Examples with DepositReceipt org.swordapp.server.DepositReceipt used on opensource projects

Example 1 with DepositReceipt

use of org.swordapp.server.DepositReceipt in project dataverse by IQSS.

the class MediaResourceManagerImpl method replaceOrAddFiles.

DepositReceipt replaceOrAddFiles(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration, boolean shouldReplace) throws SwordError, SwordAuthException, SwordServerException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, httpRequest);
    urlManager.processUrl(uri);
    String globalId = urlManager.getTargetIdentifier();
    if (urlManager.getTargetType().equals("study") && globalId != null) {
        logger.fine("looking up dataset with globalId " + globalId);
        Dataset dataset = datasetService.findByGlobalId(globalId);
        if (dataset == null) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataset with global ID of " + globalId);
        }
        UpdateDatasetCommand updateDatasetCommand = new UpdateDatasetCommand(dataset, dvReq);
        if (!permissionService.isUserAllowedOn(user, updateDatasetCommand, dataset)) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + user.getDisplayInfo().getTitle() + " is not authorized to modify dataset with global ID " + dataset.getGlobalId());
        }
        // -------------------------------------
        if (DataCaptureModuleUtil.rsyncSupportEnabled(settingsSvc.getValueForKey(SettingsServiceBean.Key.UploadMethods))) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, SettingsServiceBean.Key.UploadMethods + " contains " + SystemConfig.FileUploadMethods.RSYNC + ". Please use rsync file upload.");
        }
        /**
         * @todo decide if we want non zip files to work. Technically, now
         * that we're letting ingestService.createDataFiles unpack the zip
         * for us, the following *does* work:
         *
         * curl--data-binary @path/to/trees.png -H "Content-Disposition:
         * filename=trees.png" -H "Content-Type: image/png" -H "Packaging:
         * http://purl.org/net/sword/package/SimpleZip"
         *
         * We *might* want to continue to force API users to only upload zip
         * files so that some day we can support a including a file or files
         * that contain the metadata (i.e. description) for each file in the
         * zip: https://github.com/IQSS/dataverse/issues/723
         */
        if (!deposit.getPackaging().equals(UriRegistry.PACKAGE_SIMPLE_ZIP)) {
            throw new SwordError(UriRegistry.ERROR_CONTENT, 415, "Package format " + UriRegistry.PACKAGE_SIMPLE_ZIP + " is required but format specified in 'Packaging' HTTP header was " + deposit.getPackaging());
        }
        String uploadedZipFilename = deposit.getFilename();
        DatasetVersion editVersion = dataset.getEditVersion();
        if (deposit.getInputStream() == null) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Deposit input stream was null.");
        }
        int bytesAvailableInInputStream = 0;
        try {
            bytesAvailableInInputStream = deposit.getInputStream().available();
        } catch (IOException ex) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine number of bytes available in input stream: " + ex);
        }
        if (bytesAvailableInInputStream == 0) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Bytes available in input stream was " + bytesAvailableInInputStream + ". Please check the file you are attempting to deposit.");
        }
        /**
         * @todo Think about if we should instead pass in "application/zip"
         * rather than letting ingestService.createDataFiles() guess the
         * contentType by passing it "null". See also the note above about
         * SimpleZip vs. other contentTypes.
         */
        String guessContentTypeForMe = null;
        List<DataFile> dataFiles = new ArrayList<>();
        try {
            try {
                dataFiles = FileUtil.createDataFiles(editVersion, deposit.getInputStream(), uploadedZipFilename, guessContentTypeForMe, systemConfig);
            } catch (EJBException ex) {
                Throwable cause = ex.getCause();
                if (cause != null) {
                    if (cause instanceof IllegalArgumentException) {
                        /**
                         * @todo should be safe to remove this catch of
                         * EJBException and IllegalArgumentException once
                         * this ticket is resolved:
                         *
                         * IllegalArgumentException: MALFORMED when
                         * uploading certain zip files
                         * https://github.com/IQSS/dataverse/issues/1021
                         */
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Exception caught calling ingestService.createDataFiles. Problem with zip file, perhaps: " + cause);
                    } else {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Exception caught calling ingestService.createDataFiles: " + cause);
                    }
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Exception caught calling ingestService.createDataFiles. No cause: " + ex.getMessage());
                }
            }
        /*TODO: L.A. 4.6! catch (FileExceedsMaxSizeException ex) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Exception caught calling ingestService.createDataFiles: " + ex.getMessage());
                    //Logger.getLogger(MediaResourceManagerImpl.class.getName()).log(Level.SEVERE, null, ex);
                }*/
        } catch (IOException ex) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to add file(s) to dataset: " + ex.getMessage());
        }
        if (!dataFiles.isEmpty()) {
            Set<ConstraintViolation> constraintViolations = editVersion.validate();
            if (constraintViolations.size() > 0) {
                ConstraintViolation violation = constraintViolations.iterator().next();
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to add file(s) to dataset: " + violation.getMessage() + " The invalid value was \"" + violation.getInvalidValue() + "\".");
            } else {
                ingestService.addFiles(editVersion, dataFiles);
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No files to add to dataset. Perhaps the zip file was empty.");
        }
        try {
            dataset = commandEngine.submit(updateDatasetCommand);
        } catch (CommandException ex) {
            throw returnEarly("Couldn't update dataset " + ex);
        } catch (EJBException ex) {
            /**
             * @todo stop bothering to catch an EJBException once this has
             * been implemented:
             *
             * Have commands catch ConstraintViolationException and turn
             * them into something that inherits from CommandException ·
             * https://github.com/IQSS/dataverse/issues/1009
             */
            Throwable cause = ex;
            StringBuilder sb = new StringBuilder();
            sb.append(ex.getLocalizedMessage());
            while (cause.getCause() != null) {
                cause = cause.getCause();
                sb.append(cause + " ");
                if (cause instanceof ConstraintViolationException) {
                    ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
                    for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
                        sb.append(" Invalid value \"").append(violation.getInvalidValue()).append("\" for ").append(violation.getPropertyPath()).append(" at ").append(violation.getLeafBean()).append(" - ").append(violation.getMessage());
                    }
                }
            }
            throw returnEarly("EJBException: " + sb.toString());
        }
        ingestService.startIngestJobs(dataset, user);
        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, "Unable to determine target type or identifier from URL: " + uri);
    }
}

