@Override
public GetAccessTokenResult getAccessTokenUncached(Iterable<String> scopes) {
GetAccessTokenRequest.Builder requestBuilder = GetAccessTokenRequest.newBuilder();
for (String scope : scopes) {
requestBuilder.addScope(scope);
}
if (requestBuilder.getScopeCount() == 0) {
throw new AppIdentityServiceFailureException("No scopes specified.");
}
GetAccessTokenResponse.Builder responseBuilder = GetAccessTokenResponse.newBuilder();
try {
responseBuilder.mergeFrom(
ApiProxy.makeSyncCall(
getAccessTokenPackageName(),
GET_ACCESS_TOKEN_METHOD_NAME,
requestBuilder.build().toByteArray()));
} catch (ApiProxy.ApplicationException e) {
handleApplicationError(e);
} catch (InvalidProtocolBufferException e) {
throw new AppIdentityServiceFailureException(e.getMessage());
}
GetAccessTokenResponse response = responseBuilder.build();
return new GetAccessTokenResult(
response.getAccessToken(), new Date(response.getExpirationTime() * 1000));
}
public void deserializeFromByteArray(Message.Builder builder, byte[] array) {
try {
builder.mergeFrom(array);
} catch (InvalidProtocolBufferException e) {
log.error(e.getMessage());
}
}
/**
* Load the information in the SnapshotManifest. Called by SnapshotManifest.open()
*
* <p>If the format is v2 and there is no data-manifest, means that we are loading an in-progress
* snapshot. Since we support rolling-upgrades, we loook for v1 and v2 regions format.
*/
private void load() throws IOException {
switch (getSnapshotFormat(desc)) {
case SnapshotManifestV1.DESCRIPTOR_VERSION:
{
this.htd =
FSTableDescriptors.getTableDescriptorFromFs(fs, workingDir).getHTableDescriptor();
ThreadPoolExecutor tpool = createExecutor("SnapshotManifestLoader");
try {
this.regionManifests =
SnapshotManifestV1.loadRegionManifests(conf, tpool, fs, workingDir, desc);
} finally {
tpool.shutdown();
}
break;
}
case SnapshotManifestV2.DESCRIPTOR_VERSION:
{
SnapshotDataManifest dataManifest = readDataManifest();
if (dataManifest != null) {
htd = ProtobufUtil.convertToHTableDesc(dataManifest.getTableSchema());
regionManifests = dataManifest.getRegionManifestsList();
} else {
// Compatibility, load the v1 regions
// This happens only when the snapshot is in-progress and the cache wants to refresh.
List<SnapshotRegionManifest> v1Regions, v2Regions;
ThreadPoolExecutor tpool = createExecutor("SnapshotManifestLoader");
try {
v1Regions = SnapshotManifestV1.loadRegionManifests(conf, tpool, fs, workingDir, desc);
v2Regions = SnapshotManifestV2.loadRegionManifests(conf, tpool, fs, workingDir, desc);
} catch (InvalidProtocolBufferException e) {
throw new CorruptedSnapshotException(
"unable to parse region manifest " + e.getMessage(), e);
} finally {
tpool.shutdown();
}
if (v1Regions != null && v2Regions != null) {
regionManifests =
new ArrayList<SnapshotRegionManifest>(v1Regions.size() + v2Regions.size());
regionManifests.addAll(v1Regions);
regionManifests.addAll(v2Regions);
} else if (v1Regions != null) {
regionManifests = v1Regions;
} else /* if (v2Regions != null) */ {
regionManifests = v2Regions;
}
}
break;
}
default:
throw new CorruptedSnapshotException(
"Invalid Snapshot version: " + desc.getVersion(),
ProtobufUtil.createSnapshotDesc(desc));
}
}
/*
* Read the SnapshotDataManifest file
*/
private SnapshotDataManifest readDataManifest() throws IOException {
FSDataInputStream in = null;
try {
in = fs.open(new Path(workingDir, DATA_MANIFEST_NAME));
CodedInputStream cin = CodedInputStream.newInstance(in);
cin.setSizeLimit(manifestSizeLimit);
return SnapshotDataManifest.parseFrom(cin);
} catch (FileNotFoundException e) {
return null;
} catch (InvalidProtocolBufferException e) {
throw new CorruptedSnapshotException("unable to parse data manifest " + e.getMessage(), e);
} finally {
if (in != null) in.close();
}
}
@Override
public SigningResult signForApp(byte[] signBlob) {
