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Example 1 with CreateDatasetVersionCommand

use of edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetVersionCommand 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);
}
Also used : DatasetField(edu.harvard.iq.dataverse.DatasetField) CreateDatasetCommand(edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand) Gson(com.google.gson.Gson) JsonObject(javax.json.JsonObject) DatasetVersion(edu.harvard.iq.dataverse.DatasetVersion) JsonParseException(edu.harvard.iq.dataverse.util.json.JsonParseException) DatasetDTO(edu.harvard.iq.dataverse.api.dto.DatasetDTO) DatasetFieldValue(edu.harvard.iq.dataverse.DatasetFieldValue) StringReader(java.io.StringReader) JsonReader(javax.json.JsonReader) JsonParser(edu.harvard.iq.dataverse.util.json.JsonParser) CreateDatasetVersionCommand(edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetVersionCommand) ValidatorFactory(javax.validation.ValidatorFactory) GsonBuilder(com.google.gson.GsonBuilder) Dataset(edu.harvard.iq.dataverse.Dataset) CommandException(edu.harvard.iq.dataverse.engine.command.exception.CommandException) XMLStreamException(javax.xml.stream.XMLStreamException) ConstraintViolation(javax.validation.ConstraintViolation) Validator(javax.validation.Validator) DestroyDatasetCommand(edu.harvard.iq.dataverse.engine.command.impl.DestroyDatasetCommand)

Example 2 with CreateDatasetVersionCommand

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

the class Datasets method updateDraftVersion.

@PUT
@Path("{id}/versions/{versionId}")
public Response updateDraftVersion(String jsonBody, @PathParam("id") String id, @PathParam("versionId") String versionId) {
    if (!":draft".equals(versionId)) {
        return error(Response.Status.BAD_REQUEST, "Only the :draft version can be updated");
    }
    try (StringReader rdr = new StringReader(jsonBody)) {
        DataverseRequest req = createDataverseRequest(findUserOrDie());
        Dataset ds = findDatasetOrDie(id);
        JsonObject json = Json.createReader(rdr).readObject();
        DatasetVersion incomingVersion = jsonParser().parseDatasetVersion(json);
        // clear possibly stale fields from the incoming dataset version.
        // creation and modification dates are updated by the commands.
        incomingVersion.setId(null);
        incomingVersion.setVersionNumber(null);
        incomingVersion.setMinorVersionNumber(null);
        incomingVersion.setVersionState(DatasetVersion.VersionState.DRAFT);
        incomingVersion.setDataset(ds);
        incomingVersion.setCreateTime(null);
        incomingVersion.setLastUpdateTime(null);
        boolean updateDraft = ds.getLatestVersion().isDraft();
        DatasetVersion managedVersion = execCommand(updateDraft ? new UpdateDatasetVersionCommand(req, incomingVersion) : new CreateDatasetVersionCommand(req, ds, incomingVersion));
        return ok(json(managedVersion));
    } catch (JsonParseException ex) {
        logger.log(Level.SEVERE, "Semantic error parsing dataset version Json: " + ex.getMessage(), ex);
        return error(Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage());
    } catch (WrappedResponse ex) {
        return ex.getResponse();
    }
}
Also used : DataverseRequest(edu.harvard.iq.dataverse.engine.command.DataverseRequest) CreateDatasetVersionCommand(edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetVersionCommand) Dataset(edu.harvard.iq.dataverse.Dataset) StringReader(java.io.StringReader) JsonObject(javax.json.JsonObject) DatasetVersion(edu.harvard.iq.dataverse.DatasetVersion) JsonParseException(edu.harvard.iq.dataverse.util.json.JsonParseException) UpdateDatasetVersionCommand(edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand) Path(javax.ws.rs.Path) PUT(javax.ws.rs.PUT)

Aggregations

Dataset (edu.harvard.iq.dataverse.Dataset)2 DatasetVersion (edu.harvard.iq.dataverse.DatasetVersion)2 CreateDatasetVersionCommand (edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetVersionCommand)2 JsonParseException (edu.harvard.iq.dataverse.util.json.JsonParseException)2 StringReader (java.io.StringReader)2 JsonObject (javax.json.JsonObject)2 Gson (com.google.gson.Gson)1 GsonBuilder (com.google.gson.GsonBuilder)1 DatasetField (edu.harvard.iq.dataverse.DatasetField)1 DatasetFieldValue (edu.harvard.iq.dataverse.DatasetFieldValue)1 DatasetDTO (edu.harvard.iq.dataverse.api.dto.DatasetDTO)1 DataverseRequest (edu.harvard.iq.dataverse.engine.command.DataverseRequest)1 CommandException (edu.harvard.iq.dataverse.engine.command.exception.CommandException)1 CreateDatasetCommand (edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand)1 DestroyDatasetCommand (edu.harvard.iq.dataverse.engine.command.impl.DestroyDatasetCommand)1 UpdateDatasetVersionCommand (edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand)1 JsonParser (edu.harvard.iq.dataverse.util.json.JsonParser)1 JsonReader (javax.json.JsonReader)1 ConstraintViolation (javax.validation.ConstraintViolation)1 Validator (javax.validation.Validator)1