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High performance JSON text parsing and storing in SQLite

I'm working on some refactoring of my Android (kotlin/java) app to greatly improve the performance of an initial data synchronization that is done with our back-end systems and stored in a local SQLite db. The app is used on all kind of Android devices this sync can take up hours on the older Android devices.
The back-end system uses an JSON (UTF-8) API with around 10.000 items per batch with a lot of strings.
To achieve the highest performance possible I think I have to find a way to use / parse Strings more efficient. With just a normal JSON parser and using the Android SQLiteStatement classes I can only do this:
Parse the received JSON response (in-mem byte[]) into objects with there Strings.
These Strings are backed by new char[] and the bytes are first copied & converted to UTF-16 to the char[]. Effectively doubling the memory needed for a String.
The SQLite db uses UTF-8 encoding. So binding a string to its statement also involves some conversion steps.
I already implemented some idea's but still I have some problems;
Instead of parsing (index-overlay-parsing) to String objects I can parse these Strings to an object which has an reference to the original byte[] buffer, offset & length. The SQLiteStatement class allows to bind a byte[] as BLOB. Effectively inserting UTF-8 bytes directly in SQLite.
This approach is already much faster but still there is some memory copying involved. A neater approach will be that the SQLiteStatement allows to bind the original byte[] buffer with an offset and length. But this class is final...
Another idea was to subclass String and let this class be backed by the original byte[] buffer, offset & length. But also the String class is final...
Implementing some CharSequence sounds a neat approach but the SQLiteStatement does not have some method the bind that type...
Binary serdes does not greatly improve performance because of all the strings.
So I was wondering if you guys have some ideas how the reduce the object allocation and memory copying?
Can the Unsafe package do any help here? (proxy String?)
Another option is to copy the android.sqlite package and create my own SQLiteStatement with support for byte[]/offset/length or CharSequence.
Any other ideas?

How to write/read binary files that represent objects?

I'm new to Java programming, and I ran into this problem:
I'm creating a program that reads a .csv file, converts its lines into objects and then manipulate these objects.
Being more specific, the application reads every line giving it an index and also reads certain values from those lines and stores them in TRIE trees.
The application then can read indexes from the values stored in the trees and then retrieve the full information of the corresponding line.
My problem is that, even though I've been researching the last couple of days, I don't know how to write these structures in binary files, nor how to read them.
I want to write the lines (with their indexes) in a binary indexed file and read only the exact index that I retrieved from the TRIEs.
For the tree writing, I was looking for something like this (in C)
fwrite(tree, sizeof(struct TrieTree), 1, file)
For the "binary indexed file", I was thinking on writing objects like the TRIEs, and maybe reading each object until I've read enough to reach the corresponding index, but this probably wouldn't be very efficient.
Recapitulating, I need help in writing and reading objects in binary files and solutions on how to create an indexed file.

I think you are (for starters) best off when trying to do this with serialization.
Here is just one example from stackoverflow: What is object serialization?
(I think copy&paste of the code does not make sense, please follow the link to read)
Admittedly this does not yet solve your index creation problem.

Here is an alternative to Java native serialization, Google Protocol Buffers.
I am going to write direct quotes from documentation mostly in this answer, so be sure to follow the link at the end of answer if you are interested into more details.
What is it:
Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data – think XML, but smaller, faster, and simpler.
In other words, you can serialize your structures in Java and deserialize at .net, pyhton etc. This you don't have in java native Serialization.
Performance:
This may vary according to use case but in principle GPB should be faster, as its built with performance and interchangeability in mind.
Here is stack overflow link discussing Java native vs GPB:
High performance serialization: Java vs Google Protocol Buffers vs ...?
How does it work:
You specify how you want the information you're serializing to be structured by defining protocol buffer message types in .proto files. Each protocol buffer message is a small logical record of information, containing a series of name-value pairs. Here's a very basic example of a .proto file that defines a message containing information about a person:
message Person {
required string name = 1;
required int32 id = 2;
optional string email = 3;
enum PhoneType {
MOBILE = 0;
HOME = 1;
WORK = 2;
}
message PhoneNumber {
required string number = 1;
optional PhoneType type = 2 [default = HOME];
}
repeated PhoneNumber phone = 4;
}
Once you've defined your messages, you run the protocol buffer compiler for your application's language on your .proto file to generate data access classes. These provide simple accessors for each field (like name() and set_name()) as well as methods to serialize/parse the whole structure to/from raw bytes.
You can then use this class in your application to populate, serialize, and retrieve Person protocol buffer messages. You might then write some code like this:
Person john = Person.newBuilder()
.setId(1234)
.setName("John Doe")
.setEmail("jdoe#example.com")
.build();
output = new FileOutputStream(args[0]);
john.writeTo(output);
Read all about it here:
https://developers.google.com/protocol-buffers/
You could look at GPB as an alternative format to XSD describing XML structures, just more compact and with faster serialization.