SignForAppRequest.Builder requestBuilder = SignForAppRequest.newBuilder();
requestBuilder.setBytesToSign(ByteString.copyFrom(signBlob));
SignForAppResponse.Builder responseBuilder = SignForAppResponse.newBuilder();
try {
responseBuilder.mergeFrom(
ApiProxy.makeSyncCall(
PACKAGE_NAME, SIGN_FOR_APP_METHOD_NAME, requestBuilder.build().toByteArray()));
} catch (ApiProxy.ApplicationException e) {
handleApplicationError(e);
} catch (InvalidProtocolBufferException e) {
throw new AppIdentityServiceFailureException(e.getMessage());
}
SignForAppResponse response = responseBuilder.build();
return new SigningResult(response.getKeyName(), response.getSignatureBytes().toByteArray());
}
@Override
public String getServiceAccountName() {
GetServiceAccountNameRequest.Builder requestBuilder = GetServiceAccountNameRequest.newBuilder();
GetServiceAccountNameResponse.Builder responseBuilder =
GetServiceAccountNameResponse.newBuilder();
try {
responseBuilder.mergeFrom(
ApiProxy.makeSyncCall(
getAccessTokenPackageName(),
GET_SERVICE_ACCOUNT_NAME_METHOD_NAME,
requestBuilder.build().toByteArray()));
} catch (ApiProxy.ApplicationException e) {
handleApplicationError(e);
} catch (InvalidProtocolBufferException e) {
throw new AppIdentityServiceFailureException(e.getMessage());
}
GetServiceAccountNameResponse response = responseBuilder.build();
return response.getServiceAccountName();
}
@Override
public List<PublicCertificate> getPublicCertificatesForApp() {
GetPublicCertificateForAppRequest.Builder requestBuilder =
GetPublicCertificateForAppRequest.newBuilder();
GetPublicCertificateForAppResponse.Builder responseBuilder =
GetPublicCertificateForAppResponse.newBuilder();
try {
responseBuilder.mergeFrom(
ApiProxy.makeSyncCall(
PACKAGE_NAME, GET_CERTS_METHOD_NAME, requestBuilder.build().toByteArray()));
} catch (ApiProxy.ApplicationException e) {
handleApplicationError(e);
} catch (InvalidProtocolBufferException e) {
throw new AppIdentityServiceFailureException(e.getMessage());
}
GetPublicCertificateForAppResponse response = responseBuilder.build();
List<PublicCertificate> certs = Lists.newArrayList();
for (AppIdentityServicePb.PublicCertificate cert : response.getPublicCertificateListList()) {
certs.add(new PublicCertificate(cert.getKeyName(), cert.getX509CertificatePem()));
}
return certs;
}
@Override
public void run() {
Log.i(TAG, "Connection started");
MessageWriter writer = null;
MessageRouter router = null;
try {
MessageReader reader = new MessageReader(socket.getInputStream());
writer = new MessageWriter(socket.getOutputStream());
writers.add(writer);
router = new MessageRouter(writer);
router.register(Wire.MessageType.DO_IDENTIFY, new DoIdentifyResponder(getBaseContext()));
router.register(
Wire.MessageType.DO_ADD_ACCOUNT_MENU,
new DoAddAccountMenuResponder(getBaseContext()));
router.register(
Wire.MessageType.DO_REMOVE_ACCOUNT, new DoRemoveAccountResponder(getBaseContext()));
router.register(
Wire.MessageType.GET_ACCOUNTS, new GetAccountsResponder(getBaseContext()));
router.register(
Wire.MessageType.GET_BROWSERS, new GetBrowsersResponder(getBaseContext()));
router.register(
Wire.MessageType.GET_CLIPBOARD, new GetClipboardResponder(getBaseContext()));
router.register(Wire.MessageType.GET_DISPLAY, new GetDisplayResponder(getBaseContext()));
router.register(
Wire.MessageType.GET_PROPERTIES, new GetPropertiesResponder(getBaseContext()));
router.register(
Wire.MessageType.GET_RINGER_MODE, new GetRingerModeResponder(getBaseContext()));
router.register(
Wire.MessageType.GET_SD_STATUS, new GetSdStatusResponder(getBaseContext()));
router.register(Wire.MessageType.GET_VERSION, new GetVersionResponder(getBaseContext()));
router.register(
Wire.MessageType.GET_WIFI_STATUS, new GetWifiStatusResponder(getBaseContext()));
router.register(
Wire.MessageType.SET_CLIPBOARD, new SetClipboardResponder(getBaseContext()));
router.register(
