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

Example 91 with Dataset

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

the class Meta method dataset.

@Path("dataset/{datasetId}")
@GET
@Produces({ "application/xml" })
public String dataset(@PathParam("datasetId") Long datasetId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) throws NotFoundException /*, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/
{
    Dataset dataset = datasetService.find(datasetId);
    if (dataset == null) {
        throw new NotFoundException();
    }
    String retValue = "";
    ByteArrayOutputStream outStream = null;
    outStream = new ByteArrayOutputStream();
    try {
        ddiExportService.exportDataset(datasetId, outStream, exclude, include);
        retValue = outStream.toString();
    } catch (Exception e) {
        // metadata record requested. We simply return an empty string.
        throw new ServiceUnavailableException();
    }
    response.setHeader("Access-Control-Allow-Origin", "*");
    return retValue;
}

Example 92 with Dataset

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

the class ImportServiceBean method doImportHarvestedDataset.

@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
public Dataset doImportHarvestedDataset(DataverseRequest dataverseRequest, HarvestingClient harvestingClient, String harvestIdentifier, String metadataFormat, File metadataFile, PrintWriter cleanupLog) throws ImportException, IOException {
    if (harvestingClient == null || harvestingClient.getDataverse() == null) {
        throw new ImportException("importHarvestedDataset called wiht a null harvestingClient, or an invalid harvestingClient.");
    }
    Dataverse owner = harvestingClient.getDataverse();
    Dataset importedDataset = null;
    DatasetDTO dsDTO = null;
    String json = null;
    if ("ddi".equalsIgnoreCase(metadataFormat) || "oai_ddi".equals(metadataFormat) || metadataFormat.toLowerCase().matches("^oai_ddi.*")) {
        try {
            String xmlToParse = new String(Files.readAllBytes(metadataFile.toPath()));
            // TODO:
            // import type should be configurable - it should be possible to
            // select whether you want to harvest with or without files,
            // ImportType.HARVEST vs. ImportType.HARVEST_WITH_FILES
            logger.fine("importing DDI " + metadataFile.getAbsolutePath());
            dsDTO = importDDIService.doImport(ImportType.HARVEST_WITH_FILES, xmlToParse);
        } catch (IOException | XMLStreamException | ImportException e) {
            throw new ImportException("Failed to process DDI XML record: " + e.getClass() + " (" + e.getMessage() + ")");
        }
    } else if ("dc".equalsIgnoreCase(metadataFormat) || "oai_dc".equals(metadataFormat)) {
        logger.fine("importing DC " + metadataFile.getAbsolutePath());
        try {
            String xmlToParse = new String(Files.readAllBytes(metadataFile.toPath()));
            dsDTO = importGenericService.processOAIDCxml(xmlToParse);
        } catch (IOException | XMLStreamException e) {
            throw new ImportException("Failed to process Dublin Core XML record: " + e.getClass() + " (" + e.getMessage() + ")");
        }
    } else if ("dataverse_json".equals(metadataFormat)) {
        // This is Dataverse metadata already formatted in JSON.
        // Simply read it into a string, and pass to the final import further down:
        logger.fine("Attempting to import custom dataverse metadata from file " + metadataFile.getAbsolutePath());
        json = new String(Files.readAllBytes(metadataFile.toPath()));
    } else {
        throw new ImportException("Unsupported import metadata format: " + metadataFormat);
    }
    if (json == null) {
        if (dsDTO != null) {
            // convert DTO to Json,
            Gson gson = new GsonBuilder().setPrettyPrinting().create();
            json = gson.toJson(dsDTO);
            logger.fine("JSON produced for the metadata harvested: " + json);
        } else {
            throw new ImportException("Failed to transform XML metadata format " + metadataFormat + " into a DatasetDTO");
        }
    }
    JsonReader jsonReader = Json.createReader(new StringReader(json));
    JsonObject obj = jsonReader.readObject();
    // and call parse Json to read it into a dataset
    try {
        JsonParser parser = new JsonParser(datasetfieldService, metadataBlockService, settingsService);
        parser.setLenient(true);
        Dataset ds = parser.parseDataset(obj);
        // For ImportType.NEW, if the metadata contains a global identifier, and it's not a protocol
        // we support, it should be rejected.
        // (TODO: ! - add some way of keeping track of supported protocols!)
        // if (ds.getGlobalId() != null && !ds.getProtocol().equals(settingsService.getValueForKey(SettingsServiceBean.Key.Protocol, ""))) {
        // throw new ImportException("Could not register id " + ds.getGlobalId() + ", protocol not supported");
        // }
        ds.setOwner(owner);
        ds.getLatestVersion().setDatasetFields(ds.getLatestVersion().initDatasetFields());
        // Check data against required contraints
        List<ConstraintViolation<DatasetField>> violations = ds.getVersions().get(0).validateRequired();
        if (!violations.isEmpty()) {
            // For migration and harvest, add NA for missing required values