how to create variables at runtime

I have an byte array that contains the file data. For Khichidi-1 (224-bits), the byte array is divided into N 224-bit blocks, M(1), M(2) ,..., M(N) is there any inbuilt class in java to perform this operation. If there is none like that, then how can we create N no.of variables depending on the no.of message blocks

To create classes at runtime with Java you would have to use its reflection capabilities,
see: http://download.oracle.com/javase/tutorial/reflect/index.html
However, I don't think that would help you in this case as the data you describe is simple raw bits of a particular length. You could divvy the data up into 28-byte chunks in an array of byte arrays.

Replicating C struct padding in Java

According to here, the C compiler will pad out values when writing a structure to a binary file. As the example in the link says, when writing a struct like this:
struct {
char c;
int i;
} a;
to a binary file, the compiler will usually leave an unnamed, unused hole between the char and int fields, to ensure that the int field is properly aligned.
How could I to create an exact replica of the binary output file (generated in C), using a different language (in my case, Java)?
Is there an automatic way to apply C padding in Java output? Or do I have to go through compiler documentation to see how it works (the compiler is g++ by the way).

Don't do this, it is brittle and will lead to alignment and endianness bugs.
For external data it is much better to explicitly define the format in terms of bytes and write explicit functions to convert between internal and external format, using shift and masks (not union!).

This is true not only when writing to files, but also in memory. It is the fact that the struct is padded in memory, that leads to the padding showing up in the file, if the struct is written out byte-by-byte.
It is in general very hard to replicate with certainty the exact padding scheme, although I guess some heuristics would get you quite far. It helps if you have the struct declaration, for analysis.
Typically, fields larger than one char will be aligned so that their starting offset inside the structure is a multiple of their size. This means shorts will generally be on even offsets (divisible by 2, assuming sizeof (short) == 2), while doubles will be on offsets divisible by 8, and so on.
UPDATE: It is for reasons like this (and also reasons having to do with endianness) that it is generally a bad idea to dump whole structs out to files. It's better to do it field-by-field, like so:
put_char(out, a.c);
put_int(out, a.i);
Assuming the put-functions only write the bytes needed for the value, this will emit a padding-less version of the struct to the file, solving the problem. It is also possible to ensure a proper, known, byte-ordering by writing these functions accordingly.

Is there an automatic way to apply C
padding in Java output? Or do I have
to go through compiler documentation
to see how it works (the compiler is
g++ by the way).
Neither. Instead, you explicitly specify a data/communication format and implement that specification, rather than relying on implementation details of the C compiler. You won't even get the same output from different C compilers.

For interoperability, look at the ByteBuffer class.
Essentially, you create a buffer of a certain size, put() variables of different types at different positions, and then call array() at the end to retrieve the "raw" data representation:
ByteBuffer bb = ByteBuffer.allocate(8);
bb.order(ByteOrder.LITTLE_ENDIAN);
bb.put(0, someChar);
bb.put(4, someInteger);
byte[] rawBytes = bb.array();
But it's up to you to work out where to put padding-- i.e. how many bytes to skip between positions.
For reading data written from C, then you generally wrap() a ByteBuffer around some byte array that you've read from a file.
In case it's helpful, I've written more on ByteBuffer.

A handy way of reading/writing C structs in Java is to use the javolution Struct class (see http://www.javolution.org). This won't help you with automatically padding/aligning your data, but it does make working with raw data held in a ByteBuffer much more convenient. If you're not familiar with javolution, it's well worth a look as there's lots of other cool stuff in there too.

This hole is configurable, compiler has switches to align structs by 1/2/4/8 bytes.
So the first question is: Which alignment exactly do you want to simulate?

