Examples with DataverseRequest edu.harvard.iq.dataverse.engine.command.DataverseRequest used on opensource projects

Example 16 with DataverseRequest

use of edu.harvard.iq.dataverse.engine.command.DataverseRequest in project dataverse by IQSS.

the class CollectionListManagerImpl method listCollectionContents.

@Override
public Feed listCollectionContents(IRI iri, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordAuthException, SwordError {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, request);
    urlManager.processUrl(iri.toString());
    String dvAlias = urlManager.getTargetIdentifier();
    if (urlManager.getTargetType().equals("dataverse") && dvAlias != null) {
        Dataverse dv = dataverseService.findByAlias(dvAlias);
        if (dv != null) {
            /**
             * We'll say having AddDataset is enough to use this API
             * endpoint, which means you are a Contributor to that
             * dataverse. If we let just anyone call this endpoint, they
             * will be able to see if the supplied dataverse is published or
             * not.
             */
            if (!permissionService.requestOn(dvReq, dv).has(Permission.AddDataset)) {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + user.getDisplayInfo().getTitle() + " is not authorized to list datasets in dataverse " + dv.getAlias());
            }
            Abdera abdera = new Abdera();
            Feed feed = abdera.newFeed();
            feed.setTitle(dv.getName());
            String baseUrl = urlManager.getHostnamePlusBaseUrlPath(iri.toString());
            List<Dataset> datasets = datasetService.findByOwnerId(dv.getId());
            for (Dataset dataset : datasets) {
                /**
                 * @todo Will this be performant enough with production
                 * data, say in the root dataverse? Remove this todo if
                 * there are no complaints. :)
                 */
                if (!permissionService.isUserAllowedOn(user, new UpdateDatasetCommand(dataset, dvReq), dataset)) {
                    continue;
                }
                String editUri = baseUrl + "/edit/study/" + dataset.getGlobalId();
                String editMediaUri = baseUrl + "/edit-media/study/" + dataset.getGlobalId();
                Entry entry = feed.addEntry();
                entry.setId(editUri);
                entry.setTitle(datasetService.getTitleFromLatestVersion(dataset.getId()));
                entry.setBaseUri(new IRI(editUri));
                entry.addLink(editMediaUri, "edit-media");
                feed.addEntry(entry);
            }
            Boolean dvHasBeenReleased = dv.isReleased();
            feed.addSimpleExtension(new QName(UriRegistry.SWORD_STATE, "dataverseHasBeenReleased"), dvHasBeenReleased.toString());
            return feed;
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse: " + dvAlias);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't determine target type or identifer from URL: " + iri);
    }
}

Example 17 with DataverseRequest

use of edu.harvard.iq.dataverse.engine.command.DataverseRequest 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 18 with DataverseRequest

use of edu.harvard.iq.dataverse.engine.command.DataverseRequest in project dataverse by IQSS.

the class MediaResourceManagerImpl method deleteMediaResource.

@Override
public void deleteMediaResource(String uri, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, httpRequest);
    urlManager.processUrl(uri);
    String targetType = urlManager.getTargetType();
    String fileId = urlManager.getTargetIdentifier();
    if (targetType != null && fileId != null) {
        if ("file".equals(targetType)) {
            String fileIdString = urlManager.getTargetIdentifier();
            if (fileIdString != null) {
                Long fileIdLong;
                try {
                    fileIdLong = Long.valueOf(fileIdString);
                } catch (NumberFormatException ex) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "File id must be a number, not '" + fileIdString + "'. URL was: " + uri);
                }
                if (fileIdLong != null) {
                    logger.fine("preparing to delete file id " + fileIdLong);
                    DataFile fileToDelete = dataFileService.find(fileIdLong);
                    if (fileToDelete != null) {
                        Dataset dataset = fileToDelete.getOwner();
                        Dataset datasetThatOwnsFile = fileToDelete.getOwner();
                        Dataverse dataverseThatOwnsFile = datasetThatOwnsFile.getOwner();
                        /**
                         * @todo it would be nice to have this check higher
                         * up. Do we really need the file ID? Should the
                         * last argument to isUserAllowedOn be changed from
                         * "dataset" to "fileToDelete"?
                         */
                        UpdateDatasetCommand updateDatasetCommand = new UpdateDatasetCommand(dataset, dvReq, fileToDelete);
                        if (!permissionService.isUserAllowedOn(user, updateDatasetCommand, dataset)) {
                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + user.getDisplayInfo().getTitle() + " is not authorized to modify " + dataverseThatOwnsFile.getAlias());
                        }
                        try {
                            commandEngine.submit(updateDatasetCommand);
                        } catch (CommandException ex) {
                            throw SwordUtil.throwSpecialSwordErrorWithoutStackTrace(UriRegistry.ERROR_BAD_REQUEST, "Could not delete file: " + ex);
                        }
                    } else {
                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id " + fileIdLong + " from URL: " + uri);
                    }
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id in URL: " + uri);
                }
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not file file to delete in URL: " + uri);
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported file type found in URL: " + uri);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Target or identifer not specified in URL: " + uri);
    }
}

