public ArrayList<History> getHistory(String userId, long entryId) {
Entry entry = dao.get(entryId);
if (entry == null) return null;
authorization.expectWrite(userId, entry);
List<Audit> list = auditDAO.getAuditsForEntry(entry);
ArrayList<History> result = new ArrayList<>();
for (Audit audit : list) {
History history = audit.toDataTransferObject();
if (history.isLocalUser()) {
history.setAccount(
accountController.getByEmail(history.getUserId()).toDataTransferObject());
}
result.add(history);
}
return result;
}
private Audit auditRelationshipHelper(
Audit audit,
AuditAction action,
Vertex sourceVertex,
Vertex destVertex,
String label,
String process,
String comment,
User user,
Visibility visibility) {
visibility = orVisibility(visibility);
audit
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_RELATIONSHIP, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
audit
.getAuditRelationship()
.setSourceId(sourceVertex.getId(), visibility)
.setSourceType(CONCEPT_TYPE.getPropertyValue(sourceVertex), visibility)
.setSourceTitle(TITLE.getPropertyValue(sourceVertex), visibility)
.setDestId(destVertex.getId(), visibility)
.setDestTitle(TITLE.getPropertyValue(destVertex), visibility)
.setDestType(CONCEPT_TYPE.getPropertyValue(destVertex), visibility)
.setLabel(label, visibility);
return audit;
}
public Audit auditVertex(
AuditAction auditAction,
Object vertexId,
String process,
String comment,
User user,
FlushFlag flushFlag,
Visibility visibility) {
checkNotNull(vertexId, "vertexId cannot be null");
checkNotNull(comment, "comment cannot be null");
checkNotNull(user, "user cannot be null");
checkNotNull(process, "process cannot be null");
Audit audit = new Audit(AuditRowKey.build(vertexId));
visibility = orVisibility(visibility);
audit
.getAuditCommon()
.setUser(user, visibility)
.setAction(auditAction, visibility)
.setType(OntologyRepository.ENTITY_CONCEPT_IRI, visibility)
.setComment(comment, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
if (process.length() > 0) {
audit.getAuditCommon().setProcess(process, visibility);
}
save(audit, flushFlag);
return audit;
}
protected PartData retrieveEntryDetails(String userId, Entry entry) {
// user must be able to read if not public entry
if (!permissionsController.isPubliclyVisible(entry)) authorization.expectRead(userId, entry);
PartData partData = ModelToInfoFactory.getInfo(entry);
if (partData == null) return null;
boolean hasSequence = sequenceDAO.hasSequence(entry.getId());
partData.setHasSequence(hasSequence);
boolean hasOriginalSequence = sequenceDAO.hasOriginalSequence(entry.getId());
partData.setHasOriginalSequence(hasOriginalSequence);
// permissions
partData.setCanEdit(authorization.canWriteThoroughCheck(userId, entry));
partData.setPublicRead(permissionsController.isPubliclyVisible(entry));
// create audit event if not owner
// todo : remote access check
if (userId != null
&& authorization.getOwner(entry) != null
&& !authorization.getOwner(entry).equalsIgnoreCase(userId)) {
try {
Audit audit = new Audit();
audit.setAction(AuditType.READ.getAbbrev());
audit.setEntry(entry);
audit.setUserId(userId);
audit.setLocalUser(true);
audit.setTime(new Date(System.currentTimeMillis()));
auditDAO.create(audit);
} catch (Exception e) {
Logger.error(e);
}
}
// retrieve more information about linked entries if any (default only contains id)
if (partData.getLinkedParts() != null) {
ArrayList<PartData> newLinks = new ArrayList<>();
for (PartData link : partData.getLinkedParts()) {
Entry linkedEntry = dao.get(link.getId());
if (!authorization.canRead(userId, linkedEntry)) continue;
link = ModelToInfoFactory.createTipView(linkedEntry);
Sequence sequence = sequenceDAO.getByEntry(linkedEntry);
if (sequence != null) {
link.setBasePairCount(sequence.getSequence().length());
link.setFeatureCount(sequence.getSequenceFeatures().size());
}
newLinks.add(link);
}
partData.getLinkedParts().clear();
partData.getLinkedParts().addAll(newLinks);
}
// check if there is a parent available
List<Entry> parents = dao.getParents(entry.getId());
if (parents == null) return partData;
for (Entry parent : parents) {
if (!authorization.canRead(userId, parent)) continue;
if (parent.getVisibility() != Visibility.OK.getValue()
&& !authorization.canWriteThoroughCheck(userId, entry)) continue;
EntryType type = EntryType.nameToType(parent.getRecordType());
PartData parentData = new PartData(type);
parentData.setId(parent.getId());
parentData.setName(parent.getName());
parentData.setVisibility(Visibility.valueToEnum(parent.getVisibility()));
partData.getParents().add(parentData);
}
return partData;
}
/**
* Called by the main class to initialize defaults.
