public MobiDBFilteredMatchDAO(SignatureLibraryRelease release) { super(MobiDBMatch.class); this.release = release; this.mobidbReleaseVersion = release.getVersion(); }
@Override public String toString() { final StringBuilder sb = new StringBuilder(); sb.append("Job"); if(libraryRelease != null ) { sb.append(" (version:").append(libraryRelease.getVersion()).append(")"); } sb.append("{id='").append(id).append('\''); sb.append(", description='").append(description).append('\''); sb.append(", steps=").append(steps); sb.append('}'); return sb.toString(); }
/** * This private method is responsible for retrieving OR persisting (as appropriate) * a SignatureLibraryRelease method for the version of TMHMM being handled by this * DAO. * * @return the retrieved / persisted SignatureLibraryRelease object. */ private SignatureLibraryRelease loadTMHMMRelease() { SignatureLibraryRelease release = null; final Query releaseQuery = entityManager.createQuery("select r from SignatureLibraryRelease r where r.version = :version and r.library = :signatureLibrary"); releaseQuery.setParameter("version", signatureLibraryRelease.getVersion()); releaseQuery.setParameter("signatureLibrary", signatureLibraryRelease.getLibrary()); @SuppressWarnings("unchecked") List<SignatureLibraryRelease> releaseList = releaseQuery.getResultList(); if (releaseList.size() == 1 && releaseList.get(0) != null) { release = releaseList.get(0); } else if (releaseList.size() > 1) { throw new IllegalStateException("There is more than one SignatureLibraryRelease record for version " + signatureLibraryRelease.getVersion() + " of TMHMM in the databases."); } else { entityManager.persist(new SignatureLibraryRelease(signatureLibraryRelease.getLibrary(), signatureLibraryRelease.getVersion())); } return release; }
@XmlElement(name = "signature-library-release") private SignatureLibraryRelease getSignatureLibraryReleaseShallow() { if (this.signatureLibraryRelease == null) { return null; } return new SignatureLibraryRelease(this.signatureLibraryRelease.getLibrary(), this.signatureLibraryRelease.getVersion()); }
if (LOGGER.isDebugEnabled()) { LOGGER.debug("analysis: " + analysisJobName + " lookUpMatchAnalaysiVersion: " + lookUpMatchAnalaysVersion + " analysisJobName: " + analysisJobName + " analysisJobVersion: " + analysisJobMap.get(analysisJobName).getVersion()); if (!lookUpMatchAnalaysVersion.equals(analysisJobMap.get(analysisJobName).getVersion())) { if (LOGGER.isDebugEnabled()) { LOGGER.debug("Different versions of " + analysisJobName + " running ");
final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();
job4Debug.getId() + ": " + job4Debug.getLibraryRelease().getLibrary().getName() + ", " + job4Debug.getLibraryRelease().getVersion() + ", " + "active: " + job4Debug.isActive()); LOGGER.debug("Gene3d: " + job4Debug.getLibraryRelease().getVersion() + " - " + job4Debug.getSteps()); LOGGER.debug("panther: " + job4Debug.getLibraryRelease().getVersion() + " - " + job4Debug.getSteps()); LOGGER.debug("Name: " + signatureLibraryRelease.getLibrary().getName() + " version: " + signatureLibraryRelease.getVersion() + " name: " + signatureLibraryRelease.getLibrary().getName()); analysesToRun.append(analysisJobMap.get(key).getLibrary().getName() + "-" + analysisJobMap.get(key)); analysesToDisplay.add(String.join("-", analysisJobMap.get(key).getLibrary().getName(), analysisJobMap.get(key).getVersion()));
final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();