Examples with Dataverse edu.harvard.iq.dataverse.Dataverse used on opensource projects

Example 51 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class UpdateDataverseCommand method execute.

@Override
public Dataverse execute(CommandContext ctxt) throws CommandException {
    Dataverse result = ctxt.dataverses().save(editedDv);
    if (facetList != null) {
        ctxt.facets().deleteFacetsFor(result);
        int i = 0;
        for (DatasetFieldType df : facetList) {
            ctxt.facets().create(i++, df.getId(), result.getId());
        }
    }
    if (featuredDataverseList != null) {
        ctxt.featuredDataverses().deleteFeaturedDataversesFor(result);
        int i = 0;
        for (Object obj : featuredDataverseList) {
            Dataverse dv = (Dataverse) obj;
            ctxt.featuredDataverses().create(i++, dv.getId(), result.getId());
        }
    }
    if (inputLevelList != null) {
        ctxt.fieldTypeInputLevels().deleteFacetsFor(result);
        for (DataverseFieldTypeInputLevel obj : inputLevelList) {
            ctxt.fieldTypeInputLevels().create(obj);
        }
    }
    ctxt.index().indexDataverse(result);
    return result;
}

Example 52 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class Datasets method moveDataset.

@POST
@Path("{id}/move/{targetDataverseAlias}")
public Response moveDataset(@PathParam("id") String id, @PathParam("targetDataverseAlias") String targetDataverseAlias, @QueryParam("forceMove") Boolean force) {
    try {
        System.out.print("force: " + force);
        User u = findUserOrDie();
        Dataset ds = findDatasetOrDie(id);
        Dataverse target = dataverseService.findByAlias(targetDataverseAlias);
        if (target == null) {
            return error(Response.Status.BAD_REQUEST, "Target Dataverse not found.");
        }
        // Command requires Super user - it will be tested by the command
        execCommand(new MoveDatasetCommand(createDataverseRequest(u), ds, target, force));
        return ok("Dataset moved successfully");
    } catch (WrappedResponse ex) {
        return ex.getResponse();
    }
}

Example 53 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class ImportServiceBean method createDataverse.

/**
 * This is just a convenience method, for testing migration.  It creates
 * a dummy dataverse with the directory name as dataverse name & alias.
 * @param dvName
 * @param dataverseRequest
 * @return
 * @throws ImportException
 */
@TransactionAttribute(REQUIRES_NEW)
public Dataverse createDataverse(String dvName, DataverseRequest dataverseRequest) throws ImportException {
    Dataverse d = new Dataverse();
    Dataverse root = dataverseService.findByAlias("root");
    d.setOwner(root);
    d.setAlias(dvName);
    d.setName(dvName);
    d.setAffiliation("affiliation");
    d.setPermissionRoot(false);
    d.setDescription("description");
    d.setDataverseType(Dataverse.DataverseType.RESEARCHERS);
    DataverseContact dc = new DataverseContact();
    dc.setContactEmail("pete@mailinator.com");
    ArrayList<DataverseContact> dcList = new ArrayList<>();
    dcList.add(dc);
    d.setDataverseContacts(dcList);
    try {
        d = engineSvc.submit(new CreateDataverseCommand(d, dataverseRequest, null, null));
    } catch (EJBException ex) {
        Throwable cause = ex;
        StringBuilder sb = new StringBuilder();
        sb.append("Error creating dataverse.");
        while (cause.getCause() != null) {
            cause = cause.getCause();
            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.log(Level.SEVERE, sb.toString());
        System.out.println("Error creating dataverse: " + sb.toString());
        throw new ImportException(sb.toString());
    } catch (CommandException e) {
        throw new ImportException(e.getMessage());
    }
    return d;
}

Example 54 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class ImportServiceBean method doImportHarvestedDataset.