Example 2 with DepositReceipt

use of org.swordapp.server.DepositReceipt in project dataverse by IQSS.

the class CollectionDepositManagerImpl method createNew.

@Override
public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration config) throws SwordError, SwordServerException, SwordAuthException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, request);
    urlManager.processUrl(collectionUri);
    String dvAlias = urlManager.getTargetIdentifier();
    if (urlManager.getTargetType().equals("dataverse") && dvAlias != null) {
        logger.log(Level.FINE, "attempting deposit into this dataverse alias: {0}", dvAlias);
        Dataverse dvThatWillOwnDataset = dataverseService.findByAlias(dvAlias);
        if (dvThatWillOwnDataset != null) {
            logger.log(Level.FINE, "multipart: {0}", deposit.isMultipart());
            logger.log(Level.FINE, "binary only: {0}", deposit.isBinaryOnly());
            logger.log(Level.FINE, "entry only: {0}", deposit.isEntryOnly());
            logger.log(Level.FINE, "in progress: {0}", deposit.isInProgress());
            logger.log(Level.FINE, "metadata relevant: {0}", deposit.isMetadataRelevant());
            if (deposit.isEntryOnly()) {
                // do a sanity check on the XML received
                try {
                    SwordEntry swordEntry = deposit.getSwordEntry();
                    logger.log(Level.FINE, "deposit XML received by createNew():\n{0}", swordEntry.toString());
                } catch (ParseException ex) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Can not create dataset due to malformed Atom entry: " + ex);
                }
                Dataset dataset = new Dataset();
                dataset.setOwner(dvThatWillOwnDataset);
                String nonNullDefaultIfKeyNotFound = "";
                String protocol = settingsService.getValueForKey(SettingsServiceBean.Key.Protocol, nonNullDefaultIfKeyNotFound);
                String authority = settingsService.getValueForKey(SettingsServiceBean.Key.Authority, nonNullDefaultIfKeyNotFound);
                String separator = settingsService.getValueForKey(SettingsServiceBean.Key.DoiSeparator, nonNullDefaultIfKeyNotFound);
                dataset.setProtocol(protocol);
                dataset.setAuthority(authority);
                dataset.setDoiSeparator(separator);
                // Wait until the create command before actually getting an identifier
                // dataset.setIdentifier(datasetService.generateDatasetIdentifier(protocol, authority, separator));
                logger.log(Level.FINE, "DS Deposit identifier: {0}", dataset.getIdentifier());
                CreateDatasetCommand createDatasetCommand = new CreateDatasetCommand(dataset, dvReq, false);
                if (!permissionService.isUserAllowedOn(user, createDatasetCommand, dataset)) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + user.getDisplayInfo().getTitle() + " is not authorized to create a dataset in this dataverse.");
                }
                DatasetVersion newDatasetVersion = dataset.getEditVersion();
                String foreignFormat = SwordUtil.DCTERMS;
                try {
                    importGenericService.importXML(deposit.getSwordEntry().toString(), foreignFormat, newDatasetVersion);
                } catch (Exception ex) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "problem calling importXML: " + ex);
                }
                swordService.addDatasetContact(newDatasetVersion, user);
                swordService.addDatasetDepositor(newDatasetVersion, user);
                swordService.addDatasetSubjectIfMissing(newDatasetVersion);
                swordService.setDatasetLicenseAndTermsOfUse(newDatasetVersion, deposit.getSwordEntry());
                Dataset createdDataset = null;
                try {
                    createdDataset = engineSvc.submit(createDatasetCommand);
                } catch (EJBException | CommandException ex) {
                    Throwable cause = ex;
                    StringBuilder sb = new StringBuilder();
                    sb.append(ex.getLocalizedMessage());
                    while (cause.getCause() != null) {
                        cause = cause.getCause();
                        /**
                         * @todo move this ConstraintViolationException
                         * check to CreateDatasetCommand. Can be triggered
                         * if you don't call dataset.setIdentifier() or if
                         * you feed it date format we don't like. Once this
                         * is done we should be able to drop EJBException
                         * from the catch above and only catch
                         * CommandException
                         *
                         * See also Have commands catch
                         * ConstraintViolationException and turn them into
                         * something that inherits from CommandException ·
                         * Issue #1009 · IQSS/dataverse -
                         * https://github.com/IQSS/dataverse/issues/1009
                         */
                        if (cause instanceof ConstraintViolationException) {
                            ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
                            for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
                                sb.append(" Invalid value: '").append(violation.getInvalidValue()).append("' for ").append(violation.getPropertyPath()).append(" at ").append(violation.getLeafBean()).append(" - ").append(violation.getMessage());
                            }
                        }
                    }
                    logger.info(sb.toString());
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't create dataset: " + sb.toString());
                }
                if (createdDataset != null) {
                    ReceiptGenerator receiptGenerator = new ReceiptGenerator();
                    String baseUrl = urlManager.getHostnamePlusBaseUrlPath(collectionUri);
                    DepositReceipt depositReceipt = receiptGenerator.createDatasetReceipt(baseUrl, createdDataset);
                    return depositReceipt;
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Problem creating dataset. Null returned.");
                }
            } else if (deposit.isBinaryOnly()) {
                // curl --insecure -s --data-binary "@example.zip" -H "Content-Disposition: filename=example.zip" -H "Content-Type: application/zip" https://sword:sword@localhost:8181/dvn/api/data-deposit/v1/swordv2/collection/dataverse/sword/
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Binary deposit to the collection IRI via POST is not supported. Please POST an Atom entry instead.");
            } else if (deposit.isMultipart()) {
                // "Yeah, multipart is critically broken across all implementations" -- http://www.mail-archive.com/sword-app-tech@lists.sourceforge.net/msg00327.html
                throw new UnsupportedOperationException("Not yet implemented");
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "expected deposit types are isEntryOnly, isBinaryOnly, and isMultiPart");
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse: " + dvAlias);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine target type or identifier from URL: " + collectionUri);
    }
}