Wire.MessageType.SET_KEYGUARD_STATE, new SetKeyguardStateResponder(getBaseContext()));
router.register(
Wire.MessageType.SET_RINGER_MODE, new SetRingerModeResponder(getBaseContext()));
router.register(
Wire.MessageType.SET_WAKE_LOCK, new SetWakeLockResponder(getBaseContext()));
router.register(
Wire.MessageType.SET_WIFI_ENABLED, new SetWifiEnabledResponder(getBaseContext()));
router.register(
Wire.MessageType.SET_MASTER_MUTE, new SetMasterMuteResponder(getBaseContext()));
for (AbstractMonitor monitor : monitors) {
monitor.peek(writer);
}
while (!isInterrupted()) {
Wire.Envelope envelope = reader.read();
if (envelope == null) {
break;
}
router.route(envelope);
}
} catch (InvalidProtocolBufferException e) {
Log.e(TAG, e.getMessage());
e.printStackTrace();
} catch (IOException e) {
} catch (Exception e) {
e.printStackTrace();
} finally {
Log.i(TAG, "Connection stopping");
writers.remove(writer);
if (router != null) {
router.cleanup();
}
try {
socket.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
public List<Variant> getRecordSimpleStats(
String study, int missing_gt, float maf, String maf_allele) {
BasicDBObject compare =
new BasicDBObject("studies.stats.allele_maf", maf_allele)
.append("studies.stats.MAF", maf)
.append("studies.stats.missing", missing_gt);
List<Get> hbaseQuery = new ArrayList<>();
DBCollection collection = db.getCollection("variants");
Iterator<DBObject> result = collection.find(compare);
String chromosome = new String();
while (result.hasNext()) {
DBObject variant = result.next();
String position = variant.get("_id").toString();
// hbase query construction
Get get = new Get(position.getBytes());
hbaseQuery.add(get);
}
// Complete results, from HBase
tableName = study;
effectTableName = tableName + "effect";
Map<String, Variant> resultsMap = new HashMap<>();
try {
HTable table = new HTable(admin.getConfiguration(), tableName);
HTable effectTable = new HTable(admin.getConfiguration(), effectTableName);
Result[] hbaseResultEffect = effectTable.get(hbaseQuery);
Result[] hbaseResultStats = table.get(hbaseQuery);
// List<Variant> results = new LinkedList<>();
for (Result r : hbaseResultStats) {
String position = new String(r.getRow(), CHARSET_UTF_8);
String[] aux = position.split("_");
String inner_position = aux[1];
String chr = aux[0];
// position parsing
if (chr.startsWith("0")) {
chr = chr.substring(1);
}
while (inner_position.startsWith("0")) {
inner_position = inner_position.substring(1);
}
List<VariantFieldsProtos.VariantSample> samples = new LinkedList<>();
NavigableMap<byte[], byte[]> infoMap = r.getFamilyMap("i".getBytes());
byte[] byteStats = infoMap.get((study + "_stats").getBytes());
VariantFieldsProtos.VariantStats stats =
VariantFieldsProtos.VariantStats.parseFrom(byteStats);
byte[] byteInfo = infoMap.get((study + "_data").getBytes());
VariantFieldsProtos.VariantInfo info = VariantFieldsProtos.VariantInfo.parseFrom(byteInfo);
String alternate = StringUtils.join(info.getAlternateList(), ", ");
String reference = info.getReference();
Variant partialResult =
new Variant(
chr,
Integer.parseInt(inner_position),
Integer.parseInt(inner_position),
reference,
alternate);
String format = StringUtils.join(info.getFormatList(), ":");
NavigableMap<byte[], byte[]> sampleMap = r.getFamilyMap("d".getBytes());
Map<String, Map<String, String>> resultSampleMap = new HashMap<>();
// StringBuilder sampleRaw = new StringBuilder();
for (byte[] s : sampleMap.keySet()) {
String qual = (new String(s, CHARSET_UTF_8)).replaceAll(study + "_", "");
VariantFieldsProtos.VariantSample sample =
VariantFieldsProtos.VariantSample.parseFrom(sampleMap.get(s));
String sample1 = sample.getSample();
String[] values = sample1.split(":");
String[] fields = format.split(":");
Map<String, String> singleSampleMap = new HashMap<>();
for (int i = 0; i < fields.length; i++) {
singleSampleMap.put(fields[i], values[i]);
