private TermMentionWithGraphVertex findTermMentionWithGraphVertex(
List<TermMentionWithGraphVertex> termMentionsWithGraphVertices, TermMention termMention) {
for (TermMentionWithGraphVertex termMentionsWithGraphVertex : termMentionsWithGraphVertices) {
if (termMentionsWithGraphVertex.getTermMention().getRowKey().getStartOffset()
== termMention.getStart()
&& termMentionsWithGraphVertex.getTermMention().getRowKey().getEndOffset()
== termMention.getEnd()
&& termMentionsWithGraphVertex.getVertex() != null) {
return termMentionsWithGraphVertex;
}
}
return null;
}
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);
}