Java tutorial
/* 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. */ /* * StudyServiceBean.java * * Created on August 14, 2006, 11:47 AM * * To change this template, choose Tools | Template Manager * and open the template in the editor. */ package edu.harvard.iq.dvn.core.study; import edu.harvard.iq.dvn.core.admin.RoleServiceLocal; import edu.harvard.iq.dvn.core.admin.UserServiceLocal; import edu.harvard.iq.dvn.core.admin.VDCRole; import edu.harvard.iq.dvn.core.admin.VDCUser; import edu.harvard.iq.dvn.core.ddi.DDIServiceLocal; import edu.harvard.iq.dvn.core.doi.DOIEZIdServiceLocal; import edu.harvard.iq.dvn.core.gnrs.GNRSServiceLocal; import edu.harvard.iq.dvn.core.harvest.HarvestFormatType; import edu.harvard.iq.dvn.core.harvest.HarvestStudyServiceLocal; import edu.harvard.iq.dvn.core.index.IndexServiceLocal; import edu.harvard.iq.dvn.core.mail.MailServiceLocal; import edu.harvard.iq.dvn.core.study.StudyVersion.VersionState; import edu.harvard.iq.dvn.core.util.FileUtil; import edu.harvard.iq.dvn.core.util.StringUtil; import edu.harvard.iq.dvn.core.util.TwitterUtil; import edu.harvard.iq.dvn.core.vdc.*; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.FilenameFilter; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.io.PrintWriter; import java.io.BufferedReader; import java.io.InputStreamReader; import java.net.MalformedURLException; import java.net.URL; import java.sql.Timestamp; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Calendar; import java.util.Collection; import java.util.Date; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.logging.FileHandler; import java.util.logging.Level; import java.util.logging.Logger; import javax.annotation.Resource; import javax.ejb.EJB; import javax.ejb.EJBException; import javax.ejb.Stateless; import javax.ejb.TransactionAttribute; import javax.ejb.TransactionAttributeType; import javax.jms.Queue; import javax.jms.QueueConnectionFactory; import javax.persistence.EntityManager; import javax.persistence.PersistenceContext; import javax.persistence.Query; import javax.xml.bind.JAXBException; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerFactory; import javax.xml.transform.stream.StreamResult; import javax.xml.transform.stream.StreamSource; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.RandomStringUtils; /** * * @author Ellen Kraffmiller */ @Stateless public class StudyServiceBean implements edu.harvard.iq.dvn.core.study.StudyServiceLocal, java.io.Serializable { @PersistenceContext(unitName = "VDCNet-ejbPU") EntityManager em; @Resource(mappedName = "jms/DSBIngest") Queue queue; @Resource(mappedName = "jms/DSBQueueConnectionFactory") QueueConnectionFactory factory; @EJB GNRSServiceLocal gnrsService; @EJB VDCNetworkServiceLocal vdcNetworkService; @EJB DDIServiceLocal ddiService; @EJB UserServiceLocal userService; @EJB IndexServiceLocal indexService; @EJB VariableServiceLocal variableService; @EJB StudyExporterFactoryLocal studyExporterFactory; @EJB MailServiceLocal mailService; private static final Logger logger = Logger.getLogger("edu.harvard.iq.dvn.core.study.StudyServiceBean"); private static final SimpleDateFormat exportLogFormatter = new SimpleDateFormat("yyyy-MM-dd'T'HH-mm-ss"); @EJB StudyServiceLocal studyService; // used to force new transaction during import @EJB HarvestStudyServiceLocal harvestStudyService; @EJB VDCServiceLocal vdcService; @EJB StudyFileServiceLocal studyFileService; @EJB RoleServiceLocal roleService; @EJB GuestBookResponseServiceBean guestBookResponseServiceBean; @EJB DOIEZIdServiceLocal doiEZIdServiceLocal; /** * Creates a new instance of StudyServiceBean */ public StudyServiceBean() { } public void updateStudy(Study detachedStudy) { em.merge(detachedStudy); } public void updateStudyVersion(StudyVersion studyVersion) { em.merge(studyVersion); } public void setReadyForReview(Long studyId) { setReadyForReview(studyId, null); } public void setReadyForReview(Long studyId, String versionNote) { Study study = em.find(Study.class, studyId); StudyVersion sv = study.getLatestVersion(); setReadyForReview(sv, versionNote); } public void setReadyForReview(StudyVersion sv) { setReadyForReview(sv, null); } public void setReadyForReview(StudyVersion sv, String versionNote) { sv.setVersionState(StudyVersion.VersionState.IN_REVIEW); if (versionNote != null) { sv.setVersionNote(versionNote); } Study study = sv.getStudy(); VDCUser user = study.getCreator(); // If the user adding the study is a Contributor, send notification to all Curators in this VDC // and send an email to the Contributor about the status of the study if (user.getVDCRole(study.getOwner()) != null && user.getVDCRole(study.getOwner()).getRole().getName().equals(RoleServiceLocal.CONTRIBUTOR)) { mailService.sendStudyInReviewNotification(user.getEmail(), sv.getMetadata().getTitle()); // Notify all curators and admins that study is in review for (Iterator it = study.getOwner().getVdcRoles().iterator(); it.hasNext();) { VDCRole elem = (VDCRole) it.next(); if (elem.getRole().getName().equals(RoleServiceLocal.CURATOR) || elem.getRole().getName().equals(RoleServiceLocal.ADMIN)) { mailService.sendStudyAddedCuratorNotification(elem.getVdcUser().getEmail(), user.getUserName(), sv.getMetadata().getTitle(), study.getOwner().getName()); } } } } public void saveVersionNote(Long studyId, Long versionNumber, String newVersionNote) { Study study = em.find(Study.class, studyId); StudyVersion sv = null; if (study != null) { if (versionNumber != null) { sv = study.getStudyVersionByNumber(versionNumber); } else { sv = study.getLatestVersion(); } if (sv != null) { sv.setVersionNote(newVersionNote); } } } public void saveVersionNote(Long studyVersionId, String newVersionNote) { StudyVersion sv = em.find(StudyVersion.class, studyVersionId); if (sv != null) { sv.setVersionNote(newVersionNote); } } public void setReleased(Long studyId) { setReleased(studyId, null); } public void setReleased(Long studyId, String versionNote) { Study study = em.find(Study.class, studyId); StudyVersion latestVersion = study.getLatestVersion(); if (!latestVersion.isWorkingCopy()) { throw new EJBException( "Cannot release latestVersion, incorrect state: " + latestVersion.getVersionState()); } Date releaseDate = new Date(); // Archive the previously released or deaccessioned version StudyVersion releasedVersion = study.getReleasedVersion(); if (releasedVersion != null) { releasedVersion.setVersionState(StudyVersion.VersionState.ARCHIVED); releasedVersion.setArchiveTime(releaseDate); releasedVersion.setArchiveNote("Replaced by version " + latestVersion.getVersionNumber()); } else { StudyVersion deaccessionedVersion = study.getDeaccessionedVersion(); if (deaccessionedVersion != null) { deaccessionedVersion.setVersionState(StudyVersion.VersionState.ARCHIVED); } } latestVersion.setVersionState(StudyVersion.VersionState.RELEASED); latestVersion.setReleaseTime(releaseDate); if (versionNote != null) { latestVersion.setVersionNote(versionNote); } VDCRole studyCreatorRole = study.getCreator().getVDCRole(study.getOwner()); if (studyCreatorRole != null && studyCreatorRole.getRole().getName().equals(RoleServiceLocal.CONTRIBUTOR)) { mailService.sendStudyReleasedNotification(study.getCreator().getEmail(), latestVersion.getMetadata().getTitle(), study.getOwner().getName()); } //if DOI then publicize status if (study.getProtocol().equals("doi")) { doiEZIdServiceLocal.publicizeIdentifier(study); } // tweet release of study TwitterCredentials tc = study.getOwner().getTwitterCredentials(); if (tc != null) { String message = latestVersion.getVersionNumber() == 1 ? "New study released: " : "Study updated: "; message += latestVersion.getMetadata().getTitle(); URL url = new GlobalId(latestVersion.getStudy().getProtocol(), latestVersion.getStudy().getAuthority(), latestVersion.getStudy().getStudyId()).toURL(); TwitterUtil.tweet(tc, message, url); } // finally, re-index the study metadata: indexService.updateStudy(studyId); } public void deaccessionStudy(StudyVersion sv) { sv.setVersionState(StudyVersion.VersionState.DEACCESSIONED); sv.setArchiveTime(new Date()); em.merge(sv); indexService.deleteStudy(sv.getStudy().getId()); } public Study getStudyByHarvestInfo(VDC dataverse, String harvestIdentifier) { String queryStr = "SELECT s FROM Study s WHERE s.owner.id = '" + dataverse.getId() + "' and s.harvestIdentifier = '" + harvestIdentifier + "'"; Query query = em.createQuery(queryStr); List resultList = query.getResultList(); Study study = null; if (resultList.size() > 1) { throw new EJBException("More than one study found with owner_id= " + dataverse.getId() + " and harvestIdentifier= " + harvestIdentifier); } if (resultList.size() == 1) { study = (Study) resultList.get(0); } return study; } public void deleteStudy(Long studyId) { deleteStudy(studyId, true); } public void deleteStudyList(List<Long> studyIds) { indexService.deleteIndexList(studyIds); for (Long studyId : studyIds) { studyService.deleteStudyInNewTransaction(studyId, false); } } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void deleteStudyInNewTransaction(Long studyId, boolean deleteFromIndex) { deleteStudy(studyId, deleteFromIndex); } public void deleteStudy(Long studyId, boolean deleteFromIndex) { long start = new Date().getTime(); //System.out.println("DEBUG: 0\t - deleteStudy - BEGIN"); Study study = em.find(Study.class, studyId); if (study == null) { return; } //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - remove from collections"); for (Iterator<VDCCollection> it = study.getStudyColls().iterator(); it.hasNext();) { VDCCollection elem = it.next(); elem.getStudies().remove(study); } //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - delete data variables"); studyService.deleteDataVariables(study.getId()); //force cascade delete of deleteGuestBookResponses(study.getId()); //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - delete relationships"); study.getAllowedGroups().clear(); study.getAllowedUsers().clear(); for (Iterator<StudyFile> it = study.getStudyFiles().iterator(); it.hasNext();) { StudyFile elem = it.next(); elem.getAllowedGroups().clear(); elem.getAllowedUsers().clear(); elem.clearData(); } //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - delete physical files"); File studyDir = new File(FileUtil.getStudyFileDir() + File.separator + study.getAuthority() + File.separator + study.getStudyId()); if (studyDir.exists()) { File[] files = studyDir.listFiles(); if (files != null) { for (int i = 0; i < files.length; i++) { files[i].delete(); } } studyDir.delete(); } // remove from HarvestStudy table //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - delete from HarvestStudy"); harvestStudyService.markHarvestStudiesAsRemoved( harvestStudyService.findHarvestStudiesByGlobalId(study.getGlobalId()), new Date()); //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - delete from DB and gnrs"); em.remove(study); //ADD DOI logic if (study.getProtocol().equals("hdl")) { gnrsService.delete(study.getAuthority(), study.getStudyId()); } if (study.getProtocol().equals("doi")) { doiEZIdServiceLocal.deleteIdentifier(study); } //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - delete from Index"); if (deleteFromIndex) { indexService.deleteStudy(studyId); } //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - right before flush"); em.flush(); // Force study deletion to the database, for cases when we are calling this before deleting the owning Dataverse //System.out.println("DEBUG: " + (new Date().getTime() - start) + "\t - deleteStudy - FINISH"); logger.log(Level.INFO, "Successfully deleted Study " + studyId + "!"); } public void destroyWorkingCopyVersion(Long studyVersionId) { long start = new Date().getTime(); StudyVersion studyVersion = em.find(StudyVersion.class, studyVersionId); if (studyVersion == null) { return; } // We need to determine if there are already released versions of this // study. If so, we can destroy this version and leave the older versions // and the study intact. However, if this working version is the first // version of the study, we have to destroy the study as well -- otherwise // we'll have that version-less study shell left behind, which can mess up // ManageStudies page and possibly other partds of the system. Long studyId = null; if (studyVersion.getStudy() != null) { studyId = studyVersion.getStudy().getId(); } if (studyId != null) { if (getStudyVersion(studyId, null) == null) { deleteStudy(studyId, true); } else { // We need to make sure to delete all the Study Files that would // otherwise become "orphans" -- meaning, the files that were // only added in this working version, that are not part of // the released version of the study. // // I'm going to simply retrieve the lists of file metadata // for both versions, ordered by file Id, and delete the "tail" // of the working version list. StudyVersion releasedVersion = getStudyVersion(studyId, null); List<FileMetadata> fileMetadataList = new ArrayList<FileMetadata>(); List<FileMetadata> fileMetadataListReleased = new ArrayList<FileMetadata>(); fileMetadataList = studyFileService.getFilesByStudyVersionOrderedById(studyVersion.getId()); fileMetadataListReleased = studyFileService .getFilesByStudyVersionOrderedById(releasedVersion.getId()); int i = fileMetadataList.size(); if (i > 0) { FileMetadata fm1 = fileMetadataList.get(i - 1); Long lastReleasedStudyFileId = new Long(0); if (fileMetadataListReleased.size() > 0) { lastReleasedStudyFileId = fileMetadataListReleased.get(fileMetadataListReleased.size() - 1) .getStudyFile().getId(); } while (i > 0 && fm1 != null && fm1.getStudyFile().getId().compareTo(lastReleasedStudyFileId) > 0) { StudyFile studyFile = fm1.getStudyFile(); String fileSystemLocation = studyFile.getFileSystemLocation(); if (fileSystemLocation != null) { File fileToDelete = new File(fileSystemLocation); // For subsettable files, also remove the preserved // originals and cached format conversions: if (studyFile.isSubsettable()) { if (fileToDelete != null) { // original: File originalDataFile = new File(fileToDelete.getParent(), "_" + studyFile.getFileSystemName()); if (originalDataFile != null) { originalDataFile.delete(); } // cached alternative formats (including .RData file // that we create for Network Data files): File fileDir = new File(fileToDelete.getParent()); File[] formatConvertedFiles = fileDir .listFiles(new ConvertedFilenamesFilter(studyFile.getFileSystemName())); for (int j = 0; j < formatConvertedFiles.length; j++) { formatConvertedFiles[j].delete(); } } } // End of subsettable file special case; // For image files, we may have thumbnail files // cached on disk as well: if (studyFile.getFileType().substring(0, 6).equalsIgnoreCase("image/")) { File imageThumbnailFile = new File(fileSystemLocation + ".thumb"); if (imageThumbnailFile != null) { imageThumbnailFile.delete(); } } // End of image file special case. // And now delete the file itself: if (fileToDelete != null) { fileToDelete.delete(); } } i--; if (i > 0) { fm1 = fileMetadataList.get(i - 1); } } } em.remove(studyVersion); em.flush(); // Force deletion to the database, for cases when we are calling this before deleting the owning Dataverse logger.log(Level.INFO, "Successfully deleted StudyVersion " + studyVersionId + "!"); } } } /* these delete queires seem to take too long, so we are currently trying testing something different for deleting variables private static final String DELETE_VARIABLE_CATEGORIES = " delete from variablecategory where datavariable_id in ( " + "select dv.id from study s, filecategory fc, studyfile sf, datatable dt, datavariable dv" + " where s.id= ? " + " and s.id = fc.study_id " + " and fc.id= sf.filecategory_id " + " and sf.id=dt.studyfile_id " + " and dt.id= dv.datatable_id )"; private static final String DELETE_SUMMARY_STATISTICS = " delete from summarystatistic where datavariable_id in ( " + "select dv.id from study s, filecategory fc, studyfile sf, datatable dt, datavariable dv" + " where s.id= ? " + " and s.id = fc.study_id " + " and fc.id= sf.filecategory_id " + " and sf.id=dt.studyfile_id " + " and dt.id= dv.datatable_id )"; private static final String DELETE_VARIABLE_RANGE_ITEMS = " delete from variablerangeitem where datavariable_id in ( " + "select dv.id from study s, filecategory fc, studyfile sf, datatable dt, datavariable dv" + " where s.id= ? " + " and s.id = fc.study_id " + " and fc.id= sf.filecategory_id " + " and sf.id=dt.studyfile_id " + " and dt.id= dv.datatable_id )"; private static final String DELETE_VARIABLE_RANGES = " delete from variablerange where datavariable_id in ( " + "select dv.id from study s, filecategory fc, studyfile sf, datatable dt, datavariable dv" + " where s.id= ? " + " and s.id = fc.study_id " + " and fc.id= sf.filecategory_id " + " and sf.id=dt.studyfile_id " + " and dt.id= dv.datatable_id )"; private static final String DELETE_DATA_VARIABLES = " delete from datavariable where id in ( " + "select dv.id from study s, filecategory fc, studyfile sf, datatable dt, datavariable dv" + " where s.id= ? " + " and s.id = fc.study_id " + " and fc.id= sf.filecategory_id " + " and sf.id=dt.studyfile_id " + " and dt.id= dv.datatable_id )"; private static final String SELECT_DATAVARIABLE_IDS = "select dv.id from study s, filecategory fc, studyfile sf, datatable dt, datavariable dv" + " where s.id= ? " + " and s.id = fc.study_id " + " and fc.id= sf.filecategory_id " + " and sf.id=dt.studyfile_id " + " and dt.id= dv.datatable_id "; */ private static final String DELETE_VARIABLE_CATEGORIES_PREFIX = "delete from variablecategory where datavariable_id in "; private static final String DELETE_SUMMARY_STATISTICS_PREFIX = " delete from summarystatistic where datavariable_id in "; private static final String DELETE_VARIABLE_RANGE_ITEMS_PREFIX = " delete from variablerangeitem where datavariable_id in "; private static final String DELETE_VARIABLE_RANGES_PREFIX = "delete from variablerange where datavariable_id in "; private static final String DELETE_DATA_VARIABLES_PREFIX = "delete from datavariable where id in "; private static final String DELETE_DATA_VARIABLE_MAPPINGS_PREFIX = "delete from datavariablemapping where datavariable_id in "; private static final String SELECT_DATATABLE_IDS = "select dt.id from study s, studyfile sf, datatable dt " + "where s.id= ? " + "and s.id = sf.study_id " + "and sf.id=dt.studyfile_id "; private static final String SELECT_DATAVARIABLE_IDS_PREFIX = "select dv.id from datavariable dv where dv.datatable_id in "; public void deleteDataVariables(Long studyId) { // because the delte was taking a while, we tested spearate queires to get the info and it seemed to work much // faster, so now this delete goes in steps // step 1: determine dtIds List dtIdList = new ArrayList(); Query query = em.createNativeQuery(SELECT_DATATABLE_IDS).setParameter(1, studyId); for (Object currentResult : query.getResultList()) { dtIdList.add(new Long(((Integer) currentResult).longValue())); } if (!dtIdList.isEmpty()) { // step 2: determine variables List varList = new ArrayList(); query = em.createNativeQuery( SELECT_DATAVARIABLE_IDS_PREFIX + "(" + generateTempTableString(dtIdList) + ")"); for (Object currentResult : query.getResultList()) { varList.add(new Long(((Integer) currentResult).longValue())); } if (!varList.isEmpty()) { // step 3: delete! String varString = "(" + generateTempTableString(varList) + ")"; em.createNativeQuery(DELETE_VARIABLE_CATEGORIES_PREFIX + varString).executeUpdate(); em.createNativeQuery(DELETE_SUMMARY_STATISTICS_PREFIX + varString).executeUpdate(); em.createNativeQuery(DELETE_VARIABLE_RANGE_ITEMS_PREFIX + varString).executeUpdate(); em.createNativeQuery(DELETE_VARIABLE_RANGES_PREFIX + varString).executeUpdate(); em.createNativeQuery(DELETE_DATA_VARIABLE_MAPPINGS_PREFIX + varString).executeUpdate(); em.createNativeQuery(DELETE_DATA_VARIABLES_PREFIX + varString).executeUpdate(); } } //em.createNativeQuery(DELETE_VARIABLE_CATEGORIES).setParameter(1, studyId).executeUpdate(); //em.createNativeQuery(DELETE_SUMMARY_STATISTICS).setParameter(1, studyId).executeUpdate(); //em.createNativeQuery(DELETE_VARIABLE_RANGE_ITEMS).setParameter(1, studyId).executeUpdate(); //em.createNativeQuery(DELETE_VARIABLE_RANGES).setParameter(1, studyId).executeUpdate(); //em.createNativeQuery(DELETE_DATA_VARIABLES).setParameter(1, studyId).executeUpdate(); } private static final String DELETE_CUSTOMQUESTIONRESPONSE_PREFIX = "delete from customquestionresponse where guestbookresponse_id in "; private static final String DELETE_GUESTBOOKRESPONSE_PREFIX = "delete from guestbookresponse where id in "; private static final String SELECT_GUESTBOOK_RESPONSE_IDS = "select gbr.id from study s, guestbookresponse gbr " + "where s.id= ? " + "and s.id = gbr.study_id "; public void deleteGuestBookResponses(Long