            for (ConstraintViolation<DatasetField> v : violations) {
                DatasetField f = v.getRootBean();
                f.setSingleValue(DatasetField.NA_VALUE);
            }
        }
        // Check data against validation constraints
        // If we are migrating and "scrub migration data" is true we attempt to fix invalid data
        // if the fix fails stop processing of this file by throwing exception
        Set<ConstraintViolation> invalidViolations = ds.getVersions().get(0).validate();
        ValidatorFactory factory = Validation.buildDefaultValidatorFactory();
        Validator validator = factory.getValidator();
        if (!invalidViolations.isEmpty()) {
            for (ConstraintViolation<DatasetFieldValue> v : invalidViolations) {
                DatasetFieldValue f = v.getRootBean();
                boolean fixed = false;
                boolean converted = false;
                // TODO: Is this scrubbing something we want to continue doing?
                if (settingsService.isTrueForKey(SettingsServiceBean.Key.ScrubMigrationData, false)) {
                    fixed = processMigrationValidationError(f, cleanupLog, metadataFile.getName());
                    converted = true;
                    if (fixed) {
                        Set<ConstraintViolation<DatasetFieldValue>> scrubbedViolations = validator.validate(f);
                        if (!scrubbedViolations.isEmpty()) {
                            fixed = false;
                        }
                    }
                }
                if (!fixed) {
                    String msg = "Data modified - File: " + metadataFile.getName() + "; Field: " + f.getDatasetField().getDatasetFieldType().getDisplayName() + "; " + "Invalid value:  '" + f.getValue() + "'" + " Converted Value:'" + DatasetField.NA_VALUE + "'";
                    cleanupLog.println(msg);
                    f.setValue(DatasetField.NA_VALUE);
                }
            }
        }
        // this dataset:
        if (StringUtils.isEmpty(ds.getGlobalId())) {
            throw new ImportException("The harvested metadata record with the OAI server identifier " + harvestIdentifier + " does not contain a global unique identifier that we could recognize, skipping.");
        }
        ds.setHarvestedFrom(harvestingClient);
        ds.setHarvestIdentifier(harvestIdentifier);
        Dataset existingDs = datasetService.findByGlobalId(ds.getGlobalId());
        if (existingDs != null) {
            // we are just going to skip it!
            if (existingDs.getOwner() != null && !owner.getId().equals(existingDs.getOwner().getId())) {
                throw new ImportException("The dataset with the global id " + ds.getGlobalId() + " already exists, in the dataverse " + existingDs.getOwner().getAlias() + ", skipping.");
            }
            // skip it also:
            if (!existingDs.isHarvested()) {
                throw new ImportException("A LOCAL dataset with the global id " + ds.getGlobalId() + " already exists in this dataverse; skipping.");
            }
            // We will replace the current version with the imported version.
            if (existingDs.getVersions().size() != 1) {
                throw new ImportException("Error importing Harvested Dataset, existing dataset has " + existingDs.getVersions().size() + " versions");
            }
            // Purge all the SOLR documents associated with this client from the
            // index server:
            indexService.deleteHarvestedDocuments(existingDs);
            // DeleteFileCommand on them.
            for (DataFile harvestedFile : existingDs.getFiles()) {
                DataFile merged = em.merge(harvestedFile);
                em.remove(merged);
                harvestedFile = null;
            }
            // TODO:
            // Verify what happens with the indexed files in SOLR?
            // are they going to be overwritten by the reindexing of the dataset?
            existingDs.setFiles(null);
            Dataset merged = em.merge(existingDs);
            engineSvc.submit(new DestroyDatasetCommand(merged, dataverseRequest));
            importedDataset = engineSvc.submit(new CreateDatasetCommand(ds, dataverseRequest, false, ImportType.HARVEST));
        } else {
            importedDataset = engineSvc.submit(new CreateDatasetCommand(ds, dataverseRequest, false, ImportType.HARVEST));
        }
    } catch (JsonParseException | ImportException | CommandException ex) {
        logger.fine("Failed to import harvested dataset: " + ex.getClass() + ": " + ex.getMessage());
        FileOutputStream savedJsonFileStream = new FileOutputStream(new File(metadataFile.getAbsolutePath() + ".json"));
        byte[] jsonBytes = json.getBytes();
        int i = 0;
        while (i < jsonBytes.length) {
            int chunkSize = i + 8192 <= jsonBytes.length ? 8192 : jsonBytes.length - i;
            savedJsonFileStream.write(jsonBytes, i, chunkSize);
            i += chunkSize;
            savedJsonFileStream.flush();
        }
        savedJsonFileStream.close();
        logger.info("JSON produced saved in " + metadataFile.getAbsolutePath() + ".json");
        throw new ImportException("Failed to import harvested dataset: " + ex.getClass() + " (" + ex.getMessage() + ")", ex);
    }
    return importedDataset;
}

