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

Example 1 with UpdateDatasetCommand

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

the class DatasetPage method isLockedFromEdits.

/**
 * Authors are not allowed to edit but curators are allowed - when Dataset is inReview
 * For all other locks edit should be locked for all editors.
 */
public boolean isLockedFromEdits() {
    if (null == lockedFromEditsVar) {
        try {
            permissionService.checkEditDatasetLock(dataset, dvRequestService.getDataverseRequest(), new UpdateDatasetCommand(dataset, dvRequestService.getDataverseRequest()));
            lockedFromEditsVar = false;
        } catch (IllegalCommandException ex) {
            lockedFromEditsVar = true;
        }
    }
    return lockedFromEditsVar;
}

Example 2 with UpdateDatasetCommand

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

the class DatasetPage method save.

public String save() {
    // Validate
    Set<ConstraintViolation> constraintViolations = workingVersion.validate();
    if (!constraintViolations.isEmpty()) {
        // JsfHelper.addFlashMessage(JH.localize("dataset.message.validationError"));
        JH.addMessage(FacesMessage.SEVERITY_ERROR, JH.localize("dataset.message.validationError"));
        // FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Validation Error", "See below for details."));
        return "";
    }
    // Use the API to save the dataset:
    Command<Dataset> cmd;
    try {
        if (editMode == EditMode.CREATE) {
            if (selectedTemplate != null) {
                if (isSessionUserAuthenticated()) {
                    cmd = new CreateDatasetCommand(dataset, dvRequestService.getDataverseRequest(), false, null, selectedTemplate);
                } else {
                    JH.addMessage(FacesMessage.SEVERITY_FATAL, JH.localize("dataset.create.authenticatedUsersOnly"));
                    return null;
                }
            } else {
                cmd = new CreateDatasetCommand(dataset, dvRequestService.getDataverseRequest());
            }
        } else {
            cmd = new UpdateDatasetCommand(dataset, dvRequestService.getDataverseRequest(), filesToBeDeleted);
            ((UpdateDatasetCommand) cmd).setValidateLenient(true);
        }
        dataset = commandEngine.submit(cmd);
        if (editMode == EditMode.CREATE) {
            if (session.getUser() instanceof AuthenticatedUser) {
                userNotificationService.sendNotification((AuthenticatedUser) session.getUser(), dataset.getCreateDate(), UserNotification.Type.CREATEDS, dataset.getLatestVersion().getId());
            }
        }
        logger.fine("Successfully executed SaveDatasetCommand.");
    } catch (EJBException ex) {
        StringBuilder error = new StringBuilder();
        error.append(ex).append(" ");
        error.append(ex.getMessage()).append(" ");
        Throwable cause = ex;
        while (cause.getCause() != null) {
            cause = cause.getCause();
            error.append(cause).append(" ");
            error.append(cause.getMessage()).append(" ");
        }
        logger.log(Level.FINE, "Couldn''t save dataset: {0}", error.toString());
        populateDatasetUpdateFailureMessage();
        return returnToDraftVersion();
    } catch (CommandException ex) {
        // FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Dataset Save Failed", " - " + ex.toString()));
        logger.severe("CommandException, when attempting to update the dataset: " + ex.getMessage());
        populateDatasetUpdateFailureMessage();
        return returnToDraftVersion();
    }
    newFiles.clear();
    if (editMode != null) {
        if (editMode.equals(EditMode.CREATE)) {
            JsfHelper.addSuccessMessage(JH.localize("dataset.message.createSuccess"));
        }
        if (editMode.equals(EditMode.METADATA)) {
            JsfHelper.addSuccessMessage(JH.localize("dataset.message.metadataSuccess"));
        }
        if (editMode.equals(EditMode.LICENSE)) {
            JsfHelper.addSuccessMessage(JH.localize("dataset.message.termsSuccess"));
        }
        if (editMode.equals(EditMode.FILE)) {
            JsfHelper.addSuccessMessage(JH.localize("dataset.message.filesSuccess"));
        }
    } else {
        // must have been a bulk file update or delete:
        if (bulkFileDeleteInProgress) {
            JsfHelper.addSuccessMessage(JH.localize("dataset.message.bulkFileDeleteSuccess"));
        } else {
            JsfHelper.addSuccessMessage(JH.localize("dataset.message.bulkFileUpdateSuccess"));
        }
    }
    editMode = null;
    bulkFileDeleteInProgress = false;
    // Call Ingest Service one more time, to
    // queue the data ingest jobs for asynchronous execution:
    ingestService.startIngestJobs(dataset, (AuthenticatedUser) session.getUser());
    logger.fine("Redirecting to the Dataset page.");
    return returnToDraftVersion();
}

Example 3 with UpdateDatasetCommand

use of edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand 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 4 with UpdateDatasetCommand

use of edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand 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 5 with UpdateDatasetCommand

use of edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand 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);
    }
}