public VDC find(Object pk) {
VDC vdc = (VDC) em.find(VDC.class, pk);
VDCCollection rootCollection = vdc.getRootCollection();
rootCollection.getId();
Collection<VDCCollection> subcollections = rootCollection.getSubCollections();
traverseCollections(subcollections);
return vdc;
}
public Map getVdcTemplatesMap(Long vdcId) {
VDC vdc = em.find(VDC.class, vdcId);
Map templatesMap = new LinkedHashMap();
Template defaultNetworkTemplate = vdcNetworkService.find().getDefaultTemplate();
templatesMap.put(defaultNetworkTemplate.getName(), defaultNetworkTemplate.getId());
Collection<Template> vdcTemplates = vdc.getTemplates();
if (vdcTemplates != null) {
for (Template template : vdcTemplates) {
templatesMap.put(template.getName(), template.getId());
}
}
return templatesMap;
}
/* updateScholarDVs
*
* This is not currently used. It was
* developed for 16a, but there is an
* issue with casting and the java
* persistence layer.
* Leaving it here as a placeholder.
*
*
* @author wbossons
*/
public VDC updateScholarDVs(VDC scholarDV) {
//
String updateString =
"update vdc set firstname = '"
+ scholarDV.getFirstName()
+ "', lastname='"
+ scholarDV.getLastName()
+ "', name='"
+ scholarDV.getName()
+ "', alias='"
+ scholarDV.getAlias()
+ "', affiliation='"
+ scholarDV.getAffiliation()
+ "', dtype = 'Scholar' where id = "
+ scholarDV.getId();
Connection conn = null;
PreparedStatement updateStatement = null;
try {
conn = dvnDatasource.getConnection();
updateStatement = conn.prepareStatement(updateString);
int rowcount = updateStatement.executeUpdate();
} catch (java.sql.SQLException e) {
// Do nothing, just return null.
}
em.flush();
VDC scholardataverse = em.find(VDC.class, scholarDV.getId());
return scholardataverse;
//
}
/**
* This method implements the interface defined in DefinitionHandler to save definition to
* database backend.
*
* @param d is the Definition that is ready to be stored.
* @return true, if new version was stored and database modified, false, if the definition was
* rejected for any reason.
*/
public boolean store(Definition d) {
boolean result = false;
VDC vdc = (VDC) m_dbschema;
// NEW: remember all DVs we came across
if (m_derivations != null && d instanceof Derivation) m_derivations.add(d.shortID());
try {
if (m_rejects == null) {
// rely on saveDefinition to do "the right thing"
result = vdc.saveDefinition(d, m_overwrite);
} else {
// Is the Definition already in the database?
if (vdc.containsDefinition(d)) {
if (m_overwrite) {
// this is time-consuming and ineffective
Definition old =
vdc.loadDefinition(d.getNamespace(), d.getName(), d.getVersion(), d.getType());
old.toXML(m_rejects, " ");
result = vdc.saveDefinition(d, true);
} else {
// skip, if not forced to overwrite, but save rejects
d.toXML(m_rejects, " ");
}
} else {
// not found, insert unconditionally
result = vdc.saveDefinition(d, true);
}
}
} catch (SQLException sql) {
// database problems
for (int i = 0; sql != null; ++i) {
m_logger.log(
"database", 0, "SQL error " + i + ": " + sql.getErrorCode() + ": " + sql.getMessage());
sql = sql.getNextException();
}
m_logger.log("database", 0, "ignoring SQL exception(s)");
} catch (Exception e) {
m_logger.log("database", 0, "caught " + e + ", ignoring");
result = false;
}
if (result) m_count++;
else m_rejected++;
return result;
}
public void updateDefaultTemplate(Long vdcId, Long templateId) {
VDC vdc = em.find(VDC.class, vdcId);
Template template = em.find(Template.class, templateId);
vdc.setDefaultTemplate(template);
}
public void delete(Long vdcId) {
VDC vdc = em.find(VDC.class, vdcId);
em.refresh(vdc);
List studyIds = new ArrayList();
// Get the studyIds separately, to avoid a ConcurrentAccess Exception
// (This is necessary because the studies are deleted in Native SQL)
for (Iterator it = vdc.getOwnedStudies().iterator(); it.hasNext(); ) {
Study elem = (Study) it.next();
studyIds.add(elem.getId());
}
if (!studyIds.isEmpty()) {
studyService.deleteStudyList(studyIds);
}
vdc.getOwnedStudies().clear();
vdc.setRootCollection(null);
for (Iterator it = vdc.getOwnedCollections().iterator(); it.hasNext(); ) {
VDCCollection elem = (VDCCollection) it.next();
elem.setParentCollection(null);
elem.setOwner(null);
// Remove this Collection from all linked VDCs
for (Iterator itc = elem.getLinkedVDCs().iterator(); itc.hasNext(); ) {
VDC linkedVDC = (VDC) itc.next();
linkedVDC.getLinkedCollections().remove(elem);
}
}
for (Iterator it = vdc.getLinkedCollections().iterator(); it.hasNext(); ) {
VDCCollection elem = (VDCCollection) it.next();
VDCCollection coll = em.find(VDCCollection.class, elem.getId());
coll.getLinkedVDCs().remove(vdc);
}
for (Iterator it = vdc.getVdcGroups().iterator(); it.hasNext(); ) {
VDCGroup vdcGroup = (VDCGroup) it.next();
vdcGroup.getVdcs().remove(vdc);
}
for (Iterator it = vdc.getVdcRoles().iterator(); it.hasNext(); ) {
VDCRole vdcRole = (VDCRole) it.next();
VDCUser vdcUser = vdcRole.getVdcUser();
vdcUser.getVdcRoles().remove(vdcRole);
}
if (vdc.isHarvestingDv()) {
harvesterService.removeHarvestTimer(vdc.getHarvestingDataverse());
}
// If the vdc Default Template is in the list of dataverse templates
// (not the Network Default Template), then remove the reference before deleting the dataverse.
