/** @param bioID */
private boolean setBioID(String bioID) {
boolean toRet = false;
try {
JsonFactory factory = new JsonFactory();
JsonParser jparser = factory.createParser(bioID);
String key = "";
// Get StartObject for JSON, after first {
jparser.nextToken();
while (jparser.nextToken() != JsonToken.END_OBJECT) {
key = jparser.getText();
if (key.equals("id")) {
key = jparser.nextTextValue();
// Set bioID in Experiment
selExp.setBioID(key);
toRet = true;
} else {
jparser.skipChildren();
}
}
jparser.close();
} catch (JsonParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return toRet;
}
protected ConstExprConstruct parseAnnotationConstExprConstruct(final JsonParser jp)
throws IOException {
final ConstExprConstruct constExpr = new ConstExprConstruct();
constExpr.setType(ConstExprConstruct.Type.fromString(jp.getCurrentName()));
constExpr.setValue(jp.nextTextValue());
return constExpr;
}
@Override
public Event deserialize(JsonParser jp, DeserializationContext ctxt)
throws IOException, JsonProcessingException {
ObjectMapper mapper = (ObjectMapper) jp.getCodec();
String eventName = jp.nextTextValue();
EventKey ek = new EventKey(namespaceClass.get(), eventName);
if (!eventMapping.containsKey(ek)) {
ek = new EventKey(Namespace.DEFAULT_NAME, eventName);
if (!eventMapping.containsKey(ek)) {
return new Event(eventName, Collections.emptyList());
}
}
List<Object> eventArgs = new ArrayList<Object>();
Event event = new Event(eventName, eventArgs);
List<Class<?>> eventClasses = eventMapping.get(ek);
int i = 0;
while (true) {
JsonToken token = jp.nextToken();
if (token == JsonToken.END_ARRAY) {
break;
}
if (i > eventClasses.size() - 1) {
log.debug("Event {} has more args than declared in handler: {}", eventName, null);
break;
}
Class<?> eventClass = eventClasses.get(i);
Object arg = mapper.readValue(jp, eventClass);
eventArgs.add(arg);
i++;
}
return event;
}
private List<String> readPersons(JsonParser parser) throws IOException {
if (parser.nextToken() != JsonToken.START_ARRAY) {
reportIllegal(parser, JsonToken.START_ARRAY);
}
List<String> persons = new ArrayList<String>();
String str;
while ((str = parser.nextTextValue()) != null) {
persons.add(str);
}
verifyCurrent(parser, JsonToken.END_ARRAY);
return persons;
}
protected ReturnType parseReturnType(final JsonParser jp, final String elementName)
throws IOException {
ReturnType returnType;
if (elementName.equals(((FromXmlParser) jp).getStaxReader().getLocalName())) {
returnType = new ReturnType();
returnType.setType(jp.nextTextValue());
} else {
jp.nextToken();
returnType = jp.getCodec().readValue(jp, ReturnType.class);
}
return returnType;
}
/** Offlined version used when we do not use the default deserialization method. */
protected final String[] _deserializeCustom(
JsonParser p, DeserializationContext ctxt, String[] old) throws IOException {
final ObjectBuffer buffer = ctxt.leaseObjectBuffer();
int ix;
Object[] chunk;
if (old == null) {
ix = 0;
chunk = buffer.resetAndStart();
} else {
ix = old.length;
chunk = buffer.resetAndStart(old, ix);
}
final JsonDeserializer<String> deser = _elementDeserializer;
try {
while (true) {
/* 30-Dec-2014, tatu: This may look odd, but let's actually call method
* that suggest we are expecting a String; this helps with some formats,
* notably XML. Note, however, that while we can get String, we can't
* assume that's what we use due to custom deserializer