*
* @param projectName the project name
* @param username the authenticated username
* @exception PersisterException if an error occurs
*/
public void initParams(String projectName, String username) throws PersisterException {
audit = DomainObjectFactory.newAudit();
audit.setCreatedBy(username);
this.projectName = projectName;
// !!!! TODO Use version Too
LoaderDefault loaderDefault = loaderDAO.findByName(projectName);
if (loaderDefault == null) {
throw new PersisterException("Defaults not found. Please create a profile first.");
}
String cName = loaderDefault.getContextName();
if (cName == null) {
throw new PersisterException("Context Name not Set.");
}
context = contextDAO.findByName(cName);
if (context == null) {
throw new PersisterException("Context: " + cName + " not found.");
}
version = new Float(loaderDefault.getVersion().toString());
projectVersion = loaderDefault.getProjectVersion().toString();
workflowStatus = loaderDefault.getWorkflowStatus();
if (workflowStatus == null) {
throw new PersisterException("WorkflowStatus not Set.");
}
conceptualDomain = DomainObjectFactory.newConceptualDomain();
conceptualDomain.setPreferredName(loaderDefault.getCdName());
Context cdContext = contextDAO.findByName(loaderDefault.getCdContextName());
if (cdContext == null) {
throw new PersisterException("CD Context not found.");
}
conceptualDomain.setContext(cdContext);
try {
conceptualDomain = (ConceptualDomain) conceptualDomainDAO.find(conceptualDomain).get(0);
} catch (NullPointerException e) {
throw new PersisterException("CD: " + conceptualDomain.getPreferredName() + " not found.");
}
logger.info("List of packages that will be processed:");
String[] pkgs = loaderDefault.getPackageFilter().split(",");
for (int i = 0; i < pkgs.length; i++) {
String s = pkgs[i].trim();
int ind = s.indexOf(">");
String alias = null;
String pkg = null;
if (ind > 0) {
alias = s.substring(1, ind).trim();
pkg = s.substring(ind + 1).trim();
} else {
alias = pkg = s;
}
packageFilter.put(pkg, alias);
logger.info("Package: " + pkg + " -- Alias: " + alias);
}
logger.info("End of package list.");
}
public List<Audit> auditRelationshipProperty(
AuditAction action,
String sourceId,
String destId,
String propertyName,
Object oldValue,
Object newValue,
Edge edge,
String process,
String comment,
User user,
Visibility visibility) {
checkNotNull(action, "action cannot be null");
checkNotNull(sourceId, "sourceId cannot be null");
checkNotNull(sourceId.length() > 0, "sourceId cannot be empty");
checkNotNull(destId, "destId cannot be null");
checkNotNull(destId.length() > 0, "destId cannot be empty");
checkNotNull(propertyName, "propertyName cannot be null");
checkNotNull(propertyName.length() > 0, "propertyName cannot be empty");
checkNotNull(edge, "edge cannot be null");
checkNotNull(process, "process cannot be null");
checkNotNull(comment, "comment cannot be null");
checkNotNull(user, "user cannot be null");
Audit auditSourceDest = new Audit(AuditRowKey.build(sourceId, destId));
Audit auditDestSource = new Audit(AuditRowKey.build(destId, sourceId));
Audit auditEdge = new Audit(AuditRowKey.build(edge.getId()));
visibility = orVisibility(visibility);
auditSourceDest
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_PROPERTY, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
auditDestSource
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_PROPERTY, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
auditEdge
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_PROPERTY, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
if (oldValue != null && !oldValue.equals("")) {
auditDestSource.getAuditProperty().setPreviousValue(oldValue, visibility);
auditSourceDest.getAuditProperty().setPreviousValue(oldValue, visibility);
auditEdge.getAuditProperty().setPreviousValue(oldValue, visibility);
}
if (action == AuditAction.DELETE) {
auditDestSource.getAuditProperty().setNewValue("", visibility);
auditSourceDest.getAuditProperty().setNewValue("", visibility);
auditEdge.getAuditProperty().setNewValue("", visibility);
} else {
// TODO handle multi-valued properties