With Java, the size of data types are defined by the language specification. For example, a byte type is 1 byte, short is 2 bytes, and so on. This is unlike C, where the size of each type is architecture-dependent.
Therefore, it would be important to know how the binary file is formatted in order to be able to read the file into Java.
It may be necessary to take steps in order to be certain that fields are a specific size, to account for differences in the compiler or architecture. The mention of alignment seem to suggest that the output file will depend on the architecture.

you could try preon:
Preon is a java library for building codecs for bitstream-compressed data in a
declarative (annotation based) way. Think JAXB or Hibernate, but then for binary
encoded data.
it can handle Big/Little endian binary data, alignment (padding) and various numeric types along other features. It is a very nice library, I like it very much
my 0.02$

I highly recommend protocol buffers for exactly this problem.

As I understand it, you're saying that you don't control the output of the C program. You have to take it as given.
So do you have to read this file for some specific set of structures, or do you have to solve this in a general case? I mean, is the problem that someone said, "Here's the file created by program X, you have to read it in Java"? Or do they expect your Java program to read the C source code, find the structure definition, and then read it in Java?
If you've got a specific file to read, the problem isn't really very difficult. Either by reviewing the C compiler specifications or by studying example files, figure out where the padding is. Then on the Java side, read the file as a stream of bytes, and build the values you know are coming. Basically I'd write a set of functions to read the required number of bytes from an InputStream and turn them into the appropriate data type. Like:
int readInt(InputStream is,int len)
throws PrematureEndOfDataException
{
int n=0;
while (len-->0)
{
int i=is.read();
if (i==-1)
throw new PrematureEndOfDataException();
byte b=(byte) i;
n=(n<<8)+b;
}
return n;
}

You can alter the packing on the c side to ensure that no padding is used, or alternatively you can look at the resultant file format in a hex editor to allow you to write a parser in Java that ignores bytes that are padding.

Best way to read structured binary files with Java

I have to read a binary file in a legacy format with Java.
In a nutshell the file has a header consisting of several integers, bytes and fixed-length char arrays, followed by a list of records which also consist of integers and chars.
In any other language I would create structs (C/C++) or records (Pascal/Delphi) which are byte-by-byte representations of the header and the record. Then I'd read sizeof(header) bytes into a header variable and do the same for the records.
Something like this: (Delphi)
type
THeader = record
Version: Integer;
Type: Byte;
BeginOfData: Integer;
ID: array[0..15] of Char;
end;
...
procedure ReadData(S: TStream);
var
Header: THeader;
begin
S.ReadBuffer(Header, SizeOf(THeader));
...
end;
What is the best way to do something similar with Java? Do I have to read every single value on its own or is there any other way to do this kind of "block-read"?

To my knowledge, Java forces you to read a file as bytes rather than being able to block read. If you were serializing Java objects, it'd be a different story.
The other examples shown use the DataInputStream class with a File, but you can also use a shortcut: The RandomAccessFile class:
RandomAccessFile in = new RandomAccessFile("filename", "r");
int version = in.readInt();
byte type = in.readByte();
int beginOfData = in.readInt();
byte[] tempId;
in.read(tempId, 0, 16);
String id = new String(tempId);
Note that you could turn the responce objects into a class, if that would make it easier.

If you would be using Preon, then all you would have to do is this:
public class Header {
#BoundNumber int version;
#BoundNumber byte type;
#BoundNumber int beginOfData;
#BoundString(size="15") String id;
}
Once you have this, you create Codec using a single line:
Codec<Header> codec = Codecs.create(Header.class);
And you use the Codec like this:
Header header = Codecs.decode(codec, file);

You could use the DataInputStream class as follows:
DataInputStream in = new DataInputStream(new BufferedInputStream(
new FileInputStream("filename")));
int x = in.readInt();
double y = in.readDouble();
etc.
Once you get these values you can do with them as you please. Look up the java.io.DataInputStream class in the API for more info.

