@Override
public void handle(HttpServletRequest request, HttpServletResponse response, HandlerChain chain)
throws Exception {
final String graphEdgeId = getAttributeString(request, "graphEdgeId");
final String visibilitySource = getRequiredParameter(request, "visibilitySource");
User user = getUser(request);
Authorizations authorizations = getAuthorizations(request, user);
String workspaceId = getActiveWorkspaceId(request);
Edge graphEdge = graph.getEdge(graphEdgeId, authorizations);
if (graphEdge == null) {
respondWithNotFound(response);
return;
}
if (!graph.isVisibilityValid(new Visibility(visibilitySource), authorizations)) {
LOGGER.warn(
"%s is not a valid visibility for %s user", visibilitySource, user.getDisplayName());
respondWithBadRequest(response, "visibilitySource", getString(request, "visibility.invalid"));
chain.next(request, response);
return;
}
LOGGER.info(
"changing edge (%s) visibility source to %s",
graphEdge.getId().toString(), visibilitySource);
GraphUtil.VisibilityAndElementMutation<Edge> setPropertyResult =
GraphUtil.updateElementVisibilitySource(
visibilityTranslator,
graphEdge,
GraphUtil.getSandboxStatus(graphEdge, workspaceId),
visibilitySource,
workspaceId,
authorizations);
auditRepository.auditEdgeElementMutation(
AuditAction.UPDATE,
setPropertyResult.elementMutation,
graphEdge,
graphEdge.getVertex(Direction.OUT, authorizations),
graphEdge.getVertex(Direction.IN, authorizations),
"",
user,
setPropertyResult.visibility.getVisibility());
this.graph.flush();
this.workQueueRepository.pushGraphPropertyQueue(
graphEdge,
null,
LumifyVisibilityProperties.VISIBILITY_JSON_PROPERTY.getPropertyName(),
workspaceId,
visibilitySource);
JSONObject json = JsonSerializer.toJson(graphEdge, workspaceId, authorizations);
respondWithJson(response, json);
}
@Override
public void handle(HttpServletRequest request, HttpServletResponse response, HandlerChain chain)
throws Exception {
LumifyVisibility lumifyVisibility = new LumifyVisibility();
final String propertyName = getRequiredParameter(request, "propertyName");
final String propertyKey = getRequiredParameter(request, "propertyKey");
final String sourceId = getRequiredParameter(request, "source");
final String destId = getRequiredParameter(request, "dest");
final String edgeId = getRequiredParameter(request, "edgeId");
User user = getUser(request);
Authorizations authorizations = getAuthorizations(request, user);
String workspaceId = getActiveWorkspaceId(request);
OntologyProperty property = ontologyRepository.getProperty(propertyName);
if (property == null) {
throw new RuntimeException("Could not find property: " + propertyName);
}
// TODO remove all properties from all edges? I don't think so
Edge edge = graph.getEdge(edgeId, authorizations);
Object oldValue = null;
Property oldProperty = edge.getProperty(propertyKey, propertyName);
if (oldProperty != null) {
oldValue = oldProperty.getValue();
}
// TODO: replace "" when we implement commenting on ui
auditRepository.auditRelationshipProperty(
AuditAction.DELETE,
sourceId,
destId,
propertyKey,
property.getDisplayName(),
oldValue,
null,
edge,
"",
"",
user,
lumifyVisibility.getVisibility());
edge.removeProperty(propertyKey, propertyName, authorizations);
graph.flush();
List<Property> properties = new ArrayList<Property>();
for (Property p : edge.getProperties()) {
properties.add(p);
}
workQueueRepository.pushGraphPropertyQueue(edge, null, propertyName);
