Examples with LocalFile ubic.gemma.model.common.description.LocalFile used on opensource projects

Example 16 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class LocalFileDaoImpl method find.

@Override
public LocalFile find(LocalFile localFile) {
    BusinessKey.checkValidKey(localFile);
    HibernateTemplate t = new HibernateTemplate(this.getSessionFactory());
    t.setFlushMode(HibernateAccessor.FLUSH_COMMIT);
    List<?> results;
    if (localFile.getRemoteURL() == null) {
        results = t.findByNamedParam("from LocalFile where localURL=:u and remoteURL is null ", "u", localFile.getLocalURL());
    } else if (localFile.getLocalURL() == null) {
        results = t.findByNamedParam("from LocalFile where localURL is null and remoteURL=:r", "r", localFile.getRemoteURL());
    } else {
        results = t.findByNamedParam("from LocalFile where localURL=:u and remoteURL=:r", new String[] { "u", "r" }, new Object[] { localFile.getLocalURL(), localFile.getRemoteURL() });
    }
    Object result = null;
    if (results != null) {
        if (results.size() > 1) {
            throw new org.springframework.dao.InvalidDataAccessResourceUsageException("More than one instance of '" + LocalFile.class.getName() + "' was found when executing query");
        } else if (results.size() == 1) {
            result = results.get(0);
        }
    }
    return (LocalFile) result;
}

Example 17 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class LocalFileServiceImpl method deleteFile.

/**
 * @see LocalFileService#deleteFile(ubic.gemma.model.common.description.LocalFile)
 */
@Override
public void deleteFile(LocalFile localFile) throws IOException {
    if (localFile == null)
        return;
    File file = localFile.asFile();
    if (file == null)
        throw new IOException("Could not convert LocalFile into java.io.File");
    boolean success = false;
    if (file.exists()) {
        success = file.delete();
    }
    if (file.exists() || !success) {
        throw new IOException("Cannot remove file");
    }
    this.localFileDao.remove(localFile);
}

Example 18 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class DataUpdater method addAffyExonArrayData.

/**
 * Replaces any existing "preferred" data. Must be a single-platform study
 *
 * @param ee ee
 * @param ad ad
 */
// Possible external use
@SuppressWarnings({ "unused", "WeakerAccess" })
public void addAffyExonArrayData(ExpressionExperiment ee, ArrayDesign ad) {
    RawDataFetcher f = new RawDataFetcher();
    Collection<LocalFile> files = f.fetch(ee.getAccession().getAccession());
    if (files.isEmpty()) {
        throw new RuntimeException("Data was apparently not available");
    }
    ad = arrayDesignService.thaw(ad);
    ee = experimentService.thawLite(ee);
    Taxon primaryTaxon = ad.getPrimaryTaxon();
    ArrayDesign targetPlatform = this.prepareTargetPlatformForExonArrays(primaryTaxon);
    assert !targetPlatform.getCompositeSequences().isEmpty();
    AffyPowerToolsProbesetSummarize apt = new AffyPowerToolsProbesetSummarize();
    Collection<RawExpressionDataVector> vectors = apt.processExonArrayData(ee, targetPlatform, files);
    if (vectors.isEmpty()) {
        throw new IllegalStateException("No vectors were returned for " + ee);
    }
    ee = experimentService.replaceRawVectors(ee, vectors);
    if (!targetPlatform.equals(ad)) {
        AuditEventType eventType = ExpressionExperimentPlatformSwitchEvent.Factory.newInstance();
        auditTrailService.addUpdateEvent(ee, eventType, "Switched in course of updating vectors using AffyPowerTools (from " + ad.getShortName() + " to " + targetPlatform.getShortName() + ")");
    }
    this.audit(ee, "Data vector computation from CEL files using AffyPowerTools for " + targetPlatform, true);
    this.postprocess(ee);
}

Example 19 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class ArrayDesignPersister method persistNewArrayDesign.