Example 19 with DataverseRequest

use of edu.harvard.iq.dataverse.engine.command.DataverseRequest in project dataverse by IQSS.

the class MediaResourceManagerImpl method getMediaResourceRepresentation.

@Override
public MediaResource getMediaResourceRepresentation(String uri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
    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) {
            /**
             * @todo: support downloading of files (SWORD 2.0 Profile 6.4. -
             * Retrieving the content)
             * http://swordapp.github.io/SWORDv2-Profile/SWORDProfile.html#protocoloperations_retrievingcontent
             *
             * This ticket is mostly about terms of use:
             * https://github.com/IQSS/dataverse/issues/183
             */
            boolean getMediaResourceRepresentationSupported = false;
            if (getMediaResourceRepresentationSupported) {
                Dataverse dvThatOwnsDataset = dataset.getOwner();
                /**
                 * @todo Add Dataverse 4 style permission check here. Is
                 * there a Command we use for downloading files as zip?
                 */
                boolean authorized = false;
                if (authorized) {
                    /**
                     * @todo Zip file download is being implemented in
                     * https://github.com/IQSS/dataverse/issues/338
                     */
                    InputStream fixmeInputStream = new ByteArrayInputStream("FIXME: replace with zip of all dataset files".getBytes());
                    String contentType = "application/zip";
                    String packaging = UriRegistry.PACKAGE_SIMPLE_ZIP;
                    boolean isPackaged = true;
                    MediaResource mediaResource = new MediaResource(fixmeInputStream, contentType, packaging, isPackaged);
                    return mediaResource;
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + user.getDisplayInfo().getTitle() + " is not authorized to get a media resource representation of the dataset with global ID " + dataset.getGlobalId());
                }
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Downloading files via the SWORD-based Dataverse Data Deposit API is not (yet) supported: https://github.com/IQSS/dataverse/issues/183");
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't find dataset with global ID of " + globalId);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't dermine target type or identifier from URL: " + uri);
    }
}

Example 20 with DataverseRequest

use of edu.harvard.iq.dataverse.engine.command.DataverseRequest in project dataverse by IQSS.

the class StatementManagerImpl method getStatement.