auditDestSource.getAuditProperty().setNewValue(newValue, visibility);
auditSourceDest.getAuditProperty().setNewValue(newValue, visibility);
auditEdge.getAuditProperty().setNewValue(newValue, visibility);
}
auditDestSource.getAuditProperty().setPropertyName(propertyName, visibility);
auditSourceDest.getAuditProperty().setPropertyName(propertyName, visibility);
auditEdge.getAuditProperty().setPropertyName(propertyName, visibility);
List<Audit> audits = Lists.newArrayList(auditSourceDest, auditDestSource);
saveMany(audits);
return audits;
}
public List<Audit> auditRelationship(
AuditAction action,
Vertex sourceVertex,
Vertex destVertex,
Edge edge,
String process,
String comment,
User user,
Visibility visibility) {
checkNotNull(action, "action cannot be null");
checkNotNull(sourceVertex, "sourceVertex cannot be null");
checkNotNull(destVertex, "destVertex cannot be null");
checkNotNull(edge, "edge cannot be null");
checkNotNull(process, "process cannot be null");
checkNotNull(comment, "comment cannot be null");
checkNotNull(user, "user cannot be null");
Audit auditSourceDest = new Audit(AuditRowKey.build(sourceVertex.getId(), destVertex.getId()));
Audit auditDestSource = new Audit(AuditRowKey.build(destVertex.getId(), sourceVertex.getId()));
Audit auditEdge = new Audit(AuditRowKey.build(edge.getId()));
visibility = orVisibility(visibility);
List<Audit> audits = new ArrayList<Audit>();
String displayLabel = ontologyRepository.getDisplayNameForLabel(edge.getLabel());
audits.add(
auditRelationshipHelper(
auditSourceDest,
action,
sourceVertex,
destVertex,
displayLabel,
process,
comment,
user,
visibility));
audits.add(
auditRelationshipHelper(
auditDestSource,
action,
sourceVertex,
destVertex,
displayLabel,
process,
comment,
user,
visibility));
auditEdge
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_RELATIONSHIP, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
auditEdge
.getAuditRelationship()
.setSourceId(sourceVertex.getId(), visibility)
.setSourceType(CONCEPT_TYPE.getPropertyValue(sourceVertex), visibility)
.setSourceTitle(TITLE.getPropertyValue(sourceVertex), visibility)
.setDestId(destVertex.getId(), visibility)
.setDestTitle(TITLE.getPropertyValue(destVertex), visibility)
.setDestType(CONCEPT_TYPE.getPropertyValue(destVertex), visibility)
.setLabel(displayLabel, visibility);
audits.add(auditEdge);
saveMany(audits);
return audits;
}
public Audit auditEntityProperty(
AuditAction action,
Object id,
String propertyName,
Object oldValue,
Object newValue,
String process,
String comment,
Map<String, Object> metadata,
User user,
Visibility visibility) {
checkNotNull(action, "action cannot be null");
checkNotNull(id, "id cannot be null");
checkNotNull(propertyName, "propertyName cannot be null");
checkArgument(propertyName.length() > 0, "property name cannot be empty");
checkNotNull(process, "process cannot be null");
checkNotNull(comment, "comment cannot be null");
checkNotNull(user, "user cannot be null");
Audit audit = new Audit(AuditRowKey.build(id));
visibility = orVisibility(visibility);
audit
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_PROPERTY, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
if (oldValue != null) {
if (oldValue instanceof GeoPoint) {
String val =
String.format(
"POINT(%f,%f)",
((GeoPoint) oldValue).getLatitude(), ((GeoPoint) oldValue).getLongitude());
audit.getAuditProperty().setPreviousValue(val, visibility);
} else {
audit.getAuditProperty().setPreviousValue(oldValue.toString(), visibility);
}
}
if (action == AuditAction.DELETE) {
audit.getAuditProperty().setNewValue("", visibility);
} else {
if (newValue instanceof GeoPoint) {
String val =
String.format(
"POINT(%f,%f)",
((GeoPoint) newValue).getLatitude(), ((GeoPoint) newValue).getLongitude());
audit.getAuditProperty().setNewValue(val, visibility);
} else {
audit.getAuditProperty().setNewValue(newValue.toString(), visibility);
}
}
audit.getAuditProperty().setPropertyName(propertyName, visibility);
if (metadata != null || !metadata.isEmpty()) {
audit.getAuditProperty().setPropertyMetadata(jsonMetadata(metadata).toString(), visibility);
}
save(audit);
return audit;
}
