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

Example 21 with DataverseRequest

use of edu.harvard.iq.dataverse.engine.command.DataverseRequest 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 22 with DataverseRequest

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

the class BatchImport method startBatchJob.

private Response startBatchJob(String fileDir, String parentIdtf, String apiKey, ImportType importType, Boolean createDV) {
    if (createDV == null) {
        createDV = Boolean.FALSE;
    }
    try {
        DataverseRequest dataverseRequest;
        try {
            dataverseRequest = createDataverseRequest(findAuthenticatedUserOrDie());
        } catch (WrappedResponse wr) {
            return wr.getResponse();
        }
        if (parentIdtf == null) {
            parentIdtf = "root";
        }
        Dataverse owner = findDataverse(parentIdtf);
        if (owner == null) {
            if (createDV) {
                owner = importService.createDataverse(parentIdtf, dataverseRequest);
            } else {
                return error(Response.Status.NOT_FOUND, "Can't find dataverse with identifier='" + parentIdtf + "'");
            }
        }
        batchService.processFilePath(fileDir, parentIdtf, dataverseRequest, owner, importType, createDV);
    } catch (ImportException e) {
        return this.error(Response.Status.BAD_REQUEST, "Import Exception, " + e.getMessage());
    }
    return this.accepted();
}

Example 23 with DataverseRequest

use of edu.harvard.iq.dataverse.engine.command.DataverseRequest 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 24 with DataverseRequest

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

the class JsonParserTest method testIpGroupRoundTrip_singleIpv6Address.

@Test
public void testIpGroupRoundTrip_singleIpv6Address() {
    IpGroup original = new IpGroup();
    original.setDescription("Ip group description");
    original.setDisplayName("Test-ip-group");
    original.setId(42l);
    original.setPersistedGroupAlias("test-ip-group");
    original.setGroupProvider(new IpGroupProvider(null));
    original.add(IpAddressRange.make(IpAddress.valueOf("fe80::22c9:d0ff:fe48:ce61"), IpAddress.valueOf("fe80::22c9:d0ff:fe48:ce61")));
    JsonObject serialized = JsonPrinter.json(original).build();
    System.out.println(serialized.toString());
    IpGroup parsed = new JsonParser().parseIpGroup(serialized);
    assertEquals(original, parsed);
    assertTrue(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("fe80::22c9:d0ff:fe48:ce61"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("fe80::22c9:d0ff:fe48:ce60"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("fe80::22c9:d0ff:fe48:ce62"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("fe80::22c9:d0ff:fe47:ce61"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("fe80::22c9:d0af:fe48:ce61"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("fe79::22c9:d0ff:fe48:ce61"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("2.1.1.1"))));
}

Example 25 with DataverseRequest

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

the class JsonParserTest method testIpGroupRoundTrip_singleIpv4Address.

@Test
public void testIpGroupRoundTrip_singleIpv4Address() {
    IpGroup original = new IpGroup();
    original.setDescription("Ip group description");
    original.setDisplayName("Test-ip-group");
    original.setId(42l);
    original.setPersistedGroupAlias("test-ip-group");
    original.setGroupProvider(new IpGroupProvider(null));
    original.add(IpAddressRange.make(IpAddress.valueOf("1.1.1.1"), IpAddress.valueOf("1.1.1.1")));
    JsonObject serialized = JsonPrinter.json(original).build();
    System.out.println(serialized.toString());
    IpGroup parsed = new JsonParser().parseIpGroup(serialized);
    assertEquals(original, parsed);
    assertTrue(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("1.1.1.1"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("1.1.1.2"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("1.1.2.1"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("1.1.1.0"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("1.1.1.250"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("1.2.1.1"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("2.1.1.1"))));
    assertFalse(parsed.contains(new DataverseRequest(GuestUser.get(), IpAddress.valueOf("fe80::22c9:d0ff:fe48:ce61"))));
}