Need help choosing a robust archive format - java

I'm working on a Java application that runs on Lubuntu on single-board computers and produces thousands of image files, which are then transferred over FTP. The transfer takes several times longer for multiple files than it does for a single file of the same size as the total of the multiple files, I'm assuming because the FTP client has to establish a new connection for every file. So I thought I'd have the application put the image files in a single archive file, but the problem with this is that sometimes the SBC won't shut down cleanly for various reasons, and the entire archive may be corrupted all the images will be lost. Archiving the files afterwards is not a great option basically because it takes a long time. An intermediate solution may be to create multiple midsize archives, but I'm not happy with it.
I wrote a simple unit test to experiment with ZipOutputStream, and if I cancel the test it before it closes the stream, the resulting zip file gets corrupted, unsurprisingly. Could anyone suggest a different widely recognized archive format and/or implementation that might be more robust?

The tar format, jtar implementation seem to work pretty well. If I cancel in the middle of writing, I can still open the archive at least with 7zip and even get the partially written last entry.

Related

Does saving files in a ".zip" folder speed up file write time to network drive?

I know that when I write a new file to a folder that ends in ".zip" it compresses the file. This is when using BufferedOutputStream in JAVA and saving to a windows file system. I'm saving these files to a network drive, so the write time is dependent on network speed.
Will saving to a .zip folder speed up write time? In other words, does it transfer the data uncompressed and then compresses it (so it wouldn't speed up write time) or does it compress then write out the file? Sorry if this is an ignorant question.
There are so many misconceptions in the Question, I think it is worth going through them one at a time.
I know that when I write a new file to a folder that ends in ".zip" it compresses the file.
That is not correct. Creating a file with a ".zip" suffix does not automatically make it compressed. Writing files to a directory that has ".zip" as its filename suffix (?!?) doesn't either. Not in Java. Not in other languages.
In order to get compression, the application needs to take steps to make this happen. In Java you could use ZipOutputStream to write a file in ZIP file format. However, a ZIP file is actually an "archive" format that is designed to hold multiple files in a ZIP file. If you simply trying to compress a single file, there are better alternatives; e.g. GZIPOutputStream.
(It is also possible that this so-called "ZIP folder" you are talking about is a normal ZIP file that has been "mounted" as a loopback file system. You / someone else would have had to set that up explicitly. Anyhow, if this is what is going on here, it is nothing to do with Java. It is all happening in external software and in the operating system where the ZIP is "mounted".)
This is when using BufferedOutputStream in JAVA and saving to a windows file system.
Erm ... no. See above. However you are correct that it may be better to use a BufferedOutputStream to write files, though it only really helps if your application is writing the files in small chunks; e.g. a byte at a time. (Stream compression complicates the issue, so it is difficult to give a simple, general answer on this.)
I'm saving these files to a network drive, so the write time is dependent on network speed.
Correct. It is also dependent on network latency, the protocols used and the load on the remote file server. (If you have a ZIP "mounted", then that is going to add overheads too.)
Will saving to a .zip folder speed up write time?
Maybe. See above. It depends what you mean by a ZIP folder.
Ignoring that, writing the files (the right way) in compressed and / or archive form from Java may speed up writes. There are actually two things to consider:
For plain compression, you are trading off the time it takes the application (!!) to compress and decompress the data against the time (and disk space) you are saving by moving and storing less bytes.
For ZIP files (and similar archive formats) there is a second potential saving. Storing and retrieving lots of individual small files from a file system is slow compared with storing and retrieving a single ZIP file containing those files.
And if you are looking for optimal compression, then ZIP is not the best option.
In other words, does it transfer the data uncompressed and then compresses it (so it wouldn't speed up write time) or does it compress then write out the file?
There are so many variables that it is hard to say for sure. But unless you have done something odd, it is likely that the bytes are sent over the network in compressed form.
Finally, I would advise you NOT to try to combine mounted ZIP files and network shares:
The combination of the two could potentially interact in ways that makes performance worse.
There is a risk that you will end up with a corrupted ZIP or lost files if the network share goes offline at an inconvenient point.

