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Replicating a Looping File Backup in Java

I'm trying to implement a file storage system that is like a video recording system that loops over existing data. Say, we have a maximum file size of 10MB and append an integer value every second. We can setup a FileChannel and keep appending the values. But what to do once we've reached our 10MB? Now we want to append a new value but pop one off the head of the file. We see the problem is a sort of queue and it's easy to put and pop values from a queue in memory, but not so easy when using files.
I implemented a circular buffer with a FileChannel as the behind the scenes storage. It works but the problem is the first and last indices move through the file as data is added and removed. Ideally, I would always like the oldest data value to be at file index 0 and the most recent data at file index n-1, so that when a file is read it is from the start to end.
I saw that FileChannel supports methods transferTo() and transferFrom() and also did an implementation using these methods and again it works. The problem with this method is continually having to transfer blocks of data from the current file to a temporary file and then replace the current with the new file. It works but not particularly efficient.
Thus, I've tried a few things but not found the ideal solution or replicating a file-queue as yet and was wondering if anyone else has implemented the golden bullet solution? Maybe, a file version of a queue in which the data is shuffled along is simply not possible, but hopefully someone knows an answer. Thanks.

What is the fastest file / way to parse a large data file?

So I am working on a GAE project. I need to look up cities, Country Names and Country Codes for sign ups, LBS, ect ...
Now I figured that putting all the information in the Datastore is rather stupid as it will be used quite frequently and its gonna eat up my datastore quotations for no reason, specially that these lists arent going to change, so its pointless to put in datastore.
Now that leaves me with a few options:
API - No budget for paid services, free ones are not exactly reliable.
Upload Parse-able file - Favorable option as I like the certainty that the data will always be there.
So I got the files needed from GeoNames (link has source files for all countries in case someone needs it). The file for each country is a regular UTF-8 tab delimited file which is great.
However, now that I have the option to choose how to format and access the data, the question is:
What is the best way to format and retrieve data systematically from a static file in a Java servelet container ?
The best way being the fastest, and least resource hungry method.
Valid options:
TXT file, tab delimited
XML file Static
Java Class with Tons of enums
I know that importing country files as Java Enums and going through their values will be very fast, but do you think this is going to affect memory beyond reasonable limits ? On the other hand, every time I need to access a record, the loop will go through a few thousand lines until it finds the required record ... reading line by line so no memory issues, but incredibly slow ... I have had some experience with parsing an excel file in a Java servelet and it took something like 20 seconds just to parse 250 records, on large scale, response time WILL timeout (no doubt about it) so is XML anything like excel ??
Thank you very much guys !! Please provide opinions, all and anything is appreciated !

Easiest and fastest way would be to have the file as a static web resource file, under the WEB-INF folder and on application startup, have a context listener to load the file into memory.
In memory, it should be a Map, mapping from a key you want to search by. This will allow you like a constant access time.
Memory consumption would only matter if it is really big. A hundred thousand record for example not worth optimizing if you need to access this many times.
The static file should be plain text format or CSV, they are read and parsed most efficiently. No need XML formatting as parsing it would be slow.
If the list is really big, you can break it up into multiple, smaller files, and only parse those and only when they are required. A reasonable, easy partitioning would be to break it up by country, but any other partitioning would work (like based on its name using the first few characters from its name).
You could also consider building this Map in the memory once, and then serialize this map to a binary file, and include that binary file as a static resource file, and that way you would only have to deserialize this Map and would be no need to parse/process it as a text file and build objects yourself.
Improvements on the data file
An alternative to having the static resource file as a text/CSV file or a serialized Map
data file would be to have it as a binary data file where you could create your own custom file format.
Using DataOutputStream you can write data to a binary file in a very compact and efficient way. Then you could use DataInputStream to load data from this custom file.
This solution has the advantages that the file could be much less (compared to plain text / CSV / serialized Map), and loading it would be much faster (because DataInputStream doesn't use number parsing from a text for example, it reads the bytes of a number directly).

Hold the data in source form as XML. At start of day, or when it changes, read it into memory: that's the only time you incur the parsing cost. There are then two main options:
(a) your in-memory form is still an XML tree, and you use XPath/XQuery to query it.
(b) your in-memory form is something like a java HashMap
If the data is very simple then (b) is probably best, but it only allows you to do one kind of query, which is hard-coded. If the data is more complex or you have a variety of possible queries, then (a) is more flexible.