}
resultSampleMap.put(qual, singleSampleMap);
}
VariantStats variantStats =
new VariantStats(
chromosome,
Integer.parseInt(inner_position),
reference,
alternate,
stats.getMaf(),
stats.getMgf(),
stats.getMafAllele(),
stats.getMgfGenotype(),
stats.getMissingAlleles(),
stats.getMissingGenotypes(),
stats.getMendelianErrors(),
stats.getIsIndel(),
stats.getCasesPercentDominant(),
stats.getControlsPercentDominant(),
stats.getCasesPercentRecessive(),
stats.getControlsPercentRecessive());
partialResult.setStats(variantStats);
resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult);
}
for (Result r : hbaseResultEffect) {
if (!r.isEmpty()) {
NavigableMap<byte[], byte[]> effectMap = r.getFamilyMap("e".getBytes());
Variant partialResult = resultsMap.get(new String(r.getRow(), CHARSET_UTF_8));
System.out.println("Recuperado " + partialResult.toString());
String s = partialResult.getReference() + "_" + partialResult.getAlternate();
VariantEffectProtos.EffectInfo effectInfo =
VariantEffectProtos.EffectInfo.parseFrom(effectMap.get(s.getBytes()));
VariantEffect variantEffect =
new VariantEffect(
partialResult.getChromosome(),
(int) partialResult.getStart(),
partialResult.getReference(),
partialResult.getAlternate(),
effectInfo.getFeatureId(),
effectInfo.getFeatureName(),
effectInfo.getFeatureType(),
effectInfo.getFeatureBiotype(),
effectInfo.getFeatureChromosome(),
effectInfo.getFeatureStart(),
effectInfo.getFeatureEnd(),
effectInfo.getFeatureStrand(),
effectInfo.getSnpId(),
effectInfo.getAncestral(),
effectInfo.getAlternative(),
effectInfo.getGeneId(),
effectInfo.getTranscriptId(),
effectInfo.getGeneName(),
effectInfo.getConsequenceType(),
effectInfo.getConsequenceTypeObo(),
effectInfo.getConsequenceTypeDesc(),
effectInfo.getConsequenceTypeType(),
effectInfo.getAaPosition(),
effectInfo.getAminoacidChange(),
effectInfo.getCodonChange());
resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult);
}
}
} catch (InvalidProtocolBufferException e) {
System.err.println(e.getClass().getName() + ": " + e.getMessage());
} catch (IOException e) {
System.err.println(e.getClass().getName() + ": " + e.getMessage());
}
List<Variant> results = new ArrayList<>(resultsMap.values());
return results;
}
private Conformance.ConformanceResponse doTest(Conformance.ConformanceRequest request) {
Conformance.TestAllTypes testMessage;
switch (request.getPayloadCase()) {
case PROTOBUF_PAYLOAD:
{
try {
testMessage = Conformance.TestAllTypes.parseFrom(request.getProtobufPayload());
} catch (InvalidProtocolBufferException e) {
return Conformance.ConformanceResponse.newBuilder()
.setParseError(e.getMessage())
.build();
}
break;
}
case JSON_PAYLOAD:
{
try {
Conformance.TestAllTypes.Builder builder = Conformance.TestAllTypes.newBuilder();
JsonFormat.parser()
.usingTypeRegistry(typeRegistry)
.merge(request.getJsonPayload(), builder);
testMessage = builder.build();
} catch (InvalidProtocolBufferException e) {
return Conformance.ConformanceResponse.newBuilder()
.setParseError(e.getMessage())
.build();
}
break;
}
case PAYLOAD_NOT_SET:
{
throw new RuntimeException("Request didn't have payload.");
}
default:
{
throw new RuntimeException("Unexpected payload case.");
}
}
switch (request.getRequestedOutputFormat()) {
case UNSPECIFIED:
throw new RuntimeException("Unspecified output format.");
case PROTOBUF:
return Conformance.ConformanceResponse.newBuilder()
.setProtobufPayload(testMessage.toByteString())
.build();
case JSON:
try {
return Conformance.ConformanceResponse.newBuilder()
.setJsonPayload(
JsonFormat.printer().usingTypeRegistry(typeRegistry).print(testMessage))
.build();
} catch (InvalidProtocolBufferException | IllegalArgumentException e) {
return Conformance.ConformanceResponse.newBuilder()
.setSerializeError(e.getMessage())
.build();
}
default:
{
throw new RuntimeException("Unexpected request output.");
}
}
}
