Examples with ProjectSynchronizationException ca.corefacility.bioinformatics.irida.exceptions.ProjectSynchronizationException used on opensource projects

Example 1 with ProjectSynchronizationException

use of ca.corefacility.bioinformatics.irida.exceptions.ProjectSynchronizationException in project irida by phac-nml.

the class ProjectSynchronizationService method syncSequenceFilePair.

/**
 * Synchronize a given {@link SequenceFilePair} to the local installation.
 *
 * @param pair
 *            the {@link SequenceFilePair} to sync. This should have been
 *            read from a remote api.
 * @param sample
 *            The {@link Sample} to add the pair to.
 */
public void syncSequenceFilePair(SequenceFilePair pair, Sample sample) {
    pair.getRemoteStatus().setSyncStatus(SyncStatus.UPDATING);
    try {
        pair = pairRemoteService.mirrorSequencingObject(pair);
        pair.getFiles().forEach(s -> {
            s.setId(null);
            s.getRemoteStatus().setSyncStatus(SyncStatus.SYNCHRONIZED);
        });
        objectService.createSequencingObjectInSample(pair, sample);
        RemoteStatus pairStatus = pair.getRemoteStatus();
        pairStatus.setSyncStatus(SyncStatus.SYNCHRONIZED);
        objectService.updateRemoteStatus(pair.getId(), pairStatus);
    } catch (Exception e) {
        logger.error("Error transferring file: " + pair.getRemoteStatus().getURL(), e);
        throw new ProjectSynchronizationException("Could not synchronize pair " + pair.getRemoteStatus().getURL(), e);
    }
}

Example 2 with ProjectSynchronizationException

use of ca.corefacility.bioinformatics.irida.exceptions.ProjectSynchronizationException in project irida by phac-nml.

the class ProjectSynchronizationService method syncSingleEndSequenceFile.

/**
 * Synchronize a given {@link SingleEndSequenceFile} to the local
 * installation
 *
 * @param file
 *            the {@link SingleEndSequenceFile} to sync
 * @param sample
 *            the {@link Sample} to add the file to
 */
public void syncSingleEndSequenceFile(SingleEndSequenceFile file, Sample sample) {
    RemoteStatus fileStatus = file.getRemoteStatus();
    fileStatus.setSyncStatus(SyncStatus.UPDATING);
    try {
        file = singleEndRemoteService.mirrorSequencingObject(file);
        file.getSequenceFile().setId(null);
        file.getSequenceFile().getRemoteStatus().setSyncStatus(SyncStatus.SYNCHRONIZED);
        objectService.createSequencingObjectInSample(file, sample);
        fileStatus.setSyncStatus(SyncStatus.SYNCHRONIZED);
        objectService.updateRemoteStatus(file.getId(), fileStatus);
    } catch (Exception e) {
        logger.error("Error transferring file: " + file.getRemoteStatus().getURL(), e);
        throw new ProjectSynchronizationException("Could not synchronize file " + file.getRemoteStatus().getURL(), e);
    }
}

Example 3 with ProjectSynchronizationException

use of ca.corefacility.bioinformatics.irida.exceptions.ProjectSynchronizationException in project irida by phac-nml.

the class ProjectSynchronizationService method syncSample.

/**
 * Synchronize a given {@link Sample} to the local installation.
 *
 * @param sample          the {@link Sample} to synchronize. This should have been read
 *                        from a remote api.
 * @param project         The {@link Project} the {@link Sample} belongs in.
 * @param existingSamples A map of samples that have already been synchronized.  These will be checked to see if they've been updated
 */
public void syncSample(Sample sample, Project project, Map<String, Sample> existingSamples) {
    Sample localSample;
    if (existingSamples.containsKey(sample.getRemoteStatus().getURL())) {
        // if the sample already exists check if it's been updated
        localSample = existingSamples.get(sample.getRemoteStatus().getURL());
        // if there's changes, update the sample
        if (checkForChanges(localSample.getRemoteStatus(), sample)) {
            logger.debug("found changes for sample " + sample.getSelfHref());
            // ensure the ids are properly set
            sample = updateIds(localSample, sample);
            sample.getRemoteStatus().setSyncStatus(SyncStatus.UPDATING);
            localSample = sampleService.update(sample);
        }
    } else {
        // if the sample doesn't already exist create it
        sample.getRemoteStatus().setSyncStatus(SyncStatus.UPDATING);
        localSample = sampleService.create(sample);
        projectService.addSampleToProject(project, sample, true);
    }
    // get the local files and organize by their url
    Collection<SampleSequencingObjectJoin> localObjects = objectService.getSequencingObjectsForSample(localSample);
    Map<String, SequencingObject> objectsByUrl = new HashMap<>();
    localObjects.forEach(j -> {
        SequencingObject pair = j.getObject();
        // concatenated it
        if (pair.getRemoteStatus() != null) {
            String url = pair.getRemoteStatus().getURL();
            objectsByUrl.put(url, pair);
        }
    });
    List<SequenceFilePair> sequenceFilePairsForSample = pairRemoteService.getSequenceFilePairsForSample(sample);
    List<ProjectSynchronizationException> syncErrors = new ArrayList<>();
    for (SequenceFilePair pair : sequenceFilePairsForSample) {
        if (!objectsByUrl.containsKey(pair.getRemoteStatus().getURL())) {
            pair.setId(null);
            try {
                syncSequenceFilePair(pair, localSample);
            } catch (ProjectSynchronizationException e) {
                syncErrors.add(e);
            }
        }
    }
    List<SingleEndSequenceFile> unpairedFilesForSample = singleEndRemoteService.getUnpairedFilesForSample(sample);
    for (SingleEndSequenceFile file : unpairedFilesForSample) {
        if (!objectsByUrl.containsKey(file.getRemoteStatus().getURL())) {
            file.setId(null);
            try {
                syncSingleEndSequenceFile(file, localSample);
            } catch (ProjectSynchronizationException e) {
                syncErrors.add(e);
            }
        }
    }
    if (syncErrors.isEmpty()) {
        localSample.getRemoteStatus().setSyncStatus(SyncStatus.SYNCHRONIZED);
    } else {
        localSample.getRemoteStatus().setSyncStatus(SyncStatus.ERROR);
        logger.error("Setting sample " + localSample.getId() + "sync status to ERROR due to sync errors with files");
    }
    sampleService.update(localSample);
}