/** * Add a mutation to set this property to the provided value. * * @param mutation the element mutation * @param value the new property value * @param metadata the property metadata * @param visibility the property visibility */ public final void setProperty( final ElementMutation<?> mutation, final TRaw value, final Map<String, Object> metadata, final Visibility visibility) { mutation.setProperty(key, wrap(value), metadata, visibility); }
/** * Add a mutation to add a new value to this property. * * @param mutation the element mutation * @param multiKey the multi-valued property key * @param value the new property value * @param visibility the property visibility */ public final void addPropertyValue( final ElementMutation<?> mutation, final String multiKey, final TRaw value, final Visibility visibility) { mutation.addPropertyValue(multiKey, key, wrap(value), visibility); }
/** * Add a mutation to add a new value to this property * * @param mutation the element mutation * @param multiKey the multi-valued property key * @param value the new property value * @param metadata the property metadata * @param visibility the property visibility */ public final void addPropertyValue( final ElementMutation<?> mutation, final String multiKey, final TRaw value, final Map<String, Object> metadata, final Visibility visibility) { mutation.addPropertyValue(multiKey, propertyName, wrap(value), metadata, visibility); }
@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); }
/** * Add a mutation to set this property to the provided value. * * @param mutation the element mutation * @param value the new property value * @param visibility the property visibility */ public final void setProperty( final ElementMutation<?> mutation, final TRaw value, final Visibility visibility) { mutation.setProperty(key, wrap(value), visibility); }
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); }