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

Example 41 with CommandException

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

the class UpdateDatasetTargetURLCommand method executeImpl.

@Override
protected void executeImpl(CommandContext ctxt) throws CommandException {
    if (!(getUser() instanceof AuthenticatedUser) || !getUser().isSuperuser()) {
        throw new PermissionException("Update Target URL can only be called by superusers.", this, Collections.singleton(Permission.EditDataset), target);
    }
    IdServiceBean idServiceBean = IdServiceBean.getBean(target.getProtocol(), ctxt);
    HashMap<String, String> metadata = idServiceBean.getMetadataFromDatasetForTargetURL(target);
    try {
        String doiRetString = idServiceBean.modifyIdentifier(target, metadata);
        if (doiRetString != null && doiRetString.contains(target.getIdentifier())) {
            target.setGlobalIdCreateTime(new Timestamp(new Date().getTime()));
            ctxt.em().merge(target);
            ctxt.em().flush();
        } else {
        // do nothing - we'll know it failed because the global id create time won't have been updated.
        }
    } catch (Exception e) {
    // do nothing - idem and the problem has been logged
    }
}

Example 42 with CommandException

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

the class UpdateDataverseThemeCommand method execute.

/**
 * Update Theme and Widget related data for this dataverse, and
 * do file management needed for theme images.
 *
 * @param ctxt
 * @return
 * @throws CommandException
 */
@Override
public Dataverse execute(CommandContext ctxt) throws CommandException {
    // Get current dataverse, so we can delete current logo file if necessary
    Dataverse currentDv = ctxt.dataverses().find(editedDv.getId());
    File logoFileDir = new File(logoPath.toFile(), editedDv.getId().toString());
    File currentFile = null;
    if (currentDv.getDataverseTheme() != null && currentDv.getDataverseTheme().getLogo() != null) {
        currentFile = new File(logoFileDir, currentDv.getDataverseTheme().getLogo());
    }
    try {
        // If edited logo field is empty, and a logoFile currently exists, delete it
        if (editedDv.getDataverseTheme() == null || editedDv.getDataverseTheme().getLogo() == null) {
            if (currentFile != null) {
                currentFile.delete();
            }
        } else // If edited logo file isn't empty,and uploaded File exists, delete currentFile and copy uploaded file from temp dir to logos dir
        if (uploadedFile != null) {
            File newFile = new File(logoFileDir, editedDv.getDataverseTheme().getLogo());
            if (currentFile != null) {
                currentFile.delete();
            }
            logoFileDir.mkdirs();
            Files.copy(uploadedFile.toPath(), newFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
        }
        // save updated dataverse to db
        return ctxt.dataverses().save(editedDv);
    } catch (IOException e) {
        // improve error handling
        throw new CommandException("Error saving logo file", e, this);
    }
}

Example 43 with CommandException

use of edu.harvard.iq.dataverse.engine.command.exception.CommandException 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 44 with CommandException

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

the class EditDatafilesPage method deleteDatasetLogoAndUseThisDataFileAsThumbnailInstead.

public void deleteDatasetLogoAndUseThisDataFileAsThumbnailInstead() {
    logger.log(Level.FINE, "For dataset id {0} the current thumbnail is from a dataset logo rather than a dataset file, blowing away the logo and using this FileMetadata id instead: {1}", new Object[] { dataset.getId(), fileMetadataSelectedForThumbnailPopup });
    /**
     * @todo Rather than deleting and merging right away, try to respect how
     * this page seems to stage actions and giving the user a chance to
     * review before clicking "Save Changes".
     */
    try {
        DatasetThumbnail datasetThumbnail = commandEngine.submit(new UpdateDatasetThumbnailCommand(dvRequestService.getDataverseRequest(), dataset, UpdateDatasetThumbnailCommand.UserIntent.setDatasetFileAsThumbnail, fileMetadataSelectedForThumbnailPopup.getDataFile().getId(), null));
        // look up the dataset again because the UpdateDatasetThumbnailCommand mutates (merges) the dataset
        dataset = datasetService.find(dataset.getId());
    } catch (CommandException ex) {
        String error = "Problem setting thumbnail for dataset id " + dataset.getId() + ".: " + ex;
        // show this error to the user?
        logger.info(error);
    }
}

Example 45 with CommandException

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

the class DataversePage method save.

