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

Example 51 with DataFile

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

the class DdiExportUtil method createDataDscr.

// Methods specific to the tabular data ("<dataDscr>") section.
// Note that these do NOT operate on DTO objects, but instead directly
// on Dataverse DataVariable, DataTable, etc. objects.
// This is because for this release (4.5) we are recycling the already available
// code, and this is what we got. (We already have DTO objects for DataTable,
// and DataVariable, etc., but the current version JsonPrinter.jsonAsDatasetDto()
// does not produce JSON for these objects - it stops at DataFile. Eventually
// we want all of our objects to be exportable as JSON, and then all the exports
// can go through the same DTO state... But we don't have time for it now;
// plus, the structure of file-level metadata is currently being re-designed,
// so we probably should not invest any time into it right now). -- L.A. 4.5
private static void createDataDscr(XMLStreamWriter xmlw, DatasetVersion datasetVersion) throws XMLStreamException {
    if (datasetVersion.getFileMetadatas() == null || datasetVersion.getFileMetadatas().isEmpty()) {
        return;
    }
    boolean tabularData = false;
    // tabular datafile.
    for (FileMetadata fileMetadata : datasetVersion.getFileMetadatas()) {
        DataFile dataFile = fileMetadata.getDataFile();
        if (dataFile != null && dataFile.isTabularData()) {
            if (!tabularData) {
                xmlw.writeStartElement("dataDscr");
                tabularData = true;
            }
            List<DataVariable> vars = dataFile.getDataTable().getDataVariables();
            for (DataVariable var : vars) {
                createVarDDI(xmlw, var);
            }
        }
    }
    if (tabularData) {
        // dataDscr
        xmlw.writeEndElement();
    }
}

Example 52 with DataFile

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

the class DeleteHarvestingClientCommand method executeImpl.

@Override
public void executeImpl(CommandContext ctxt) throws CommandException {
    if (harvestingClient == null) {
        throw new IllegalCommandException("DeleteHarvestingClientCommand: attempted to execute with null harvesting client; dataverse: " + motherDataverse.getAlias(), this);
    }
    HarvestingClient merged = ctxt.em().merge(harvestingClient);
    for (DataFile harvestedFile : ctxt.files().findHarvestedFilesByClient(merged)) {
        DataFile mergedFile = ctxt.em().merge(harvestedFile);
        ctxt.em().remove(mergedFile);
        harvestedFile = null;
    }
    ctxt.em().remove(merged);
}

Example 53 with DataFile

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

the class HarvestingClientServiceBean method deleteClient.

// Deleting a client, with all the associated content, can take a while -
// hence it's an async action:
// TOFIGUREOUT:
// for whatever reason I cannot call the DeleteHarvestingClientCommand from
// inside this method; something to do with it being asynchronous?
@Asynchronous
public void deleteClient(Long clientId) {
    String errorMessage = null;
    HarvestingClient victim = find(clientId);
    if (victim == null) {
        return;
    }
    try {
        // engineService.submit(new DeleteHarvestingClientCommand(dvRequestService.getDataverseRequest(), victim));
        HarvestingClient merged = em.merge(victim);
        // if this was a scheduled harvester, make sure the timer is deleted:
        dataverseTimerService.removeHarvestTimer(victim);
        // purge indexed objects:
        indexService.deleteHarvestedDocuments(victim);
        // proceed removing the client itself.
        for (DataFile harvestedFile : dataFileService.findHarvestedFilesByClient(merged)) {
            DataFile mergedFile = em.merge(harvestedFile);
            em.remove(mergedFile);
            harvestedFile = null;
        }
        em.remove(merged);
    } catch (Exception e) {
        errorMessage = "Failed to delete cleint. Unknown exception: " + e.getMessage();
    }
    if (errorMessage != null) {
        logger.warning(errorMessage);
    }
}

Example 54 with DataFile

use of edu.harvard.iq.dataverse.DataFile 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 55 with DataFile

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

the class DdiExportUtil method createFileDscr.

private static void createFileDscr(XMLStreamWriter xmlw, DatasetVersion datasetVersion) throws XMLStreamException {
    String dataverseUrl = getDataverseSiteUrl();
    for (FileMetadata fileMetadata : datasetVersion.getFileMetadatas()) {
        DataFile dataFile = fileMetadata.getDataFile();
        if (dataFile != null && dataFile.isTabularData()) {
            DataTable dt = dataFile.getDataTable();
            xmlw.writeStartElement("fileDscr");
            writeAttribute(xmlw, "ID", "f" + dataFile.getId());
            writeAttribute(xmlw, "URI", dataverseUrl + "/api/access/datafile/" + dataFile.getId());
            xmlw.writeStartElement("fileTxt");
            xmlw.writeStartElement("fileName");
            xmlw.writeCharacters(fileMetadata.getLabel());
            // fileName
            xmlw.writeEndElement();
            if (dt.getCaseQuantity() != null || dt.getVarQuantity() != null || dt.getRecordsPerCase() != null) {
                xmlw.writeStartElement("dimensns");
                if (dt.getCaseQuantity() != null) {
                    xmlw.writeStartElement("caseQnty");
                    xmlw.writeCharacters(dt.getCaseQuantity().toString());
                    // caseQnty
                    xmlw.writeEndElement();
                }
                if (dt.getVarQuantity() != null) {
                    xmlw.writeStartElement("varQnty");
                    xmlw.writeCharacters(dt.getVarQuantity().toString());
                    // varQnty
                    xmlw.writeEndElement();
                }
                if (dt.getRecordsPerCase() != null) {
                    xmlw.writeStartElement("recPrCas");
                    xmlw.writeCharacters(dt.getRecordsPerCase().toString());
                    // recPrCas
                    xmlw.writeEndElement();
                }
                // dimensns
                xmlw.writeEndElement();
            }
            xmlw.writeStartElement("fileType");
            xmlw.writeCharacters(dataFile.getContentType());
            // fileType
            xmlw.writeEndElement();
            // fileTxt
            xmlw.writeEndElement();
            // (Universal Numeric Fingerprint) signature:
            if (dt.getUnf() != null && !dt.getUnf().equals("")) {
                xmlw.writeStartElement("notes");
                writeAttribute(xmlw, "level", LEVEL_FILE);
                writeAttribute(xmlw, "type", NOTE_TYPE_UNF);
                writeAttribute(xmlw, "subject", NOTE_SUBJECT_UNF);
                xmlw.writeCharacters(dt.getUnf());
                // notes
                xmlw.writeEndElement();
            }
            if (dataFile.getTags() != null) {
                for (int i = 0; i < dataFile.getTags().size(); i++) {
                    xmlw.writeStartElement("notes");
                    writeAttribute(xmlw, "level", LEVEL_FILE);
                    writeAttribute(xmlw, "type", NOTE_TYPE_TAG);
                    writeAttribute(xmlw, "subject", NOTE_SUBJECT_TAG);
                    xmlw.writeCharacters(dataFile.getTags().get(i).getTypeLabel());
                    // notes
                    xmlw.writeEndElement();
                }
            }
            // TODO: add the remaining fileDscr elements!
            // fileDscr
            xmlw.writeEndElement();
        }
    }
}