*/
String value;
if (p.nextTextValue() == null) {
JsonToken t = p.getCurrentToken();
if (t == JsonToken.END_ARRAY) {
break;
}
// Ok: no need to convert Strings, but must recognize nulls
value =
(t == JsonToken.VALUE_NULL) ? deser.getNullValue(ctxt) : deser.deserialize(p, ctxt);
} else {
value = deser.deserialize(p, ctxt);
}
if (ix >= chunk.length) {
chunk = buffer.appendCompletedChunk(chunk);
ix = 0;
}
chunk[ix++] = value;
}
} catch (Exception e) {
// note: pass String.class, not String[].class, as we need element type for error info
throw JsonMappingException.wrapWithPath(e, String.class, ix);
}
String[] result = buffer.completeAndClearBuffer(chunk, ix, String.class);
ctxt.returnObjectBuffer(buffer);
return result;
}
@Override
public String[] deserialize(JsonParser p, DeserializationContext ctxt, String[] intoValue)
throws IOException {
// Ok: must point to START_ARRAY (or equivalent)
if (!p.isExpectedStartArrayToken()) {
String[] arr = handleNonArray(p, ctxt);
if (arr == null) {
return intoValue;
}
final int offset = intoValue.length;
String[] result = new String[offset + arr.length];
System.arraycopy(intoValue, 0, result, 0, offset);
System.arraycopy(arr, 0, result, offset, arr.length);
return result;
}
if (_elementDeserializer != null) {
return _deserializeCustom(p, ctxt, intoValue);
}
final ObjectBuffer buffer = ctxt.leaseObjectBuffer();
int ix = intoValue.length;
Object[] chunk = buffer.resetAndStart(intoValue, ix);
try {
while (true) {
String value = p.nextTextValue();
if (value == null) {
JsonToken t = p.getCurrentToken();
if (t == JsonToken.END_ARRAY) {
break;
}
if (t != JsonToken.VALUE_NULL) {
value = _parseString(p, ctxt);
}
}
if (ix >= chunk.length) {
chunk = buffer.appendCompletedChunk(chunk);
ix = 0;
}
chunk[ix++] = value;
}
} catch (Exception e) {
throw JsonMappingException.wrapWithPath(e, chunk, buffer.bufferedSize() + ix);
}
String[] result = buffer.completeAndClearBuffer(chunk, ix, String.class);
ctxt.returnObjectBuffer(buffer);
return result;
}
@Override
public List<Video> fetchSource(String embedPageUrl) throws OnErrorThrowable {
String body = GeneralUtils.getWebPage(embedPageUrl);
String elementHtml =
Jsoup.parse(body).select("div.progress").first().nextElementSibling().html();
String onlyJson =
elementHtml.substring(
elementHtml.indexOf("var vars = ") + 11, elementHtml.indexOf("var fixed_player_size"));
List<Video> videos = new ArrayList<>(1);
try {
String regex = "url\\d+";
Pattern pattern = Pattern.compile(regex, Pattern.CASE_INSENSITIVE);
JsonParser jsonParser = new JsonFactory().createParser(onlyJson);
while (!jsonParser.isClosed()) {
JsonToken jsonToken = jsonParser.nextToken();
String currentName = jsonParser.getCurrentName();
if (jsonToken != null && currentName != null) {
Matcher matcher = pattern.matcher(currentName);
if (matcher.find()) {
String nextValue = jsonParser.nextTextValue();
if (nextValue != null) {
videos.add(new Video(currentName.substring(3) + "p", nextValue));
}
}
}
}
} catch (IOException io) {
throw OnErrorThrowable.from(new Throwable("Vk video retrieval failed.", io));
}
return videos;
}
@Override
protected ReferentialConstraintRole doDeserialize(
final JsonParser jp, final DeserializationContext ctxt)
throws IOException, JsonProcessingException {
final ReferentialConstraintRole refConstRole = new ReferentialConstraintRole();
