I have following code to serialize my data into a file:
out = new ObjectOutputStream(new FileOutputStream(file));
out.writeObject(chunk);
out.flush();
I read with the following:
in = new ObjectInputStream(new FileInputStream(file));
Chunk chunk = (Chunk) in.readObject();
The weird thing is, when I read the data, all members are set to default and I get no data back that I wrote before.
If I use the XML variant all works fine.
e = new XMLEncoder(new FileOutputStream(file));
e.writeObject(chunk);
e.flush();
and
e = new XMLDecoder(new FileInputStream(file));
Chunk chunk = (Chunk) e.readObject();
What is wrong with the binary format?
Update
Ok i got this now: Chunk is a complex class with classes in, other classes with other classes in and so on. At some point the contained classes is declared as Object and should be Serializable. As Steve mentioned.
Thank you for your answers.
While I can't think of a good reason why one decoder would work differently than another, I'd suggest posting the code of the Chunk object. Things to look at:
Are you declaring any fields transient? These won't get serialized
Are any of the problems occurring with nested objects or collections which themselves may not be serializable?
Are the defaults overwritten in the constructor , or somewhere else that's not going to be called in a deserialization operation?
The only reason I can think of for fields being set to default during serialization would be that they're defined as transient.
If that's not it, try distilling your code to a small, self-contained program that reproduces the problem. Most likely, you will spot the cause of the problem while you do that, otherwise post it here.
Another (admittedly unlikely) possibility besides the obvious transient fields mentioned by others is that Chunk might implement Externalizable but not actually override the necessary writeExternal / readExternal methods. That would also explain why XMLEncoder works.
Related
I am relatively new to using the netcdf-java library, and I've immediately run into a problem when trying to load a file. The problem is that there doesn't seem to be a way to load a NetcdfFile from a byte array stored in memory, and that is the base form of my data. To elaborate a little, it is actually a .cdf file uploaded through a client, which the client then converts into a byte array for the server code to read. So the server, where my code is running, cannot see the uploaded file at all. I also cannot assume the server itself is writable, so essentially there is no "location" to pass into the typical NetcdfFile loading methods.
The FAQ on ucar.edu does mention the possibility of reading from a non-file source, here. It says I should write my own IOSP, which I am happy to do. However, there is very little guidance on how to do this.
I don't know how to implement isValidFile when the only thing passed into the function is a RandomAccessFile, which the FAQ says can be ignored.
I don't know how my IOSP will obtain the byte array in question for use in readData.
I don't know why the minimal example in the FAQ advises me to make a new NetcdfFile class, when it seems I could just use the default one but pass in my custom IOSP.
This question is a little vague, but I am truly lost without many clues on where to even begin. Any guidance would be appreciated.
EDIT: I'm using 5.4.2 of the netcdf-java library.
I found this answer in the support archives. The solution is to use InMemoryRandomAccessFile. The constructor takes a String location and a byte array containing the file's contents. From my testing, I think the location can be any arbitrary string. Here is the code that worked for me.
byte[] filebytes = retrieveFileBytes(clientFilepath);
InMemoryRandomAccessFile raf = new InMemoryRandomAccessFile(clientFilepath, filebytes);
NetcdfFile file = NetcdfFiles.open(raf, clientFilepath, null, null);
Variable peakRetentionTime = file.findVariable("peak_retention_time");
if (peakRetentionTime == null) {
displayWarning("peak_retention_time null!");
} else {
Array data = peakRetentionTime.read();
displayInfo(Ncdump.printArray(data));
}
I'm using an ObjectInputStream to call readObject for reading in serialized Objects. I would like to avoid having this method block, so I'm looking to use something like Inputstream.available().
InputStream.available() will tell you there are bytes available and that read() will not block. Is there an equivalent method for seriailzation that will tell you if there are Objects available and readObject will not block?
No. Although you could use the ObjectInputStream in another thread and check to see whether that has an object available. Generally polling isn't a great idea, particularly with the poor guarantees of InputStream.available.
The Java serialization API was not designed to support an available() function. If you implement your own object reader/writer functions, you can read any amount of data off the stream you like, and there is no reporting method.
So readObject() does not know how much data it will read, so it does not know how many objects are available.
As the other post suggested, your best bet is to move the reading into a separate thread.
I have an idea that by adding another InputStream into the chain one can make availability information readable by the client:
HACK!
InputStream is = ... // where we actually read the data
BufferedInputStream bis = new BufferedInputStream(is);
ObjectInputStream ois = new ObjectInputStream(bis);
if( bis.available() > N ) {
Object o = ois.readObject();
}
The tricky point is value of N. It should be big enough to cover both serialization header and object data. If those are varying wildly, no luck.
The BufferedInputStream works for me, and why not just check if(bis.available() > 0) instead of a N value, this works perfectly for me.