@Override
public Statement getStatement(String editUri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordError, SwordAuthException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, httpRequest);
    urlManager.processUrl(editUri);
    String globalId = urlManager.getTargetIdentifier();
    if (urlManager.getTargetType().equals("study") && globalId != null) {
        logger.fine("request for sword statement by user " + user.getDisplayInfo().getTitle());
        Dataset dataset = datasetService.findByGlobalId(globalId);
        if (dataset == null) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "couldn't find dataset with global ID of " + globalId);
        }
        Dataverse dvThatOwnsDataset = dataset.getOwner();
        if (!permissionService.isUserAllowedOn(user, new GetDraftDatasetVersionCommand(dvReq, dataset), dataset)) {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + user.getDisplayInfo().getTitle() + " is not authorized to view dataset with global ID " + globalId);
        }
        String feedUri = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit/study/" + dataset.getGlobalId();
        String author = dataset.getLatestVersion().getAuthorsStr();
        String title = dataset.getLatestVersion().getTitle();
        // in the statement, the element is called "updated"
        Date lastUpdatedFinal = new Date();
        Date lastUpdateTime = dataset.getLatestVersion().getLastUpdateTime();
        if (lastUpdateTime != null) {
            lastUpdatedFinal = lastUpdateTime;
        } else {
            logger.info("lastUpdateTime was null, trying createtime");
            Date createtime = dataset.getLatestVersion().getCreateTime();
            if (createtime != null) {
                lastUpdatedFinal = createtime;
            } else {
                logger.info("creatime was null, using \"now\"");
                lastUpdatedFinal = new Date();
            }
        }
        AtomDate atomDate = new AtomDate(lastUpdatedFinal);
        String datedUpdated = atomDate.toString();
        Statement statement = new AtomStatement(feedUri, author, title, datedUpdated);
        Map<String, String> states = new HashMap<>();
        states.put("latestVersionState", dataset.getLatestVersion().getVersionState().toString());
        Boolean isMinorUpdate = dataset.getLatestVersion().isMinorUpdate();
        states.put("isMinorUpdate", isMinorUpdate.toString());
        if (dataset.isLocked()) {
            states.put("locked", "true");
            states.put("lockedDetail", dataset.getLocks().stream().map(l -> l.getInfo()).collect(joining(",")));
            Optional<DatasetLock> earliestLock = dataset.getLocks().stream().min((l1, l2) -> (int) Math.signum(l1.getStartTime().getTime() - l2.getStartTime().getTime()));
            states.put("lockedStartTime", earliestLock.get().getStartTime().toString());
        } else {
            states.put("locked", "false");
        }
        statement.setStates(states);
        List<FileMetadata> fileMetadatas = dataset.getLatestVersion().getFileMetadatas();
        for (FileMetadata fileMetadata : fileMetadatas) {
            DataFile dataFile = fileMetadata.getDataFile();
            // We are exposing the filename for informational purposes. The file id is what you
            // actually operate on to delete a file, etc.
            // 
            // Replace spaces to avoid IRISyntaxException
            String fileNameFinal = fileMetadata.getLabel().replace(' ', '_');
            String fileUrlString = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit-media/file/" + dataFile.getId() + "/" + fileNameFinal;
            IRI fileUrl;
            try {
                fileUrl = new IRI(fileUrlString);
            } catch (IRISyntaxException ex) {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid URL for file ( " + fileUrlString + " ) resulted in " + ex.getMessage());
            }
            ResourcePart resourcePart = new ResourcePart(fileUrl.toString());
            // default to something that doesn't throw a org.apache.abdera.util.MimeTypeParseException
            String finalFileFormat = "application/octet-stream";
            String contentType = dataFile.getContentType();
            if (contentType != null) {
                finalFileFormat = contentType;
            }
            resourcePart.setMediaType(finalFileFormat);
            /**
             * @todo: Why are properties set on a ResourcePart not exposed
             * when you GET a Statement? Asked about this at
             * http://www.mail-archive.com/sword-app-tech@lists.sourceforge.net/msg00394.html
             */
            // Map<String, String> properties = new HashMap<String, String>();
            // properties.put("filename", studyFile.getFileName());
            // properties.put("category", studyFile.getLatestCategory());
            // properties.put("originalFileType", studyFile.getOriginalFileType());
            // properties.put("id", studyFile.getId().toString());
            // properties.put("UNF", studyFile.getUnf());
            // resourcePart.setProperties(properties);
            statement.addResource(resourcePart);
        /**
         * @todo it's been noted at
         * https://github.com/IQSS/dataverse/issues/892#issuecomment-54159284
         * that at the file level the "updated" date is always "now",
         * which seems to be set here:
         * https://github.com/swordapp/JavaServer2.0/blob/sword2-server-1.0/src/main/java/org/swordapp/server/AtomStatement.java#L70
         */
        }
        return statement;
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine target type or identifier from URL: " + editUri);
    }
}