package io.lumify.web.routes.vertex;
import com.google.inject.Inject;
import io.lumify.core.config.Configuration;
import io.lumify.core.exception.LumifyException;
import io.lumify.core.model.audit.AuditAction;
import io.lumify.core.model.audit.AuditRepository;
import io.lumify.core.model.ontology.Concept;
import io.lumify.core.model.ontology.OntologyRepository;
import io.lumify.core.model.properties.LumifyProperties;
import io.lumify.core.model.termMention.TermMentionBuilder;
import io.lumify.core.model.termMention.TermMentionRepository;
import io.lumify.core.model.user.UserRepository;
import io.lumify.core.model.workQueue.WorkQueueRepository;
import io.lumify.core.model.workspace.Workspace;
import io.lumify.core.model.workspace.WorkspaceRepository;
import io.lumify.core.security.LumifyVisibility;
import io.lumify.core.security.VisibilityTranslator;
import io.lumify.core.user.User;
import io.lumify.core.util.GraphUtil;
import io.lumify.core.util.LumifyLogger;
import io.lumify.core.util.LumifyLoggerFactory;
import io.lumify.miniweb.HandlerChain;
import io.lumify.web.BaseRequestHandler;
import io.lumify.web.clientapi.model.VisibilityJson;
import org.securegraph.Authorizations;
import org.securegraph.Edge;
import org.securegraph.Graph;
import org.securegraph.Vertex;
import org.securegraph.mutation.ElementMutation;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.util.HashMap;
import java.util.Map;
public class ResolveTermEntity extends BaseRequestHandler {
private static final LumifyLogger LOGGER = LumifyLoggerFactory.getLogger(ResolveTermEntity.class);
private static final String MULTI_VALUE_KEY = ResolveTermEntity.class.getName();
private final Graph graph;
private final AuditRepository auditRepository;
private final OntologyRepository ontologyRepository;
private final VisibilityTranslator visibilityTranslator;
private final WorkspaceRepository workspaceRepository;
private final WorkQueueRepository workQueueRepository;
private final String artifactHasEntityIri;
@Inject
public ResolveTermEntity(
final Graph graphRepository,
final AuditRepository auditRepository,
final OntologyRepository ontologyRepository,
final UserRepository userRepository,
final VisibilityTranslator visibilityTranslator,
final Configuration configuration,
final TermMentionRepository termMentionRepository,
final WorkspaceRepository workspaceRepository,
final WorkQueueRepository workQueueRepository) {
super(userRepository, workspaceRepository, configuration);
this.graph = graphRepository;
this.auditRepository = auditRepository;
this.ontologyRepository = ontologyRepository;
this.visibilityTranslator = visibilityTranslator;
this.workspaceRepository = workspaceRepository;
this.workQueueRepository = workQueueRepository;
this.artifactHasEntityIri = this.getConfiguration().get(Configuration.ONTOLOGY_IRI_ARTIFACT_HAS_ENTITY);
if (this.artifactHasEntityIri == null) {
throw new LumifyException("Could not find configuration for " + Configuration.ONTOLOGY_IRI_ARTIFACT_HAS_ENTITY);
}
}
@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");
User user = getUser(request);
String workspaceId = getActiveWorkspaceId(request);
Workspace workspace = workspaceRepository.findById(workspaceId, user);
Authorizations authorizations = getAuthorizations(request, user);
VisibilityJson 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", getString(request, "visibility.invalid"));
chain.next(request, response);
return;
}
String 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>();
LumifyProperties.VISIBILITY_JSON.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);
LumifyProperties.CONCEPT_TYPE.setProperty(vertexMutation, conceptId, metadata, lumifyVisibility.getVisibility());
LumifyProperties.TITLE.addPropertyValue(vertexMutation, MULTI_VALUE_KEY, title, metadata, lumifyVisibility.getVisibility());
vertex = vertexMutation.save(authorizations);
auditRepository.auditVertexElementMutation(AuditAction.UPDATE, vertexMutation, vertex, "", user, lumifyVisibility.getVisibility());
LumifyProperties.VISIBILITY_JSON.setProperty(vertexMutation, visibilityJson, metadata, lumifyVisibility.getVisibility());
this.graph.flush();
workspaceRepository.updateEntityOnWorkspace(workspace, vertex.getId(), false, 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);
LumifyProperties.VISIBILITY_JSON.setProperty(edge, visibilityJson, metadata, lumifyVisibility.getVisibility(), authorizations);
auditRepository.auditRelationship(AuditAction.CREATE, artifactVertex, vertex, edge, "", "", user, lumifyVisibility.getVisibility());
new TermMentionBuilder()
.sourceVertex(artifactVertex)
.propertyKey(propertyKey)
.start(mentionStart)
.end(mentionEnd)
.title(title)
.conceptIri(concept.getIRI())
.visibilityJson(visibilityJson)
.resolvedTo(vertex, edge)
.process(getClass().getSimpleName())
.save(this.graph, visibilityTranslator, authorizations);
vertexMutation.save(authorizations);
this.graph.flush();
workQueueRepository.pushTextUpdated(artifactId);
workQueueRepository.pushElement(edge);
respondWithSuccessJson(response);
}
}