Example 93 with Dataset

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

the class ContainerManagerImpl method getEntry.

@Override
public DepositReceipt getEntry(String uri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordError, SwordAuthException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, httpRequest);
    logger.fine("getEntry called with url: " + uri);
    urlManager.processUrl(uri);
    String targetType = urlManager.getTargetType();
    if (!targetType.isEmpty()) {
        logger.fine("operating on target type: " + urlManager.getTargetType());
        if ("study".equals(targetType)) {
            String globalId = urlManager.getTargetIdentifier();
            Dataset dataset = datasetService.findByGlobalId(globalId);
            if (dataset != null) {
                if (!permissionService.isUserAllowedOn(user, new GetDraftDatasetVersionCommand(dvReq, dataset), dataset)) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + user.getDisplayInfo().getTitle() + " is not authorized to retrieve entry for " + dataset.getGlobalId());
                }
                Dataverse dvThatOwnsDataset = dataset.getOwner();
                ReceiptGenerator receiptGenerator = new ReceiptGenerator();
                String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
                DepositReceipt depositReceipt = receiptGenerator.createDatasetReceipt(baseUrl, dataset);
                if (depositReceipt != null) {
                    return depositReceipt;
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not generate deposit receipt.");
                }
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataset based on URL: " + uri);
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported target type (" + targetType + ") in URL: " + uri);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine target type from URL: " + uri);
    }
}

Example 94 with Dataset

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

the class ContainerManagerImpl method deleteContainer.

