Examples with Dataset edu.harvard.iq.dataverse.Dataset used on opensource projects

Example 76 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class XgetRecordHandler method createRecord.

private Xrecord createRecord(OAICompiledRequest parameters, Item item) throws BadArgumentException, CannotDisseminateRecordException, OAIException, NoMetadataFormatsException, CannotDisseminateFormatException {
    MetadataFormat format = getContext().formatForPrefix(parameters.getMetadataPrefix());
    Header header = new Header();
    Dataset dataset = ((Xitem) item).getDataset();
    Xrecord xrecord = new Xrecord().withFormatName(parameters.getMetadataPrefix()).withDataset(dataset);
    header.withIdentifier(item.getIdentifier());
    ItemHelper itemHelperWrap = new ItemHelper(item);
    header.withDatestamp(item.getDatestamp());
    for (Set set : itemHelperWrap.getSets(getContext(), getRepository().getFilterResolver())) header.withSetSpec(set.getSpec());
    if (item.isDeleted())
        header.withStatus(Header.Status.DELETED);
    xrecord.withHeader(header);
    xrecord.withMetadata(item.getMetadata());
    return xrecord;
}

Example 77 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class IngestServiceBean method addFilesToDataset.

// addFilesToDataset() takes a list of new DataFiles and attaches them to the parent
// Dataset (the files are attached to the dataset, and the fileMetadatas to the
// supplied version).
public void addFilesToDataset(DatasetVersion version, List<DataFile> newFiles) {
    if (newFiles != null && newFiles.size() > 0) {
        Dataset dataset = version.getDataset();
        for (DataFile dataFile : newFiles) {
            // These are all brand new files, so they should all have
            // one filemetadata total. -- L.A.
            FileMetadata fileMetadata = dataFile.getFileMetadatas().get(0);
            String fileName = fileMetadata.getLabel();
            // Attach the file to the dataset and to the version:
            dataFile.setOwner(dataset);
            version.getFileMetadatas().add(dataFile.getFileMetadata());
            dataFile.getFileMetadata().setDatasetVersion(version);
            dataset.getFiles().add(dataFile);
        }
    }
}

Example 78 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class XitemRepository method getItem.

@Override
public Item getItem(String identifier) throws IdDoesNotExistException, OAIException {
    logger.fine("getItem; calling findOaiRecordsByGlobalId, identifier " + identifier);
    List<OAIRecord> oaiRecords = recordService.findOaiRecordsByGlobalId(identifier);
    if (oaiRecords != null && !oaiRecords.isEmpty()) {
        Xitem xoaiItem = null;
        for (OAIRecord record : oaiRecords) {
            if (xoaiItem == null) {
                Dataset dataset = datasetService.findByGlobalId(record.getGlobalId());
                if (dataset != null) {
                    xoaiItem = new Xitem(record).withDataset(dataset);
                }
            } else {
                // is part of multiple sets:
                if (!StringUtil.isEmpty(record.getSetName())) {
                    xoaiItem.getSets().add(new Set(record.getSetName()));
                }
            }
        }
        if (xoaiItem != null) {
            return xoaiItem;
        }
    }
    throw new IdDoesNotExistException();
}

Example 79 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class XitemRepository method getItems.