JSONArray resultsJson = JsonSerializer.toJsonProperties(properties, workspaceId);
respondWithJson(response, resultsJson);
}
@Override
public void handle(HttpServletRequest request, HttpServletResponse response, HandlerChain chain)
throws Exception {
final String artifactId = getRequiredParameter(request, "artifactId");
final String propertyKey = getRequiredParameter(request, "propertyKey");
final long mentionStart = getRequiredParameterAsLong(request, "mentionStart");
final long mentionEnd = getRequiredParameterAsLong(request, "mentionEnd");
final String title = getRequiredParameter(request, "sign");
final String conceptId = getRequiredParameter(request, "conceptId");
final String visibilitySource = getRequiredParameter(request, "visibilitySource");
final String resolvedVertexId = getOptionalParameter(request, "resolvedVertexId");
final String justificationText = getOptionalParameter(request, "justificationText");
final String sourceInfo = getOptionalParameter(request, "sourceInfo");
String termMentionRowKeyString = getOptionalParameter(request, "rowKey");
User user = getUser(request);
String workspaceId = getActiveWorkspaceId(request);
Workspace workspace = workspaceRepository.findById(workspaceId, user);
Authorizations authorizations = getAuthorizations(request, user);
JSONObject visibilityJson =
GraphUtil.updateVisibilitySourceAndAddWorkspaceId(null, visibilitySource, workspaceId);
LumifyVisibility visibility = this.visibilityTranslator.toVisibility(visibilityJson);
if (!graph.isVisibilityValid(visibility.getVisibility(), authorizations)) {
LOGGER.warn(
"%s is not a valid visibility for %s user", visibilitySource, user.getDisplayName());
respondWithBadRequest(response, "visibilitySource", STRINGS.getString("visibility.invalid"));
chain.next(request, response);
return;
}
Object id = resolvedVertexId == null ? graph.getIdGenerator().nextId() : resolvedVertexId;
Concept concept = ontologyRepository.getConceptByIRI(conceptId);
final Vertex artifactVertex = graph.getVertex(artifactId, authorizations);
LumifyVisibility lumifyVisibility = visibilityTranslator.toVisibility(visibilityJson);
Map<String, Object> metadata = new HashMap<String, Object>();
LumifyVisibilityProperties.VISIBILITY_JSON_PROPERTY.setMetadata(metadata, visibilityJson);
ElementMutation<Vertex> vertexMutation;
Vertex vertex;
if (resolvedVertexId != null) {
vertex = graph.getVertex(id, authorizations);
vertexMutation = vertex.prepareMutation();
} else {
vertexMutation = graph.prepareVertex(id, lumifyVisibility.getVisibility());
GraphUtil.addJustificationToMutation(
vertexMutation, justificationText, sourceInfo, lumifyVisibility);
CONCEPT_TYPE.setProperty(
vertexMutation, conceptId, metadata, lumifyVisibility.getVisibility());
TITLE.addPropertyValue(
vertexMutation, MULTI_VALUE_KEY, title, metadata, lumifyVisibility.getVisibility());
vertex = vertexMutation.save(authorizations);
auditRepository.auditVertexElementMutation(
AuditAction.UPDATE, vertexMutation, vertex, "", user, lumifyVisibility.getVisibility());
LumifyVisibilityProperties.VISIBILITY_JSON_PROPERTY.setProperty(
vertexMutation, visibilityJson, metadata, lumifyVisibility.getVisibility());
this.graph.flush();
workspaceRepository.updateEntityOnWorkspace(
workspace, vertex.getId(), false, null, null, user);
}
// TODO: a better way to check if the same edge exists instead of looking it up every time?