studyId) { // because the delte was taking a while, we tested spearate queires to get the info and it seemed to work much // faster, so now this delete goes in steps // step 1: determine dtIds List gbrIdList = new ArrayList(); Query query = em.createNativeQuery(SELECT_GUESTBOOK_RESPONSE_IDS).setParameter(1, studyId); for (Object currentResult : query.getResultList()) { gbrIdList.add(new Long(((Integer) currentResult).longValue())); } if (!gbrIdList.isEmpty()) { // step 2: determine variables String varString = "(" + generateTempTableString(gbrIdList) + ")"; em.createNativeQuery(DELETE_CUSTOMQUESTIONRESPONSE_PREFIX + varString).executeUpdate(); em.createNativeQuery(DELETE_GUESTBOOKRESPONSE_PREFIX + varString).executeUpdate(); } } /** * Gets Study without any of its dependent objects * */ public Study getStudy(Long studyId) { Study study = em.find(Study.class, studyId); if (study == null) { throw new IllegalArgumentException("Unknown studyId: " + studyId); } return study; } /** * Gets Study and dependent objects based on Map parameter; * Should only be used for studies with Released versions * used by studyListingPage * */ @TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED) public Study getStudyForSearch(Long studyId, Map studyFields) { Study study = em.find(Study.class, studyId); if (study == null) { throw new IllegalArgumentException("Unknown studyId: " + studyId); } Metadata metadata = null; if (study.getReleasedVersion() != null) { metadata = study.getReleasedVersion().getMetadata(); } else { throw new IllegalArgumentException("No released version available for this study: " + studyId); } if (studyFields != null) { for (Object studyField : studyFields.keySet()) { String fieldName = (String) studyField; if ("authorName".equals(fieldName)) { for (Iterator<StudyAuthor> it = metadata.getStudyAuthors().iterator(); it.hasNext();) { StudyAuthor elem = it.next(); elem.getId(); } } else if ("abstractText".equals(fieldName)) { for (Iterator<StudyAbstract> it = metadata.getStudyAbstracts().iterator(); it.hasNext();) { StudyAbstract elem = it.next(); elem.getId(); } } else if ("producerName".equals(fieldName)) { for (Iterator<StudyProducer> it = metadata.getStudyProducers().iterator(); it.hasNext();) { StudyProducer elem = it.next(); elem.getId(); } } else if ("distributorName".equals(fieldName)) { for (Iterator<StudyDistributor> it = metadata.getStudyDistributors().iterator(); it .hasNext();) { StudyDistributor elem = it.next(); elem.getId(); } } else if ("relatedStudies".equals(fieldName)) { for (Iterator<StudyRelStudy> it = metadata.getStudyRelStudies().iterator(); it.hasNext();) { StudyRelStudy elem = it.next(); elem.getId(); } } else if ("relatedMaterial".equals(fieldName)) { for (Iterator<StudyRelMaterial> it = metadata.getStudyRelMaterials().iterator(); it .hasNext();) { StudyRelMaterial elem = it.next(); elem.getId(); } } else if ("relatedPublications".equals(fieldName)) { for (Iterator<StudyRelPublication> it = metadata.getStudyRelPublications().iterator(); it .hasNext();) { StudyRelPublication elem = it.next(); elem.getId(); } } } } return study; } public List getStudies() { String query = "SELECT s FROM Study s ORDER BY s.id"; return (List) em.createQuery(query).getResultList(); } public List getStudiesByIdRange(long begin, long end) { String query = "SELECT s FROM Study s WHERE s.id > " + begin + " AND s.id < " + end + " ORDER BY s.id"; logger.info("query: " + query); try { return (List) em.createQuery(query).getResultList(); } catch (Exception ex) { return null; } } public List getRecentStudies(Long vdcId, int numResults) { String query = "SELECT s FROM Study s " + "ORDER BY s.createTime desc"; if (vdcId != null) { query = "SELECT s FROM Study s WHERE s.owner.id = " + vdcId + " ORDER BY s.createTime desc"; } if (numResults == -1) { return (List) em.createQuery(query).getResultList(); } else { return (List) em.createQuery(query).setMaxResults(numResults).getResultList(); } } public List getRecentlyReleasedStudyIds(Long vdcId, Long vdcNetworkId, int numResults) { String linkedStudyClause = ""; String networkClause = ""; if (vdcNetworkId != null && !vdcNetworkId.equals(vdcNetworkService.findRootNetwork().getId())) { networkClause = " and v.vdcnetwork_id = " + vdcNetworkId + " "; VDCNetwork vdcNetwork = vdcNetworkService.findById(vdcNetworkId); List<Study> linkedStudys = (List) vdcNetwork.getLinkedStudies(); List<Long> studyIdList = new ArrayList<Long>(); for (Study study : linkedStudys) { studyIdList.add(study.getId()); } if (studyIdList != null && studyIdList.size() > 0) { String studyIds = generateTempTableString(studyIdList); linkedStudyClause = " or sv.study_id in (" + studyIds + ") "; } } String queryStr = " SELECT sv.study_id FROM StudyVersion sv where sv.versionstate = " + "'" + StudyVersion.VersionState.RELEASED + "'" + " and (sv.study_id in ( " + " select s.id FROM VDC v, Study s, StudyVersion sv where s.id = sv.study_id and sv.versionstate = " + "'" + StudyVersion.VersionState.RELEASED + "'" + " and s.owner_id = v.id and v.restricted = false " + networkClause + ") " + linkedStudyClause + ") ORDER BY sv.releaseTime desc"; if (vdcId != null) { queryStr = "SELECT s.id FROM Study s, StudyVersion sv where s.id = sv.study_id " + " and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + " and s.owner_id = " + vdcId + " ORDER BY sv.releaseTime desc"; } //System.out.print("release data query " + queryStr); Query query = em.createNativeQuery(queryStr); List<Long> returnList = new ArrayList<Long>(); if (numResults == -1) { for (Object currentResult : query.getResultList()) { if (currentResult instanceof Integer) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } else { returnList.add(new Long(((Long) currentResult).longValue())); } } } else { int i = 0; for (Object currentResult : query.getResultList()) { i++; if (i > numResults) { break; } else { if (currentResult instanceof Integer) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } else { returnList.add(new Long(((Long) currentResult).longValue())); } } } } return returnList; } public List getMostDownloadedStudyIds(Long vdcId, Long vdcNetworkId, int numResults) { String dataverseClause = ""; if (vdcId != null) { dataverseClause = " and s.owner_id = " + vdcId + " "; } String linkedStudyClause = ""; String networkClause = ""; if (vdcNetworkId != null && !vdcNetworkId.equals(vdcNetworkService.findRootNetwork().getId())) { networkClause = " and v.vdcnetwork_id = " + vdcNetworkId + " "; VDCNetwork vdcNetwork = vdcNetworkService.findById(vdcNetworkId); List<Study> linkedStudys = (List) vdcNetwork.getLinkedStudies(); List<Long> studyIdList = new ArrayList<Long>(); for (Study study : linkedStudys) { studyIdList.add(study.getId()); } if (studyIdList != null && studyIdList.size() > 0) { String studyIds = generateTempTableString(studyIdList); linkedStudyClause = " or s.id in (" + studyIds + ") "; } } String queryStr = "select s.id " + "from Study s " + "left outer JOIN StudyFileActivity sfa on s.id = sfa.study_id " + "where s.id in ( select s.id from Study s, VDC v, StudyVersion sv " + " where s.id = sv.study_id " + " and s.owner_id = v.id " + " and v.restricted = false " + " and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + dataverseClause + networkClause + ")" + linkedStudyClause + " group by s.id " + " order by " + "(CASE WHEN sum(downloadcount) is null THEN -1 ELSE sum(downloadcount) END) desc"; //System.out.print("Download count query " + queryStr); Query query = em.createNativeQuery(queryStr); List<Long> returnList = new ArrayList<Long>(); if (numResults == -1) { for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } } else { int i = 0; for (Object currentResult : query.getResultList()) { i++; if (i > numResults) { break; } else { returnList.add(new Long(((Integer) currentResult).longValue())); } } } return returnList; } public List<Long> getStudyIdsForExport() { String queryStr = "select s.id from study s, studyversion sv where s.id = sv.study_id and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "' and s.isharvested='false' and (sv.releasetime > s.lastexporttime or s.lastexporttime is null)"; Query query = em.createNativeQuery(queryStr); List<Long> returnList = new ArrayList<Long>(); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } return returnList; } public List<Long> getAllStudyIds() { String queryStr = "select id from study order by id"; Query query = em.createNativeQuery(queryStr); List<Long> returnList = new ArrayList<Long>(); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } return returnList; } // This method is used by the IndexServiceBean in order to find and // reindex the studies that are no longer cross-linked by any foreign // subnetworks. public List<Long> getAllLinkedStudyIds() { List<Long> returnList = new ArrayList<Long>(); String queryStr = "SELECT DISTINCT study_id FROM linked_network_studies ORDER BY study_id"; Query query = em.createNativeQuery(queryStr); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add((Long) currentResult); } return returnList; } public List<Long> getAllNonHarvestedStudyIds() { String queryStr = "select id from study where isharvested='false'"; Query query = em.createNativeQuery(queryStr); List<Long> returnList = new ArrayList<Long>(); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } return returnList; } /** * this method only returns released studies * @param studyIdList * @param orderBy * @return list of oredered ids */ public List getOrderedStudies(List studyIdList, String orderBy) { if (orderBy == null || studyIdList == null || studyIdList.size() == 0) { return studyIdList; } String studyIds = generateTempTableString(studyIdList); String queryStr = null; if (orderBy.equals("globalId")) { queryStr = "SELECT s.id " + "from study s " + "where s.id in (" + studyIds + ") " + "ORDER BY s.protocol, s.authority, s.studyId"; } else if (orderBy.equals("title")) { queryStr = "SELECT s.id " + "from metadata m, studyversion sv, study s " + "where sv.metadata_id = m.id " + "and s.id = sv.study_id " + "and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + "and s.id in (" + studyIds + ") " + "ORDER BY m.title"; } else if (orderBy.equals("releaseTime")) { queryStr = "SELECT s.id " + "from studyversion sv, study s " + "where s.id = sv.study_id " + "and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + "and s.id in (" + studyIds + ") " + "ORDER BY sv.releasetime