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

Example 6 with UpdateDatasetCommand

use of edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand 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 7 with UpdateDatasetCommand

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

the class FilePage 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 == dataset) {
        dataset = fileMetadata.getDataFile().getOwner();
    }
    if (null == lockedFromEditsVar) {
        try {
            permissionService.checkEditDatasetLock(dataset, dvRequestService.getDataverseRequest(), new UpdateDatasetCommand(dataset, dvRequestService.getDataverseRequest()));
            lockedFromEditsVar = false;
        } catch (IllegalCommandException ex) {
            lockedFromEditsVar = true;
        }
    }
    return lockedFromEditsVar;
}

Example 8 with UpdateDatasetCommand

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

the class AddReplaceFileHelper method step_070_run_update_dataset_command.

/**
 * Create and run the update dataset command
 *
 * @return
 */
private boolean step_070_run_update_dataset_command() {
    if (this.hasError()) {
        return false;
    }
    Command<Dataset> update_cmd;
    update_cmd = new UpdateDatasetCommand(dataset, dvRequest);
    ((UpdateDatasetCommand) update_cmd).setValidateLenient(true);
    try {
        // Submit the update dataset command
        // and update the local dataset object
        // 
        dataset = commandEngine.submit(update_cmd);
    } catch (CommandException ex) {
        /**
         * @todo Add a test to exercise this error.
         */
        this.addErrorSevere(getBundleErr("add.add_file_error"));
        logger.severe(ex.getMessage());
        return false;
    } catch (EJBException ex) {
        /**
         * @todo Add a test to exercise this error.
         */
        this.addErrorSevere("add.add_file_error (see logs)");
        logger.severe(ex.getMessage());
        return false;
    }
    return true;
}

Example 9 with UpdateDatasetCommand

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

the class EditDatafilesPage method save.

