@Before
public void setup() {
Visibility visibility = new Visibility("");
Authorizations authorizations = new InMemoryAuthorizations();
InMemoryGraphConfiguration config = new InMemoryGraphConfiguration(new HashMap());
idGenerator = new QueueIdGenerator();
graph = new InMemoryGraph(config, idGenerator, new DefaultSearchIndex(config.getConfig()));
authorizationRepository = new InMemoryAuthorizationRepository();
Configuration lumifyConfiguration =
new HashMapConfigurationLoader(new HashMap()).createConfiguration();
InMemoryUserRepository userRepository =
new InMemoryUserRepository(lumifyConfiguration, userListenerUtil);
user1 = (InMemoryUser) userRepository.addUser("user2", "user2", null, "none", new String[0]);
graph.addVertex(user1.getUserId(), visibility, authorizations);
user2 = (InMemoryUser) userRepository.addUser("user2", "user2", null, "none", new String[0]);
graph.addVertex(user2.getUserId(), visibility, authorizations);
when(ontologyRepository.getConceptByIRI(eq(OntologyRepository.ROOT_CONCEPT_IRI)))
.thenReturn(rootConcept);
when(ontologyRepository.getOrCreateConcept(
(Concept) isNull(),
eq(WorkspaceRepository.WORKSPACE_CONCEPT_NAME),
anyString(),
(java.io.File) anyObject()))
.thenReturn(workspaceConcept);
when(workspaceConcept.getTitle()).thenReturn(WorkspaceRepository.WORKSPACE_CONCEPT_NAME);
when(workspaceToEntityRelationship.getIRI()).thenReturn("workspaceToEntityRelationshipId");
when(ontologyRepository.getOrCreateRelationshipType(
eq(workspaceConcept),
eq(rootConcept),
eq(WorkspaceRepository.WORKSPACE_TO_ENTITY_RELATIONSHIP_NAME),
anyString()))
.thenReturn(workspaceToEntityRelationship);
when(workspaceToUserRelationship.getIRI()).thenReturn("workspaceToUserRelationshipId");
when(ontologyRepository.getOrCreateRelationshipType(
eq(workspaceConcept),
eq(rootConcept),
eq(WorkspaceRepository.WORKSPACE_TO_USER_RELATIONSHIP_NAME),
anyString()))
.thenReturn(workspaceToUserRelationship);
workspaceRepository =
new SecureGraphWorkspaceRepository(
ontologyRepository, graph, userRepository, authorizationRepository, workspaceDiff);
String entity1VertexId = "entity1Id";
entity1Vertex =
graph.addVertex(
entity1VertexId, new LumifyVisibility().getVisibility(), new InMemoryAuthorizations());
}
private void verifyWikipediaPageConcept(OntologyRepository ontologyRepository) {
Concept wikipediaPageConcept =
ontologyRepository.getConceptByIRI(WikipediaConstants.WIKIPEDIA_PAGE_CONCEPT_URI);
if (wikipediaPageConcept == null) {
throw new RuntimeException(
WikipediaConstants.WIKIPEDIA_PAGE_CONCEPT_URI + " concept not found");
}
}
private void verifyWikipediaPageInternalLinkWikipediaPageRelationship(
OntologyRepository ontologyRepository) {
Relationship wikipediaPageInternalLinkWikipediaPageRelationship =
ontologyRepository.getRelationshipByIRI(
WikipediaConstants.WIKIPEDIA_PAGE_INTERNAL_LINK_WIKIPEDIA_PAGE_CONCEPT_URI);
if (wikipediaPageInternalLinkWikipediaPageRelationship == null) {
throw new RuntimeException(
WikipediaConstants.WIKIPEDIA_PAGE_INTERNAL_LINK_WIKIPEDIA_PAGE_CONCEPT_URI
+ " relationship not found");
}
}
@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 {
ClientApiOntology result = ontologyRepository.getClientApiObject();
String json = ObjectMapperFactory.getInstance().writeValueAsString(result);
String eTag = generateETag(json.getBytes());
if (testEtagHeaders(request, response, eTag)) {
return;
}
addETagHeader(response, eTag);
respondWithClientApiObject(response, result);
}
@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);
}
@Override
public void handle(HttpServletRequest request, HttpServletResponse response, HandlerChain chain)
throws Exception {
long totalStartTime = System.nanoTime();
final String query;
final String filter = getRequiredParameter(request, "filter");
final int offset = (int) getOptionalParameterLong(request, "offset", 0);
final int size = (int) getOptionalParameterLong(request, "size", DEFAULT_RESULT_COUNT);
final String conceptType = getOptionalParameter(request, "conceptType");
