public static WorksheetEntry fromParser(XmlPullParser parser)
throws XmlPullParserException, IOException {
final int depth = parser.getDepth();
final WorksheetEntry entry = new WorksheetEntry();
String tag = null;
int type;
while (((type = parser.next()) != END_TAG || parser.getDepth() > depth)
&& type != END_DOCUMENT) {
if (type == START_TAG) {
tag = parser.getName();
if (LINK.equals(tag)) {
final String rel = parser.getAttributeValue(null, REL);
final String href = parser.getAttributeValue(null, HREF);
if (REL_LISTFEED.equals(rel)) {
entry.mListFeed = href;
}
}
} else if (type == END_TAG) {
tag = null;
} else if (type == TEXT) {
final String text = parser.getText();
if (TITLE.equals(tag)) {
entry.mTitle = text;
} else if (UPDATED.equals(tag)) {
entry.mUpdated = ParserUtils.parseTime(text);
}
}
}
return entry;
}
private Audit auditRelationshipHelper(
Audit audit,
AuditAction action,
Vertex sourceVertex,
Vertex destVertex,
String label,
String process,
String comment,
User user,
Visibility visibility) {
visibility = orVisibility(visibility);
audit
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_RELATIONSHIP, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
audit
.getAuditRelationship()
.setSourceId(sourceVertex.getId(), visibility)
.setSourceType(CONCEPT_TYPE.getPropertyValue(sourceVertex), visibility)
.setSourceTitle(TITLE.getPropertyValue(sourceVertex), visibility)
.setDestId(destVertex.getId(), visibility)
.setDestTitle(TITLE.getPropertyValue(destVertex), visibility)
.setDestType(CONCEPT_TYPE.getPropertyValue(destVertex), visibility)
.setLabel(label, visibility);
return audit;
}
@Override
protected void execute(Search search, SearchKey key, SolrDocumentList documents)
throws ActionException {
Parameter param = em.find(Parameter.class, "SEARCH_REPO");
String repo = param.getValue();
File repoDir =
new File(
repo + File.separator + search.getConfig().getId() + File.separator + search.getId());
repoDir.mkdirs();
ImageRenderer imageRenderer = new ImageRenderer();
Transcoder transcoder = new PDFTranscoder();
for (SolrDocument doc : documents) {
String docUrl = (String) doc.getFieldValue(URL.toString());
String docTitle = (String) doc.getFieldValue(TITLE.toString());
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
File outputFile = new File(repoDir.getAbsolutePath() + File.separator + docTitle + ".pdf");
try {
imageRenderer.renderURL(docUrl, outputStream, ImageRenderer.Type.SVG);
} catch (IOException | SAXException e) {
log.error("SVG rendering problem", e);
createErrorFile(docUrl, outputFile, e);
continue;
}
byte[] svgBytes = outputStream.toByteArray();
ByteArrayInputStream inputStream = new ByteArrayInputStream(svgBytes);
TranscoderInput transcoderInput = new TranscoderInput(inputStream);
TranscoderOutput transcoderOutput = null;
try {
transcoderOutput = new TranscoderOutput(new FileOutputStream(outputFile));
} catch (FileNotFoundException e) {
log.warn("this shouldn't happen!", e);
createErrorFile(docUrl, outputFile, e);
continue;
}
try {
transcoder.transcode(transcoderInput, transcoderOutput);
} catch (TranscoderException e) {
log.warn("Transcoding problem", e);
createErrorFile(docUrl, outputFile, e);
continue;
}
}
}
@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);
}
public List<Audit> auditRelationship(
AuditAction action,
Vertex sourceVertex,
Vertex destVertex,
Edge edge,
String process,
String comment,
User user,
Visibility visibility) {
checkNotNull(action, "action cannot be null");
checkNotNull(sourceVertex, "sourceVertex cannot be null");
checkNotNull(destVertex, "destVertex cannot be null");
checkNotNull(edge, "edge cannot be null");
checkNotNull(process, "process cannot be null");
checkNotNull(comment, "comment cannot be null");
checkNotNull(user, "user cannot be null");
Audit auditSourceDest = new Audit(AuditRowKey.build(sourceVertex.getId(), destVertex.getId()));
Audit auditDestSource = new Audit(AuditRowKey.build(destVertex.getId(), sourceVertex.getId()));
Audit auditEdge = new Audit(AuditRowKey.build(edge.getId()));
visibility = orVisibility(visibility);
List<Audit> audits = new ArrayList<Audit>();
String displayLabel = ontologyRepository.getDisplayNameForLabel(edge.getLabel());
audits.add(
auditRelationshipHelper(
auditSourceDest,
action,
sourceVertex,
destVertex,
displayLabel,
process,
comment,
user,
visibility));
audits.add(
auditRelationshipHelper(
auditDestSource,
action,
sourceVertex,
destVertex,
displayLabel,
process,
comment,
user,
visibility));
auditEdge
.getAuditCommon()
.setUser(user, visibility)
.setAction(action, visibility)
.setType(OntologyRepository.TYPE_RELATIONSHIP, visibility)
.setComment(comment, visibility)
.setProcess(process, visibility)
.setUnixBuildTime(
versionService.getUnixBuildTime() != null ? versionService.getUnixBuildTime() : -1L,
visibility)
.setScmBuildNumber(
versionService.getScmBuildNumber() != null ? versionService.getScmBuildNumber() : "",
visibility)
.setVersion(
versionService.getVersion() != null ? versionService.getVersion() : "", visibility);
auditEdge
.getAuditRelationship()
.setSourceId(sourceVertex.getId(), visibility)
.setSourceType(CONCEPT_TYPE.getPropertyValue(sourceVertex), visibility)
.setSourceTitle(TITLE.getPropertyValue(sourceVertex), visibility)
.setDestId(destVertex.getId(), visibility)
.setDestTitle(TITLE.getPropertyValue(destVertex), visibility)
.setDestType(CONCEPT_TYPE.getPropertyValue(destVertex), visibility)
.setLabel(displayLabel, visibility);
audits.add(auditEdge);
saveMany(audits);
return audits;
}