@Override
public ListItemsResults getItems(List<ScopedFilter> filters, int offset, int length, String setSpec, Date from, Date until) throws OAIException {
    logger.fine("calling getItems; offset=" + offset + ", length=" + length + ", setSpec=" + setSpec + ", from=" + from + ", until=" + until);
    List<OAIRecord> oaiRecords = recordService.findOaiRecordsBySetName(setSpec, from, until);
    logger.fine("total " + oaiRecords.size() + " returned");
    List<Item> xoaiItems = new ArrayList<>();
    if (oaiRecords != null && !oaiRecords.isEmpty()) {
        for (int i = offset; i < offset + length && i < oaiRecords.size(); i++) {
            OAIRecord oaiRecord = oaiRecords.get(i);
            Dataset dataset = datasetService.findByGlobalId(oaiRecord.getGlobalId());
            if (dataset != null) {
                Xitem xItem = new Xitem(oaiRecord).withDataset(dataset);
                xoaiItems.add(xItem);
            }
        }
        if (!StringUtil.isEmpty(setSpec)) {
            addExtraSets(xoaiItems, setSpec, from, until);
        }
        boolean hasMore = offset + length < oaiRecords.size();
        ListItemsResults result = new ListItemsResults(hasMore, xoaiItems);
        logger.fine("returning result with " + xoaiItems.size() + " items.");
        return result;
    }
    return new ListItemsResults(false, xoaiItems);
}

Example 80 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class IngestMessageBean method onMessage.

@TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
public void onMessage(Message message) {
    IngestMessage ingestMessage = null;
    Long datafile_id = null;
    try {
        ObjectMessage om = (ObjectMessage) message;
        ingestMessage = (IngestMessage) om.getObject();
        Iterator iter = ingestMessage.getFileIds().iterator();
        datafile_id = null;
        // -- L.A. Aug. 13 2014
        while (iter.hasNext()) {
            datafile_id = (Long) iter.next();
            logger.fine("Start ingest job;");
            try {
                if (ingestService.ingestAsTabular(datafile_id)) {
                    // Thread.sleep(10000);
                    logger.fine("Finished ingest job;");
                } else {
                    logger.warning("Error occurred during ingest job!");
                }
            } catch (Exception ex) {
                // ex.printStackTrace();
                // TODO:
                // this solution is working - but it would be cleaner to instead
                // make sure that all the exceptions are interrupted and appropriate
                // action taken still on the ingest service side.
                // -- L.A. Aug. 13 2014;
                logger.info("Unknown exception occurred  during ingest (supressed stack trace); re-setting ingest status.");
                if (datafile_id != null) {
                    logger.fine("looking up datafile for id " + datafile_id);
                    DataFile datafile = datafileService.find(datafile_id);
                    if (datafile != null) {
                        datafile.SetIngestProblem();
                        IngestReport errorReport = new IngestReport();
                        errorReport.setFailure();
                        if (ex.getMessage() != null) {
                            errorReport.setReport("Ingest succeeded, but failed to save the ingested tabular data in the database: " + ex.getMessage());
                        } else {
                            errorReport.setReport("Ingest succeeded, but failed to save the ingested tabular data in the database; no further information is available");
                        }
                        errorReport.setDataFile(datafile);
                        datafile.setIngestReport(errorReport);
                        datafile.setDataTables(null);
                        logger.info("trying to save datafile and the failed ingest report, id=" + datafile_id);
                        datafile = datafileService.save(datafile);
                        Dataset dataset = datafile.getOwner();
                        if (dataset != null && dataset.getId() != null) {
                            // logger.info("attempting to remove dataset lock for dataset " + dataset.getId());
                            // datasetService.removeDatasetLock(dataset.getId());
                            ingestService.sendFailNotification(dataset.getId());
                        }
                    }
                }
            }
        }
        // packed into this IngestMessage belong to the same dataset)
        if (datafile_id != null) {
            DataFile datafile = datafileService.find(datafile_id);
            if (datafile != null) {
                Dataset dataset = datafile.getOwner();
                if (dataset != null && dataset.getId() != null) {
                    datasetService.removeDatasetLocks(dataset.getId(), DatasetLock.Reason.Ingest);
                }
            }
        }
    } catch (JMSException ex) {
        // error in getting object from message; can't send e-mail
        ex.printStackTrace();
    } finally {
        // when we're done, go ahead and remove the lock (not yet)
        try {
        // datasetService.removeDatasetLock( ingestMessage.getDatasetId() );
        } catch (Exception ex) {
            // application was unable to remove the datasetLock
            ex.printStackTrace();
        }
    }
}