/*
Copyright (C) 2005-2012, by the President and Fellows of Harvard College.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Dataverse Network - A web application to share, preserve and analyze research data.
Developed at the Institute for Quantitative Social Science, Harvard University.
Version 3.0.
*/
package edu.harvard.iq.dvn.api.datadeposit;
import edu.harvard.iq.dvn.core.admin.VDCUser;
import edu.harvard.iq.dvn.core.study.EditStudyFilesService;
import edu.harvard.iq.dvn.core.study.EditStudyService;
import edu.harvard.iq.dvn.core.study.Study;
import edu.harvard.iq.dvn.core.study.StudyFile;
import edu.harvard.iq.dvn.core.study.StudyFileEditBean;
import edu.harvard.iq.dvn.core.study.StudyFileServiceLocal;
import edu.harvard.iq.dvn.core.study.StudyLock;
import edu.harvard.iq.dvn.core.study.StudyServiceLocal;
import edu.harvard.iq.dvn.core.study.TabularDataFile;
import edu.harvard.iq.dvn.core.util.FileUtil;
import edu.harvard.iq.dvn.core.vdc.VDC;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import javax.ejb.EJB;
import javax.ejb.EJBException;
import javax.inject.Inject;
import javax.naming.Context;
import javax.naming.InitialContext;
import javax.naming.NamingException;
import org.swordapp.server.AuthCredentials;
import org.swordapp.server.Deposit;
import org.swordapp.server.DepositReceipt;
import org.swordapp.server.MediaResource;
import org.swordapp.server.MediaResourceManager;
import org.swordapp.server.SwordAuthException;
import org.swordapp.server.SwordConfiguration;
import org.swordapp.server.SwordError;
import org.swordapp.server.SwordServerException;
import org.swordapp.server.UriRegistry;
@EJB(name = "editStudyFiles", beanInterface = edu.harvard.iq.dvn.core.study.EditStudyFilesService.class)
public class MediaResourceManagerImpl implements MediaResourceManager {
@EJB
StudyServiceLocal studyService;
@EJB
StudyFileServiceLocal studyFileService;
@Inject
SwordAuth swordAuth;
@Inject
UrlManager urlManager;
private static final Logger logger = Logger.getLogger(MediaResourceManagerImpl.class.getCanonicalName());
@Override
public MediaResource getMediaResourceRepresentation(String uri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
VDCUser vdcUser = swordAuth.auth(authCredentials);
urlManager.processUrl(uri);
String globalId = urlManager.getTargetIdentifier();
if (urlManager.getTargetType().equals("study") && globalId != null) {
EditStudyService editStudyService;
Context ctx;
try {
ctx = new InitialContext();
editStudyService = (EditStudyService) ctx.lookup("java:comp/env/editStudy");
} catch (NamingException ex) {
logger.info("problem looking up editStudyService");
throw new SwordServerException("problem looking up editStudyService");
}
logger.fine("looking up study with globalId " + globalId);
Study study = editStudyService.getStudyByGlobalId(globalId);
if (study != null) {
/**
* @todo: support this
*/
boolean getMediaResourceRepresentationSupported = false;
if (getMediaResourceRepresentationSupported) {
VDC dvThatOwnsStudy = study.getOwner();
if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
InputStream fixmeInputStream = new ByteArrayInputStream("FIXME: replace with zip of all study files".getBytes());
String contentType = "application/zip";
String packaging = UriRegistry.PACKAGE_SIMPLE_ZIP;
boolean isPackaged = true;
MediaResource mediaResource = new MediaResource(fixmeInputStream, contentType, packaging, isPackaged);
return mediaResource;
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to get a media resource representation of the study with global ID " + study.getGlobalId());
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Please use the Dataverse Network Data Sharing API instead");
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "couldn't find study with global ID of " + globalId);
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't dermine target type or identifier from URL: " + uri);
}
}
@Override
public DepositReceipt replaceMediaResource(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
/**
* @todo: Perhaps create a new version of a study here?
