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

Example 36 with DatasetVersion

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

the class OAIRecordServiceBean method updateOaiRecordsForDataset.

// Updates any existing OAI records for this dataset
// Should be called whenever there's a change in the release status of the Dataset
// (i.e., when it's published or deaccessioned), so that the timestamps and
// on the records could be freshened before the next reexport of the corresponding
// sets.
// *Note* that the method assumes that a full metadata reexport has already
// been attempted on the dataset. (Meaning that if getLastExportTime is null,
// we'll just assume that the exports failed and the OAI records must be marked
// as "deleted".
@TransactionAttribute(REQUIRES_NEW)
public void updateOaiRecordsForDataset(Dataset dataset) {
    // create Map of OaiRecords
    List<OAIRecord> oaiRecords = findOaiRecordsByGlobalId(dataset.getGlobalId());
    if (oaiRecords != null) {
        DatasetVersion releasedVersion = dataset.getReleasedVersion();
        if (releasedVersion == null || dataset.getLastExportTime() == null) {
            // Datast must have been deaccessioned.
            markOaiRecordsAsRemoved(oaiRecords, new Date(), logger);
            return;
        }
        for (OAIRecord record : oaiRecords) {
            if (record.isRemoved()) {
                logger.fine("\"un-deleting\" an existing OAI Record for " + dataset.getGlobalId());
                record.setRemoved(false);
                record.setLastUpdateTime(new Date());
            } else if (dataset.getLastExportTime().after(record.getLastUpdateTime())) {
                record.setLastUpdateTime(new Date());
            }
        }
    } else {
        logger.fine("Null returned - no records found.");
    }
}

Example 37 with DatasetVersion

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

the class OAIRecordServiceBean method updateOaiRecords.

public void updateOaiRecords(String setName, List<Long> datasetIds, Date updateTime, boolean doExport, Logger setUpdateLogger) {
    // create Map of OaiRecords
    List<OAIRecord> oaiRecords = findOaiRecordsBySetName(setName);
    Map<String, OAIRecord> recordMap = new HashMap<>();
    if (oaiRecords != null) {
        for (OAIRecord record : oaiRecords) {
            // look for duplicates here? delete?
            recordMap.put(record.getGlobalId(), record);
        }
    } else {
        setUpdateLogger.fine("Null returned - no records found.");
    }
    if (!recordMap.isEmpty()) {
        setUpdateLogger.fine("Found " + recordMap.size() + " existing records");
    } else {
        setUpdateLogger.fine("No records in the set yet.");
    }
    if (datasetIds != null) {
        for (Long datasetId : datasetIds) {
            setUpdateLogger.fine("processing dataset id=" + datasetId);
            Dataset dataset = datasetService.find(datasetId);
            if (dataset == null) {
                setUpdateLogger.fine("failed to find dataset!");
            } else {
                setUpdateLogger.fine("found dataset.");
                // TODO: option to *force* export?
                if (doExport) {
                    // TODO:
                    // Review this logic - specifically for handling of
                    // deaccessioned datasets. -- L.A. 4.5
                    // OK, it looks like we can't rely on .getPublicationDate() -
                    // as it is essentially the *first publication* date;
                    // and we are interested in the *last*
                    DatasetVersion releasedVersion = dataset.getReleasedVersion();
                    Date publicationDate = releasedVersion == null ? null : releasedVersion.getReleaseTime();
                    if (publicationDate != null && (dataset.getLastExportTime() == null || dataset.getLastExportTime().before(publicationDate))) {
                        setUpdateLogger.fine("Attempting to run export on dataset " + dataset.getGlobalId());
                        exportAllFormats(dataset);
                    }
                }
                setUpdateLogger.fine("\"last exported\" timestamp: " + dataset.getLastExportTime());
                em.refresh(dataset);
                setUpdateLogger.fine("\"last exported\" timestamp, after db refresh: " + dataset.getLastExportTime());
                updateOaiRecordForDataset(dataset, setName, recordMap, setUpdateLogger);
            }
        }
    }
    // anything left in the map should be marked as removed!
    markOaiRecordsAsRemoved(recordMap.values(), updateTime, setUpdateLogger);
}

Example 38 with DatasetVersion

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

the class RestrictFileCommand method executeImpl.

@Override
protected void executeImpl(CommandContext ctxt) throws CommandException {
    // check if public install & don't allow
    boolean defaultValue = false;
    boolean publicInstall = ctxt.settings().isTrueForKey(SettingsServiceBean.Key.PublicInstall, defaultValue);
    if (publicInstall) {
        throw new CommandExecutionException("Restricting files is not permitted on a public installation.", this);
    }
    if (file.getOwner() == null) {
        // this is a new file through upload, restrict
        file.getFileMetadata().setRestricted(restrict);
        file.setRestricted(restrict);
    } else {
        Dataset dataset = file.getOwner();
        DatasetVersion workingVersion = dataset.getEditVersion();
        // check if this file is already restricted or already unrestricted
        if ((restrict && file.getFileMetadata().isRestricted()) || (!restrict && !file.getFileMetadata().isRestricted())) {
            String text = restrict ? "restricted" : "unrestricted";
            throw new CommandExecutionException("File " + file.getDisplayName() + " is already " + text, this);
        }
        // check if this dataset is a draft (should be), then we can update restrict
        if (workingVersion.isDraft()) {
            // because we must update the working version metadata
            if (dataset.isReleased()) {
                for (FileMetadata fmw : workingVersion.getFileMetadatas()) {
                    if (file.equals(fmw.getDataFile())) {
                        fmw.setRestricted(restrict);
                        if (!file.isReleased()) {
                            file.setRestricted(restrict);
                        }
                    }
                }
            } else {
                file.getFileMetadata().setRestricted(restrict);
                if (!file.isReleased()) {
                    file.setRestricted(restrict);
                }
                if (file.getFileMetadata().isRestricted() != restrict) {
                    throw new CommandExecutionException("Failed to update the file metadata", this);
                }
            }
        } else {
            throw new CommandExecutionException("Working version must be a draft", this);
        }
    }
}

Example 39 with DatasetVersion

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

the class DDIExportServiceBean method export.