@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
public Dataset doImportHarvestedDataset(DataverseRequest dataverseRequest, HarvestingClient harvestingClient, String harvestIdentifier, String metadataFormat, File metadataFile, PrintWriter cleanupLog) throws ImportException, IOException {
    if (harvestingClient == null || harvestingClient.getDataverse() == null) {
        throw new ImportException("importHarvestedDataset called wiht a null harvestingClient, or an invalid harvestingClient.");
    }
    Dataverse owner = harvestingClient.getDataverse();
    Dataset importedDataset = null;
    DatasetDTO dsDTO = null;
    String json = null;
    if ("ddi".equalsIgnoreCase(metadataFormat) || "oai_ddi".equals(metadataFormat) || metadataFormat.toLowerCase().matches("^oai_ddi.*")) {
        try {
            String xmlToParse = new String(Files.readAllBytes(metadataFile.toPath()));
            // TODO:
            // import type should be configurable - it should be possible to
            // select whether you want to harvest with or without files,
            // ImportType.HARVEST vs. ImportType.HARVEST_WITH_FILES
            logger.fine("importing DDI " + metadataFile.getAbsolutePath());
            dsDTO = importDDIService.doImport(ImportType.HARVEST_WITH_FILES, xmlToParse);
        } catch (IOException | XMLStreamException | ImportException e) {
            throw new ImportException("Failed to process DDI XML record: " + e.getClass() + " (" + e.getMessage() + ")");
        }
    } else if ("dc".equalsIgnoreCase(metadataFormat) || "oai_dc".equals(metadataFormat)) {
        logger.fine("importing DC " + metadataFile.getAbsolutePath());
        try {
            String xmlToParse = new String(Files.readAllBytes(metadataFile.toPath()));
            dsDTO = importGenericService.processOAIDCxml(xmlToParse);
        } catch (IOException | XMLStreamException e) {
            throw new ImportException("Failed to process Dublin Core XML record: " + e.getClass() + " (" + e.getMessage() + ")");
        }
    } else if ("dataverse_json".equals(metadataFormat)) {
        // This is Dataverse metadata already formatted in JSON.
        // Simply read it into a string, and pass to the final import further down:
        logger.fine("Attempting to import custom dataverse metadata from file " + metadataFile.getAbsolutePath());
        json = new String(Files.readAllBytes(metadataFile.toPath()));
    } else {
        throw new ImportException("Unsupported import metadata format: " + metadataFormat);
    }
    if (json == null) {
        if (dsDTO != null) {
            // convert DTO to Json,
            Gson gson = new GsonBuilder().setPrettyPrinting().create();
            json = gson.toJson(dsDTO);
            logger.fine("JSON produced for the metadata harvested: " + json);
        } else {
            throw new ImportException("Failed to transform XML metadata format " + metadataFormat + " into a DatasetDTO");
        }
    }
    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(true);
        Dataset ds = parser.parseDataset(obj);
        // For ImportType.NEW, if the metadata contains a global identifier, and it's not a protocol
        // we support, it should be rejected.
        // (TODO: ! - add some way of keeping track of supported protocols!)
        // 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()) {
            // For migration and harvest, add NA for missing required values
            for (ConstraintViolation<DatasetField> v : violations) {
                DatasetField f = v.getRootBean();
                f.setSingleValue(DatasetField.NA_VALUE);
            }
        }
        // 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;
                // TODO: Is this scrubbing something we want to continue doing?
                if (settingsService.isTrueForKey(SettingsServiceBean.Key.ScrubMigrationData, false)) {
                    fixed = processMigrationValidationError(f, cleanupLog, metadataFile.getName());
                    converted = true;
                    if (fixed) {
                        Set<ConstraintViolation<DatasetFieldValue>> scrubbedViolations = validator.validate(f);
                        if (!scrubbedViolations.isEmpty()) {
                            fixed = false;
                        }
                    }
                }
                if (!fixed) {
                    String msg = "Data modified - File: " + metadataFile.getName() + "; Field: " + f.getDatasetField().getDatasetFieldType().getDisplayName() + "; " + "Invalid value:  '" + f.getValue() + "'" + " Converted Value:'" + DatasetField.NA_VALUE + "'";
                    cleanupLog.println(msg);
                    f.setValue(DatasetField.NA_VALUE);
                }
            }
        }
        // this dataset:
        if (StringUtils.isEmpty(ds.getGlobalId())) {
            throw new ImportException("The harvested metadata record with the OAI server identifier " + harvestIdentifier + " does not contain a global unique identifier that we could recognize, skipping.");
        }
        ds.setHarvestedFrom(harvestingClient);
        ds.setHarvestIdentifier(harvestIdentifier);
        Dataset existingDs = datasetService.findByGlobalId(ds.getGlobalId());
        if (existingDs != null) {
            // we are just going to skip it!
            if (existingDs.getOwner() != null && !owner.getId().equals(existingDs.getOwner().getId())) {
                throw new ImportException("The dataset with the global id " + ds.getGlobalId() + " already exists, in the dataverse " + existingDs.getOwner().getAlias() + ", skipping.");
            }
            // skip it also:
            if (!existingDs.isHarvested()) {
                throw new ImportException("A LOCAL dataset with the global id " + ds.getGlobalId() + " already exists in this dataverse; skipping.");
            }
            // 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");
            }
            // Purge all the SOLR documents associated with this client from the
            // index server:
            indexService.deleteHarvestedDocuments(existingDs);
            // DeleteFileCommand on them.
            for (DataFile harvestedFile : existingDs.getFiles()) {
                DataFile merged = em.merge(harvestedFile);
                em.remove(merged);
                harvestedFile = null;
            }
            // TODO:
            // Verify what happens with the indexed files in SOLR?
            // are they going to be overwritten by the reindexing of the dataset?
            existingDs.setFiles(null);
            Dataset merged = em.merge(existingDs);
            engineSvc.submit(new DestroyDatasetCommand(merged, dataverseRequest));
            importedDataset = engineSvc.submit(new CreateDatasetCommand(ds, dataverseRequest, false, ImportType.HARVEST));
        } else {
            importedDataset = engineSvc.submit(new CreateDatasetCommand(ds, dataverseRequest, false, ImportType.HARVEST));
        }
    } catch (JsonParseException | ImportException | CommandException ex) {
        logger.fine("Failed to import harvested dataset: " + ex.getClass() + ": " + ex.getMessage());
        FileOutputStream savedJsonFileStream = new FileOutputStream(new File(metadataFile.getAbsolutePath() + ".json"));
        byte[] jsonBytes = json.getBytes();
        int i = 0;
        while (i < jsonBytes.length) {
            int chunkSize = i + 8192 <= jsonBytes.length ? 8192 : jsonBytes.length - i;
            savedJsonFileStream.write(jsonBytes, i, chunkSize);
            i += chunkSize;
            savedJsonFileStream.flush();
        }
        savedJsonFileStream.close();
        logger.info("JSON produced saved in " + metadataFile.getAbsolutePath() + ".json");
        throw new ImportException("Failed to import harvested dataset: " + ex.getClass() + " (" + ex.getMessage() + ")", ex);
    }
    return importedDataset;
}