*
* "The server MUST effectively replace all the existing content in the
* item, although implementations may choose to provide versioning or
* some other mechanism for retaining the overwritten content." --
* http://swordapp.github.io/SWORDv2-Profile/SWORDProfile.html#protocoloperations_editingcontent_binary
*
* Also, if you enable this method, think about the SwordError currently
* being returned by replaceOrAddFiles with shouldReplace set to true
* and an empty zip uploaded. If no files are unzipped the user will see
* a error about this but the files will still be deleted!
*/
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Replacing the files of a study is not supported. Please delete and add files separately instead.");
}
@Override
public void deleteMediaResource(String uri, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
VDCUser vdcUser = swordAuth.auth(authCredentials);
urlManager.processUrl(uri);
String targetType = urlManager.getTargetType();
String fileId = urlManager.getTargetIdentifier();
if (targetType != null && fileId != null) {
if ("file".equals(targetType)) {
String fileIdString = urlManager.getTargetIdentifier();
if (fileIdString != null) {
Long fileIdLong;
try {
fileIdLong = Long.valueOf(fileIdString);
} catch (NumberFormatException ex) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "File id must be a number, not '" + fileIdString + "'. URL was: " + uri);
}
if (fileIdLong != null) {
logger.fine("preparing to delete file id " + fileIdLong);
StudyFile fileToDelete;
try {
fileToDelete = studyFileService.getStudyFile(fileIdLong);
} catch (EJBException ex) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id " + fileIdLong);
}
if (fileToDelete != null) {
Study study = fileToDelete.getStudy();
StudyLock studyLock = study.getStudyLock();
if (studyLock != null) {
String message = Util.getStudyLockMessage(studyLock, study.getGlobalId());
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, message);
}
String globalId = study.getGlobalId();
VDC dvThatOwnsFile = fileToDelete.getStudy().getOwner();
if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsFile)) {
EditStudyFilesService editStudyFilesService;
try {
Context ctx = new InitialContext();
editStudyFilesService = (EditStudyFilesService) ctx.lookup("java:comp/env/editStudyFiles");
} catch (NamingException ex) {
logger.info("problem looking up editStudyFilesService");
throw new SwordServerException("problem looking up editStudyFilesService");
}
editStudyFilesService.setStudyVersionByGlobalId(globalId);
// editStudyFilesService.findStudyFileEditBeanById() would be nice
List studyFileEditBeans = editStudyFilesService.getCurrentFiles();
for (Iterator it = studyFileEditBeans.iterator(); it.hasNext();) {
StudyFileEditBean studyFileEditBean = (StudyFileEditBean) it.next();
if (studyFileEditBean.getStudyFile().getId().equals(fileToDelete.getId())) {
logger.fine("marked for deletion: " + studyFileEditBean.getStudyFile().getFileName());
studyFileEditBean.setDeleteFlag(true);
} else {
logger.fine("not marked for deletion: " + studyFileEditBean.getStudyFile().getFileName());
}
}
editStudyFilesService.save(dvThatOwnsFile.getId(), vdcUser.getId());
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + vdcUser.getUserName() + " is not authorized to modify " + dvThatOwnsFile.getAlias());
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id " + fileIdLong + " from URL: " + uri);
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id in URL: " + uri);
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not file file to delete in URL: " + uri);
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported file type found in URL: " + uri);
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Target or identifer not specified in URL: " + uri);
}
}
@Override
public DepositReceipt addResource(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
boolean shouldReplace = false;
return replaceOrAddFiles(uri, deposit, authCredentials, swordConfiguration, shouldReplace);
}
DepositReceipt replaceOrAddFiles(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration, boolean shouldReplace) throws SwordError, SwordAuthException, SwordServerException {
VDCUser vdcUser = swordAuth.auth(authCredentials);