for (; jp.getCurrentToken() != JsonToken.END_OBJECT; jp.nextToken()) {
final JsonToken token = jp.getCurrentToken();
if (token == JsonToken.FIELD_NAME) {
if ("Role".equals(jp.getCurrentName())) {
refConstRole.setRole(jp.nextTextValue());
} else if ("PropertyRef".equals(jp.getCurrentName())) {
jp.nextToken();
refConstRole.getPropertyRefs().add(jp.getCodec().readValue(jp, PropertyRef.class));
}
}
}
return refConstRole;
}
private Image readImage(JsonParser parser) throws IOException {
boolean haveWidth = false;
boolean haveHeight = false;
Image image = new Image();
if (parser.nextFieldName(FIELD_URI)) {
image.uri = parser.nextTextValue();
if (parser.nextFieldName(FIELD_TITLE)) {
image.title = parser.nextTextValue();
if (parser.nextFieldName(FIELD_WIDTH)) {
image.width = parser.nextIntValue(-1);
haveWidth = true;
if (parser.nextFieldName(FIELD_HEIGHT)) {
image.height = parser.nextIntValue(-1);
haveHeight = true;
if (parser.nextFieldName(FIELD_SIZE)) {
image.size = Image.Size.valueOf(parser.nextTextValue());
parser.nextToken();
verifyCurrent(parser, JsonToken.END_OBJECT);
return image;
}
}
}
}
}
for (; parser.getCurrentToken() == JsonToken.FIELD_NAME; parser.nextToken()) {
String field = parser.getCurrentName();
// read value token (or START_ARRAY)
parser.nextToken();
Integer I = fullFieldToIndex.get(field);
if (I != null) {
switch (I) {
case FIELD_IX_URI:
image.uri = parser.getText();
continue;
case FIELD_IX_TITLE:
image.title = parser.getText();
continue;
case FIELD_IX_WIDTH:
image.width = parser.getIntValue();
haveWidth = true;
continue;
case FIELD_IX_HEIGHT:
image.height = parser.getIntValue();
haveHeight = true;
continue;
case FIELD_IX_SIZE:
image.size = Image.Size.valueOf(parser.getText());
continue;
}
}
throw new IllegalStateException("Unexpected field '" + field + "'");
}
if (image.uri == null) throw new IllegalStateException("Missing field: " + FIELD_URI);
if (!haveWidth) throw new IllegalStateException("Missing field: " + FIELD_WIDTH);
if (!haveHeight) throw new IllegalStateException("Missing field: " + FIELD_HEIGHT);
if (image.size == null) throw new IllegalStateException("Missing field: " + FIELD_SIZE);
verifyCurrent(parser, JsonToken.END_OBJECT);
return image;
}
private Media readMedia(JsonParser parser) throws IOException {
if (parser.nextToken() != JsonToken.START_OBJECT) {
reportIllegal(parser, JsonToken.START_OBJECT);
}
Media media = new Media();
boolean haveWidth = false;
boolean haveHeight = false;
boolean haveDuration = false;
boolean haveSize = false;
// As with above, first fast path
if (parser.nextFieldName(FIELD_PLAYER)) {
media.player = Media.Player.find(parser.nextTextValue());
if (parser.nextFieldName(FIELD_URI)) {
media.uri = parser.nextTextValue();
if (parser.nextFieldName(FIELD_TITLE)) {
media.title = parser.nextTextValue();
if (parser.nextFieldName(FIELD_WIDTH)) {
haveWidth = true;
media.width = parser.nextIntValue(-1);
if (parser.nextFieldName(FIELD_HEIGHT)) {
haveHeight = true;
media.height = parser.nextIntValue(-1);
if (parser.nextFieldName(FIELD_FORMAT)) {
media.format = parser.nextTextValue();
if (parser.nextFieldName(FIELD_DURATION)) {
haveDuration = true;
media.duration = parser.nextLongValue(-1L);
if (parser.nextFieldName(FIELD_SIZE)) {
haveSize = true;
media.size = parser.nextLongValue(-1L);
if (parser.nextFieldName(FIELD_BITRATE)) {
media.bitrate = parser.nextIntValue(-1);