Example 55 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class ContainerManagerImpl method getEntry.

@Override
public DepositReceipt getEntry(String uri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordError, SwordAuthException {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, httpRequest);
    logger.fine("getEntry called with url: " + uri);
    urlManager.processUrl(uri);
    String targetType = urlManager.getTargetType();
    if (!targetType.isEmpty()) {
        logger.fine("operating on target type: " + urlManager.getTargetType());
        if ("study".equals(targetType)) {
            String globalId = urlManager.getTargetIdentifier();
            Dataset dataset = datasetService.findByGlobalId(globalId);
            if (dataset != null) {
                if (!permissionService.isUserAllowedOn(user, new GetDraftDatasetVersionCommand(dvReq, dataset), dataset)) {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + user.getDisplayInfo().getTitle() + " is not authorized to retrieve entry for " + dataset.getGlobalId());
                }
                Dataverse dvThatOwnsDataset = dataset.getOwner();
                ReceiptGenerator receiptGenerator = new ReceiptGenerator();
                String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
                DepositReceipt depositReceipt = receiptGenerator.createDatasetReceipt(baseUrl, dataset);
                if (depositReceipt != null) {
                    return depositReceipt;
                } else {
                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not generate deposit receipt.");
                }
            } else {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataset based on URL: " + uri);
            }
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported target type (" + targetType + ") in URL: " + uri);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine target type from URL: " + uri);
    }
}