getSpecies(), getMessage(MessagesConstants.NULL_SPECIES_FOR_GENOME, reference.getName())); return find(readSequence, reference.getSpecies()); } }
BlatSearchManager { public List<PSLRecord> findBlatReadSequence(Long referenceId, String readSequence) throws ExternalDbUnavailableException, IOException { Assert.isTrue(referenceId != null && StringUtils.isNotBlank(readSequence), MessagesConstants.ERROR_NULL_PARAM); Reference reference = referenceGenomeManager.load(referenceId); Assert.notNull(reference.getSpecies(), getMessage(MessagesConstants.NULL_SPECIES_FOR_GENOME, reference.getName())); return find(readSequence, reference.getSpecies()); }  }
BlatSearchManager { public List<PSLRecord> findBlatReadSequence(Long referenceId, String readSequence) throws ExternalDbUnavailableException, IOException { Assert.isTrue(referenceId != null && StringUtils.isNotBlank(readSequence), MessagesConstants.ERROR_NULL_PARAM); Reference reference = referenceGenomeManager.load(referenceId); Assert.notNull(reference.getSpecies(), getMessage(MessagesConstants.NULL_SPECIES_FOR_GENOME, reference.getName())); return find(readSequence, reference.getSpecies()); }  List<PSLRecord> find(String readSequence, Species species); List<PSLRecord> findBlatReadSequence(Long referenceId, String readSequence); }
BlatSearchManager { public List<PSLRecord> findBlatReadSequence(Long referenceId, String readSequence) throws ExternalDbUnavailableException, IOException { Assert.isTrue(referenceId != null && StringUtils.isNotBlank(readSequence), MessagesConstants.ERROR_NULL_PARAM); Reference reference = referenceGenomeManager.load(referenceId); Assert.notNull(reference.getSpecies(), getMessage(MessagesConstants.NULL_SPECIES_FOR_GENOME, reference.getName())); return find(readSequence, reference.getSpecies()); }  List<PSLRecord> find(String readSequence, Species species); List<PSLRecord> findBlatReadSequence(Long referenceId, String readSequence);  }