urlManager.processUrl(uri);
String globalId = urlManager.getTargetIdentifier();
if (urlManager.getTargetType().equals("study") && globalId != null) {
EditStudyService editStudyService;
Context ctx;
try {
ctx = new InitialContext();
editStudyService = (EditStudyService) ctx.lookup("java:comp/env/editStudy");
} catch (NamingException ex) {
logger.info("problem looking up editStudyService");
throw new SwordServerException("problem looking up editStudyService");
}
logger.fine("looking up study with globalId " + globalId);
Study study = editStudyService.getStudyByGlobalId(globalId);
if (study == null) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study with global ID of " + globalId);
}
StudyLock studyLock = study.getStudyLock();
if (studyLock != null) {
String message = Util.getStudyLockMessage(studyLock, study.getGlobalId());
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, message);
}
Long studyId;
try {
studyId = study.getId();
} catch (NullPointerException ex) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "couldn't find study with global ID of " + globalId);
}
VDC dvThatOwnsStudy = study.getOwner();
if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
editStudyService.setStudyVersion(studyId);
editStudyService.save(dvThatOwnsStudy.getId(), vdcUser.getId());
EditStudyFilesService editStudyFilesService;
try {
editStudyFilesService = (EditStudyFilesService) ctx.lookup("java:comp/env/editStudyFiles");
} catch (NamingException ex) {
logger.info("problem looking up editStudyFilesService");
throw new SwordServerException("problem looking up editStudyFilesService");
}
editStudyFilesService.setStudyVersionByGlobalId(globalId);
List studyFileEditBeans = editStudyFilesService.getCurrentFiles();
List<String> exisitingFilenames = new ArrayList<String>();
for (Iterator it = studyFileEditBeans.iterator(); it.hasNext();) {
StudyFileEditBean studyFileEditBean = (StudyFileEditBean) it.next();
if (shouldReplace) {
studyFileEditBean.setDeleteFlag(true);
logger.fine("marked for deletion: " + studyFileEditBean.getStudyFile().getFileName());
} else {
String filename = studyFileEditBean.getStudyFile().getFileName();
exisitingFilenames.add(filename);
}
}
editStudyFilesService.save(dvThatOwnsStudy.getId(), vdcUser.getId());
if (!deposit.getPackaging().equals(UriRegistry.PACKAGE_SIMPLE_ZIP)) {
throw new SwordError(UriRegistry.ERROR_CONTENT, 415, "Package format " + UriRegistry.PACKAGE_SIMPLE_ZIP + " is required but format specified in 'Packaging' HTTP header was " + deposit.getPackaging());
}
// Right now we are only supporting UriRegistry.PACKAGE_SIMPLE_ZIP but
// in the future maybe we'll support other formats? Rdata files? Stata files?
// That's what the uploadDir was going to be for, but for now it's commented out
//
// String uploadDirString;
// File uploadDir;
String importDirString;
File importDir;
String swordTempDirString = swordConfiguration.getTempDirectory();
if (swordTempDirString == null) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine temp directory");
} else {
// uploadDirString = swordTempDirString + File.separator + "uploads" + File.separator + study.getId().toString();
// uploadDir = new File(uploadDirString);
// if (!uploadDir.exists()) {
// if (!uploadDir.mkdirs()) {
// logger.info("couldn't create directory: " + uploadDir.getAbsolutePath());
// throw new SwordServerException("couldn't create upload directory");
// }
// }
importDirString = swordTempDirString + File.separator + "import" + File.separator + study.getId().toString();
importDir = new File(importDirString);
if (!importDir.exists()) {
if (!importDir.mkdirs()) {
logger.info("couldn't create directory: " + importDir.getAbsolutePath());
throw new SwordServerException("couldn't create import directory");
}
}
}
// the first character of the filename is truncated with the official jar
// so we use include the bug fix at https://github.com/IQSS/swordv2-java-server-library/commit/aeaef83
// and use this jar: https://build.hmdc.harvard.edu:8443/job/swordv2-java-server-library-iqss/2/
String uploadedZipFilename = deposit.getFilename();
ZipInputStream ziStream = new ZipInputStream(deposit.getInputStream());
ZipEntry zEntry;
FileOutputStream tempOutStream = null;
List<StudyFileEditBean> fbList = new ArrayList<StudyFileEditBean>();