Edge edge =
graph.addEdge(
artifactVertex,
vertex,
this.artifactHasEntityIri,
lumifyVisibility.getVisibility(),
authorizations);
LumifyVisibilityProperties.VISIBILITY_JSON_PROPERTY.setProperty(
edge, visibilityJson, metadata, lumifyVisibility.getVisibility(), authorizations);
auditRepository.auditRelationship(
AuditAction.CREATE,
artifactVertex,
vertex,
edge,
"",
"",
user,
lumifyVisibility.getVisibility());
TermMentionRowKey termMentionRowKey;
if (termMentionRowKeyString != null) {
termMentionRowKey = new TermMentionRowKey(RowKeyHelper.jsonDecode(termMentionRowKeyString));
} else {
termMentionRowKey =
new TermMentionRowKey(
artifactId, propertyKey, mentionStart, mentionEnd, edge.getId().toString());
}
TermMentionModel termMention = new TermMentionModel(termMentionRowKey);
termMention
.getMetadata()
.setSign(title, lumifyVisibility.getVisibility())
.setOntologyClassUri(concept.getDisplayName(), lumifyVisibility.getVisibility())
.setConceptGraphVertexId(concept.getTitle(), lumifyVisibility.getVisibility())
.setVertexId(vertex.getId().toString(), lumifyVisibility.getVisibility())
.setEdgeId(edge.getId().toString(), lumifyVisibility.getVisibility());
termMentionRepository.save(termMention);
vertexMutation.addPropertyValue(
graph.getIdGenerator().nextId().toString(),
LumifyProperties.ROW_KEY.getPropertyName(),
termMentionRowKey.toString(),
metadata,
lumifyVisibility.getVisibility());
vertexMutation.save(authorizations);
this.graph.flush();
workQueueRepository.pushTextUpdated(artifactId);
workQueueRepository.pushElement(edge);
JSONObject result = new JSONObject();
result.put("success", true);
respondWithJson(response, result);
}
private TermMentionWithGraphVertex saveTermMention(
Vertex artifactGraphVertex,
TermMention termMention,
String workspaceId,
String visibilitySource) {
LOGGER.debug(
"Saving term mention '%s':%s:%s (%d:%d)",
termMention.getSign(),
termMention.getOntologyClassUri(),
termMention.getPropertyKey(),
termMention.getStart(),
termMention.getEnd());
Vertex vertex = null;
if (visibilitySource == null) {
visibilitySource = termMention.getVisibility().getVisibilityString();
}
JSONObject visibilityJson = new JSONObject();
visibilityJson.put(VisibilityTranslator.JSON_SOURCE, visibilitySource);
Visibility visibility = visibilityTranslator.toVisibility(visibilityJson).getVisibility();
Visibility visibilityWithWorkspaceId;
JSONObject visibilityJsonWithWorkspaceId;
if (!workspaceId.equals("")) {
visibilityJsonWithWorkspaceId =
GraphUtil.updateVisibilitySourceAndAddWorkspaceId(null, visibilitySource, workspaceId);
visibilityWithWorkspaceId =
visibilityTranslator.toVisibility(visibilityJsonWithWorkspaceId).getVisibility();
} else {
visibilityWithWorkspaceId = visibility;
visibilityJsonWithWorkspaceId = visibilityJson;
}
TermMentionRowKey termMentionRowKey =
new TermMentionRowKey(
artifactGraphVertex.getId().toString(),
termMention.getPropertyKey(),
termMention.getStart(),
termMention.getEnd());
TermMentionModel termMentionModel = new TermMentionModel(termMentionRowKey);
termMentionModel.getMetadata().setSign(termMention.getSign(), visibility);
termMentionModel
.getMetadata()
.setOntologyClassUri(termMention.getOntologyClassUri(), visibility);
if (termMention.getProcess() != null && !termMention.getProcess().equals("")) {
termMentionModel.getMetadata().setAnalyticProcess(termMention.getProcess(), visibility);
}
Concept concept = ontologyRepository.getConceptByIRI(termMention.getOntologyClassUri());
if (concept == null) {
LOGGER.error("Could not find ontology graph vertex '%s'", termMention.getOntologyClassUri());
return null;
}