read/write to a large size file in java

i have a binary file with following format :
[N bytes identifier & record length] [n1 bytes data]
[N bytes identifier & record length] [n2 bytes data]
[N bytes identifier & record length] [n3 bytes data]
as you see i have records with different lengths. in each record i have N bytes fixed which contains and id and the length of data in record.
this file is very big and can contains 3 millions records.
I want to open this file by an application and let user to browse and edit the records.
( Insert / Update / Delete records)
my initial plan is to create and index file from original file and for each record, keep next and previous record address to navigate forward and backward easily. (some sort of linked list but in file not in memory)
is there library (java library) to help me to implement this requirement ?
any recommendation or experience that you think is useful?
----------------- EDIT ----------------------------------------------
Thanks for guides and suggestions,
some more info:
the original file and its format is out of my control (it's a third party file) and i can't change the file format. but i have to read it, let user to navigate over records and edit some of them (insert new record/ update an existing record/ delete a record) and at the end save it back to original file format.
do u still recommend DataBase instead of a normal index file ?
----------------- SECOND EDIT ----------------------------------------------
record size in update mode is fixed. it means updated (edited) record has same length as original record's, unless user delete the record and create another record with different format.
Many Thanks

Seriously, you should NOT be using a binary file for this. You should use a database.
The problems with trying to implement this as a regular file stem from the fact that operating systems do not allow you to insert extra bytes into the middle of an existing file. So if you need to insert a record (anywhere but the end), update a record (with a different size) or remove a record, you would need to:
rewrite other records (after the insertion/update/deletion point) to make or reclaim space, or
implement some kind of free space management within the file.
All of this is complicated and / or expensive.
Fortunately, there is a class of software that implements this kind of thing. It is called database software. There are a wide range of options, ranging from using a full-scale RDBMS to light-weight solutions like BerkeleyDB files.
In response to your 1st and 2nd edits, a database will still be simpler.
However, here's an alternative that might perform better for this use-case than using a DB... without doing complicated free-space management.
Read the file and build an in-memory index that maps ids to file locations.
Create a second file to hold new and updated records.
Perform the record adds/updates/deletes:
An addition is handled by writing the new record to the end of the second file, and adding an index entry for it.
An update is handled by writing the updated record to the end of the second file, and changing the existing index entry to point to it.
A delete is handled by deleting the index entry for the record's key.
Compact the file as follows:
Create a new file.
Read each record in the old file in order, and check the index for the record's key. If the entry still points to the location of the record, copy the record to the new file. Otherwise skip it.
Repeat the step 4.2 for the second file.
If we completed all of the above successfully, delete the old file and second file.
Note this relies on being able to keep the index in memory. If that is not feasible, then the implementation is going to be more complicated ... and more like a database.

Having a data file and an index file would be the general base idea for such an implementation, but you'd pretty much find yourself dealing with data fragmentation upon repeated data updates/deletion, etc. This kind of project, in itself, should be a separate project and should not be part of your main application. However, essentially, a database is what you need as it is specifically designed for such operations and use cases and will also allow you to search, sort, and extend (alter) your data structure without having to refactor an in-house (custom) solution.
May I suggest you to download Apache Derby and create a local embedded database (derby does it for you want you create a new embedded connection at run-time). It will not only be faster than anything you'll write yourself, but will make your application easier to maintain.
Apache Derby is a single jar file that you can simply include and distribute with your project (check the license if any legal issue may apply in your app). There is no need for a database server or third party software; it's all pure Java.
Bottom line as that it all depends on how large is your application, if you need to share the data across many clients, if speed is a critical aspect of your app, etc.
For a stand-alone, single user project, I recommend Apache Derby. For a n-tier application, you might want to look into MySQL, PostgreSQL or (hrm) even Oracle. Using already made and tested solutions is not only smart, but will cut down your development time (and maintenance efforts).
Cheers.

Generally you are better off letting a library or database do the work for you.
You may not want to have an SQL database and there are plenty of simple databases which don't use SQL. http://nosql-database.org/ lists 122 of them.
At a minimum, if you are going to write this I suggest you read the source for one of these databases to see how they work.
Depending on the size of the records, 3 million isn't that much and I would suggest you keep as much in memory as possible.
The problem you are likely to have is ensuring the data is consistent and recovering the data when a corruption occurs. The second problem is dealing with fragmentation efficiently (some thing the brightest minds working on the GC deal with) The third problem is likely to be maintain the index in a transaction fashion with the source data to ensure there are no inconsistencies.
While this may appear simple at first, there are significant complexities in making sure there data is reliable, maintainable and can be accessed efficiently. This is why most developers use an existing database/datastore library and concentrate on the features which are unqiue to their application.

(Note: My answer is about the problem in general, not considering any Java libraries or - like the other answers also proposed - using a database (library), which might be better than reinventing the wheel)
The idea to create an index is good and will be very helpful performance-wise (although you wrote "index file", I think it should be kept in memory). Generating the index should be quite fast if you read the ID and record length for each entry and then just skip the data with a file seek.
You should also think about the edit functionality. Especially inserting and deleting can be very slow on such a big file if you do it wrong (f.e. deleting and then moving all the following entries to close the gap).
The best option would be to only mark deleted entries as deleted. When inserting, you can overwrite one of those or append to the end of the file.