media.hasBitrate = true;
if (parser.nextFieldName(FIELD_COPYRIGHT)) {
media.copyright = parser.nextTextValue();
if (parser.nextFieldName(FIELD_PERSONS)) {
media.persons = readPersons(parser);
parser.nextToken();
verifyCurrent(parser, JsonToken.END_OBJECT);
return media;
}
}
}
}
}
}
}
}
}
}
}
// and if something reorder or missing, general loop:
for (; parser.getCurrentToken() == JsonToken.FIELD_NAME; parser.nextToken()) {
String field = parser.getCurrentName();
Integer I = fullFieldToIndex.get(field);
if (I != null) {
switch (I) {
case FIELD_IX_PLAYER:
media.player = Media.Player.find(parser.nextTextValue());
continue;
case FIELD_IX_URI:
media.uri = parser.nextTextValue();
continue;
case FIELD_IX_TITLE:
media.title = parser.nextTextValue();
continue;
case FIELD_IX_WIDTH:
media.width = parser.nextIntValue(-1);
haveWidth = true;
continue;
case FIELD_IX_HEIGHT:
media.height = parser.nextIntValue(-1);
haveHeight = true;
continue;
case FIELD_IX_FORMAT:
media.format = parser.nextTextValue();
continue;
case FIELD_IX_DURATION:
media.duration = parser.nextLongValue(-1L);
haveDuration = true;
continue;
case FIELD_IX_SIZE:
media.size = parser.nextLongValue(-1L);
haveSize = true;
continue;
case FIELD_IX_BITRATE:
media.bitrate = parser.nextIntValue(-1);
media.hasBitrate = true;
continue;
case FIELD_IX_PERSONS:
media.persons = readPersons(parser);
continue;
case FIELD_IX_COPYRIGHT:
media.copyright = parser.nextTextValue();
continue;
}
}
throw new IllegalStateException("Unexpected field '" + field + "'");
}
verifyCurrent(parser, JsonToken.END_OBJECT);
if (media.uri == null) throw new IllegalStateException("Missing field: " + FIELD_URI);
if (!haveWidth) throw new IllegalStateException("Missing field: " + FIELD_WIDTH);
if (!haveHeight) throw new IllegalStateException("Missing field: " + FIELD_HEIGHT);
if (media.format == null) throw new IllegalStateException("Missing field: " + FIELD_FORMAT);
if (!haveDuration) throw new IllegalStateException("Missing field: " + FIELD_DURATION);
if (!haveSize) throw new IllegalStateException("Missing field: " + FIELD_SIZE);
if (media.persons == null) media.persons = new ArrayList<String>();
if (media.player == null) throw new IllegalStateException("Missing field: " + FIELD_PLAYER);
return media;
}
@Override
protected AbstractEntityType doDeserialize(final JsonParser jp, final DeserializationContext ctxt)
throws IOException, JsonProcessingException {
final AbstractEntityType entityType =
ODataServiceVersion.V30 == version
? new org.apache.olingo.client.core.edm.xml.v3.EntityTypeImpl()
: new org.apache.olingo.client.core.edm.xml.v4.EntityTypeImpl();
for (; jp.getCurrentToken() != JsonToken.END_OBJECT; jp.nextToken()) {
final JsonToken token = jp.getCurrentToken();
if (token == JsonToken.FIELD_NAME) {
if ("Name".equals(jp.getCurrentName())) {
entityType.setName(jp.nextTextValue());
} else if ("Abstract".equals(jp.getCurrentName())) {
entityType.setAbstractEntityType(BooleanUtils.toBoolean(jp.nextTextValue()));
} else if ("BaseType".equals(jp.getCurrentName())) {
entityType.setBaseType(jp.nextTextValue());
} else if ("OpenType".equals(jp.getCurrentName())) {
entityType.setOpenType(BooleanUtils.toBoolean(jp.nextTextValue()));
} else if ("HasStream".equals(jp.getCurrentName())) {
entityType.setHasStream(BooleanUtils.toBoolean(jp.nextTextValue()));
} else if ("Key".equals(jp.getCurrentName())) {