I think ObjectInputStream.readObject blocks(= waits until) when no input is to be read. So if there is any input at all in the stream aka if(bis.available() > 0) ObjectInputStream.readObject will not block. Keep in mind that ObjectInputStream.readObject might throw a ClassNotFoundException, and that is't a problem at all to me.
I am new to Java. I want to learn to use GZIPstreams. I already have tried this:
ArrayList<SubImage>myObject = new ArrayList<SubImage>(); // SubImage is a Serializable class
ObjectOutputStream compressedOutput = new ObjectOutputStream(
new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(
new File("....")))));
compressedOutput.writeObject(myObject);
and
ObjectInputStream compressedInput = new ObjectInputStream(
new BufferedInputStream(new GZIPInputStream(new FileInputStream(
new File("....")))));
myObject=(ArrayList<SubImage>)compressedInput.readObject();
When the program writes myObject to a file without throwing any exception, but when it reaches the line
myObject=(ArrayList<SubImage>)compressedInput.readObject();
it throws this exception:
Exception in thread "main" java.io.EOFException: Unexpected end of ZLIB input stream
How can I solve this problem?
You have to flush and close your outputstream. Otherwhise, at least, the BufferedOutputStream will not write everything to the file (it does in big chucks to avoid penalizing performance).
If you call compressedOutput.flush() and compressedOutput.close() it will suffice.
You can try writing a simple string object and checking if the file is well written.
How? If you write a xxx.txt.gz file you can open it with your preferred zip app and look at the xxx.txt. If the app complains, then the content is not full written.
Extended answer to a comment: compressing even more the data
Changing serialization
You could change the standard serialization of SubImage object if it's an object of your own. Check java.io.Serializable javadoc to know how to do it. It's pretty straightforward.
Writing just what you need
Serialization has the drawback that needs to write "it's a SubImage" just before every instance you write. It's not necessary if you know what's going to be there beforehand. So you could try to serialize it more manually.
To write your list, instead of writing an object write directly the values that conform your list. You will need just a DataOutputStream (but ObjectOutputStream is a DOS so you can use it anyway).
dos.writeInt(yourList.size()); // tell how many items
for (SubImage si: yourList) {
// write every field, in order (this should be a method called writeSubImage :)
dos.writeInt(...);
dos.writeInt(...);
...
}
// to read the thing just:
int size = dis.readInt();
for (int i=0; i<size; i++) {
// read every field, in the same order (this should be a method called readSubImage :)
dis.readInt(...);
dis.readInt(...);
...
// create the subimage
// add it to the list you are recreating
}
This method is more manual but if:
you know what's going to be written
you will not need this kind of serialization for many types
it's pretty affordable and definitively more compressed than the Serializable counterpart.
Have in mind that there are alternative frameworks to serialize objects or create string messages (XStream for xml, Google Protocol Buffers for binary messages, and so on). That frameworks could work directly to binary or writing a string that could be then written.
If your app will need more on this, or just curious, maybe you should look at them.
Alternative serialization frameworks
Just looked in SO and found several questions (and answers) addressing this issue:
https://stackoverflow.com/search?q=alternative+serialization+frameworks+java
I've found that XStream is pretty easy and straightforward to use. And JSON is a format pretty readable and succint (and Javascript compatible which could be a plus :).
I should go for:
Object -> JSON -> OutputStreamWriter(UTF-8) -> GZippedOutputStream -> FileOutputStream
how can I write many serializable objects to a single file and then read a few of the objects as and when needed?
You'd have to implement the indexing aspect yourself, but otherwise this could be done. When you serialize an object you essentially get back an OutputStream, which you can point to wherever you want. Storing multiple objects into a file this way would be straightforward.
The tough part comes when you want to read "a few" objects back. How are you going to know how to seek to the position in the file that contains the specific object you want? If you're always reading objects back in the same order you wrote them, from the start of the file onwards, this will not be a problem. But if you want to have random access to objects in the "middle" of the stream, you're going to have to come up with some way to determine the byte offset of the specific object you're interested in.
(This method would have nothing to do with synchronization or even Java per se; you've got to design a scheme that will fit with your requirements and environment.)
The writing part is easy. You just have to remember that you have to write all objects 'at once'. You can't create a file with serialized objects, close it and open it again to append more objects. If you try it, you'll get error messages on reading.
For deserializing, I think you have to process the complete file and keep the objects you're interested in. The others will be created but collected by the gc on the next occasion.
Make Object[] for storing your objects. It worked for me.