desc"; } else if (orderBy.equals("productionDate")) { queryStr = "SELECT s.id " + "from metadata m, studyversion sv, study s " + "where sv.metadata_id = m.id " + "and s.id = sv.study_id " + "and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + "and s.id in (" + studyIds + ") " + "ORDER BY m.productionDate desc"; } else if (orderBy.equals("downloadCount")) { // this query runs fine in Postgres, but will need to be tested with other DBs if they are used queryStr = "select s.id " + "from metadata m, studyversion sv, study s " + "LEFT OUTER JOIN studyfileactivity sfa on s.id = sfa.study_id " + "where sv.metadata_id = m.id " + "and s.id = sv.study_id " + "and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + "and s.id in (" + studyIds + ")" + "group by s.id, m.title " + "order by " + "(CASE WHEN sum(downloadcount) is null THEN -1 ELSE sum(downloadcount) END) desc, m.title"; } if (queryStr != null) { Query query = em.createNativeQuery(queryStr); System.out.print("sort Test global-Id-sort " + queryStr); List<Long> returnList = new ArrayList<Long>(); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } return returnList; } else { return studyIdList; // invalid order by } } public List getDvOrderedStudyVersionIds(Long vdcId, String orderBy, boolean ascending) { List<Long> returnList = new ArrayList<Long>(); if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String queryStr = "SELECT v.id" + " from studyversion v, study s, metadata m, vdcuser cr" + " WHERE v.study_id = s.id" + " and v.metadata_id = m.id" + " and s.creator_id = cr.id" + " and s.owner_id = " + vdcId + " and v.id in (SELECT max(v.id) from studyversion v group by v.study_id)" + " ORDER BY " + orderBy; if (!ascending) { queryStr += " desc"; } Query query = em.createNativeQuery(queryStr); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult)).longValue()); } return returnList; } public List getDvOrderedDeaccessionedStudyVersionIds(Long vdcId, String orderBy, boolean ascending) { List<Long> returnList = new ArrayList<Long>(); if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String queryStr = "SELECT v.id" + " from studyversion v, study s, metadata m, vdcuser cr" + " WHERE v.study_id = s.id" + " and v.metadata_id = m.id" + " and s.creator_id = cr.id" + " and s.owner_id = " + vdcId + " and v.versionstate = '" + StudyVersion.VersionState.DEACCESSIONED + "'" + " and v.id in (SELECT max(v.id) from studyversion v group by v.study_id)" + " ORDER BY " + orderBy; if (!ascending) { queryStr += " desc"; } Query query = em.createNativeQuery(queryStr); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult)).longValue()); } return returnList; } public List getAllDeaccessionedStudyVersionIdsByContributor(Long contributorId, String orderBy, boolean ascending) { List<Long> returnList = new ArrayList<Long>(); if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String queryStr = "SELECT v.id" + " from studyversion v, study s, metadata m, vdcuser cr " + " WHERE v.study_id = s.id" + " and v.metadata_id = m.id" + " and s.creator_id = cr.id" + " and v.versionstate = '" + StudyVersion.VersionState.DEACCESSIONED + "'" + " and v.id in (SELECT max(v.id) from studyversion v, versioncontributor c " + " where c.studyversion_id = v.id and c.contributor_id = " + contributorId + " group by v.study_id)" + " ORDER BY " + orderBy; if (!ascending) { queryStr += " desc"; } Query query = em.createNativeQuery(queryStr); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult)).longValue()); } return returnList; } public List getAllStudyVersionIdsByContributor(Long contributorId, String orderBy, boolean ascending) { List<Long> returnList = new ArrayList<Long>(); if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String queryStr = "SELECT v.id" + " from studyversion v, study s, metadata m, vdcuser cr " + " WHERE v.study_id = s.id" + " and v.metadata_id = m.id" + " and s.creator_id = cr.id" + " and v.id in (SELECT max(v.id) from studyversion v, versioncontributor c " + " where c.studyversion_id = v.id and c.contributor_id = " + contributorId + " group by v.study_id)" + " ORDER BY " + orderBy; if (!ascending) { queryStr += " desc"; } Query query = em.createNativeQuery(queryStr); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult)).longValue()); } return returnList; } public List getDvOrderedStudyVersionIdsByContributor(Long vdcId, Long contributorId, String orderBy, boolean ascending) { List<Long> returnList = new ArrayList<Long>(); if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String queryStr = "SELECT v.id" + " from studyversion v, study s, metadata m, vdcuser cr " + " WHERE v.study_id=s.id" + " and v.metadata_id = m.id" + " and s.creator_id = cr.id" + " and s.owner_id = " + vdcId + " and v.id in (SELECT max(v.id) from studyversion v, versioncontributor c " + " where c.studyversion_id = v.id and c.contributor_id = " + contributorId + " group by v.study_id)" + " ORDER BY " + orderBy; if (!ascending) { queryStr += " desc"; } Query query = em.createNativeQuery(queryStr); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult)).longValue()); } return returnList; } public List getDvOrderedDeaccessionedStudyVersionIdsByContributor(Long vdcId, Long contributorId, String orderBy, boolean ascending) { List<Long> returnList = new ArrayList<Long>(); if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String queryStr = "SELECT v.id" + " from studyversion v, study s, metadata m, vdcuser cr " + " WHERE v.study_id=s.id" + " and v.metadata_id = m.id" + " and s.creator_id = cr.id" + " and s.owner_id = " + vdcId + " and v.versionstate = '" + StudyVersion.VersionState.DEACCESSIONED + "'" + " and v.id in (SELECT max(v.id) from studyversion v, versioncontributor c " + " where c.studyversion_id = v.id and c.contributor_id = " + contributorId + " group by v.study_id)" + " ORDER BY " + orderBy; if (!ascending) { queryStr += " desc"; } Query query = em.createNativeQuery(queryStr); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult)).longValue()); } return returnList; } public List getDvOrderedStudyIds(Long vdcId, String orderBy, boolean ascending) { if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String query = "SELECT s.id FROM Study s WHERE s.owner.id = " + vdcId + " ORDER BY s." + orderBy; if (!ascending) { query += " desc"; } return (List) em.createQuery(query).getResultList(); } public List getDvOrderedStudyIdsByCreator(Long vdcId, Long creatorId, String orderBy, boolean ascending) { if (!ascending && orderBy.equals("s.protocol, s.authority, s.studyId")) { orderBy = "s.protocol desc, s.authority desc, s.studyId "; } String query = "SELECT s.id FROM Study s WHERE s.owner.id = " + vdcId + " and s.creator.id = " + creatorId + " ORDER BY s." + orderBy; if (!ascending) { query += " desc"; } return (List) em.createQuery(query).getResultList(); } public List<DataFileFormatType> getDataFileFormatTypes() { return em.createQuery("select object(t) from DataFileFormatType as t").getResultList(); } public String generateStudyIdSequence(String protocol, String authority) { // Date now = new Date(); // return ""+now.getTime(); // return em.createNamedQuery("getStudyIdSequence").getSingleResult().toString(); String studyId = null; studyId = gnrsService.getNewObjectId(protocol, authority); /* do { Vector result = (Vector)em.createNativeQuery("select nextval('studyid_seq')").getSingleResult(); studyId = result.get(0).toString(); } while (!isUniqueStudyId(studyId, protocol, authority)); */ return studyId; } /** * Check that a studyId entered by the user is unique (not currently used for any other study in this Dataverse Network) */ @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public boolean isUniqueStudyId(String userStudyId, String protocol, String authority) { String queryStr = "SELECT s from Study s where s.studyId = :studyId and s.protocol= :protocol and s.authority= :authority"; Study study = null; Query query = em.createQuery(queryStr); query.setParameter("studyId", userStudyId); query.setParameter("protocol", protocol); query.setParameter("authority", authority); return query.getResultList().size() == 0; } public void exportStudyFilesToLegacySystem(String lastUpdateTime, String authority) { // Get list of studies that have been updated yesterday, // and export them to legacy VDC system Logger logger = null; String exportLogDirStr = System.getProperty("vdc.export.log.dir"); if (exportLogDirStr == null) { System.out.println("Missing system property: vdc.export.log.dir. Please add to JVM options"); return; } File exportLogDir = new File(exportLogDirStr); if (!exportLogDir.exists()) { exportLogDir.mkdir(); } logger = Logger.getLogger("edu.harvard.iq.dvn.core.web.servlet.VDCExportServlet"); // Everytime export runs, we want to write to a separate log file (handler). // So if export has run previously, remove the previous handler if (logger.getHandlers() != null && logger.getHandlers().length > 0) { int numHandlers = logger.getHandlers().length; for (int i = 0; i < numHandlers; i++) { logger.removeHandler(logger.getHandlers()[i]); } } SimpleDateFormat formatter = new SimpleDateFormat("yyyy_MM_dd"); FileHandler handler = null; try { handler = new FileHandler( exportLogDirStr + File.separator + "export_" + formatter.format(new Date()) + ".log"); } catch (IOException e) { throw new EJBException(e); } // Add handler to the desired logger logger.addHandler(handler); logger.info("Begin Exporting Studies"); int studyCount = 0; int deletedStudyCount = 0; try { /* THIS IS LEGACY CODE AND SHOULD BE DELETED // For all studies that have been deleted in the dataverse since last export, remove study directory in VDC String query = "SELECT s from DeletedStudy s where s.authority = '" + authority + "' "; List deletedStudies = em.createQuery(query).getResultList(); for (Iterator it = deletedStudies.iterator(); it.hasNext();) { DeletedStudy deletedStudy = (DeletedStudy) it.next(); logger.info("Deleting study " + deletedStudy.getGlobalId()); Study study = em.find(Study.class, deletedStudy.getId()); File legacyStudyDir = new File(FileUtil.getLegacyFileDir() + File.separatorChar + study.getAuthority() + File.separatorChar + study.getStudyId()); // Remove files in the directory, then delete the directory. File[] studyFiles = legacyStudyDir.listFiles(); if (studyFiles != null) { for (int i = 0; i < studyFiles.length; i++) { studyFiles[i].delete(); } } legacyStudyDir.delete(); deletedStudyCount++; em.remove(deletedStudy); } */ // Do export of all studies updated at "lastUpdateTime"" if (authority == null) { authority = vdcNetworkService.find().getAuthority(); } String beginTime = null; String endTime = null; if (lastUpdateTime == null) { Calendar cal = Calendar.getInstance(); cal.add(Calendar.DAY_OF_YEAR, -1); beginTime = new SimpleDateFormat("yyyy-MM-dd").format(cal.getTime()); // Use yesterday as default value cal.add(Calendar.DAY_OF_YEAR, 1); endTime = new SimpleDateFormat("yyyy-MM-dd").format(cal.getTime()); } else { beginTime = lastUpdateTime; Date date = new SimpleDateFormat("yyyy-MM-dd").parse(lastUpdateTime); Calendar cal = Calendar.getInstance(); cal.setTime(date); cal.add(Calendar.DAY_OF_YEAR, 1); endTime = new SimpleDateFormat("yyyy-MM-dd").format(cal.getTime()); } String query = "SELECT s from Study s where s.authority = '" + authority + "' "; query += " and s.lastUpdateTime >'" + beginTime + "'"; // query+=" and s.lastUpdateTime <'" +endTime+"'"; query += " order by s.studyId"; List updatedStudies = em.createQuery(query).getResultList(); for (Iterator it = updatedStudies.iterator(); it.hasNext();) { Study study = (Study) it.next(); logger.info("Exporting study " + study.getStudyId()); exportStudyToLegacySystem(study, authority); studyCount++; } } catch (Exception e) { logger.severe(e.getMessage()); String stackTrace = "StackTrace: \n"; logger.severe("Exception caused by: " + e + "\n"); StackTraceElement[] ste = e.getStackTrace(); for (int m = 0; m < ste.length; m++) { stackTrace += ste[m].toString() + "\n"; } logger.severe(stackTrace); } logger.info("End export, " + studyCount + " studies successfully exported, " + deletedStudyCount + " studies deleted."); } private void exportStudyToLegacySystem(Study study, String authority) throws IOException, JAXBException { throw new EJBException("This feature is no longer supported!!"); /* // For each study // update study file locations for legacy system // Write ddi to an output stream // If data file dir exists, delete everything from it // copy ddi to study.xml, // copy study files. File studyDir = new File(FileUtil.getStudyFileDir() + File.separatorChar + authority + File.separatorChar + study.getStudyId()); File legacyStudyDir = new File(FileUtil.getLegacyFileDir() + File.separatorChar + authority + File.separatorChar + study.getStudyId()); // If the directory exists in the legacy system, then clear out all the files contained in it if (legacyStudyDir.exists() && legacyStudyDir.isDirectory()) { File[] files = legacyStudyDir.listFiles(); for (int i = 0; i < files.length; i++) { files[i].delete(); } } else { legacyStudyDir.mkdirs(); } // Export the study to study.xml in the legacy directory FileWriter fileWriter = new FileWriter(new File(legacyStudyDir, "study.xml")); try { ddiService.exportStudy(study, fileWriter, true, true); fileWriter.flush(); } finally { fileWriter.close(); } // Copy all the study files to the legacy directory for (Iterator it = study.getStudyFiles().iterator(); it.hasNext();) { StudyFile studyFile = (StudyFile) it.next(); FileUtil.copyFile(new File(studyDir, studyFile.getFileSystemName()), new File(legacyStudyDir, studyFile.getFileSystemName())); } */ } public String generateFileSystemNameSequence() { String fileSystemName = null; do { //Vector result = (Vector) em.createNativeQuery("select nextval('filesystemname_seq')").getSingleResult(); //fileSystemName = result.get(0).toString(); Long result = (Long) em.createNativeQuery("select nextval('filesystemname_seq')").getSingleResult(); fileSystemName = result.toString(); } while (!isUniqueFileSystemName(fileSystemName)); return fileSystemName; } /** * Check that a fileId unique (not currently used for any other file in this study) */ public boolean isUniqueFileSystemName(String fileSystemName) { String query = "SELECT f FROM StudyFile f WHERE f.fileSystemName = '" + fileSystemName + "'"; return em.createQuery(query).getResultList().size() == 0; } public List<StudyLock> getStudyLocks() { String query = "SELECT sl FROM StudyLock sl"; return (List<StudyLock>) em.createQuery(query).getResultList(); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void addStudyLock(Long studyId, Long userId, String detail) { Study study = em.find(Study.class, studyId); VDCUser user = em.find(VDCUser.class, userId); StudyLock lock = new StudyLock(); lock.setStudy(study); lock.setUser(user); lock.setDetail(detail); lock.setStartTime(new Date()); study.setStudyLock(lock); if (user.getStudyLocks() == null) { user.setStudyLocks(new ArrayList()); } user.getStudyLocks().add(lock); em.persist(lock); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void removeStudyLock(Long studyId) { Study study = em.find(Study.class, studyId); em.refresh(study); StudyLock lock = study.getStudyLock(); if (lock != null) { VDCUser user = lock.getUser(); study.setStudyLock(null); user.getStudyLocks().remove(lock); em.remove(lock); } } public void incrementNumberOfDownloads(Long studyFileId, Long currentVDCId) { incrementNumberOfDownloads(studyFileId, currentVDCId, new Date(), (GuestBookResponse) null); } public void incrementNumberOfDownloads(Long studyFileId, Long currentVDCId, Date lastDownloadTime) { incrementNumberOfDownloads(studyFileId, currentVDCId, lastDownloadTime, (GuestBookResponse) null); } @Override public void incrementNumberOfDownloads(Long studyFileId, Long currentVDCId, GuestBookResponse guestbookResponse) { incrementNumberOfDownloads(studyFileId, currentVDCId, new Date(), guestbookResponse); } public void incrementNumberOfDownloads(Long studyFileId, Long currentVDCId, Date lastDownloadTime, GuestBookResponse guestbookResponse) { StudyFile sf = studyFileService.getStudyFile(studyFileId); Study study = sf.getStudy(); StudyFileActivity sfActivity = sf.getStudyFileActivity(); if (guestbookResponse.getStudyVersion() == null || guestbookResponse.getStudyVersion().isDraft()) { //if our studyversion is in draft or doesn't exist we don't want to count it or save GB responses. return; } addGuestbookRecords(sf, guestbookResponse); if (sfActivity == null) { sfActivity = new StudyFileActivity(); sfActivity.setStudyFile(sf); sfActivity.setStudy(study); sf.setStudyFileActivity(sfActivity); study.getStudyFileActivity().add(sfActivity); } sfActivity.setDownloadCount(sfActivity.getDownloadCount() + 1); sfActivity.setLastDownloadTime(lastDownloadTime); if (currentVDCId == null) { VDCActivity vdcActivity = study.getOwner().getVDCActivity(); vdcActivity.setLocalStudyNetworkDownloadCount(vdcActivity.getLocalStudyNetworkDownloadCount() + 1); } else if (currentVDCId.equals(study.getOwner().getId())) { VDCActivity vdcActivity = study.getOwner().getVDCActivity(); vdcActivity.setLocalStudyLocalDownloadCount(vdcActivity.getLocalStudyLocalDownloadCount() + 1); } else { VDCActivity vdcActivity1 = study.getOwner().getVDCActivity(); vdcActivity1.setLocalStudyForeignDownloadCount(vdcActivity1.getLocalStudyForeignDownloadCount() + 1); VDCActivity vdcActivity2 = vdcService.findById(currentVDCId).getVDCActivity(); vdcActivity2.setForeignStudyLocalDownloadCount(vdcActivity2.getForeignStudyLocalDownloadCount() + 1); } } private void addGuestbookRecords(StudyFile file, GuestBookResponse guestbookResponse) { if (guestbookResponse != null) { guestbookResponse.setStudyFile(file); guestbookResponse.setResponseTime(new Date()); guestBookResponseServiceBean.update(guestbookResponse); } } public RemoteAccessAuth lookupRemoteAuthByHost(String hostName) { String queryStr = "SELECT r FROM RemoteAccessAuth r WHERE r.hostName= :hostName"; RemoteAccessAuth remoteAuth = null; try { Query query = em.createQuery(queryStr); query.setParameter("hostName", hostName); List resultList = query.getResultList(); if (resultList.size() > 0) { remoteAuth = (RemoteAccessAuth) resultList.get(0); } } catch (javax.persistence.NoResultException e) { // DO nothing, just return null. } return remoteAuth; } public Study getStudyByGlobalId(String identifier) { String protocol = null; String authority = null; String studyId = null; int index1 = identifier.indexOf(':'); int index2 = identifier.indexOf('/'); int index3 = 0; if (index1 == -1) { throw new EJBException("Error parsing identifier: " + identifier + ". ':' not found in string"); } else { protocol = identifier.substring(0, index1); } if (index2 == -1) { throw new EJBException("Error parsing identifier: " + identifier + ". '/' not found in string"); } else { authority = identifier.substring(index1 + 1, index2); } if (protocol.equals("doi")) { index3 = identifier.indexOf('/', index2 + 1); if (index3 == -1) { studyId = identifier.substring(index2 + 1).toUpperCase(); } else { authority = identifier.substring(index1 + 1, index3); studyId = identifier.substring(index3 + 1).toUpperCase(); } } else { studyId = identifier.substring(index2 + 1).toUpperCase(); } String queryStr = "SELECT s from Study s where s.studyId = :studyId and s.protocol= :protocol and s.authority= :authority"; Study study = null; try { Query query = em.createQuery(queryStr); query.setParameter("studyId", studyId); query.setParameter("protocol", protocol); query.setParameter("authority", authority); study = (Study) query.getSingleResult(); } catch (javax.persistence.NoResultException e) { // DO nothing, just return null. } return study; } public StudyVersion getStudyVersion(String globalId, Long versionNumber) { Study study = getStudyByGlobalId(globalId); if (study != null) { return getStudyVersion(study.getId(), versionNumber); } else { return null; } } public StudyVersion getStudyVersion(Long studyId, Long versionNumber) { Study study = em.find(Study.class, studyId); StudyVersion studyVersion = null; if (study != null) { if (versionNumber == null) { // return either the released or deaccessioned version studyVersion = study.getReleasedVersion(); if (studyVersion == null) { studyVersion = study.getDeaccessionedVersion(); } } else if (versionNumber == -1) { // return the latest version studyVersion = study.getLatestVersion(); } else { studyVersion = study.getStudyVersionByNumber(versionNumber); } } //String queryStr = "SELECT sv FROM StudyVersion sv WHERE sv.study.id = '" + studyId; //if (versionNumber != null) { // queryStr += "' and sv.versionNumber = '" + versionNumber + "'"; //} else { // get reelased version // queryStr += "' and sv.versionState = :releasedState "; //} //Query query = em.createQuery(queryStr); //if (versionNumber == null) { // query.setParameter("releasedState", VersionState.RELEASED); //} //List resultList = query.getResultList(); //StudyVersion studyVersion = null; //if (resultList.size() > 1) { // throw new EJBException("More than one study version found with studyId = " + studyId + " and versionNumber = " + versionNumber); //} //if (resultList.size() == 1) { // studyVersion = (StudyVersion) resultList.get(0); //} return studyVersion; } public StudyVersion getStudyVersionById(Long versionId) { StudyVersion sv = em.find(StudyVersion.class, versionId); if (sv == null) { throw new IllegalArgumentException("Unknown version id " + versionId); } return sv; } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public Study importHarvestStudy(File xmlFile, Long vdcId, Long userId, String harvestIdentifier) { VDC vdc = em.find(VDC.class, vdcId); em.refresh(vdc); // workaround to get correct value for harvesting dataverse (to be investigated) if (vdc.getHarvestingDataverse() == null) { throw new EJBException("importHarvestStudy(...) should only be called for a harvesting dataverse."); } Study study = doImportStudy(xmlFile, vdc.getHarvestingDataverse().getHarvestFormatType().getId(), vdcId, userId, harvestIdentifier, null); // new create exports files for these studies studyService.exportStudy(study); logger.info("completed importHarvestStudy() returning study" + study.getGlobalId()); return study; } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public Study importStudy(File xmlFile, Long harvestFormatTypeId, Long vdcId, Long userId) { return doImportStudy(xmlFile, harvestFormatTypeId, vdcId, userId, null, null); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public Study importStudy(File xmlFile, Long harvestFormatTypeId, Long vdcId, Long userId, List<StudyFileEditBean> filesToUpload) { return doImportStudy(xmlFile, harvestFormatTypeId, vdcId, userId, null, filesToUpload); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public Study importStudy(File xmlFile, Long harvestFormatTypeId, Long vdcId, Long userId, String harvestIdentifier, List<StudyFileEditBean> filesToUpload) { return doImportStudy(xmlFile, harvestFormatTypeId, vdcId, userId, harvestIdentifier, filesToUpload); } private File transformToDDI(File xmlFile, String xslFileName) { File ddiFile = null; InputStream in = null; OutputStream out = null; try { // prepare source in = new FileInputStream(xmlFile); StreamSource source = new StreamSource(in); // prepare result ddiFile = File.createTempFile("ddi", ".xml"); out = new FileOutputStream(ddiFile); StreamResult result = new StreamResult(out); // now transform StreamSource xslSource = new StreamSource(new File(xslFileName)); Transformer transformer = TransformerFactory.newInstance().newTransformer(xslSource); transformer.transform(source, result); } catch (Exception ex) { ex.printStackTrace(); throw new EJBException("Error occurred while attempting to transform file: " + ex.getMessage()); } finally { try { if (in != null) { in.close(); } } catch (Exception e) { } try { if (out != null) { out.close(); } } catch (Exception e) { } } return ddiFile; } public File transformToDDI(String xml, String xslFileName, String tmpDirPath) { File uploadDir = new File(tmpDirPath); if (!uploadDir.exists()) { if (!uploadDir.mkdirs()) { throw new EJBException("Could not create directory: " + uploadDir.getAbsolutePath()); } } String tmpFilePath = tmpDirPath + File.separator + "study.xml"; File tmpFile = new File(tmpFilePath); try { FileUtils.writeStringToFile(tmpFile, xml); } catch (IOException ex) { throw new EJBException("Could not write temporary file"); } finally { uploadDir.delete(); } File ddiFile = transformToDDI(tmpFile, xslFileName); tmpFile.delete(); uploadDir.delete(); return ddiFile; } private void copyXMLFile(Study study, File xmlFile, String xmlFileName) { try { // create, if needed, the directory File newDir = FileUtil.getStudyFileDir(study); if (!newDir.exists()) { newDir.mkdirs(); } FileUtil.copyFile(xmlFile, new File(newDir, xmlFileName)); } catch (IOException ex) { ex.printStackTrace(); String msg = "ImportStudy failed: "; if (ex.getMessage() != null) { msg += ex.getMessage(); } EJBException e = new EJBException(msg); e.initCause(ex); throw e; } } private void clearCollection(Collection collection) { if (collection != null) { for (Iterator it = collection.iterator(); it.hasNext();) { Object elem = it.next(); it.remove(); em.remove(elem); } } } private void resetStudyForHarvesting(StudyVersion studyVersion) { // first delete variables via query (for performance) Study study = studyVersion.getStudy(); deleteDataVariables(study.getId()); for (StudyFile elem : study.getStudyFiles()) { elem.clearData(); } // then delete files clearCollection(study.getStudyFiles()); // now create new, empty metadata object and delete old one Metadata m = new Metadata(); em.persist(m); // persist because otherwise update study can fail with non null metadata id exception em.remove(studyVersion.getMetadata()); studyVersion.setMetadata(m); // clear global id componenents study.setProtocol(null); study.setAuthority(null); study.setStudyId(null); // finally, flush, so that everything is removed and new objects get properly created em.flush(); } public Study saveStudyVersion(StudyVersion studyVersion, Long userId) { VDCUser user = em.find(VDCUser.class, userId); Date lastUpdateTime = new Date(); studyVersion.setLastUpdateTime(lastUpdateTime); studyVersion.getStudy().setLastUpdateTime(lastUpdateTime); VDC studyVDC = studyVersion.getStudy().getOwner(); if (!user.isNetworkAdmin()) { userService.makeContributor(user.getId(), studyVDC.getId()); VDCRole vdcRole = roleService.findByUserVDC(userId, studyVDC.getId()); if (vdcRole.getRole().getName().equals(RoleServiceLocal.CONTRIBUTOR)) { studyVersion.setVersionState(VersionState.DRAFT); } } studyVersion.updateVersionContributors(user); studyVersion.getMetadata().setDisplayOrders(); return studyVersion.getStudy(); } // visible studies are defined as those that are released and not in a restricted vdc // (unless you are in vdc) public List getVisibleStudies(List studyIds, Long vdcId) { List returnList = new ArrayList(); if (studyIds != null && studyIds.size() > 0) { generateTempTableString(studyIds); String queryString = "SELECT s.id " + "FROM study s, studyversion sv, vdc v, tempid ts " + "WHERE s.id = sv.study_id " + "AND s.owner_id = v.id " + "AND sv.versionState = '" + StudyVersion.VersionState.RELEASED + "' " + "AND s.id = ts.tempid " + "AND (v.restricted = false " + (vdcId != null ? "OR v.id = " + vdcId : "") + ") ORDER BY ts.orderby"; Query query = em.createNativeQuery(queryString); for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } } return returnList; } private String generateTempTableString(List<Long> studyIds) { // first step: create the temp table with the ids em.createNativeQuery(" BEGIN; SET TRANSACTION READ WRITE; DROP TABLE IF EXISTS tempid; END;") .executeUpdate(); em.createNativeQuery( " BEGIN; SET TRANSACTION READ WRITE; CREATE TEMPORARY TABLE tempid (tempid integer primary key, orderby integer); END;") .executeUpdate(); em.createNativeQuery(" BEGIN; SET TRANSACTION READ WRITE; INSERT INTO tempid VALUES " + generateIDsforTempInsert(studyIds) + "; END;").executeUpdate(); return "select tempid from tempid"; } private String generateIDsforTempInsert(List idList) { int count = 0; StringBuffer sb = new StringBuffer(); Iterator iter = idList.iterator(); while (iter.hasNext()) { Long id = (Long) iter.next(); sb.append("(").append(id).append(",").append(count++).append(")"); if (iter.hasNext()) { sb.append(","); } } return sb.toString(); } // this method will return only the subset of studies that are public public List getViewableStudies(List<Long> studyIds) { return getViewableStudies(studyIds, null, null, null); } // viewable studies are those that are defined as not restricted to the user public List getViewableStudies(List<Long> studyIds, Long userId, Long ipUserGroupId, Long vdcId) { List returnList = new ArrayList(); if (studyIds != null && studyIds.size() > 0) { // we first create a temp table with all the study ids; this is because when the list is too large // SQL cannot handle it generateTempTableString(studyIds); // dynamically generate the query StringBuffer queryString = new StringBuffer("select id from study s, tempid ts "); StringBuffer whereClause = new StringBuffer("where s.id = ts.tempid "); whereClause.append("and ( restricted = false "); boolean groupJoinAdded = false; if (vdcId != null) { // if this parameter is passed, the user is an admin or curator of this vdc whereClause.append("or owner_id = ? "); } if (userId != null) { queryString.append("left join study_vdcuser su on (s.id = su.studies_id) "); queryString.append("left join study_usergroup sg on (s.id = sg.studies_id ) "); whereClause.append("or su.allowedusers_id = ? "); whereClause.append( "or sg.allowedgroups_id in (select usergroups_id from vdcuser_usergroup where users_id = ?) "); groupJoinAdded = true; } if (ipUserGroupId != null) { if (!groupJoinAdded) { queryString.append("left join study_usergroup sg on (s.id = sg.studies_id ) "); } whereClause.append("or sg.allowedgroups_id = ? "); } whereClause.append(") "); // we are now ready to create the query Query query = em.createNativeQuery(queryString.toString() + whereClause.toString()); // now set parameters int parameterCount = 1; if (vdcId != null) { query.setParameter(parameterCount++, vdcId); } if (userId != null) { query.setParameter(parameterCount++, userId); query.setParameter(parameterCount++, userId); } if (ipUserGroupId != null) { query.setParameter(parameterCount++, ipUserGroupId); } for (Object currentResult : query.getResultList()) { // convert results into Longs returnList.add(new Long(((Integer) currentResult).longValue())); } } return returnList; } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void exportStudy(Study study) { List<String> exportFormats = studyExporterFactory.getExportFormats(); for (String exportFormat : exportFormats) { exportStudyToFormat(study, exportFormat); } study.setLastExportTime(new Date()); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void exportStudy(Long studyId) { Study study = em.find(Study.class, studyId); exportStudy(study); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void exportStudyToFormat(Long studyId, String exportFormat) { Study study = em.find(Study.class, studyId); exportStudyToFormat(study, exportFormat); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void exportStudyToFormat(Study study, String exportFormat) { // only export released studies // TODO: we should clean up the export logic to handle export of versions if (study.getReleasedVersion() == null) { return; } File studyDir = FileUtil.getStudyFileDir(study); StudyExporter studyExporter = studyExporterFactory.getStudyExporter(exportFormat); String fileName = "export_" + exportFormat; if (studyExporter.isXmlFormat()) { fileName += ".xml"; } File exportFile = new File(studyDir, fileName); OutputStream os = null; try { exportFile.createNewFile(); os = new FileOutputStream(exportFile); studyExporter.exportStudy(study, os); } catch (IOException e) { throw new EJBException(e); } finally { try { if (os != null) { os.close(); } } catch (IOException ex) { } } // study.setLastExportTime(new Date()); } public void exportUpdatedStudies() { exportStudies(studyService.getStudyIdsForExport()); harvestStudyService.updateHarvestStudies(); } public void exportStudies(List<Long> studyIds, String exportFormat) { String logTimestamp = exportLogFormatter.format(new Date()); Logger exportLogger = Logger .getLogger("edu.harvard.iq.dvn.core.study.StudyServiceBean.export." + logTimestamp); List<Long> harvestedStudyIds = new ArrayList<Long>(); try { exportLogger.addHandler(new FileHandler( FileUtil.getExportFileDir() + File.separator + "export_" + logTimestamp + ".log")); } catch (IOException e) { logger.severe("Exception adding log file handler " + FileUtil.getExportFileDir() + File.separator + "export_" + logTimestamp + ".log"); return; } try { int exportCount = 0; exportLogger.info("Begin exporting studies, number of possible studies to export: " + studyIds.size()); for (Long studyId : studyIds) { Study study = em.find(Study.class, studyId); if (study.getReleasedVersion() != null) { exportLogger.info("Begin export for study " + study.getGlobalId()); if (exportFormat == null) { studyService.exportStudy(studyId); //TODO check why do we pass the id and not the study } else { studyService.exportStudyToFormat(studyId, exportFormat); //TODO check why do we pass the id and not the study } exportLogger.info("Complete export for study " + study.getGlobalId()); exportCount++; } else { exportLogger .info("No released version for study " + study.getGlobalId() + "; skipping export."); } } exportLogger.info("Completed exporting studies. Actual number of studies exported: " + exportCount); } catch (EJBException e) { logException(e, exportLogger); throw e; } } public void exportStudies(List<Long> studyIds) { exportStudies(studyIds, null); } private void logException(Throwable e, Logger logger) { boolean cause = false; String fullMessage = ""; do { String message = e.getClass().getName() + " " + e.getMessage(); if (cause) { message = "\nCaused By Exception.................... " + e.getClass().getName() + " " + e.getMessage(); } StackTraceElement[] ste = e.getStackTrace(); message += "\nStackTrace: \n"; for (int m = 0; m < ste.length; m++) { message += ste[m].toString() + "\n"; } fullMessage += message; cause = true; } while ((e = e.getCause()) != null); logger.severe(fullMessage); } private Study doImportStudy(File xmlFile, Long harvestFormatTypeId, Long vdcId, Long userId, String harvestIdentifier, List<StudyFileEditBean> filesToUpload) { logger.info("Begin doImportStudy"); Study study = null; StudyVersion studyVersion = null; boolean newStudy = true; VDC vdc = em.find(VDC.class, vdcId); // Note on the logic below: // It IS possible for the method to be called on a Harvested study, but without the // harvestIdentifier supplied! This happens when harvesting from Nesstar sources // (see more comments on Nesstar harvesting below). // --L.A. boolean isHarvest = (harvestIdentifier != null || (vdc.getHarvestingDataverse() != null)); boolean isNesstarHarvest = ((vdc.getHarvestingDataverse() != null) && vdc.getHarvestingDataverse().isNesstar()); Map<String, String> globalIdComponents = null; // used if this is an update of a harvested study VDCUser creator = em.find(VDCUser.class, userId); // Step 1: determine format and transform if necessary File ddiFile = xmlFile; boolean fileTransformed = false; HarvestFormatType hft = em.find(HarvestFormatType.class, harvestFormatTypeId); if (hft.getStylesheetFileName() != null) { ddiFile = transformToDDI(xmlFile, hft.getStylesheetFileName()); fileTransformed = true; } // Step 2a: if harvested, check if exists if (isHarvest) { if (harvestIdentifier == null) { // When harvesting from Nesstar sources, no unique identifiers // are provided on the protocol level. Instead, we have to // check the actual DDI metadata and see if it provides // an ID we could use as the harvestidentifier. // -- L.A. if (isNesstarHarvest) { Study tmpStudy = new Study(vdc, creator, StudyVersion.VersionState.RELEASED); StudyVersion tmpStudyVersion = tmpStudy.getLatestVersion(); String tmpStudyId = null; // We are doing an extra run of ddiService.mapDDI in order // to achieve this; note that mapDDI is a fairly cheap // operation, since it doesn't parse the data portion of the // ddi. // an experimental hack: // it appears that some Nesstar-provided DDIs are failing to // import because of the illegal "xml:lang=..." attributes in // them; and some fail because of the DTD-style schema headers // (<?DOCTYPE codeBook ...) Let's try to just strip them out - // and see if that helps: BufferedReader rd = null; PrintWriter ddiProcessedOut = null; File ddiFileProcessed = null; try { ddiFileProcessed = File.createTempFile("NesstarDdiProcessed.", ".xml"); FileOutputStream ddiProcessedStream = new FileOutputStream(ddiFileProcessed); ddiProcessedOut = new PrintWriter(ddiProcessedStream, true); rd = new BufferedReader(new InputStreamReader(new FileInputStream(ddiFile))); String line = null; while ((line = rd.readLine()) != null) { if (line.matches("^<.DOCTYPE codeBook.*") || line.equals("")) { // skip this line } else { line = line.replaceAll(" xml:lang=\"[^\"]*\"", ""); ddiProcessedOut.println(line); } } } catch (IOException ex) { throw new EJBException("Failed to process and parse Nesstar ddi."); } finally { if (rd != null) { try { rd.close(); } catch (Exception ex) { } } ddiFile.delete(); if (ddiProcessedOut != null) { ddiProcessedOut.close(); } } ddiFile = ddiFileProcessed; ddiService.mapDDI(ddiFile, tmpStudyVersion, true); if (tmpStudyVersion.getMetadata().getStudyOtherIds().size() > 0) { tmpStudyId = tmpStudyVersion.getMetadata().getStudyOtherIds().get(0).getOtherId(); // We may need to go through the list of "other Ids" (instead of // just grabbing the first one); and apply some logic to get the // best one. -- L.A. } if (tmpStudyId == null || !isValidStudyIdString(tmpStudyId)) { throw new EJBException("No suitable ID was found in the Nesstar-harvested metadata."); } harvestIdentifier = tmpStudyId; } else { throw new EJBException("No Identifier available for a harvested (non-Nesstar) study."); } } study = getStudyByHarvestInfo(vdc, harvestIdentifier); if (study != null) { // if (!study.isIsHarvested()) { // // This study actually belongs to the local DVN, so don't continue with harvest // // TODO: this check is probably no longer needed, now that we get study by harvestIdentifier // throw new EJBException("This study originated in the local DVN - we don't need to harvest it."); // } newStudy = false; // store old global ID components globalIdComponents = new HashMap<String, String>(); globalIdComponents.put("globalId", study.getGlobalId()); globalIdComponents.put("protocol", study.getProtocol()); globalIdComponents.put("authority", study.getAuthority()); globalIdComponents.put("studyId", study.getStudyId()); studyVersion = study.getLatestVersion(); resetStudyForHarvesting(studyVersion); } } // Step 2b: initialize new Study if (study == null) { VersionState newVersionState = isHarvest ? StudyVersion.VersionState.RELEASED : StudyVersion.VersionState.DRAFT; study = new Study(vdc, creator, newVersionState); studyVersion = study.getLatestVersion(); // if not a harvest, set initial date of deposit (this may get overridden during map ddi step if (!isHarvest) { studyVersion.getMetadata().setDateOfDeposit(new SimpleDateFormat("yyyy-MM-dd").format(new Date())); } } em.persist(study); // Step 3: map the ddi Map dataFilesMap = null; if (isNesstarHarvest) { dataFilesMap = ddiService.mapDDI(ddiFile, studyVersion, true); } else { dataFilesMap = ddiService.mapDDI(ddiFile, studyVersion, false); } logger.info("doImportStudy: ddi mapped"); //Step 4: post mapping processing if (isHarvest) { study.setIsHarvested(true); study.setHarvestIdentifier(harvestIdentifier); // for Nesstar studies, we are also cooking a link pointing to // the location of this study on their web server, to provide as a // "holdings"/"original archive" in the DVN Study UI. if (isNesstarHarvest) { String nServerURL = vdc.getHarvestingDataverse().getServerUrl(); // chop any trailing slashes in the server URL - or they will result // in multiple slashes in the final URL pointing to the study // on server of origin; Nesstar doesn't like it, apparently. nServerURL = nServerURL.replaceAll("/*$", ""); String nServerURLencoded = nServerURL; nServerURLencoded.replace(":", "%3A"); nServerURLencoded.replace("/", "%2F"); String nWebviewLocation = nServerURL + "/webview/?mode=documentation&submode=abstract&studydoc=" + nServerURLencoded + "%2Fobj%2FfStudy%2F" + harvestIdentifier + "&top=yes"; studyVersion.getMetadata().setHarvestHoldings(nWebviewLocation); } } else { // clear fields related to harvesting studyVersion.getMetadata().setHarvestHoldings(null); studyVersion.getMetadata().setHarvestDVTermsOfUse(null); studyVersion.getMetadata().setHarvestDVNTermsOfUse(null); } //em.flush(); // This flush statement may in fact produce an error condition, // since some of our StudyFiles may not have been persisted yet // We are going to take care of that in the next step; but we // shouldn't be trying to flush until we do. So I'm commenting it // out. -- L.A. // step 5: persist files from ddi (since studyFile is not persisted when the new FileMetadata objects are created - since // the studyFile often already exists - we need to manually persist the study files here) for (FileMetadata fmd : studyVersion.getFileMetadatas()) { em.persist(fmd.getStudyFile()); } if (!isNesstarHarvest) { Map variablesMap = ddiService.reMapDDI(ddiFile, studyVersion, dataFilesMap); logger.info("doImportStudy: ddi re-mapped"); logger.info("reading the variables map;"); if (variablesMap != null) { for (Object mapKey : variablesMap.keySet()) { List<DataVariable> variablesMapEntry = (List<DataVariable>) variablesMap.get(mapKey); Long fileId = (Long) mapKey; if (variablesMapEntry != null) { logger.info("found non-empty map entry for datatable id " + fileId); DataVariable dv = variablesMapEntry.get(0); DataTable tmpDt = dv.getDataTable(); if (tmpDt != null) { tmpDt.setDataVariables(variablesMapEntry); logger.info("added variables to datatable " + tmpDt.getId()); } else { logger.info("first variable on the map for id " + tmpDt.getId() + " is referencing NULL datatable! WTF?"); } } else { logger.info("found empty map entry for datatable id " + fileId); } } } } saveStudyVersion(studyVersion, userId); if (isHarvest) { studyVersion.setReleaseTime(new Date()); } boolean registerHandle = determineId(studyVersion, vdc, globalIdComponents); if (newStudy && !studyService.isUniqueStudyId(study.getStudyId(), study.getProtocol(), study.getAuthority())) { throw new EJBException( "A study with this globalId already exists (likely cause: the study was previously harvested into a different dataverse)."); } // step 5: upload files if (filesToUpload != null) { studyFileService.addFiles(studyVersion, filesToUpload, creator); } // step 6: store the original study files copyXMLFile(study, ddiFile, "original_imported_study.xml"); if (fileTransformed) { copyXMLFile(study, xmlFile, "original_imported_study_pretransform.xml"); } // step 7: register if necessary if (registerHandle && vdcNetworkService.find().isHandleRegistration()) { if (study.getProtocol().equals("hdl") || isHarvest) { study.setProtocol("hdl"); String handle = study.getAuthority() + "/" + study.getStudyId(); gnrsService.createHandle(handle); } if (study.getProtocol().equals("doi")) { doiEZIdServiceLocal.createIdentifier(studyVersion.getStudy()); } } logger.info("completed doImportStudy() returning study" + study.getGlobalId()); return study; } private boolean determineId(StudyVersion sv, VDC vdc, Map<String, String> globalIdComponents) { Study study = sv.getStudy(); VDCNetwork vdcNetwork = vdcNetworkService.find(); String protocol = vdcNetwork.getProtocol(); String authority = vdcNetwork.getAuthority(); String globalId = null; if (!StringUtil.isEmpty(study.getStudyId())) { globalId = study.getGlobalId(); } if (vdc.getHarvestingDataverse() != null) { if (vdc.getHarvestingDataverse().getHandlePrefix() != null) { // FOR THIS HARVESTED DATAVERSE, WE TAKE CARE OF HANDLE GENERATION if (globalId != null) { throw new EJBException("DDI should not specify a handle, but does."); } if (globalIdComponents != null) { study.setProtocol(globalIdComponents.get("protocol")); study.setAuthority(globalIdComponents.get("authority")); study.setStudyId(globalIdComponents.get("studyId")); } else { boolean generateRandom = vdc.getHarvestingDataverse().isGenerateRandomIds(); authority = vdc.getHarvestingDataverse().getHandlePrefix().getPrefix(); generateHandle(sv.getMetadata(), protocol, authority, generateRandom); return true; } } else { if (globalId == null) { // FOR THIS HARVESTED DATAVERSE, THE DDI SHOULD SPECIFY THE HANDLE throw new EJBException("DDI should specify a handle, but does not."); } else if (globalIdComponents != null && !globalId.equals(globalIdComponents.get("globalId"))) { throw new EJBException( "DDI specifies a handle that is different from current handle for this study."); } } } else { // imported study if (globalId == null) { generateHandle(sv.getMetadata(), protocol, authority, true); return true; } } return false; } private void generateHandle(Metadata metadata, String protocol, String authority, boolean generateRandom) { String studyId = null; if (generateRandom) { do { studyId = RandomStringUtils.randomAlphanumeric(5); } while (!isUniqueStudyId(studyId, protocol, authority)); } else { if (metadata.getStudyOtherIds().size() > 0) { studyId = metadata.getStudyOtherIds().get(0).getOtherId(); if (!isValidStudyIdString(studyId)) { throw new EJBException("The Other ID (from DDI) was invalid."); } } else { throw new EJBException("No Other ID (from DDI) was available for generating a handle."); } } Study study = metadata.getStudyVersion().getStudy(); study.setProtocol(protocol); study.setAuthority(authority); study.setStudyId(studyId); } public boolean isValidStudyIdString(String str) { final char[] chars = str.toCharArray(); for (int x = 0; x < chars.length; x++) { final char c = chars[x]; if (StringUtil.isAlphaNumericChar(c) || c == '-' || c == '_' || c == '.') { continue; } return false; } return true; } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public void setIndexTime(Long studyId, Date indexTime) { Study study = em.find(Study.class, studyId); study.setLastIndexTime(indexTime); em.merge(study); } @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) public Study setLinkedToNetworks(Long studyId, List<VDCNetwork> linkedToNetworks) { Study study = em.find(Study.class, studyId); study.setLinkedToNetworks(linkedToNetworks); return em.merge(study); } public Timestamp getLastUpdatedTime(Long vdcId) { String queryString = "SELECT max(lastupdatetime) from study where owner_id=" + vdcId; Query query = em.createNativeQuery(queryString); Timestamp timestamp = (Timestamp) query.getSingleResult(); return timestamp; } public long getStudyDownloadCount(List studyIds) { String queryString = "select sum(downloadcount) " + "from studyfileactivity sfa " + "where sfa.study_id in (" + generateTempTableString(studyIds) + ")"; Long studyDownloadCount = null; Query query = em.createNativeQuery(queryString); try { studyDownloadCount = (Long) query.getSingleResult(); } catch (Exception nre) { } // empty catch; return 0 return studyDownloadCount != null ? studyDownloadCount.longValue() : 0; } public long getStudyDownloadCount(Long studyId) { String queryString = "select sum(downloadcount) " + "from studyfileactivity sfa " + "where sfa.study_id = " + studyId; Long studyDownloadCount = null; Query query = em.createNativeQuery(queryString); try { studyDownloadCount = (Long) query.getSingleResult(); } catch (Exception nre) { } // empty catch; return 0 return studyDownloadCount != null ? studyDownloadCount.longValue() : 0; } public long getStudyFileCount(Long studyId) { String queryString = "SELECT count(f.*) FROM FileMetadata f, studyversion sv " + "WHERE f.studyVersion_id = sv.id" + " and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + " AND SV.STUDY_ID =" + studyId; Long studyDownloadCount = null; Query query = em.createNativeQuery(queryString); try { studyDownloadCount = (Long) query.getSingleResult(); } catch (Exception nre) { } // empty catch; return 0 return studyDownloadCount != null ? studyDownloadCount.longValue() : 0; } public long getStudyFileCount(List studyIds) { String queryString = "SELECT count(f.*) FROM FileMetadata f, studyversion sv " + "WHERE f.studyVersion_id = sv.id" + " and sv.versionstate = '" + StudyVersion.VersionState.RELEASED + "'" + " AND sv.study_id in (" + generateTempTableString(studyIds) + ")"; Long studyDownloadCount = null; Query query = em.createNativeQuery(queryString); try { studyDownloadCount = (Long) query.getSingleResult(); } catch (Exception nre) { } // empty catch; return 0 return studyDownloadCount != null ? studyDownloadCount.longValue() : 0; } // get the sum of downloads of files associated with a particular version public long getStudyVersionDownloadCount(Long studyVersionId) { String queryString = "select sum(downloadcount) " + "from studyfileactivity sfa, studyversion sv, filemetadata fmd " + "where sfa.study_id = sv.study_id " + "and fmd.studyversion_id=sv.id " + "and sfa.studyfile_id=fmd.studyfile_id " + "and sv.id = " + studyVersionId; Long studyDownloadCount = null; Query query = em.createNativeQuery(queryString); try { studyDownloadCount = (Long) query.getSingleResult(); } catch (Exception nre) { } // empty catch; return 0 return studyDownloadCount != null ? studyDownloadCount.longValue() : 0; } public Long getActivityCount(Long vdcId) { String queryString = " select sum(downloadcount) " + "from studyfileactivity sfa, study s " + "where sfa.study_id = s.id " + "and s.owner_id = " + vdcId; Long longValue = null; Query query = em.createNativeQuery(queryString); try { longValue = (Long) query.getSingleResult(); } catch (Exception nre) { longValue = new Long("0"); } finally { return longValue; } } public Long getTotalActivityCount() { String queryString = "select sum(downloadcount) " + "from studyfileactivity sfa, study s " + "where sfa.study_id = s.id"; Query query = em.createNativeQuery(queryString); Long longValue = (Long) query.getSingleResult(); return longValue; } public List<MetadataFormatType> findAllMetadataExportFormatTypes() { String queryStr = "SELECT f FROM MetadataFormatType f"; Query query = em.createQuery(queryStr); return query.getResultList(); } public class ConvertedFilenamesFilter implements FilenameFilter { private String baseName; public ConvertedFilenamesFilter(String baseName) { super(); this.baseName = baseName; } public boolean accept(File dir, String name) { return (name.matches(baseName + "\\.D[0-9]*") || name.equals(baseName + ".RData")); } } public void determineStudiesFromFiles(List studyFiles, List studies, Map fileMap) { Iterator iter = studyFiles.iterator(); while (iter.hasNext()) { Long sfId = (Long) iter.next(); StudyFile studyFile = null; try { studyFile = studyFileService.getStudyFile(sfId); } catch (IllegalArgumentException ex) { System.out.println("Study File (ID=" + sfId + ") was found in index, but is not in DB!"); } if (studyFile != null) { Long studyId = studyFile.getStudy().getId(); if (studies.contains(studyId)) { List fileList = (List) fileMap.get(studyId); fileList.add(studyFile); fileMap.put(studyId, fileList); } else { studies.add(studyId); List fileList = new ArrayList(); fileList.add(studyFile); fileMap.put(studyId, fileList); } } } } public Long getMaxStudyTableId() { Long lastId = null; String queryStr = "SELECT s.id FROM Study s ORDER BY s.id DESC"; Query query = em.createQuery(queryStr).setMaxResults(1); try { lastId = (Long) query.getSingleResult(); } catch (Exception ex) { logger.info("caught exception while trying to determine the last id in the study table."); lastId = null; } return lastId; } }