termMentionModel.getMetadata().setConceptGraphVertexId(concept.getTitle(), visibility);
if (termMention.isResolved()) {
String title = termMention.getSign();
ElementMutation<Vertex> vertexElementMutation;
if (termMention.getUseExisting()) {
graph.flush(); // make sure the previous term mentions have made it into the graph
if (termMention.getId() != null) {
vertex = graph.getVertex(termMention.getId(), getAuthorizations());
} else {
vertex =
singleOrDefault(
graph
.query(getAuthorizations())
.has(LumifyProperties.TITLE.getPropertyName(), title)
.has(LumifyProperties.CONCEPT_TYPE.getPropertyName(), concept.getTitle())
.vertices(),
null);
}
}
Map<String, Object> metadata = new HashMap<String, Object>();
LumifyVisibilityProperties.VISIBILITY_JSON_PROPERTY.setMetadata(
metadata, visibilityJsonWithWorkspaceId);
if (vertex == null) {
if (termMention.getId() != null) {
vertexElementMutation =
graph.prepareVertex(termMention.getId(), visibilityWithWorkspaceId);
} else {
vertexElementMutation = graph.prepareVertex(visibilityWithWorkspaceId);
}
LumifyProperties.TITLE.setProperty(
vertexElementMutation, title, metadata, visibilityWithWorkspaceId);
LumifyProperties.CONCEPT_TYPE.setProperty(
vertexElementMutation, concept.getTitle(), metadata, visibilityWithWorkspaceId);
} else {
vertexElementMutation = vertex.prepareMutation();
}
for (TermMention.TermMentionProperty termMentionProperty : termMention.getNewProperties()) {
vertexElementMutation.addPropertyValue(
termMentionProperty.getKey(),
termMentionProperty.getName(),
termMentionProperty.getValue(),
metadata,
visibilityWithWorkspaceId);
}
LumifyVisibilityProperties.VISIBILITY_JSON_PROPERTY.setProperty(
vertexElementMutation,
visibilityJsonWithWorkspaceId,
metadata,
visibilityWithWorkspaceId);
vertexElementMutation.addPropertyValue(
graph.getIdGenerator().nextId(),
LumifyProperties.ROW_KEY.getPropertyName(),
termMentionRowKey.toString(),
metadata,
visibilityWithWorkspaceId);
if (!(vertexElementMutation instanceof ExistingElementMutation)) {
vertex = vertexElementMutation.save(getAuthorizations());
auditRepository.auditVertexElementMutation(
AuditAction.UPDATE,
vertexElementMutation,
vertex,
termMention.getProcess(),
getUser(),
visibilityWithWorkspaceId);
} else {
auditRepository.auditVertexElementMutation(
AuditAction.UPDATE,
vertexElementMutation,
vertex,
termMention.getProcess(),
getUser(),
visibilityWithWorkspaceId);
vertex = vertexElementMutation.save(getAuthorizations());
}
// TODO: a better way to check if the same edge exists instead of looking it up every time?
Edge edge =
singleOrDefault(
artifactGraphVertex.getEdges(
vertex, Direction.OUT, artifactHasEntityIri, getAuthorizations()),
null);
if (edge == null) {
edge =
graph.addEdge(
artifactGraphVertex, vertex, artifactHasEntityIri, visibility, getAuthorizations());
LumifyVisibilityProperties.VISIBILITY_JSON_PROPERTY.setProperty(
edge,
visibilityJsonWithWorkspaceId,
metadata,
visibilityWithWorkspaceId,
getAuthorizations());
auditRepository.auditRelationship(
AuditAction.CREATE,
artifactGraphVertex,
vertex,
edge,
termMention.getProcess(),
"",
getUser(),
visibilityWithWorkspaceId);
}
graph.flush();
if (workspaceId != null && !workspaceId.equals("")) {
Workspace workspace = workspaceRepository.findById(workspaceId, getUser());
workspaceRepository.updateEntityOnWorkspace(
workspace, vertex.getId(), null, null, null, getUser());
}
termMentionModel
.getMetadata()
.setVertexId(vertex.getId().toString(), visibility)
.setEdgeId(edge.getId().toString(), visibility);
}
getTermMentionRepository().save(termMentionModel, FlushFlag.NO_FLUSH);
return new TermMentionWithGraphVertex(termMentionModel, vertex);
}