I'd use a Flat File Database (e. g. Berkeley DB Java Edition). Just write your nodes as rows in a table like:
Node
----
id
value
parent_id
To read more Objects from file:
public class ReadObjectFromFile {
public static Object[] readObject() throws IOException {
Object[] list = null;
try {
byte[] bytes = Files.readAllBytes(Paths.get("src/objectFile.txt"));
ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(bytes));
list = (Object[]) ois.readObject();
ois.close();
} catch (IOException | ClassNotFoundException e) {
e.printStackTrace();
}
return list;
}
}
I have a very large object which I wish to serialize. During the process of serialization, it comes to occupy some 130MB of heap as an weblogic.utils.io.UnsyncByteArrayOutputStream. I am using a BufferedOutputStream to speed up writing the data to disk, which reduces the amount of time for which this object is held in memory.
Is it possible to use a buffer to reduce the size of the object in memory though? It would be good if there was a way to serialize it x bytes at a time and write those bytes to disk.
Sample code follows if it is of any use. There's not much to go on though I don't think. If it's the case that there needs to be a complete in-memory copy of the object to be serialised (and therefore no concept of a serialization buffer) then I suppose I am stuck.
ObjectOutputStream tmpSerFileObjectStream = null;
OutputStream tmpSerFileStream = null;
BufferedOutputStream bufferedStream = null;
try {
tmpSerFileStream = new FileOutputStream(tmpSerFile);
bufferedStream = new BufferedOutputStream(tmpSerFileStream);
tmpSerFileObjectStream = new ObjectOutputStream(bufferedStream);
tmpSerFileObjectStream.writeObject(siteGroup);
tmpSerFileObjectStream.flush();
} catch (InvalidClassException invalidClassEx) {
throw new SiteGroupRepositoryException(
"Problem encountered with class being serialised", invalidClassEx);
} catch (NotSerializableException notSerializableEx) {
throw new SiteGroupRepositoryException(
"Object to be serialized does not implement " + Serializable.class,
notSerializableEx);
} catch (IOException ioEx) {
throw new SiteGroupRepositoryException(
"Problem encountered while writing ser file", ioEx);
} catch (Exception ex) {
throw new SiteGroupRepositoryException(
"Unexpected exception encountered while writing ser file", ex);
} finally {
if (tmpSerFileObjectStream != null) {
try {
tmpSerFileObjectStream.close();
if(null!=tmpSerFileStream)tmpSerFileStream.close();
if(null!=bufferedStream)bufferedStream.close();
} catch (IOException ioEx) {
logger.warn("Exception caught on trying to close ser file stream", ioEx);
}
}
}
This is wrong on so many levels. This is a massive abuse of serialization. Serialization is mostly intended for temporarily storing an object. For example,
session objects between tomcat server restarts.
transferring objects between jvms ( load balancing at website )
Java's serialization makes no effort to handle long-term storage of objects (No versioning support) and may not handle large objects well.
For something so big, I would suggest some investigation first:
Ensure that you are not trying to persist the entire JVM Heap.
Look for member variables that can be labeled as 'transient' to avoid including them it the serialization ( perhaps you have references to service objects )
Consider possibility that there is a memory leak and the object is excessively large.
If everything is indeed correct, you will have to research alternatives to java.io.Serialization. Taking more control via java.io.Externalization might work. But I would suggest something like a json or xml representation.
Update:
Investigate :
google's protocol buffer
facebook's Thrift
Avro
Cisco's Etch
Take a look at this benchmarkings as well.
What is the "siteGroup" object that you're trying to save? I ask, because it's unlikely that any one object is 130MB in size, unless it has a ginormous list/array/map/whatever in it -- and if that's the case, the answer would be to persist that data in a database.
But if there's no monster collection in the object, then the problem is likely that the object tree contains references to a bagillion objects, and the serialization of course does a deep copy (this fact has been used as a shortcut to implement clone() a lot of times), so everything gets cataloged all at once in a top-down fashion.
If that's the problem, then the solution would be to implement your own serialization scheme where each object gets serialized in a bottom-up fashion, possibly in multiple files, and only references are maintained to other objects, instead of the whole thing. This would allow you to write each object out individually, which would have the effect you're looking for: smaller memory footprint due to writing the data out in chunks.
However, implementing your own serialization, like implementing a clone() method, is not all that easy. So it's a cost/benefit thing.
It sounds like whatever runtime you are using has a less-than-ideal implementation of object serialization that you likely don't have any control over.
A similar complaint is mentioned here, although it is quite old.
http://objectmix.com/weblogic/523772-outofmemoryerror-adapter.html
Can you use a newer version of weblogic? Can you reproduce this in a unit test? If so, try running it under a different JVM and see what happens.
I don't know about weblogic (that is - JRockit I suppose) serialization in particular: honestly I see no reason for using ByteArrayOutputStreams...
You may want to implement java.io.Externalizable if you need more control on how your object is serialized - or switch to an entirely different serialization system (eg: Terracotta) if you don't want to write read/write methods yourself (if you have many big classes).
Why does it occupy all those bytes as an unsync byte array output stream?
That's not how default serialization works. You must have some special code in there to make it do that. Solution: don't.