I may have misunderstood you, but it seems to me you're creating in-memory structures you hope will be a byte-per-byte accurate representation of what you want to read from hard-disk, then copy the whole stuff onto memory and manipulate thence?
If that's indeed the case, you're playing a very dangerous game. At least in C, the standard doesn't enforce things like padding or aligning of members of a struct. Not to mention things like big/small endianness or parity bits... So even if your code happens to run it's very non-portable and risky - you depend on the compiler's creator not changing its mind on future versions.
Better to create an automaton to both validate the structure being read (byte per byte) from HD is valid, and filling an in-memory structure if it's indeed OK. You may loose some milliseconds (not so much as it may seem for modern OSes do a lot of disk read caching) though you gain platform and compiler independence. Plus, your code will be easily ported to another language.
Post Edit: In a way I sympathize with you. In the good-ol' days of DOS/Win3.11, I once created a C program to read BMP files. And used exactly the same technique. Everything was nice until I tried to compile it for Windows - oops!! Int was now 32 bits long, rather than 16! When I tried to compile on Linux, discovered gcc had very different rules for bit fields allocation than Microsoft C (6.0!). I had to resort to macro tricks to make it portable...

I used Javolution and javastruct, both handles the conversion between bytes and objects.
Javolution provides classes that represent C types. All you need to do is to write a class that describes the C structure. For example, from the C header file,
struct Date {
unsigned short year;
unsigned byte month;
unsigned byte day;
};
should be translated into:
public static class Date extends Struct {
public final Unsigned16 year = new Unsigned16();
public final Unsigned8 month = new Unsigned8();
public final Unsigned8 day = new Unsigned8();
}
Then call setByteBuffer to initialize the object:
Date date = new Date();
date.setByteBuffer(ByteBuffer.wrap(bytes), 0);
javastruct uses annotation to define fields in a C structure.
#StructClass
public class Foo{
#StructField(order = 0)
public byte b;
#StructField(order = 1)
public int i;
}
To initialize an object:
Foo f2 = new Foo();
JavaStruct.unpack(f2, b);

I guess FileInputStream lets you read in bytes. So, opening the file with FileInputStream and read in the sizeof(header). I am assuming that the header has a fixed format and size. I don't see that mentioned in the initial post, but assuming that is the case as it would get much more complex if the header has optional args and different sizes.
Once you have the info, there can be a header class in which you assign the contents of the buffer that you've already read. And then parse the records in a similar fashion.

Here is a link to read byte using a ByteBuffer (Java NIO)
http://exampledepot.com/egs/java.nio/ReadChannel.html

As other people mention DataInputStream and Buffers are probably the low-level API's you are after for dealing with binary data in java.
However you probably want something like Construct (wiki page has good examples too: http://en.wikipedia.org/wiki/Construct_(python_library), but for Java.
I don't know of any (Java versions) off hand, but taking that approach (declaratively specifying the struct in code) would probably be the right way to go. With a suitable fluent interface in Java it would probably be quite similar to a DSL.
EDIT: bit of googling reveals this:
http://javolution.org/api/javolution/io/Struct.html
Which might be the kind of thing you are looking for. I have no idea whether it works or is any good, but it looks like a sensible place to start.

I would create an object that wraps around a ByteBuffer representation of the data and provide getters to read directly from the buffer. In this way, you avoid copying data from the buffer to primitive types. Furthermore, you could use a MappedByteBuffer to get the byte buffer. If your binary data is complex, you can model it using classes and give each class a sliced version of your buffer.
class SomeHeader {
private final ByteBuffer buf;
SomeHeader( ByteBuffer fileBuffer){
// you may need to set limits accordingly before
// fileBuffer.limit(...)
this.buf = fileBuffer.slice();
// you may need to skip the sliced region
// fileBuffer.position(endPos)
}
public short getVersion(){
return buf.getShort(POSITION_OF_VERSION_IN_BUFFER);
}
}
Also useful are the methods for reading unsigned values from byte buffers.
HTH

I've written up a technique to do this sort of thing in java - similar to the old C-like idiom of reading bit-fields. Note it is just a start but could be expanded upon.
here

In the past I used DataInputStream to read data of arbitrary types in a specified order. This will not allow you to easily account for big-endian/little-endian issues.
As of 1.4 the java.nio.Buffer family might be the way to go, but it seems that the your code might actually be more complicated. These classes do have support for handling endian issues.

A while ago I found this article on using reflection and parsing to read binary data. In this case, the author is using reflection to read the java binary .class files. But if you are reading the data into a class file, it may be of some help.