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

Example 1 with CreateDatasetCommand

use of edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand 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 2 with CreateDatasetCommand

use of edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand 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 CreateDatasetCommand

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

the class ImportServiceBean method doImport.

public JsonObjectBuilder doImport(DataverseRequest dataverseRequest, Dataverse owner, String xmlToParse, String fileName, ImportType importType, PrintWriter cleanupLog) throws ImportException, IOException {
    String status = "";
    Long createdId = null;
    DatasetDTO dsDTO = null;
    try {
        dsDTO = importDDIService.doImport(importType, xmlToParse);
    } catch (XMLStreamException e) {
        throw new ImportException("XMLStreamException" + e);
    }
    // convert DTO to Json,
    Gson gson = new GsonBuilder().setPrettyPrinting().create();
    String json = gson.toJson(dsDTO);
    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(!importType.equals(ImportType.NEW));
        Dataset ds = parser.parseDataset(obj);
        // we support, it will be rejected.
        if (importType.equals(ImportType.NEW)) {
            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()) {
            if (importType.equals(ImportType.MIGRATION) || importType.equals(ImportType.HARVEST)) {
                // For migration and harvest, add NA for missing required values
                for (ConstraintViolation<DatasetField> v : violations) {
                    DatasetField f = v.getRootBean();
                    f.setSingleValue(DatasetField.NA_VALUE);
                }
            } else {
                // when importing a new dataset, the import will fail
                // if required values are missing.
                String errMsg = "Error importing data:";
                for (ConstraintViolation<DatasetField> v : violations) {
                    errMsg += " " + v.getMessage();
                }
                throw new ImportException(errMsg);
            }
        }
        // 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;
                if ((importType.equals(ImportType.MIGRATION) || importType.equals(ImportType.HARVEST)) && settingsService.isTrueForKey(SettingsServiceBean.Key.ScrubMigrationData, false)) {
                    fixed = processMigrationValidationError(f, cleanupLog, fileName);
                    converted = true;
                    if (fixed) {
                        Set<ConstraintViolation<DatasetFieldValue>> scrubbedViolations = validator.validate(f);
                        if (!scrubbedViolations.isEmpty()) {
                            fixed = false;
                        }
                    }
                }
                if (!fixed) {
                    if (importType.equals(ImportType.HARVEST)) {
                        String msg = "Data modified - File: " + fileName + "; Field: " + f.getDatasetField().getDatasetFieldType().getDisplayName() + "; " + "Invalid value:  '" + f.getValue() + "'" + " Converted Value:'" + DatasetField.NA_VALUE + "'";
                        cleanupLog.println(msg);
                        f.setValue(DatasetField.NA_VALUE);
                    } else {
                        String msg = " Validation error for ";
                        if (converted) {
                            msg += "converted ";
                        }
                        msg += "value: " + f.getValue() + ", " + f.getValidationMessage();
                        throw new ImportException(msg);
                    }
                }
            }
        }
        Dataset existingDs = datasetService.findByGlobalId(ds.getGlobalId());
        if (existingDs != null) {
            if (importType.equals(ImportType.HARVEST)) {
                // 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");
                }
                engineSvc.submit(new DestroyDatasetCommand(existingDs, dataverseRequest));
                Dataset managedDs = engineSvc.submit(new CreateDatasetCommand(ds, dataverseRequest, false, importType));
                status = " updated dataset, id=" + managedDs.getId() + ".";
            } else {
                // check that the version number isn't already in the dataset
                for (DatasetVersion dsv : existingDs.getVersions()) {
                    if (dsv.getVersionNumber().equals(ds.getLatestVersion().getVersionNumber())) {
                        throw new ImportException("VersionNumber " + ds.getLatestVersion().getVersionNumber() + " already exists in dataset " + existingDs.getGlobalId());
                    }
                }
                DatasetVersion dsv = engineSvc.submit(new CreateDatasetVersionCommand(dataverseRequest, existingDs, ds.getVersions().get(0)));
                status = " created datasetVersion, for dataset " + dsv.getDataset().getGlobalId();
                createdId = dsv.getId();
            }
        } else {
            Dataset managedDs = engineSvc.submit(new CreateDatasetCommand(ds, dataverseRequest, false, importType));
            status = " created dataset, id=" + managedDs.getId() + ".";
            createdId = managedDs.getId();
        }
    } catch (JsonParseException ex) {
        logger.log(Level.INFO, "Error parsing datasetVersion: {0}", ex.getMessage());
        throw new ImportException("Error parsing datasetVersion: " + ex.getMessage(), ex);
    } catch (CommandException ex) {
        logger.log(Level.INFO, "Error excuting Create dataset command: {0}", ex.getMessage());
        throw new ImportException("Error excuting dataverse command: " + ex.getMessage(), ex);
    }
    return Json.createObjectBuilder().add("message", status);
}

Example 4 with CreateDatasetCommand

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

the class FilePage method isLockedFromDownload.

public boolean isLockedFromDownload() {
    if (null == dataset) {
        dataset = fileMetadata.getDataFile().getOwner();
    }
    if (null == lockedFromDownloadVar) {
        try {
            permissionService.checkDownloadFileLock(dataset, dvRequestService.getDataverseRequest(), new CreateDatasetCommand(dataset, dvRequestService.getDataverseRequest()));
            lockedFromDownloadVar = false;
        } catch (IllegalCommandException ex) {
            lockedFromDownloadVar = true;
        }
    }
    return lockedFromDownloadVar;
}

Example 5 with CreateDatasetCommand

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

the class DatasetPage method isLockedFromDownload.

public boolean isLockedFromDownload() {
    if (null == lockedFromDownloadVar) {
        try {
            permissionService.checkDownloadFileLock(dataset, dvRequestService.getDataverseRequest(), new CreateDatasetCommand(dataset, dvRequestService.getDataverseRequest()));
            lockedFromDownloadVar = false;
        } catch (IllegalCommandException ex) {
            lockedFromDownloadVar = true;
            return true;
        }
    }
    return lockedFromDownloadVar;
}