public String save() {
    if (!saveEnabled) {
        return "";
    }
    if (isFileReplaceOperation()) {
        try {
            return saveReplacementFile();
        } catch (FileReplaceException ex) {
            String errMsg = ex.getMessage();
            FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Dataset Save Failed", errMsg));
            logger.log(Level.SEVERE, "Dataset save failed for replace operation: {0}", errMsg);
            return null;
        }
    }
    // Save the NEW files permanently:
    ingestService.addFiles(workingVersion, newFiles);
    if (workingVersion.getId() == null || datasetUpdateRequired) {
        logger.fine("issuing the dataset update command");
        if (datasetUpdateRequired) {
            for (int i = 0; i < workingVersion.getFileMetadatas().size(); i++) {
                for (FileMetadata fileMetadata : fileMetadatas) {
                    if (fileMetadata.getDataFile().getStorageIdentifier() != null) {
                        if (fileMetadata.getDataFile().getStorageIdentifier().equals(workingVersion.getFileMetadatas().get(i).getDataFile().getStorageIdentifier())) {
                            workingVersion.getFileMetadatas().set(i, fileMetadata);
                        }
                    }
                }
            }
            if (tabularDataTagsUpdated) {
                for (int i = 0; i < dataset.getFiles().size(); i++) {
                    for (FileMetadata fileMetadata : fileMetadatas) {
                        if (fileMetadata.getDataFile().getStorageIdentifier() != null) {
                            if (fileMetadata.getDataFile().getStorageIdentifier().equals(dataset.getFiles().get(i).getStorageIdentifier())) {
                                dataset.getFiles().set(i, fileMetadata.getDataFile());
                            }
                        }
                    }
                }
                tabularDataTagsUpdated = false;
            }
        }
        Command<Dataset> cmd;
        try {
            cmd = new UpdateDatasetCommand(dataset, dvRequestService.getDataverseRequest(), filesToBeDeleted);
            ((UpdateDatasetCommand) cmd).setValidateLenient(true);
            dataset = commandEngine.submit(cmd);
        } 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.INFO, "Couldn''t save dataset: {0}", error.toString());
            populateDatasetUpdateFailureMessage();
            return null;
        } catch (CommandException ex) {
            FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Dataset Save Failed", " - " + ex.toString()));
            logger.severe(ex.getMessage());
            populateDatasetUpdateFailureMessage();
            return null;
        }
        datasetUpdateRequired = false;
        saveEnabled = false;
    } else {
        // This is an existing Draft version (and nobody has explicitly
        // requested that the entire dataset is updated). So we'll try to update
        // only the filemetadatas and/or files affected, and not the
        // entire version.
        // TODO: in 4.3, create SaveDataFileCommand!
        // -- L.A. Sep. 21 2015, 4.2
        Timestamp updateTime = new Timestamp(new Date().getTime());
        workingVersion.setLastUpdateTime(updateTime);
        dataset.setModificationTime(updateTime);
        StringBuilder saveError = new StringBuilder();
        for (FileMetadata fileMetadata : fileMetadatas) {
            if (fileMetadata.getDataFile().getCreateDate() == null) {
                fileMetadata.getDataFile().setCreateDate(updateTime);
                fileMetadata.getDataFile().setCreator((AuthenticatedUser) session.getUser());
            }
            fileMetadata.getDataFile().setModificationTime(updateTime);
            try {
                // DataFile savedDatafile = datafileService.save(fileMetadata.getDataFile());
                fileMetadata = datafileService.mergeFileMetadata(fileMetadata);
                logger.fine("Successfully saved DataFile " + fileMetadata.getLabel() + " in the database.");
            } catch (EJBException ex) {
                saveError.append(ex).append(" ");
                saveError.append(ex.getMessage()).append(" ");
                Throwable cause = ex;
                while (cause.getCause() != null) {
                    cause = cause.getCause();
                    saveError.append(cause).append(" ");
                    saveError.append(cause.getMessage()).append(" ");
                }
            }
        }
        // Remove / delete any files that were removed
        for (FileMetadata fmd : filesToBeDeleted) {
            // check if this file is being used as the default thumbnail
            if (fmd.getDataFile().equals(dataset.getThumbnailFile())) {
                logger.fine("deleting the dataset thumbnail designation");
                dataset.setThumbnailFile(null);
            }
            if (!fmd.getDataFile().isReleased()) {
                // if file is draft (ie. new to this version, delete; otherwise just remove filemetadata object)
                try {
                    commandEngine.submit(new DeleteDataFileCommand(fmd.getDataFile(), dvRequestService.getDataverseRequest()));
                    dataset.getFiles().remove(fmd.getDataFile());
                    workingVersion.getFileMetadatas().remove(fmd);
                    // todo: clean this up some when we clean the create / update dataset methods
                    for (DataFileCategory cat : dataset.getCategories()) {
                        cat.getFileMetadatas().remove(fmd);
                    }
                } catch (CommandException cmde) {
                // TODO:
                // add diagnostics reporting for individual data files that
                // we failed to delete.
                }
            } else {
                datafileService.removeFileMetadata(fmd);
                fmd.getDataFile().getFileMetadatas().remove(fmd);
                workingVersion.getFileMetadatas().remove(fmd);
            }
        }
        String saveErrorString = saveError.toString();
        if (saveErrorString != null && !saveErrorString.isEmpty()) {
            logger.log(Level.INFO, "Couldn''t save dataset: {0}", saveErrorString);
            populateDatasetUpdateFailureMessage();
            return null;
        }
        // the id for null, just in case)
        if (mode == FileEditMode.UPLOAD) {
            if (dataset.getId() != null) {
                dataset = datasetService.find(dataset.getId());
            }
        }
    }
    newFiles.clear();
    workingVersion = dataset.getEditVersion();
    logger.fine("working version id: " + workingVersion.getId());
    if (mode == FileEditMode.SINGLE) {
        JsfHelper.addSuccessMessage(getBundleString("file.message.editSuccess"));
    } else {
        JsfHelper.addSuccessMessage(getBundleString("dataset.message.filesSuccess"));
    }
    // queue the data ingest jobs for asynchronous execution:
    if (mode == FileEditMode.UPLOAD) {
        ingestService.startIngestJobs(dataset, (AuthenticatedUser) session.getUser());
    }
    if (mode == FileEditMode.SINGLE && fileMetadatas.size() > 0) {
        // If this was a "single file edit", i.e. an edit request sent from
        // the individual File Landing page, we want to redirect back to
        // the landing page. BUT ONLY if the file still exists - i.e., if
        // the user hasn't just deleted it!
        versionString = "DRAFT";
        return returnToFileLandingPage();
    }
    // if (newDraftVersion) {
    // return returnToDraftVersionById();
    // }
    logger.fine("Redirecting to the dataset page, from the edit/upload page.");
    return returnToDraftVersion();
}

Example 10 with UpdateDatasetCommand

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

the class DatasetPage method registerDataset.

public String registerDataset() {
    UpdateDatasetCommand cmd;
    try {
        cmd = new UpdateDatasetCommand(dataset, dvRequestService.getDataverseRequest());
        cmd.setValidateLenient(true);
        dataset = commandEngine.submit(cmd);
    } catch (CommandException ex) {
        FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_WARN, "Dataset Registration Failed", " - " + ex.toString()));
        logger.severe(ex.getMessage());
    }
    FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_INFO, "DatasetRegistered", "Your dataset is now registered.");
    FacesContext.getCurrentInstance().addMessage(null, message);
    return returnToDatasetOnly();
}