What is the best way to transfer bytes between files on network in Java [duplicate]

This question already exists:
Does java FileChannnel.transferTo() work cleverly when files are on network?
Closed 7 years ago.
The code is written in Java 1.7
I want to make some major modifications to a binary file on a slow network.To protect against the network connection being lost instead of writing directly to the file I write to a new file. When I have completed writing to the new file I delete the old file and rename the new file to the old file.
My question is is it better for the new file to be
1. On the same location as the original file
2. Locally on the computer
With 1. writing to the file could be slower, but the rename should be quicker in fact with most oses would be immediate . With 2 writing to the file should be quicker but then renaming the filwe would be slower.
I feel the answer is 1.
Actually if I open a Filechannel to both files and transfer files directly from one channel to another do the bytes have to come from network to my computer and back to network or can they been copied directly from one place on network to the the ther.
I'm guessing here but the files are probably mounted via some network file system (NFS, SMB) on your computer. So you can access them like local files; they are just slower.
As for the first question: You're not gaining anything by first writing the file locally. In the end, you always have to move the file to correct place in the network and that always involves a "copy all bytes" operation. For example, Java's File.rename() will fail when the two files aren't on the same harddisk / mount. So you have to manually copy the bytes to the destination folder anyway. Some IO frameworks do that for you when necessary but it always happens.
As for directly copying data between two remote hosts: There are a few network filesystems which support such operations but it's a special feature. The usual culprits (NFS and SMB) don't. They always download the whole file from the source and then upload it to the target.

Writing a ZIP on the fly?

At the moment I am tracing a load of files that come into my system to a directory. The issue is that I am running out of iNodes (the number of files I can store). For "replay" reasons (there are other reasons too), I would like the files to be separate files, so I can't just write to one file.
I am wondering whether I can replace this with code that will write the files to a ZIP on the fly. However, my concern is - what happens if the JVM crashes during procesing for whatever reason, do will I end up with a corrupt ZIP file? Or is there a way that I can ensure that the ZIP is valid after every "write"?

How to know if file is complete on the server using FTP?

I have a file scanner application in Java, that keeps scanning a directory on a server using FTP. gets list of files of the directory and downloads them one by one. on the other side, on the server, there's a process that writes these files. if I'm lucky I wouldn't try to download an incomplete file but how can I make sure if the write process on the server is complete and the file handle is closed, and file is ready to be downloaded?
I have no control on the write process which is on the server. moreover, I don't have write permission on the directory to try to get a write-handle in order to check if there's already a write handle open, so this option is off the table.
Is there an FTP function addressing this problem?
This is a very old and well-known problem.
There is no way to be absolutely certain a file being written by the FTP daemon is complete. It's even possible that the file transfer failed and then gets restarted and completed. You must poll the file's size and set a time limit, say 5 minutes. If the size does not change during that time you assume the file is complete.
If possible, the program that processes the file should be able to deal with partial files.
A much better alternative is rsync, which is much more robust and deterministic. It can even be configured (via command-line option) to write the data initially to a temporary location and move it to its final destination path upon successful completion. If the file exists where you expect it, then it is by definition complete.
A possible solution would be first uploading the file with a different filename (e.g. adding ".partial") and then renaming it to its final name.
If the server finds the final name then the upload has been completed.
If you cannot control the upload process then what you are asking is impossible by definition: the file upload could stop because of a network problem or because the sending process is stopped for whatever reason.
What the receiving end will observe is just a closing of the incoming stream; there is no way to guarantee that the data will not be a partial transfer.
Other workarounds could be checking for an end-of-data marker or using a request to the sending server to check if (in their view) the transfer has been completed.
This is more fundamental than FTP: you'd have a similar problem reading those files even if they were being created on the local machine.
If you can't modify the writing process, you'll need to jump through some hoops. None are great, but some are safer than others.
Keep reading until nothing changes for some window (maybe a minute, like David Schwartz suggests). You could optimize this a bit by watching the file size.
Figure out if the files are written serially in a reliable order. When you see file N appear, you know that file N-1 is ready. (Assumes that the directory is empty before the files are written, though you could also look at timestamps.) The downside is that your logic will break if the writer ever changes order or starts writing in parallel.
The reliable, safe solutions require improving the writer process.
Writer can write the files to hidden or temporary locations and only make them visible once the entire file (or directory) is ready, using symlinks or file-moving or chmod.
Writer creates a special file (e.g., "./DONE") only after all other files have been written, and reader doesn't read any files until that file is present.
Depending on the file type, the writer could add some kind of end-of-file record/line at the end of the file, and the reader could ensure that it's present.
You can use Ftp library from Apache common API
get more information
boolean flag = retrieveFile(String remote, OutputStream local);
This flag check output stream is available of the current file.

How to be sure a file has been successfully written?