try {
// copied from createStudyFilesFromZip in AddFilesPage
while ((zEntry = ziStream.getNextEntry()) != null) {
// Note that some zip entries may be directories - we
// simply skip them:
if (!zEntry.isDirectory()) {
String fileEntryName = zEntry.getName();
logger.fine("file found: " + fileEntryName);
String dirName = null;
String finalFileName = null;
int ind = fileEntryName.lastIndexOf('/');
if (ind > -1) {
finalFileName = fileEntryName.substring(ind + 1);
if (ind > 0) {
dirName = fileEntryName.substring(0, ind);
dirName = dirName.replace('/', '-');
}
} else {
finalFileName = fileEntryName;
}
if (".DS_Store".equals(finalFileName)) {
continue;
}
// http://superuser.com/questions/212896/is-there-any-way-to-prevent-a-mac-from-creating-dot-underscore-files
if (finalFileName.startsWith("._")) {
continue;
}
File tempUploadedFile = new File(importDir, finalFileName);
tempOutStream = new FileOutputStream(tempUploadedFile);
byte[] dataBuffer = new byte[8192];
int i = 0;
while ((i = ziStream.read(dataBuffer)) > 0) {
tempOutStream.write(dataBuffer, 0, i);
tempOutStream.flush();
}
tempOutStream.close();
// We now have the unzipped file saved in the upload directory;
// zero-length dta files (for example) are skipped during zip
// upload in the GUI, so we'll skip them here as well
if (tempUploadedFile.length() != 0) {
StudyFileEditBean tempFileBean = new StudyFileEditBean(tempUploadedFile, studyService.generateFileSystemNameSequence(), study);
tempFileBean.setSizeFormatted(tempUploadedFile.length());
String finalFileNameAfterReplace = finalFileName;
if (tempFileBean.getStudyFile() instanceof TabularDataFile) {
// predict what the tabular file name will be
finalFileNameAfterReplace = FileUtil.replaceExtension(finalFileName);
}
validateFileName(exisitingFilenames, finalFileNameAfterReplace, study);
// And, if this file was in a legit (non-null) directory,
// we'll use its name as the file category:
if (dirName != null) {
tempFileBean.getFileMetadata().setCategory(dirName);
}
fbList.add(tempFileBean);
}
} else {
logger.fine("directory found: " + zEntry.getName());
}
}
} catch (IOException ex) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Problem with file: " + uploadedZipFilename);
} finally {
// if (!uploadDir.delete()) {
// logger.fine("Unable to delete " + uploadDir.getAbsolutePath());
// }
}
if (fbList.size() > 0) {
StudyFileServiceLocal studyFileService;
try {
studyFileService = (StudyFileServiceLocal) ctx.lookup("java:comp/env/studyFileService");
} catch (NamingException ex) {
logger.info("problem looking up studyFileService");
throw new SwordServerException("problem looking up studyFileService");
}
try {
studyFileService.addFiles(study.getLatestVersion(), fbList, vdcUser);
} catch (EJBException ex) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to add file(s) to study: " + ex.getMessage());
}
ReceiptGenerator receiptGenerator = new ReceiptGenerator();
String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
DepositReceipt depositReceipt = receiptGenerator.createReceipt(baseUrl, study);
return depositReceipt;
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Problem with zip file '" + uploadedZipFilename + "'. Number of files unzipped: " + fbList.size());
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to modify study with global ID " + study.getGlobalId());
}
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine target type or identifier from URL: " + uri);
}
}
// copied from AddFilesPage
private void validateFileName(List<String> existingFilenames, String fileName, Study study) throws SwordError {
if (fileName.contains("\\")
|| fileName.contains("/")
|| fileName.contains(":")
|| fileName.contains("*")
|| fileName.contains("?")
|| fileName.contains("\"")
|| fileName.contains("<")
|| fileName.contains(">")
|| fileName.contains("|")
|| fileName.contains(";")
|| fileName.contains("#")) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid File Name - cannot contain any of the following characters: \\ / : * ? \" < > | ; . Filename was '" + fileName + "'");
}
if (existingFilenames.contains(fileName)) {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Filename " + fileName + " already exists in study " + study.getGlobalId());
}
}
}