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API for Java to rename/move files based on rulesets

I'm looking for an API to move/copy and rename files based on rulesets. Is there a better way than using only java.io and regexp?
Background: I want to write a small program to convert files (images) between different similar tools, but they all have different folder structures and different filenaming rules.

Ant knows to do this very well. Why not to write a task for ant that does what you want and use Ant filter for file filtering? Take a look on http://ant.apache.org/manual/Tasks/filter.html

Extract a particular folder from a jar and copy it to a desired destination on my system

I need to extract the resource folder from inside a jar to a desired location in my system. I want to do it by calling a function in a class, which is in the same jar.
I don't want to copy one file at a time. Can you please suggest me a way in which I can copy the entire folder?
I initially thought of compressing them into a zip, and copying it elsewhere, and extracting it.
How will this work? Is there a more efficient way to do this?
Thanks in advance.

If you are going to do this using java API I know only one way: you have to use JarInputStream or ZipInputStream, iterate over Zip entries, detect which entries belong to the folder and extract them, i.e. read from zip and write to disk. There is no other "magical" way.
But if you want you can probably use some kind of higher level API. Check VFS from Jakarta: http://commons.apache.org/vfs/
It provides API that probably does what you need.

You could use Runtime.exec api to execute something similar to the following :
jar xf <your_jar_file_name> <path_to_directory_to_be_extracted>
In this way, you do not have to create specialized class to handle Jar files and you can focus on solving actual problem at hand.
Note : this is restricted to JDK may not work on JRE.

Alternative to ZIP as a project file format. SQLite or Other?

My Java application is currently using ZIP as a project file format. The project files contain a few XML files and many image and sound files.
The project files are getting pretty big, and since I can't find a way with the java.util.zip classes to write to a ZIP file without recreating it, my file saves are becoming very slow. So for example, if I just want to update one XML file, I need to rewrite the entire ZIP.
Is there some other Java ZIP library that will allow me to do random writes to a ZIP file?
I know switching to something like SQLite solves the random write issue. Would using SQLite just to write XML, Sound and Images as blobs be an appropriate use?
I suppose I could come up with my own file format and use RandomAccessFile but then there would be a lot of bookkeeping I'd have to write.
Update...
My file format is very much like Office Open XML. It is a ZIP file containing XML and other resources.
Someone must have solved the problem of how to do random writes to update a ZIP file. Does anyone know how?

There exist so-called single-file virtual file systems, that let you create file-based containers and provide file-system like structure and APIs. One of the samples is SolFS (it has C-written core with JNI wrapper) and some other C- and Delphi-written solutions (I don't remember their names at the moment). I guess there exist similar native Java solutions as well.

First of all I would separate your app's resources in those that are static (such as images) and those that can be changed (the xml files you mentioned).
Since the static files won't be re-written, you can continue to store them in a zip file, which IMHO is a good approach to deploy any resources.
Now you have 2 options:
Since the non-static files are probably not too big (the xml files are likely to be smaller than images+sounds), you can stick with your current solution (zip file) and simply maintain 2 zip files, of which only one (the smaller one with the changeable files) can/will be re-written.
You could use a in-memory-database (such as hsqldb) to store the changeable files and only persist them (transferring from the database to a file on the drive) when your application shuts down or that operation is explicitly needed.

sqlite is not always fast (at least in my experience). I would suggest individually compressing the XML files -- you'll still get decent compression, and just use the file system to save them. You could experiment with btrfs, or just go with ext4. If you're not on Linux, then this should still work okay, but it might not be as fast until things are cached in memory.
the idea is that if you do not have redundancy between XML files, then you don't get that much saving by compressing them in one "solid" archive.

Before offering another answer along the lines of using properly structured JARs, I have to ask -- why does the project need to be encapsulated in one file? How do you distribute the program to users to run?

If you must keep a project contained within a single file and be able to replace resources efficiently, yes I would say SQLite is a good choice.
If you do choose to use SQLite, also consider converting some of the XML schemas to one or more SQL tables rather than storing large XML documents as BLOBs.

Shipping Java code with data baked into the .jar

I need to ship some Java code that has an associated set of data. It's a simulator for a device, and I want to be able to include all of the data used for the simulated records in the one .JAR file. In this case, each simulated record contains four fields (calling party, called party, start of call, call duration).
What's the best way to do that? I've gone down the path of generating the data as Java statements, but IntelliJ doesn't seem particularly happy dealing with a 100,000 line Java source file!
Is there a smarter way to do this?
In the C#/.NET world I'd create the data as a separate file, embed it in the assembly as a resource, and then use reflection to pull that out at runtime and access it. I'm unsure of what the appropriate analogy is in the Java world.
FWIW, Java 1.6, shipping for Solaris.

It is perfectly OK to include static resource files in the JAR. This is commonly done with properties files. You can access the resource with the following:
Class.getResourceAsStream ("/some/pkg/resource.properties");
Where / is relative to the root of the classpath.
This article deals with the subject Smartly load your properties.

Sure, just include them in your jar and do
InputStream is = this.getClass().getClassLoader().getResourceAsStream("file.name");
If you put them under some folders, like "data" then just do
InputStream is = this.getClass().getClassLoader().getResourceAsStream("data/file.name");

Any way to get a File object from a JAR

I have a JAR file that contains an API that uses external model files. I would like to include the model files in the JAR itself so it easier to use for other developers. The API will accept a File object only, is there any way to do this? I have already tried the following, and they have failed:
Using class.getResourceAsStream(). This would work if the API accepted an InputStream.
Parsing the classpath and trying to build from the entries (the JAR will show as app.jar)
I suppose an option is to use getResourceAsStream and move the files to a permanent location on the HDD but, I do not like this option. There has to be something better, any thoughts?

Resources in a .jar file are not files in the sense that the OS can access them directly via normal file access APIs.
And since java.io.File represents exactly that kind of file (i.e. a thing that looks like a file to the OS), it can't be used to refer to anything in a .jar file.
A possible workaround is to extract the resource to a temporary file and refer to that with a File.
Note that generally APIs that try to handle files should be written to handle InputStream/OutputStream as well to allow this kind of operations to suceed.