I'm adding autosave functionality to a graphics application in Java. The application periodically autosaves the current document and also autosaves on exit. When the user starts the application, the autosave file is reloaded.
If the autosave file is corrupted in any way (I assume a power cut when the file is in the middle of being saved would do this?), the user will lose their work. How can I prevent such situations and do all I can to guarantee that the autosave document is in a consistent state?
To further complicate matters, to autosave the document I need to save one .xml file and several .png files. Also, the .png saving occurs in C code over JNI.
My current strategy is to write each .png with the extension .png.tmp, write the .xml file with the extension .xml.tmp, and then rename each file to remove the .tmp part leaving the .xml until last. On startup, I only load the autosave document if I can find a .xml file and ignore .xml.tmp files. I also don't delete the previous autosave document until the .xml.tmp file for the new document is renamed.
I guess my knowledge of what happens when you write to disk is poor. I know you can have software read/write buffers when using files, as well as OS and hardware buffers and that all of these need to be flushed. I'm confused how I can know for sure when something really has been written to disk and what I can do to protect myself. Does the renaming operation do anything to make sure buffers are flushed?
If the autosave file is corrupted in any way (I assume a power cut when the file is in the middle of being saved would do this?), the user will lose their work. How can I prevent such situations and do all I can to guarantee that the autosave document is in a consistent state?
To prevent loss of data due to partially written autosave file, don't overwrite the autosave file. Instead, write to a new file each time, and then rename it once the file has been safely written.
To guard against not noticing that an autosave file has not been correctly written:
Pay attention to the exceptions thrown as the autosave file is written and closed in case a disc error, file system full, etc.
Keep a running checksum of the file as it is written and write it at the end of the file. Then when you load the autosave file, check that the checksum is there and is correct.
If the checkpointed state involves multiple files, make sure that you write the files in a well known order (without overwriting!), and write the checksum on the autosave file after all of the other files have been safely closed. You might want to create a directory for each checkpoint.
FOLLOW UP
No. I'm not saying that rename always succeeds. However, it is atomic - it either succeeds (and completes) or the file system is not changed. So, if you do this:
write "file.new" and close,
delete "file",
rename "file.new" to "file"
then provided the first step succeeds you are guaranteed to have the latest "file" safely on disc. And it is simple to add a couple of steps so that you have a backup of "file" at all times. (If the 3rd step fails, you are left with "file.new" and no "file". This can be recovered manually, or automatically by the application next time you run it.)
Also, I'm not saying that writes always succeed, or that applications don't crash, or that the power never goes off. And the point of the checksum is to allow you to detect the cases where these things have happened and the autosave file is incomplete.
Finally, it is a good idea to have two autosaves in case your application gets itself into a state where its data structures are messed up and the last autosave is nonsensical as a result. (The checksum won't protect against this.) Be cautious about autosaving when the application crashes for the same reason.
As an aside, since you have several different files as part of this one document, consider using either a project directory to hold them all together, or using some encapsulation format (like .zip) to put them all inside one file.
What you want to do is atomically replace the old backup files with new ones. Unfortunately, I don't believe that Java gives you enough control do this directly. You also need to reason about what operations are atomic in the underlying operating system. I know Linux file systems, so my answer will be biased towards a Java program running on that system. I would be shocked if Windows didn't do the same thing, but I can't say for certain.
Most Linux file systems (e.g. the meta-data journaled ones) let you rename files atomically. If the system crashes half-way through a rename, when you restart, it will be as if you never renamed a file in the first place. For this reason, a common way to atomically update an existing file F is to write your new data to a temporary file T and then rename T to F. Any system or application crash up to that rename will not affect F, so it will always be consistent.
Of course, before you rename, you need to make sure that your temporary file is consistent. Make sure that all streaming buffers for the file are flushed to the OS (Channel.force() or OutputStream.flush()) and the OS buffers are flushed to the disk (FileOutputStream.getFD.sync()). Of course, unless your OS disables the write cache on the hard disk itself (it probably hasn't), there's still a chance that your data can be corrupted. Add a checksum to the XML if you really want to be really sure. If you're truly paranoid, you should flush the OS and hard disk buffer caches and re-read the file to verify that it is consistent. This is beyond any reasonable expectation for normal consumer applications.
But that's just to atomically write write a single file. Your propblem is more complex: you have many files to update atomically. For example, I'll say that you have two files, img.png and main.xml. I'd do one of these:
The easy solution is to make a per-savefile directory. You wouldn't need to worry about renaming each individual file, and you could still atomically rename the new backup dir over the old backup dir you're replacing. That is, if your old backup is bak/img.png and bak/main.xml, write bak.tmp/img.png and bak.tmp/main.xml and rename bak.tmp to bak.
Name the new auxiliary files something else and let them coexist with the old ones for a little while. That is, write img.2.png and main.xml.tmp (which should refer to img.2.png, not img.png) and only rename main.xml.tmp to main.xml. Then delete img.png.
addition: If you don't have atomic renames, the next best thing extends on #2. Whenever you save the project, give it a new name (e.g. ver342.xml). When you load, just find the most recent XML that is consistent (i.e. its checksum verifies). Keep around 2 or 3 to be safe. Only delete an auto-save if you have successfully restored from a more-recent copy.

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