jp.nextToken();
entityType.setKey(jp.readValueAs(EntityKeyImpl.class));
} else if ("Property".equals(jp.getCurrentName())) {
jp.nextToken();
if (entityType instanceof org.apache.olingo.client.core.edm.xml.v3.EntityTypeImpl) {
((org.apache.olingo.client.core.edm.xml.v3.EntityTypeImpl) entityType)
.getProperties()
.add(jp.readValueAs(org.apache.olingo.client.core.edm.xml.v3.PropertyImpl.class));
} else {
((org.apache.olingo.client.core.edm.xml.v4.EntityTypeImpl) entityType)
.getProperties()
.add(jp.readValueAs(org.apache.olingo.client.core.edm.xml.v4.PropertyImpl.class));
}
} else if ("NavigationProperty".equals(jp.getCurrentName())) {
jp.nextToken();
if (entityType instanceof org.apache.olingo.client.core.edm.xml.v3.EntityTypeImpl) {
((org.apache.olingo.client.core.edm.xml.v3.EntityTypeImpl) entityType)
.getNavigationProperties()
.add(
jp.readValueAs(
org.apache.olingo.client.core.edm.xml.v3.NavigationPropertyImpl.class));
} else {
((org.apache.olingo.client.core.edm.xml.v4.EntityTypeImpl) entityType)
.getNavigationProperties()
.add(
jp.readValueAs(
org.apache.olingo.client.core.edm.xml.v4.NavigationPropertyImpl.class));
}
} else if ("Annotation".equals(jp.getCurrentName())) {
jp.nextToken();
((org.apache.olingo.client.core.edm.xml.v4.EntityTypeImpl) entityType)
.setAnnotation(jp.readValueAs(AnnotationImpl.class));
}
}
}
return entityType;
}
/**
* Query Watchman for file change events. If too many events are pending or an error occurs an
* overflow event is posted to the EventBus signalling that events may have been lost (and so
* typically caches must be cleared to avoid inconsistency). Interruptions and IOExceptions are
* propagated to callers, but typically if overflow events are handled conservatively by
* subscribers then no other remedial action is required.
*/
@Override
public void postEvents(BuckEventBus buckEventBus) throws IOException, InterruptedException {
ProcessExecutor.LaunchedProcess watchmanProcess =
processExecutor.launchProcess(
ProcessExecutorParams.builder()
.addCommand("watchman", "--server-encoding=json", "--no-pretty", "-j")
.build());
try {
LOG.debug("Writing query to Watchman: %s", query);
watchmanProcess.getOutputStream().write(query.getBytes(Charsets.US_ASCII));
watchmanProcess.getOutputStream().close();
LOG.debug("Parsing JSON output from Watchman");
final long parseStartTimeMillis = clock.currentTimeMillis();
InputStream jsonInput = watchmanProcess.getInputStream();
if (LOG.isVerboseEnabled()) {
byte[] fullResponse = ByteStreams.toByteArray(jsonInput);
jsonInput.close();
jsonInput = new ByteArrayInputStream(fullResponse);
LOG.verbose("Full JSON: " + new String(fullResponse, Charsets.UTF_8).trim());
}
JsonParser jsonParser = objectMapper.getJsonFactory().createJsonParser(jsonInput);
PathEventBuilder builder = new PathEventBuilder();
JsonToken token = jsonParser.nextToken();
/*
* Watchman returns changes as an array of JSON objects with potentially unstable key
* ordering:
* {
* "files": [
* {
* "new": false,
* "exists": true,
* "name": "bin/buckd",
* },
* ]
* }
* A simple way to parse these changes is to collect the relevant values from each object
* in a builder and then build an event when the end of a JSON object is reached. When the end
* of the enclosing JSON object is processed the builder will not contain a complete event, so
* the object end token will be ignored.