@Override
public void deleteContainer(String uri, AuthCredentials authCredentials, SwordConfiguration sc) throws SwordError, SwordServerException, SwordAuthException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvRequest = new DataverseRequest(user, httpRequest);
    logger.fine("deleteContainer called with url: " + uri);
    urlManager.processUrl(uri);
    logger.fine("original url: " + urlManager.getOriginalUrl());
    if (!"edit".equals(urlManager.getServlet())) {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "edit servlet expected, not " + urlManager.getServlet());
    }
    String targetType = urlManager.getTargetType();
    if (!targetType.isEmpty()) {
        logger.fine("operating on target type: " + urlManager.getTargetType());
        if ("dataverse".equals(targetType)) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Dataverses can not be deleted via the Data Deposit API but other Dataverse APIs may support this operation.");
        } else if ("study".equals(targetType)) {
            String globalId = urlManager.getTargetIdentifier();
            logger.fine("globalId: " + globalId);
            if (globalId != null) {
                Dataset dataset = dataset = datasetService.findByGlobalId(globalId);
                if (dataset != null) {
                    Dataverse dvThatOwnsDataset = dataset.getOwner();
                    /**
                     * We are checking if DeleteDatasetVersionCommand can be
                     * called even though DeleteDatasetCommand can be called
                     * when a dataset hasn't been published. They should be
                     * equivalent in terms of a permission check.
                     */
                    DeleteDatasetVersionCommand deleteDatasetVersionCommand = new DeleteDatasetVersionCommand(dvRequest, dataset);
                    if (!permissionService.isUserAllowedOn(user, deleteDatasetVersionCommand, dataset)) {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + user.getDisplayInfo().getTitle() + " is not authorized to modify " + dvThatOwnsDataset.getAlias());
                    }
                    DatasetVersion.VersionState datasetVersionState = dataset.getLatestVersion().getVersionState();
                    if (dataset.isReleased()) {
                        if (datasetVersionState.equals(DatasetVersion.VersionState.DRAFT)) {
                            logger.info("destroying working copy version of dataset " + dataset.getGlobalId());
                            try {
                                engineSvc.submit(deleteDatasetVersionCommand);
                            } catch (CommandException ex) {
                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Can't delete dataset version for " + dataset.getGlobalId() + ": " + ex);
                            }
                            logger.info("dataset version deleted for dataset id " + dataset.getId());
                        } else if (datasetVersionState.equals(DatasetVersion.VersionState.RELEASED)) {
                            throw new SwordError(UriRegistry.ERROR_METHOD_NOT_ALLOWED, "Deaccessioning a dataset is no longer supported as of Data Deposit API version in URL (" + swordConfiguration.getBaseUrlPathV1() + ") Equivalent functionality is being developed at https://github.com/IQSS/dataverse/issues/778");
                        } else if (datasetVersionState.equals(DatasetVersion.VersionState.DEACCESSIONED)) {
                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Lastest version of dataset " + dataset.getGlobalId() + " has already been deaccessioned.");
                        } else if (datasetVersionState.equals(DatasetVersion.VersionState.ARCHIVED)) {
                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Lastest version of dataset " + dataset.getGlobalId() + " has been archived and can not be deleted or deaccessioned.");
                        } else {
                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Operation not valid for dataset " + dataset.getGlobalId() + " in state " + datasetVersionState);
                        }
                    /**
                     * @todo Reformat else below properly so you can
                     * just reformat the whole file in Netbeans or
                     * similar.
                     */
                    } else {
                        // dataset has never been published, this is just a sanity check (should always be draft)
                        if (datasetVersionState.equals(DatasetVersion.VersionState.DRAFT)) {
                            try {
                                engineSvc.submit(new DeleteDatasetCommand(dvRequest, dataset));
                                logger.fine("dataset deleted");
                            } catch (CommandExecutionException ex) {
                                // internal error
                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Can't delete dataset: " + ex.getMessage());
                            } catch (CommandException ex) {
                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Can't delete dataset: " + ex.getMessage());
                            }
                        } else {
                            // we should never get here. throw an error explaining why
                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "dataset is in illegal state (not published yet not in draft)");
                        }
                    }
                } else {
                    throw new SwordError(404);
                }
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataset to delete from URL: " + uri);
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported delete target in URL:" + uri);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No target for deletion specified");
    }
}

Example 95 with Dataset

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

the class ContainerManagerImpl method useHeaders.

