private void initialize() {
try {
dataSetManager = new DataSetManager();
dataSetManager.addDataSetFactory(
new LuceneDataSetFactory<Object, Object, Object>(
dataSetManager,
null,
new FileUtils(),
new NullCytoscapeUtils<Object, Object, Object>(),
null),
Collections.emptyMap());
data = dataSetManager.open(DirectorySettings.getGeneManiaDirectory());
human = getHumanOrganism(data);
networkUtils = new NetworkUtils();
cache =
new DataCache(
new SynchronizedObjectCache(
new MemObjectCache(data.getObjectCache(NullProgressReporter.instance(), false))));
mania = new Mania2(cache);
setGeneLimit(DEFAULT_GENE_LIMIT);
setCombiningMethod(DEFAULT_COMBINING_METHOD);
setNetworks(new HashSet<String>(Arrays.asList(DEFAULT_NETWORKS)));
} catch (Exception e) {
LOG.error(e);
}
}
private RelatedGenesEngineResponseDto runQuery(RelatedGenesEngineRequestDto request)
throws DataStoreException {
try {
request.setProgressReporter(NullProgressReporter.instance());
RelatedGenesEngineResponseDto result;
result = mania.findRelated(request);
request.setCombiningMethod(result.getCombiningMethodApplied());
networkUtils.normalizeNetworkWeights(result);
return result;
} catch (ApplicationException e) {
Logger logger = Logger.getLogger(getClass());
logger.error("Unexpected error", e); // $NON-NLS-1$
return null;
}
}
private EnrichmentEngineRequestDto createEnrichmentRequest(
RelatedGenesEngineResponseDto response) {
if (human.getOntology() == null) {
return null;
}
EnrichmentEngineRequestDto request = new EnrichmentEngineRequestDto();
request.setProgressReporter(NullProgressReporter.instance());
request.setMinCategories(MIN_CATEGORIES);
request.setqValueThreshold(Q_VALUE_THRESHOLD);
request.setOrganismId(human.getId());
request.setOntologyId(human.getOntology().getId());
Set<Long> nodes = new HashSet<Long>();
for (NetworkDto network : response.getNetworks()) {
for (InteractionDto interaction : network.getInteractions()) {
nodes.add(interaction.getNodeVO1().getId());
nodes.add(interaction.getNodeVO2().getId());
}
}
request.setNodes(nodes);
return request;
}
/**
* add a user-network to data set, then compute a result using BP combining from the core networks
* *not* including the user network that was just uploaded
*/
@Test
public void testBPCombiningWithoutUserNetwork() throws Exception {
System.out.println("averageCombiningWithUserNetworkChaChaCha");
int orgId = 1;
int userNetworkId = -1;
String userName = "******";
// add a user network
// INetworkSymMatrixProvider provider = new CacheNetworkSymMatrixProvider(userName,
// orgId, randomCacheBuilder.getCache());
UserNetworkProcessor instance =
new UserNetworkProcessor(randomCacheBuilder.getCache(), randomCacheBuilder.getCacheDir());
UploadNetworkEngineRequestDto uploadRequest = new UploadNetworkEngineRequestDto();
uploadRequest.setLayout(DataLayout.PROFILE);
uploadRequest.setMethod(NetworkProcessingMethod.PEARSON);
uploadRequest.setNamespace(userName);
uploadRequest.setProgressReporter(NullProgressReporter.instance());
uploadRequest.setOrganismId(orgId);
uploadRequest.setNetworkId(userNetworkId);
uploadRequest.setSparsification(50);
String data = "id\tf1\tf2\tf3\n10000\t1.5\t3.0\t4.0\n10001\t2.0\t2.2\t2.1\n";
uploadRequest.setData(new StringReader(data));
UploadNetworkEngineResponseDto uploadResponse = instance.process(uploadRequest);
assertNotNull(uploadResponse);
// now send in a request for related genes, involving all the old networks plus
// the new one
IMania mania = new Mania2(randomCacheBuilder.getCache());
// create request for organism 1
RelatedGenesEngineRequestDto relatedRequest = new RelatedGenesEngineRequestDto();
relatedRequest.setNamespace(userName);
relatedRequest.setOrganismId(orgId);
relatedRequest.setCombiningMethod(CombiningMethod.BP);
relatedRequest.setScoringMethod(ScoringMethod.DISCRIMINANT);
long[] nodeIds = randomCacheBuilder.getCache().getNodeIds(orgId).getNodeIds();
// first 10 nodes as +ve
ArrayList<Long> posNodes = new ArrayList<Long>();
for (int i = 0; i < 10; i++) {