Example 3 with DepositReceipt

use of org.swordapp.server.DepositReceipt in project dataverse by IQSS.

the class ContainerManagerImpl method replaceMetadata.

@Override
public DepositReceipt replaceMetadata(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, httpRequest);
    logger.fine("replaceMetadata called with url: " + uri);
    urlManager.processUrl(uri);
    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, "Metadata replace of dataverse is not supported.");
        } else if ("study".equals(targetType)) {
            logger.fine("replacing metadata for dataset");
            // do a sanity check on the XML received
            try {
                SwordEntry swordEntry = deposit.getSwordEntry();
                logger.fine("deposit XML received by replaceMetadata():\n" + swordEntry);
            } catch (ParseException ex) {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Can not replace dataset metadata due to malformed Atom entry: " + ex);
            }
            String globalId = urlManager.getTargetIdentifier();
            Dataset dataset = datasetService.findByGlobalId(globalId);
            if (dataset != null) {
                Dataverse dvThatOwnsDataset = dataset.getOwner();
                UpdateDatasetCommand updateDatasetCommand = new UpdateDatasetCommand(dataset, dvReq);
                if (!permissionService.isUserAllowedOn(user, updateDatasetCommand, dataset)) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + user.getDisplayInfo().getTitle() + " is not authorized to modify dataverse " + dvThatOwnsDataset.getAlias());
                }
                DatasetVersion datasetVersion = dataset.getEditVersion();
                // erase all metadata before creating populating dataset version
                List<DatasetField> emptyDatasetFields = new ArrayList<>();
                datasetVersion.setDatasetFields(emptyDatasetFields);
                String foreignFormat = SwordUtil.DCTERMS;
                try {
                    importGenericService.importXML(deposit.getSwordEntry().toString(), foreignFormat, datasetVersion);
                } catch (Exception ex) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "problem calling importXML: " + ex);
                }
                swordService.addDatasetContact(datasetVersion, user);
                swordService.addDatasetDepositor(datasetVersion, user);
                swordService.addDatasetSubjectIfMissing(datasetVersion);
                swordService.setDatasetLicenseAndTermsOfUse(datasetVersion, deposit.getSwordEntry());
                try {
                    engineSvc.submit(updateDatasetCommand);
                } catch (CommandException ex) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "problem updating dataset: " + ex);
                }
                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, "Could not find dataset based on global id (" + globalId + ") in URL: " + uri);
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unknown target type specified on which to replace metadata: " + uri);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No target specified on which to replace metadata: " + uri);
    }
}

Example 4 with DepositReceipt

use of org.swordapp.server.DepositReceipt in project mycore by MyCoRe-Org.

the class MCRSwordUtil method buildDepositReceipt.

public static DepositReceipt buildDepositReceipt(IRI iri) throws SwordError {
    DepositReceipt depositReceipt = new DepositReceipt();
    depositReceipt.setEditIRI(iri);
    return depositReceipt;
}

Example 5 with DepositReceipt

use of org.swordapp.server.DepositReceipt 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);
    }
}