@Override
@RunAsSystem
public void initialize() {
Resource resource = new ClassPathResource("roc-curve.R");
if (resource.exists()) {
long count =
dataService.count(
Script.ENTITY_NAME, new QueryImpl().eq(Script.NAME, ROC_CURVE_SCRIPT_NAME));
if (count == 0) {
Entity scriptType =
dataService.findOne(ScriptType.ENTITY_NAME, new QueryImpl().eq(ScriptType.NAME, "R"));
if (scriptType == null) throw new UnknownEntityException("ScriptType R does not exist!");
String scriptContent;
try {
scriptContent =
FileCopyUtils.copyToString(new InputStreamReader(resource.getInputStream(), "UTF-8"));
} catch (IOException e) {
throw new UncheckedIOException(e);
}
if (dataService.count(
ScriptParameter.ENTITY_NAME,
new QueryImpl().eq(ScriptParameter.NAME, ROC_CURVE_SCRIPT_PARAMETER))
== 0) {
dataService.add(
ScriptParameter.ENTITY_NAME,
new MapEntity(ImmutableMap.of(ScriptParameter.NAME, ROC_CURVE_SCRIPT_PARAMETER)));
}
Entity scriptParameterEntity =
dataService.findOne(
ScriptParameter.ENTITY_NAME,
new QueryImpl().eq(ScriptParameter.NAME, ROC_CURVE_SCRIPT_PARAMETER));
MapEntity scriptEntity = new MapEntity();
scriptEntity.set(Script.NAME, ROC_CURVE_SCRIPT_NAME);
scriptEntity.set(Script.GENERATE_TOKEN, true);
scriptEntity.set(Script.TYPE, scriptType);
scriptEntity.set(Script.RESULT_FILE_EXTENSION, "png");
scriptEntity.set(Script.CONTENT, scriptContent);
scriptEntity.set(Script.PARAMETERS, Arrays.asList(scriptParameterEntity));
dataService.add(Script.ENTITY_NAME, scriptEntity);
LOG.info("Script entity \"roc\" has been added to the database!");
} else {
LOG.info("Script entity \"roc\" already exists in the database!");
}
} else {
LOG.info("R script \"roc-curve.R\" does not exist on classpath!");
}
}
private EntityCollectionResponseV2 createEntityCollectionResponse(
String entityName, EntityCollectionRequestV2 request, HttpServletRequest httpRequest) {
EntityMetaData meta = dataService.getEntityMetaData(entityName);
Query q = request.getQ() != null ? request.getQ().createQuery(meta) : new QueryImpl();
q.pageSize(request.getNum()).offset(request.getStart()).sort(request.getSort());
Fetch fetch =
AttributeFilterToFetchConverter.convert(
request.getAttrs(), meta, languageService.getCurrentUserLanguageCode());
if (fetch != null) {
q.fetch(fetch);
}
if (request.getAggs() != null) {
// return aggregates for aggregate query
AggregateQuery aggsQ = request.getAggs().createAggregateQuery(meta, q);
AttributeMetaData xAttr = aggsQ.getAttributeX();
AttributeMetaData yAttr = aggsQ.getAttributeY();
if (xAttr == null && yAttr == null) {
throw new MolgenisQueryException("Aggregate query is missing 'x' or 'y' attribute");
}
AggregateResult aggs = dataService.aggregate(entityName, aggsQ);
AttributeMetaDataResponseV2 xAttrResponse =
xAttr != null
? new AttributeMetaDataResponseV2(
entityName, meta, xAttr, fetch, permissionService, dataService, languageService)
: null;
AttributeMetaDataResponseV2 yAttrResponse =
yAttr != null
? new AttributeMetaDataResponseV2(
entityName, meta, yAttr, fetch, permissionService, dataService, languageService)
: null;
return new EntityAggregatesResponse(
aggs, xAttrResponse, yAttrResponse, BASE_URI + '/' + entityName);
} else {
Long count = dataService.count(entityName, q);
Iterable<Entity> it;
if (count > 0) {
it =
new Iterable<Entity>() {
@Override
public Iterator<Entity> iterator() {
return dataService.findAll(entityName, q).iterator();
}
};
} else {
it = Collections.emptyList();
}
EntityPager pager = new EntityPager(request.getStart(), request.getNum(), count, it);
List<Map<String, Object>> entities = new ArrayList<>();
for (Entity entity : it) {
Map<String, Object> responseData = new LinkedHashMap<String, Object>();
createEntityValuesResponse(entity, fetch, responseData);
entities.add(responseData);
}
UriComponentsBuilder builder = UriComponentsBuilder.fromUriString(getFullURL(httpRequest));
String prevHref = null;
if (pager.getPrevStart() != null) {
builder.replaceQueryParam("start", pager.getPrevStart());
prevHref = builder.build(false).toUriString();
}
String nextHref = null;
if (pager.getNextStart() != null) {
builder.replaceQueryParam("start", pager.getNextStart());
nextHref = builder.build(false).toUriString();
}
return new EntityCollectionResponseV2(
pager,
entities,
fetch,
BASE_URI + '/' + entityName,
meta,
permissionService,
dataService,
languageService,
prevHref,
nextHref);
}
}