public String save() {
    List<DataverseFieldTypeInputLevel> listDFTIL = new ArrayList<>();
    if (editMode != null && editMode.equals(EditMode.INFO)) {
        List<MetadataBlock> selectedBlocks = new ArrayList<>();
        if (dataverse.isMetadataBlockRoot()) {
            dataverse.getMetadataBlocks().clear();
        }
        for (MetadataBlock mdb : this.allMetadataBlocks) {
            if (dataverse.isMetadataBlockRoot() && (mdb.isSelected() || mdb.isRequired())) {
                selectedBlocks.add(mdb);
                for (DatasetFieldType dsft : mdb.getDatasetFieldTypes()) {
                    if (dsft.isRequiredDV() && !dsft.isRequired() && ((!dsft.isHasParent() && dsft.isInclude()) || (dsft.isHasParent() && dsft.getParentDatasetFieldType().isInclude()))) {
                        DataverseFieldTypeInputLevel dftil = new DataverseFieldTypeInputLevel();
                        dftil.setDatasetFieldType(dsft);
                        dftil.setDataverse(dataverse);
                        dftil.setRequired(true);
                        dftil.setInclude(true);
                        listDFTIL.add(dftil);
                    }
                    if ((!dsft.isHasParent() && !dsft.isInclude()) || (dsft.isHasParent() && !dsft.getParentDatasetFieldType().isInclude())) {
                        DataverseFieldTypeInputLevel dftil = new DataverseFieldTypeInputLevel();
                        dftil.setDatasetFieldType(dsft);
                        dftil.setDataverse(dataverse);
                        dftil.setRequired(false);
                        dftil.setInclude(false);
                        listDFTIL.add(dftil);
                    }
                }
            }
        }
        if (!selectedBlocks.isEmpty()) {
            dataverse.setMetadataBlocks(selectedBlocks);
        }
        if (!dataverse.isFacetRoot()) {
            facets.getTarget().clear();
        }
    }
    Command<Dataverse> cmd = null;
    // TODO change to Create - for now the page is expecting INFO instead.
    Boolean create;
    if (dataverse.getId() == null) {
        if (session.getUser().isAuthenticated()) {
            dataverse.setOwner(ownerId != null ? dataverseService.find(ownerId) : null);
            create = Boolean.TRUE;
            cmd = new CreateDataverseCommand(dataverse, dvRequestService.getDataverseRequest(), facets.getTarget(), listDFTIL);
        } else {
            JH.addMessage(FacesMessage.SEVERITY_FATAL, BundleUtil.getStringFromBundle("dataverse.create.authenticatedUsersOnly"));
            return null;
        }
    } else {
        create = Boolean.FALSE;
        if (editMode != null && editMode.equals(EditMode.FEATURED)) {
            cmd = new UpdateDataverseCommand(dataverse, null, featuredDataverses.getTarget(), dvRequestService.getDataverseRequest(), null);
        } else {
            cmd = new UpdateDataverseCommand(dataverse, facets.getTarget(), null, dvRequestService.getDataverseRequest(), listDFTIL);
        }
    }
    try {
        dataverse = commandEngine.submit(cmd);
        if (session.getUser() instanceof AuthenticatedUser) {
            if (create) {
                userNotificationService.sendNotification((AuthenticatedUser) session.getUser(), dataverse.getCreateDate(), Type.CREATEDV, dataverse.getId());
            }
        }
        String message;
        if (editMode != null && editMode.equals(EditMode.FEATURED)) {
            message = "The featured dataverses for this dataverse have been updated.";
        } else {
            message = (create) ? BundleUtil.getStringFromBundle("dataverse.create.success", Arrays.asList(settingsWrapper.getGuidesBaseUrl(), systemConfig.getGuidesVersion())) : BundleUtil.getStringFromBundle("dataverse.update.success");
        }
        JsfHelper.addSuccessMessage(message);
        editMode = null;
        return returnRedirect();
    } catch (CommandException ex) {
        logger.log(Level.SEVERE, "Unexpected Exception calling dataverse command", ex);
        String errMsg = create ? BundleUtil.getStringFromBundle("dataverse.create.failure") : BundleUtil.getStringFromBundle("dataverse.update.failure");
        JH.addMessage(FacesMessage.SEVERITY_FATAL, errMsg);
        return null;
    } catch (Exception e) {
        logger.log(Level.SEVERE, "Unexpected Exception calling dataverse command", e);
        String errMsg = create ? BundleUtil.getStringFromBundle("dataverse.create.failure") : BundleUtil.getStringFromBundle("dataverse.update.failure");
        JH.addMessage(FacesMessage.SEVERITY_FATAL, errMsg);
        return null;
    }
}