final String getLeafNodes = getOptionalParameter(request, "leafNodes");
final String relatedToVertexId = getOptionalParameter(request, "relatedToVertexId");
if (relatedToVertexId == null) {
query = getRequiredParameter(request, "q");
} else {
query = getOptionalParameter(request, "q");
}
long startTime = System.nanoTime();
User user = getUser(request);
Authorizations authorizations = getAuthorizations(request, user);
String workspaceId = getActiveWorkspaceId(request);
ModelUserContext modelUserContext =
userRepository.getModelUserContext(authorizations, workspaceId);
JSONArray filterJson = new JSONArray(filter);
ontologyRepository.resolvePropertyIds(filterJson);
graph.flush();
LOGGER.debug("search %s\n%s", query, filterJson.toString(2));
Query graphQuery;
if (relatedToVertexId == null) {
graphQuery = graph.query(query, authorizations);
} else if (query == null || StringUtils.isBlank(query)) {
graphQuery = graph.getVertex(relatedToVertexId, authorizations).query(authorizations);
} else {
graphQuery = graph.getVertex(relatedToVertexId, authorizations).query(query, authorizations);
}
for (int i = 0; i < filterJson.length(); i++) {
JSONObject obj = filterJson.getJSONObject(i);
if (obj.length() > 0) {
updateQueryWithFilter(graphQuery, obj);
}
}
if (conceptType != null) {
Concept concept = ontologyRepository.getConceptByIRI(conceptType);
if (getLeafNodes == null || !getLeafNodes.equals("false")) {
List<Concept> leafNodeList = ontologyRepository.getAllLeafNodesByConcept(concept);
if (leafNodeList.size() > 0) {
String[] conceptIds = new String[leafNodeList.size()];
int count = 0;
for (Concept c : leafNodeList) {
conceptIds[count] = c.getTitle();
count++;
}
graphQuery.has(CONCEPT_TYPE.getPropertyName(), Compare.IN, conceptIds);
}
} else {
graphQuery.has(CONCEPT_TYPE.getPropertyName(), conceptType);
}
}
graphQuery.limit(size);
graphQuery.skip(offset);
Iterable<Vertex> searchResults;
try {
searchResults = graphQuery.vertices();
} catch (SearchPhaseExecutionException ex) {
respondWithBadRequest(response, "q", "Invalid Query");
return;
}
Map<Object, Double> scores = null;
if (searchResults instanceof IterableWithScores) {
scores = ((IterableWithScores) searchResults).getScores();
}
long retrievalStartTime = System.nanoTime();
List<JSONObject> verticesJsonList = new ArrayList<JSONObject>();
for (Vertex vertex : searchResults) {
JSONObject vertexJson = JsonSerializer.toJson(vertex, workspaceId);
if (scores != null) {
vertexJson.put("score", scores.get(vertex.getId()));
}
vertexJson.put(
"detectedObjects",
detectedObjectRepository.toJSON(vertex, modelUserContext, authorizations, workspaceId));
verticesJsonList.add(vertexJson);
}
long retrievalEndTime = System.nanoTime();
Collections.sort(
verticesJsonList,
new Comparator<JSONObject>() {
@Override
public int compare(JSONObject o1, JSONObject o2) {
double score1 = o1.optDouble("score", 0.0);
double score2 = o2.optDouble("score", 0.0);
return -Double.compare(score1, score2);
}
});
JSONArray verticesJson = new JSONArray();
for (JSONObject vertexJson : verticesJsonList) {
verticesJson.put(vertexJson);
}
long totalEndTime = System.nanoTime();
JSONObject results = new JSONObject();
results.put("vertices", verticesJson);
results.put("nextOffset", offset + size);
results.put("retrievalTime", retrievalEndTime - retrievalStartTime);
results.put("totalTime", totalEndTime - totalStartTime);
if (searchResults instanceof IterableWithTotalHits) {
results.put("totalHits", ((IterableWithTotalHits) searchResults).getTotalHits());
}
if (searchResults instanceof IterableWithSearchTime) {
results.put(
"searchTime", ((IterableWithSearchTime) searchResults).getSearchTimeNanoSeconds());
}
long endTime = System.nanoTime();
LOGGER.info(
"Search for \"%s\" found %d vertices in %dms",
query, verticesJsonList.size(), (endTime - startTime) / 1000 / 1000);
respondWithJson(response, results);
}
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);
}