Insert / Update / Delete records
Inserting (rather than merely appending) and deleting records to a file is expensive because you have to move all the following content of the file to create space for the new record or to remove the space it used. Updating is similarly expensive if the update changes the length of the record (you say they are variable length).
The file format you propose is fundamentally unsuitable for the kinds of operations you want to perform. Others have suggested using a data-base. If you don't want to go that far, adding an index file (as you suggest) is the way to go. I recommend making the index records all the same length.

As others have stated a database would seem a better solution. The following are Java SQL DB's that could be used: H2, Derby or HSQLDB
If you want to use an index file look at Berkley DB or No Sql
If there is some reason for using a file, look at JRecord . It has
Several Classes for reading/writing files with variable length binary records (they where written for Cobol VB files). Any of Mainframe / Fujitsu / Open Cobol VB file structures should do the job.
An Editor for editing JRecord files. The latest version of the Editor can handle large files (it uses Compression / spill file). The editor suffers from having to download the whole file and only one user can edit the file at one time.
The JRecord solution will only work if
There is a limited number (preferably one) users all located in the one location
Fast infostructure

Is it possible to prepend data to an file without rewriting?

I deal with very large binary files ( several GB to multiple TB per file ). These files exist in a legacy format and upgrading requires writing a header to the FRONT of the file. I can create a new file and rewrite the data but sometimes this can take a long time. I'm wondering if there is any faster way to accomplish this upgrade. The platform is limited to Linux and I'm willing to use low-level functions (ASM, C, C++) / file system tricks to make this happen. The primimary library is Java and JNI is completely acceptable.

There's no general way to do this natively.
Maybe some file-systems provide some functions to do this (cannot give any hint about this), but your code will then be file-system dependent.
A solution could be that of simulating a file-system: you could store your data on a set of several files, and then provide some functions to open, read and write data as if it was a single file.

Sounds crazy, but you can store the file data in reverse order, if it is possible to change function that reads data from file. In that case you can append data (in reverse order) at the end of the file. It is just a general idea, so I can't recommend anything particular.
The code for reversing of current file can looks like this:
std::string records;
ofstream out;
std::copy( records.rbegin(), records.rend(), std::ostream_iterator<string>(out));

It depends on what you mean by "filesystem tricks". If you're willing to get down-and-dirty with the filesystem's on-disk format, and the size of the header you want to add is a multiple of the filesystem block size, then you could write a program to directly manipulate the filesystem's on-disk structures (with the filesystem unmounted).
This enterprise is about as hairy as it sounds though - it'd likely only be worth it if you had hundreds of these giant files to process.

I would just use the standard Linux tools to do it.
Writting another application to do it seems like it would be sub-optimal.
cat headerFile oldFile > tmpFile && mv tmpFile oldFile

I know this is an old question, but I hope this helps someone in the future. Similar to simulating a filesystem, you could simply use a named pipe:
mkfifo /path/to/file_to_be_read
{ echo "HEADER"; cat /path/to/source_file; } > /path/to/file_to_be_read
Then, you run your legacy program against /path/to/file_to_be_read, and the input would be:
HEADER
contents of /path/to/source_file
...
This will work as long as the program reads the file sequentially and doesn't do mmap() or rewind() past the buffer.

Reading a gz file and keeping track of position in file

So, here is the situation:
I have to read big .gz archives (GBs) and kind of "index" them to later on be able to retrieve specific pieces using random access.
In other words, I wish to read the archive line by line, and be able to get the specific location in the file for any such line. (so that I can jump directly to these specific locations upon request). (PS: ...and it's UTF-8 so we cannot assume 1 byte == 1 char.)
So, basically, what I just need is a BufferedReader which keeps track of its location in the file. However, this doesn't seem to exist.
Is there anything available or do I have to roll my own?
A few additional comments:
I cannot use BufferedReader directly since the file location corresponds to what has been buffered so far. In other words, a multiple of the internal buffer size instead of the line location.
I cannot use InputStreamReader directly for performance reasons. Unbuffered would be way to slow, and, btw, lacks convenience methods to read lines.
I cannot use RandomAccessFile since 1. it's zipped, and 2. RandomAccessFile uses "modified" UTF-8
I guess the best would be use a kind of of buffered reader keeping track of file location and buffer offset ...but this sounds quite cumbersome. But maybe I missed something. Perhaps there is already something existing to do that, to read files line by lines and keep track of location (even if zipped).
Thanks for tips,
Arnaud

I think jzran could be pretty much what you're looking for:
It's a Java library based on the
zran.c sample from zlib.
You can preprocess a large gzip
archive, producing an "index" that can
be used for random read access.
You can balance between index size and
access speed.

What you are looking for is called mark(), markSupported() and skip().
This methods are declared both in InputStream and Reader, so you are welcome to use them.

GZIP compression does not support seeking. Previous data blocks are needed to build compression tables...