// If not removed, you will get a foreign key violation when the persistence logic deletes
// the collection of templates.
if (vdc.getTemplates().contains(vdc.getDefaultTemplate())) {
vdc.setDefaultTemplate(null);
}
em.remove(vdc);
}
public List getLinkedCollections(VDC vdc, boolean getHiddenCollections) {
// getHiddenCollections is no longer used
return vdc.getLinkedCollections();
}
private void create(VDCUser user, String name, String alias, String dtype, List studyFields) {
VDC addedSite = new VDC();
addedSite.setCreator(user);
VDCNetwork vdcNetwork = vdcNetworkService.find(new Long(1));
addedSite.setDefaultTemplate(vdcNetwork.getDefaultTemplate());
em.persist(addedSite);
addedSite.setName(name);
addedSite.setAlias(alias);
addedSite.setDtype(dtype);
addedSite.setCreatedDate(DateUtil.getTimestamp());
addedSite.getRootCollection().setName(name);
addedSite.setDefaultTemplate(vdcNetwork.getDefaultTemplate());
addedSite.setHeader(vdcNetwork.getDefaultVDCHeader());
addedSite.setFooter(vdcNetwork.getDefaultVDCFooter());
addedSite.setRestricted(true);
addedSite.setDisplayAnnouncements(false);
ArrayList advancedSearchFields = new ArrayList();
ArrayList searchResultsFields = new ArrayList();
for (Iterator it = studyFields.iterator(); it.hasNext(); ) {
StudyField elem = (StudyField) it.next();
if (elem.isAdvancedSearchField()) {
advancedSearchFields.add(elem);
}
if (elem.isSearchResultField()) {
searchResultsFields.add(elem);
}
}
addedSite.setAdvSearchFields(advancedSearchFields);
addedSite.setSearchResultFields(searchResultsFields);
userService.addVdcRole(
user.getId(), findByAlias(addedSite.getAlias()).getId(), roleService.ADMIN);
}
/** scholar dataverse */
private void createScholarDataverse(
Long userId,
String firstName,
String lastName,
String name,
String affiliation,
String alias,
String dataverseType,
List studyFields) {
VDC sDV = new VDC();
em.persist(sDV);
sDV.setCreator(em.find(VDCUser.class, userId));
sDV.setName(name);
sDV.setFirstName(firstName);
sDV.setLastName(lastName);
sDV.setAffiliation(affiliation);
sDV.setName(name);
sDV.setAlias(alias);
sDV.setDtype(dataverseType);
sDV.setCreatedDate(DateUtil.getTimestamp());
sDV.getRootCollection().setName(name);
VDCNetwork vdcNetwork = vdcNetworkService.find(new Long(1));
sDV.setDefaultTemplate(vdcNetwork.getDefaultTemplate());
sDV.setHeader(vdcNetwork.getDefaultVDCHeader());
sDV.setFooter(vdcNetwork.getDefaultVDCFooter());
sDV.setRestricted(true);
sDV.setDisplayAnnouncements(false);
ArrayList advancedSearchFields = new ArrayList();
ArrayList searchResultsFields = new ArrayList();
for (Iterator it = studyFields.iterator(); it.hasNext(); ) {
StudyField elem = (StudyField) it.next();
if (elem.isAdvancedSearchField()) {
advancedSearchFields.add(elem);
}
if (elem.isSearchResultField()) {
searchResultsFields.add(elem);
}
}
sDV.setAdvSearchFields(advancedSearchFields);
sDV.setSearchResultFields(searchResultsFields);
userService.addVdcRole(userId, findByAlias(sDV.getAlias()).getId(), roleService.ADMIN);
}
public void addContributorRequest(Long vdcId, Long userId) {
Role contributor = (Role) roleService.findByName(RoleServiceLocal.CONTRIBUTOR);
VDC vdc = em.find(VDC.class, vdcId);
VDCUser user = em.find(VDCUser.class, userId);
RoleRequest roleRequest = new RoleRequest();
roleRequest.setRole(contributor);
roleRequest.setVdcUser(user);
roleRequest.setVdc(vdc);
vdc.getRoleRequests().add(roleRequest);
}