/*
     * Workhorse methods, that do all the work: 
     */
private void export(String objectTag, Long objectId, OutputStream os, String partialExclude, String partialInclude) {
    /*
         * Some checks will need to be here, to see if the corresponding dataset
         * is released, if all the permissions are satisfied, etc., with 
         * approrpiate exceptions thrown otherwise. 
         *
         *      something like
        
         throw new IllegalArgumentException("ExportStudy called with a null study.");
         throw new IllegalArgumentException("Study does not have released version, study.id = " + s.getId());
         */
    Set<String> includedFieldSet = null;
    Set<String> excludedFieldSet = null;
    DatasetVersion releasedVersion = null;
    if (partialExclude != null && !"".equals(partialExclude)) {
        excludedFieldSet = new HashSet<String>();
        String[] splitTokens = partialExclude.split(",");
        for (int i = 0; i < splitTokens.length; i++) {
            if (splitTokens[i] != null && !splitTokens[i].equals("")) {
                excludedFieldSet.add(splitTokens[i]);
            }
        }
    }
    if (partialInclude != null && !"".equals(partialInclude)) {
        includedFieldSet = new HashSet<String>();
        String[] splitTokens = partialInclude.split(",");
        for (int i = 0; i < splitTokens.length; i++) {
            if (splitTokens[i] != null && !splitTokens[i].equals("")) {
                includedFieldSet.add(splitTokens[i]);
            }
        }
    }
    // Create XML Stream Writer, using the supplied OutputStream:
    XMLStreamWriter xmlw = null;
    // Try to resolve the supplied object id:
    Object dataObject = null;
    if (OBJECT_TAG_VARIABLE.equals(objectTag)) {
        dataObject = variableService.find(objectId);
        if (dataObject == null) {
            throw new IllegalArgumentException("Metadata Export: Invalid variable id supplied.");
        }
    } else if (OBJECT_TAG_DATAFILE.equals(objectTag)) {
        dataObject = fileService.find(objectId);
        if (dataObject == null) {
            throw new IllegalArgumentException("Metadata Export: Invalid datafile id supplied.");
        }
    } else if (OBJECT_TAG_DATASET.equals(objectTag)) {
        dataObject = datasetService.find(objectId);
        if (dataObject == null) {
            throw new IllegalArgumentException("Metadata Export: Invalid dataset id supplied.");
        }
        releasedVersion = ((Dataset) dataObject).getReleasedVersion();
        if (releasedVersion == null) {
            throw new IllegalArgumentException("Metadata Export: Dataset not released.");
        }
    } else {
        throw new IllegalArgumentException("Metadata Export: Unsupported export requested.");
    }
    try {
        xmlw = xmlOutputFactory.createXMLStreamWriter(os);
        xmlw.writeStartDocument();
        if (OBJECT_TAG_VARIABLE.equals(objectTag)) {
            createVarDDI(xmlw, excludedFieldSet, includedFieldSet, (DataVariable) dataObject);
        } else if (OBJECT_TAG_DATAFILE.equals(objectTag)) {
            createDataFileDDI(xmlw, excludedFieldSet, includedFieldSet, (DataFile) dataObject);
        } else if (OBJECT_TAG_DATASET.equals(objectTag)) {
            createDatasetDDI(xmlw, excludedFieldSet, includedFieldSet, releasedVersion);
        }
        xmlw.writeEndDocument();
    } catch (XMLStreamException ex) {
        Logger.getLogger("global").log(Level.SEVERE, null, ex);
        throw new EJBException("ERROR occurred during partial export of a study.", ex);
    } finally {
        try {
            if (xmlw != null) {
                xmlw.close();
            }
        } catch (XMLStreamException ex) {
        }
    }
}

Example 40 with DatasetVersion

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

the class ExportService method exportAllFormats.

// This method goes through all the Exporters and calls
// the "chacheExport()" method that will save the produced output
// in a file in the dataset directory, on each Exporter available.
public void exportAllFormats(Dataset dataset) throws ExportException {
    try {
        clearAllCachedFormats(dataset);
    } catch (IOException ex) {
        Logger.getLogger(ExportService.class.getName()).log(Level.SEVERE, null, ex);
    }
    try {
        DatasetVersion releasedVersion = dataset.getReleasedVersion();
        if (releasedVersion == null) {
            throw new ExportException("No released version for dataset " + dataset.getGlobalId());
        }
        JsonPrinter jsonPrinter = new JsonPrinter(settingsService);
        final JsonObjectBuilder datasetAsJsonBuilder = jsonPrinter.jsonAsDatasetDto(releasedVersion);
        JsonObject datasetAsJson = datasetAsJsonBuilder.build();
        Iterator<Exporter> exporters = loader.iterator();
        while (exporters.hasNext()) {
            Exporter e = exporters.next();
            String formatName = e.getProviderName();
            cacheExport(releasedVersion, formatName, datasetAsJson, e);
        }
    } catch (ServiceConfigurationError serviceError) {
        throw new ExportException("Service configuration error during export. " + serviceError.getMessage());
    }
    // Finally, if we have been able to successfully export in all available
    // formats, we'll increment the "last exported" time stamp:
    dataset.setLastExportTime(new Timestamp(new Date().getTime()));
}