posNodes.add((long) nodeIds[i]);
}
relatedRequest.setPositiveNodes(posNodes);
// all networks less one
Collection<Collection<Long>> requestNetworks = new ArrayList<Collection<Long>>();
ArrayList<Long> group = new ArrayList<Long>();
for (int i = 0; i < networkIds.length; i++) {
group.add(networkIds[i]);
}
// group.add((long) userNetworkId);
requestNetworks.add(group);
relatedRequest.setInteractionNetworks(requestNetworks);
relatedRequest.setLimitResults(10);
relatedRequest.setProgressReporter(NullProgressReporter.instance());
// compute result
RelatedGenesEngineResponseDto relatedResponse = mania.findRelated(relatedRequest);
assertNotNull(relatedResponse);
assertNotNull(relatedResponse.getNetworks());
assertFalse(relatedResponse.getNetworks().size() == 0);
System.out.println("num networks in result: " + relatedResponse.getNetworks().size());
for (NetworkDto n : relatedResponse.getNetworks()) {
System.out.println(
" network id: "
+ n.getId()
+ " weight: "
+ n.getWeight()
+ " num interactions: "
+ n.getInteractions().size());
for (InteractionDto interaction : n.getInteractions()) {
/*
System.out.println(String.format(" inter: node %s %s, node %s %s, %s",
interaction.getNodeVO1().getId(),
interaction.getNodeVO1().getScore(),
interaction.getNodeVO2().getId(),
interaction.getNodeVO2().getScore(),
interaction.getWeight()
));
*/
}
}
// TODO: send the same request through again, but this time using the old mania api
}
/*
* helper to add a small user network to the test data set, then
* call a related genes request with given combining method, and
* other params set to std values
*/
public RelatedGenesEngineResponseDto regressionHelper(CombiningMethod method) throws Exception {
int orgId = 1;
int userNetworkId = -1;
String userName = "******";
// add a user network
// INetworkSymMatrixProvider provider = new CacheNetworkSymMatrixProvider(userName,
// orgId, randomCacheBuilder.getCache());
UserNetworkProcessor instance =
new UserNetworkProcessor(randomCacheBuilder.getCache(), randomCacheBuilder.getCacheDir());
UploadNetworkEngineRequestDto uploadRequest = new UploadNetworkEngineRequestDto();
uploadRequest.setLayout(DataLayout.PROFILE);
uploadRequest.setMethod(NetworkProcessingMethod.PEARSON);
uploadRequest.setNamespace(userName);
uploadRequest.setProgressReporter(NullProgressReporter.instance());
uploadRequest.setOrganismId(orgId);
uploadRequest.setNetworkId(userNetworkId);
uploadRequest.setSparsification(50);
String data = "id\tf1\tf2\tf3\n10000\t1.5\t3.0\t4.0\n10001\t2.0\t2.2\t2.1\n";
uploadRequest.setData(new StringReader(data));
UploadNetworkEngineResponseDto uploadResponse = instance.process(uploadRequest);
assertNotNull(uploadResponse);
// now send in a request for related genes, involving all the old networks plus
// the new one
IMania mania = new Mania2(randomCacheBuilder.getCache());
// create request for organism 1
RelatedGenesEngineRequestDto relatedRequest = new RelatedGenesEngineRequestDto();
relatedRequest.setNamespace(userName);
relatedRequest.setOrganismId(orgId);
relatedRequest.setCombiningMethod(method);
relatedRequest.setScoringMethod(ScoringMethod.DISCRIMINANT);
long[] nodeIds = randomCacheBuilder.getCache().getNodeIds(orgId).getNodeIds();
// first 10 nodes as +ve
ArrayList<Long> posNodes = new ArrayList<Long>();
for (int i = 0; i < 10; i++) {
posNodes.add(nodeIds[i]);
}
relatedRequest.setPositiveNodes(posNodes);
// all networks
Collection<Collection<Long>> requestNetworks = new ArrayList<Collection<Long>>();
ArrayList<Long> group = new ArrayList<Long>();
for (int i = 0; i < networkIds.length; i++) {
group.add((long) networkIds[i]);
}
group.add((long) userNetworkId);
requestNetworks.add(group);
relatedRequest.setInteractionNetworks(requestNetworks);
relatedRequest.setLimitResults(10);
relatedRequest.setProgressReporter(NullProgressReporter.instance());
// compute result
RelatedGenesEngineResponseDto relatedResponse = mania.findRelated(relatedRequest);
return relatedResponse;
}