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

Example 31 with FileMetadata

use of edu.harvard.iq.dataverse.FileMetadata 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 32 with FileMetadata

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

the class IngestUtil method checkForDuplicateFileNamesFinal.

/**
 * Checks a list of new data files for duplicate names, renaming any
 * duplicates to ensure that they are unique.
 *
 * @param version the dataset version
 * @param newFiles the list of new data files to add to it
 */
public static void checkForDuplicateFileNamesFinal(DatasetVersion version, List<DataFile> newFiles) {
    // Step 1: create list of existing path names from all FileMetadata in the DatasetVersion
    // unique path name: directoryLabel + file separator + fileLabel
    Set<String> pathNamesExisting = existingPathNamesAsSet(version);
    // Step 2: check each new DataFile against the list of path names, if a duplicate create a new unique file name
    for (Iterator<DataFile> dfIt = newFiles.iterator(); dfIt.hasNext(); ) {
        FileMetadata fm = dfIt.next().getFileMetadata();
        fm.setLabel(duplicateFilenameCheck(fm, pathNamesExisting));
    }
}

Example 33 with FileMetadata

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

the class TestIngest method datafile.

// @EJB
@Path("test/file")
@GET
@Produces({ "text/plain" })
public String datafile(@QueryParam("fileName") String fileName, @QueryParam("fileType") String fileType, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/
{
    String output = "";
    if (StringUtil.isEmpty(fileName) || StringUtil.isEmpty(fileType)) {
        output = output.concat("Usage: /api/ingest/test/file?fileName=PATH&fileType=TYPE");
        return output;
    }
    BufferedInputStream fileInputStream = null;
    try {
        fileInputStream = new BufferedInputStream(new FileInputStream(new File(fileName)));
    } catch (FileNotFoundException notfoundEx) {
        fileInputStream = null;
    }
    if (fileInputStream == null) {
        output = output.concat("Could not open file " + fileName + ".");
        return output;
    }
    TabularDataFileReader ingestPlugin = ingestService.getTabDataReaderByMimeType(fileType);
    if (ingestPlugin == null) {
        output = output.concat("Could not locate an ingest plugin for type " + fileType + ".");
        return output;
    }
    TabularDataIngest tabDataIngest = null;
    try {
        tabDataIngest = ingestPlugin.read(fileInputStream, null);
    } catch (IOException ingestEx) {
        output = output.concat("Caught an exception trying to ingest file " + fileName + ".");
        return output;
    }
    try {
        if (tabDataIngest != null) {
            File tabFile = tabDataIngest.getTabDelimitedFile();
            if (tabDataIngest.getDataTable() != null && tabFile != null && tabFile.exists()) {
                String tabFilename = FileUtil.replaceExtension(fileName, "tab");
                java.nio.file.Files.copy(Paths.get(tabFile.getAbsolutePath()), Paths.get(tabFilename), StandardCopyOption.REPLACE_EXISTING);
                DataTable dataTable = tabDataIngest.getDataTable();
                DataFile dataFile = new DataFile();
                dataFile.setStorageIdentifier(tabFilename);
                FileMetadata fileMetadata = new FileMetadata();
                fileMetadata.setLabel(fileName);
                dataFile.setDataTable(dataTable);
                dataTable.setDataFile(dataFile);
                fileMetadata.setDataFile(dataFile);
                dataFile.getFileMetadatas().add(fileMetadata);
                output = output.concat("NVARS: " + dataTable.getVarQuantity() + "\n");
                output = output.concat("NOBS: " + dataTable.getCaseQuantity() + "\n");
                try {
                    ingestService.produceSummaryStatistics(dataFile, tabFile);
                    output = output.concat("UNF: " + dataTable.getUnf() + "\n");
                } catch (IOException ioex) {
                    output = output.concat("UNF: failed to calculate\n" + "\n");
                }
                for (int i = 0; i < dataTable.getVarQuantity(); i++) {
                    String vartype = "";
                    // if ("continuous".equals(dataTable.getDataVariables().get(i).getVariableIntervalType().getName())) {
                    if (dataTable.getDataVariables().get(i).isIntervalContinuous()) {
                        vartype = "numeric-continuous";
                    } else {
                        if (dataTable.getDataVariables().get(i).isTypeNumeric()) {
                            vartype = "numeric-discrete";
                        } else {
                            String formatCategory = dataTable.getDataVariables().get(i).getFormatCategory();
                            if ("time".equals(formatCategory)) {
                                vartype = "character-time";
                            } else if ("date".equals(formatCategory)) {
                                vartype = "character-date";
                            } else {
                                vartype = "character";
                            }
                        }
                    }
                    output = output.concat("VAR" + i + " ");
                    output = output.concat(dataTable.getDataVariables().get(i).getName() + " ");
                    output = output.concat(vartype + " ");
                    output = output.concat(dataTable.getDataVariables().get(i).getUnf());
                    output = output.concat("\n");
                }
            } else {
                output = output.concat("Ingest failed to produce tab file or data table for file " + fileName + ".");
                return output;
            }
        } else {
            output = output.concat("Ingest resulted in a null tabDataIngest object for file " + fileName + ".");
            return output;
        }
    } catch (IOException ex) {
        output = output.concat("Caught an exception trying to save ingested data for file " + fileName + ".");
        return output;
    }
    return output;
}

Example 34 with FileMetadata

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

the class FileUtilTest method testIsPubliclyDownloadable2.

@Test
public void testIsPubliclyDownloadable2() {
    FileMetadata nonRestrictedFileMetadata = new FileMetadata();
    DatasetVersion dsv = new DatasetVersion();
    TermsOfUseAndAccess termsOfUseAndAccess = new TermsOfUseAndAccess();
    termsOfUseAndAccess.setTermsOfUse("be excellent to each other");
    dsv.setTermsOfUseAndAccess(termsOfUseAndAccess);
    dsv.setVersionState(DatasetVersion.VersionState.RELEASED);
    nonRestrictedFileMetadata.setDatasetVersion(dsv);
    Dataset dataset = new Dataset();
    dsv.setDataset(dataset);
    nonRestrictedFileMetadata.setRestricted(false);
    assertEquals(false, FileUtil.isPubliclyDownloadable(nonRestrictedFileMetadata));
}

Example 35 with FileMetadata

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

the class FileUtilTest method testIsPubliclyDownloadable.

@Test
public void testIsPubliclyDownloadable() {
    assertEquals(false, FileUtil.isPubliclyDownloadable(null));
    FileMetadata restrictedFileMetadata = new FileMetadata();
    restrictedFileMetadata.setRestricted(true);
    assertEquals(false, FileUtil.isPubliclyDownloadable(restrictedFileMetadata));
    FileMetadata nonRestrictedFileMetadata = new FileMetadata();
    DatasetVersion dsv = new DatasetVersion();
    dsv.setVersionState(DatasetVersion.VersionState.RELEASED);
    nonRestrictedFileMetadata.setDatasetVersion(dsv);
    Dataset dataset = new Dataset();
    dsv.setDataset(dataset);
    nonRestrictedFileMetadata.setRestricted(false);
    assertEquals(true, FileUtil.isPubliclyDownloadable(nonRestrictedFileMetadata));
}