*/
int eventCount = 0;
while (token != null) {
boolean shouldOverflow = false;
if (eventCount > overflow) {
LOG.warn(
"Received too many events from Watchmen (%d > overflow max %d), posting overflow "
+ "event and giving up.",
eventCount, overflow);
shouldOverflow = true;
} else {
long elapsedMillis = clock.currentTimeMillis() - parseStartTimeMillis;
if (elapsedMillis >= timeoutMillis) {
LOG.warn(
"Parsing took too long (timeout %d ms), posting overflow event and giving up.",
timeoutMillis);
shouldOverflow = true;
}
}
if (shouldOverflow) {
postWatchEvent(createOverflowEvent());
processExecutor.destroyLaunchedProcess(watchmanProcess);
processExecutor.waitForLaunchedProcess(watchmanProcess);
return;
}
switch (token) {
case FIELD_NAME:
String fieldName = jsonParser.getCurrentName();
switch (fieldName) {
case "is_fresh_instance":
// Force caches to be invalidated --- we have no idea what's happening.
Boolean newInstance = jsonParser.nextBooleanValue();
if (newInstance) {
LOG.info(
"Fresh watchman instance detected. "
+ "Posting overflow event to flush caches.");
postWatchEvent(createOverflowEvent());
}
break;
case "name":
builder.setPath(Paths.get(jsonParser.nextTextValue()));
break;
case "new":
if (jsonParser.nextBooleanValue()) {
builder.setCreationEvent();
}
break;
case "exists":
if (!jsonParser.nextBooleanValue()) {
builder.setDeletionEvent();
}
break;
case "error":
WatchmanWatcherException e =
new WatchmanWatcherException(jsonParser.nextTextValue());
LOG.error(
e, "Error in Watchman output. Posting an overflow event to flush the caches");
postWatchEvent(createOverflowEvent());
throw e;
case "warning":
String message = jsonParser.nextTextValue();
buckEventBus.post(
ConsoleEvent.warning("Watchman has produced a warning: %s", message));
LOG.warn("Watchman has produced a warning: %s", message);
break;
}
break;
case END_OBJECT:
if (builder.canBuild()) {
postWatchEvent(builder.build());
++eventCount;
}
builder = new PathEventBuilder();
break;
// $CASES-OMITTED$
default:
break;
}
token = jsonParser.nextToken();
}
int watchmanExitCode;
LOG.debug("Posted %d Watchman events. Waiting for subprocess to exit...", eventCount);
watchmanExitCode = processExecutor.waitForLaunchedProcess(watchmanProcess);
if (watchmanExitCode != 0) {
LOG.error("Watchman exited with error code %d", watchmanExitCode);
postWatchEvent(createOverflowEvent()); // Events may have been lost, signal overflow.
ByteArrayOutputStream buffer = new ByteArrayOutputStream();
ByteStreams.copy(watchmanProcess.getErrorStream(), buffer);
throw new WatchmanWatcherException(
"Watchman failed with exit code " + watchmanExitCode + ": " + buffer.toString());
} else {
LOG.debug("Watchman exited cleanly.");
}
} catch (InterruptedException e) {
LOG.warn(e, "Killing Watchman process on interrupted exception");
postWatchEvent(createOverflowEvent()); // Events may have been lost, signal overflow.
processExecutor.destroyLaunchedProcess(watchmanProcess);
processExecutor.waitForLaunchedProcess(watchmanProcess);
Thread.currentThread().interrupt();
throw e;
} catch (IOException e) {
LOG.error(e, "Killing Watchman process on I/O exception");
postWatchEvent(createOverflowEvent()); // Events may have been lost, signal overflow.
processExecutor.destroyLaunchedProcess(watchmanProcess);
processExecutor.waitForLaunchedProcess(watchmanProcess);
throw e;
}
}