@Override
public DepositReceipt useHeaders(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
    logger.fine("uri was " + uri);
    logger.fine("isInProgress:" + deposit.isInProgress());
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvRequest = new DataverseRequest(user, httpRequest);
    urlManager.processUrl(uri);
    String targetType = urlManager.getTargetType();
    if (!targetType.isEmpty()) {
        logger.fine("operating on target type: " + urlManager.getTargetType());
        if ("study".equals(targetType)) {
            String globalId = urlManager.getTargetIdentifier();
            if (globalId != null) {
                Dataset dataset = null;
                try {
                    dataset = datasetService.findByGlobalId(globalId);
                } catch (EJBException ex) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataset based on global id (" + globalId + ") in URL: " + uri);
                }
                if (dataset != null) {
                    Dataverse dvThatOwnsDataset = dataset.getOwner();
                    boolean doMinorVersionBump = false;
                    // if dataset is unreleased, major version; if released, then check if can be minor
                    if (dataset.isReleased() && dataset.getLatestVersion().isMinorUpdate()) {
                        doMinorVersionBump = true;
                    }
                    PublishDatasetCommand publishDatasetCommand = new PublishDatasetCommand(dataset, dvRequest, doMinorVersionBump);
                    if (!permissionService.isUserAllowedOn(user, publishDatasetCommand, dataset)) {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + user.getDisplayInfo().getTitle() + " is not authorized to modify dataverse " + dvThatOwnsDataset.getAlias());
                    }
                    if (!deposit.isInProgress()) {
                        /**
                         * We are considering a draft version of a study to
                         * be incomplete and are saying that sending
                         * isInProgress=false means the study version is
                         * complete and can be released.
                         *
                         * 9.2. Deposit Incomplete
                         *
                         * "If In-Progress is true, the server SHOULD expect
                         * the client to provide further updates to the item
                         * some undetermined time in the future. Details of
                         * how this is implemented is dependent on the
                         * server's purpose. For example, a repository
                         * system may hold items which are marked
                         * In-Progress in a workspace until such time as a
                         * client request indicates that the deposit is
                         * complete." --
                         * http://swordapp.github.io/SWORDv2-Profile/SWORDProfile.html#continueddeposit_incomplete
                         */
                        if (!dataset.getLatestVersion().getVersionState().equals(DatasetVersion.VersionState.RELEASED)) {
                            try {
                                dataset = engineSvc.submit(publishDatasetCommand).getDataset();
                            } catch (CommandException ex) {
                                String msg = "Unable to publish dataset: " + ex;
                                logger.severe(msg + ": " + ex.getMessage());
                                throw SwordUtil.throwRegularSwordErrorWithoutStackTrace(msg);
                            }
                            ReceiptGenerator receiptGenerator = new ReceiptGenerator();
                            String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
                            DepositReceipt depositReceipt = receiptGenerator.createDatasetReceipt(baseUrl, dataset);
                            return depositReceipt;
                        } else {
                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Latest version of dataset " + globalId + " has already been published.");
                        }
                    } else {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Pass 'In-Progress: false' header to publish a dataset.");
                    }
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataset using globalId " + globalId);
                }
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find globalId for dataset in URL:" + uri);
            }
        } else if ("dataverse".equals(targetType)) {
            String dvAlias = urlManager.getTargetIdentifier();
            if (dvAlias != null) {
                Dataverse dvToRelease = dataverseService.findByAlias(dvAlias);
                if (dvToRelease != null) {
                    PublishDataverseCommand publishDataverseCommand = new PublishDataverseCommand(dvRequest, dvToRelease);
                    if (!permissionService.isUserAllowedOn(user, publishDataverseCommand, dvToRelease)) {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + user.getDisplayInfo().getTitle() + " is not authorized to modify dataverse " + dvAlias);
                    }
                    if (deposit.isInProgress()) {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unpublishing a dataverse is not supported.");
                    }
                    try {
                        engineSvc.submit(publishDataverseCommand);
                        ReceiptGenerator receiptGenerator = new ReceiptGenerator();
                        String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
                        DepositReceipt depositReceipt = receiptGenerator.createDataverseReceipt(baseUrl, dvToRelease);
                        return depositReceipt;
                    } catch (CommandException ex) {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't publish dataverse " + dvAlias + ": " + ex);
                    }
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse based on alias in URL: " + uri);
                }
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find dataverse alias in URL: " + uri);
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "unsupported target type (" + targetType + ") in URL:" + uri);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Target type missing from URL: " + uri);
    }
}