/**
 * Persist an entirely new array design, including composite sequences and any associated new sequences.
 */
private ArrayDesign persistNewArrayDesign(ArrayDesign arrayDesign) {
    if (arrayDesign == null)
        return null;
    AbstractPersister.log.info("Persisting new platform " + arrayDesign.getName());
    try {
        this.getSessionFactory().getCurrentSession().setFlushMode(FlushMode.COMMIT);
        if (arrayDesign.getDesignProvider() != null)
            arrayDesign.setDesignProvider(this.persistContact(arrayDesign.getDesignProvider()));
        if (arrayDesign.getLocalFiles() != null) {
            for (LocalFile file : arrayDesign.getLocalFiles()) {
                this.persistLocalFile(file);
            }
        }
        if (arrayDesign.getPrimaryTaxon() == null) {
            throw new IllegalArgumentException("Primary taxon cannot be null");
        }
        arrayDesign.setPrimaryTaxon((Taxon) this.persist(arrayDesign.getPrimaryTaxon()));
        for (DatabaseEntry externalRef : arrayDesign.getExternalReferences()) {
            externalRef.setExternalDatabase(this.persistExternalDatabase(externalRef.getExternalDatabase()));
        }
        AbstractPersister.log.info("Persisting " + arrayDesign);
        if (arrayDesign.getAuditTrail() != null && this.isTransient(arrayDesign.getAuditTrail()))
            arrayDesign.getAuditTrail().setId(null);
        Collection<CompositeSequence> scs = new ArrayList<>(arrayDesign.getCompositeSequences());
        arrayDesign.getCompositeSequences().clear();
        arrayDesign = arrayDesignDao.create(arrayDesign);
        arrayDesign.getCompositeSequences().addAll(scs);
        arrayDesign = this.persistArrayDesignCompositeSequenceAssociations(arrayDesign);
        arrayDesignDao.update(arrayDesign);
    } finally {
        this.getSessionFactory().getCurrentSession().setFlushMode(FlushMode.AUTO);
    }
    return arrayDesign;
}

Example 20 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class ExpressionPersister method fillInBioAssayAssociations.

private void fillInBioAssayAssociations(BioAssay bioAssay, ArrayDesignsForExperimentCache c) {
    ArrayDesign arrayDesign = bioAssay.getArrayDesignUsed();
    ArrayDesign arrayDesignUsed;
    if (!this.isTransient(arrayDesign)) {
        arrayDesignUsed = arrayDesign;
    } else if (c == null || !c.getArrayDesignCache().containsKey(arrayDesign.getShortName())) {
        throw new UnsupportedOperationException("You must provide the persistent platforms in a cache object");
    } else {
        arrayDesignUsed = c.getArrayDesignCache().get(arrayDesign.getShortName());
        if (arrayDesignUsed == null || arrayDesignUsed.getId() == null) {
            throw new IllegalStateException("You must provide the platform in the cache object");
        }
        arrayDesignUsed = (ArrayDesign) this.getSessionFactory().getCurrentSession().load(ArrayDesign.class, arrayDesignUsed.getId());
        if (arrayDesignUsed == null) {
            throw new IllegalStateException("No platform matching " + arrayDesign.getShortName());
        }
        AbstractPersister.log.debug("Setting platform used for bioassay to " + arrayDesignUsed.getId());
    }
    assert !this.isTransient(arrayDesignUsed);
    bioAssay.setArrayDesignUsed(arrayDesignUsed);
    boolean hadFactors = false;
    BioMaterial material = bioAssay.getSampleUsed();
    for (FactorValue factorValue : material.getFactorValues()) {
        // Factors are not compositioned in any more, but by association with the ExperimentalFactor.
        this.fillInFactorValueAssociations(factorValue);
        this.persistFactorValue(factorValue);
        hadFactors = true;
    }
    if (hadFactors)
        AbstractPersister.log.debug("factor values done");
    // DatabaseEntries are persisted by composition, so we just need to fill in the ExternalDatabase.
    if (bioAssay.getAccession() != null) {
        bioAssay.getAccession().setExternalDatabase(this.persistExternalDatabase(bioAssay.getAccession().getExternalDatabase()));
        // IN CASE we are retrying.
        bioAssay.getAccession().setId(null);
        AbstractPersister.log.debug("external database done");
    }
    // BioMaterials
    bioAssay.setSampleUsed((BioMaterial) this.persist(bioAssay.getSampleUsed()));
    AbstractPersister.log.debug("biomaterials done");
    LocalFile rawDataFile = bioAssay.getRawDataFile();
    if (rawDataFile != null) {
        if (this.isTransient(rawDataFile)) {
            // in case of retry.
            rawDataFile.setId(null);
            // raw file is unique for bioassay.
            bioAssay.setRawDataFile(this.persistLocalFile(rawDataFile, true));
        } else {
            // re-sync.
            this.localFileDao.update(rawDataFile);
        }
        AbstractPersister.log.debug("raw data file done");
    }
    for (LocalFile file : bioAssay.getDerivedDataFiles()) {
        if (this.isTransient(file))
            // in case of retry
            file.setId(null);
        this.persistLocalFile(file);
    }
    if (this.isTransient(bioAssay.getAuditTrail()) && bioAssay.getAuditTrail() != null)
        // in case of retry;
        bioAssay.getAuditTrail().setId(null);
    AbstractPersister.log.debug("Done with " + bioAssay);
}