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  • Reliable file copy (move) process - mostly Unix/Linux

    - by mfinni
    Short story : We have a need for a rock-solid reliable file mover process. We have source directories that are often being written to that we need to move files from. The files come in pairs - a big binary, and a small XML index. We get a CTL file that defines these file bundles. There is a process that operates on the files once they are in the destination directory; that gets rid of them when it's done. Would rsync do the best job, or do we need to get more complex? Long story as follows : We have multiple sources to pull from : one set of directories are on a Windows machine (that does have Cygwin and an SSH daemon), and a whole pile of directories are on a set of SFTP servers (Most of these are also Windows.) Our destinations are a list of directories on AIX servers. We used to use a very reliable Perl script on the Windows/Cygwin machine when it was our only source. However, we're working on getting rid of that machine, and there are other sources now, the SFTP servers, that we cannot presently run our own scripts on. For security reasons, we can't run the copy jobs on our AIX servers - they have no access to the source servers. We currently have a homegrown Java program on a Linux machine that uses SFTP to pull from the various new SFTP source directories, copies to a local tmp directory, verifies that everything is present, then copies that to the AIX machines, and then deletes the files from the source. However, we're finding any number of bugs or poorly-handled error checking. None of us are Java experts, so fixing/improving this may be difficult. Concerns for us are: With a remote source (SFTP), will rsync leave alone any file still being written? Some of these files are large. From reading the docs, it seems like rysnc will be very good about not removing the source until the destination is reliably written. Does anyone have experience confirming or disproving this? Additional info We will be concerned about the ingestion process that operates on the files once they are in the destination directory. We don't want it operating on files while we are in the process of copying them; it waits until the small XML index file is present. Our current copy job are supposed to copy the XML file last. Sometimes the network has problems, sometimes the SFTP source servers crap out on us. Sometimes we typo the config files and a destination directory doesn't exist. We never want to lose a file due to this sort of error. We need good logs If you were presented with this, would you just script up some rsync? Or would you build or buy a tool, and if so, what would it be (or what technologies would it use?) I (and others on my team) are decent with Perl.

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  • Copy mdf file and use it in run time

    - by Anibas
    After I copy mdf file (and his log file) I tries to Insert data. I receive the following message: "An attempt to attach an auto-named database for file [fileName].mdf failed. A database with the same name exists, or specified file cannot be opened, or it is located on UNC share. When I copied the file manual everything worked normally. Is it correct the order File.Copy leaves the file engaged?

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  • Parse a text file into multiple text file

    - by Vijay Kumar Singh
    I want to get multiple file by parsing a input file Through Java. The Input file contains many fasta format of thousands of protein sequence and I want to generate raw format(i.e., without any comma semicolon and without any extra symbol like "", "[", "]" etc) of each protein sequence. A fasta sequence starts form "" symbol followed by description of protein and then sequence of protein. For example ? lcl|NC_000001.10_cdsid_XP_003403591.1 [gene=LOC100652771] [protein=hypothetical protein LOC100652771] [protein_id=XP_003403591.1] [location=join(12190..12227,12595..12721,13403..13639)] MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCL PSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH Like above formate the input file contains 1000s of protein sequence. I have to generate thousands of raw file containing only individual protein sequence without any special symbol or gaps. I have developed the code for it in Java but out put is : Cannot open a file followed by cannot find file. Please help me to solve my problem. Regards Vijay Kumar Garg Varanasi Bharat (India) The code is /*Java code to convert FASTA format to a raw format*/ import java.io.*; import java.util.*; import java.util.regex.*; import java.io.FileInputStream; // java package for using regular expression public class Arrayren { public static void main(String args[]) throws IOException { String a[]=new String[1000]; String b[][] =new String[1000][1000]; /*open the id file*/ try { File f = new File ("input.txt"); //opening the text document containing genbank ids FileInputStream fis = new FileInputStream("input.txt"); //Reading the file contents through inputstream BufferedInputStream bis = new BufferedInputStream(fis); // Writing the contents to a buffered stream DataInputStream dis = new DataInputStream(bis); //Method for reading Java Standard data types String inputline; String line; String separator = System.getProperty("line.separator"); // reads a line till next line operator is found int i=0; while ((inputline=dis.readLine()) != null) { i++; a[i]=inputline; a[i]=a[i].replaceAll(separator,""); //replaces unwanted patterns like /n with space a[i]=a[i].trim(); // trims out if any space is available a[i]=a[i]+".txt"; //takes the file name into an array try // to handle run time error /*take the sequence in to an array*/ { BufferedReader in = new BufferedReader (new FileReader(a[i])); String inline = null; int j=0; while((inline=in.readLine()) != null) { j++; b[i][j]=inline; Pattern q=Pattern.compile(">"); //Compiling the regular expression Matcher n=q.matcher(inline); //creates the matcher for the above pattern if(n.find()) { /*appending the comment line*/ b[i][j]=b[i][j].replaceAll(">gi",""); //identify the pattern and replace it with a space b[i][j]=b[i][j].replaceAll("[a-zA-Z]",""); b[i][j]=b[i][j].replaceAll("|",""); b[i][j]=b[i][j].replaceAll("\\d{1,15}",""); b[i][j]=b[i][j].replaceAll(".",""); b[i][j]=b[i][j].replaceAll("_",""); b[i][j]=b[i][j].replaceAll("\\(",""); b[i][j]=b[i][j].replaceAll("\\)",""); } /*printing the sequence in to a text file*/ b[i][j]=b[i][j].replaceAll(separator,""); b[i][j]=b[i][j].trim(); // trims out if any space is available File create = new File(inputline+"R.txt"); try { if(!create.exists()) { create.createNewFile(); // creates a new file } else { System.out.println("file already exists"); } } catch(IOException e) // to catch the exception and print the error if cannot open a file { System.err.println("cannot create a file"); } BufferedWriter outt = new BufferedWriter(new FileWriter(inputline+"R.txt", true)); outt.write(b[i][j]); // printing the contents to a text file outt.close(); // closing the text file System.out.println(b[i][j]); } } catch(Exception e) { System.out.println("cannot open a file"); } } } catch(Exception ex) // catch the exception and prints the error if cannot find file { System.out.println("cannot find file "); } } } If you provide me correct it will be much easier to understand.

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  • Designing a database file format

    - by RoliSoft
    I would like to design my own database engine for educational purposes, for the time being. Designing a binary file format is not hard nor the question, I've done it in the past, but while designing a database file format, I have come across a very important question: How to handle the deletion of an item? So far, I've thought of the following two options: Each item will have a "deleted" bit which is set to 1 upon deletion. Pro: relatively fast. Con: potentially sensitive data will remain in the file. 0x00 out the whole item upon deletion. Pro: potentially sensitive data will be removed from the file. Con: relatively slow. Recreating the whole database. Pro: no empty blocks which makes the follow-up question void. Con: it's a really good idea to overwrite the whole 4 GB database file because a user corrected a typo. I will sell this method to Twitter ASAP! Now let's say you already have a few empty blocks in your database (deleted items). The follow-up question is how to handle the insertion of a new item? Append the item to the end of the file. Pro: fastest possible. Con: file will get huge because of all the empty blocks that remain because deleted items aren't actually deleted. Search for an empty block exactly the size of the one you're inserting. Pro: may get rid of some blocks. Con: you may end up scanning the whole file at each insert only to find out it's very unlikely to come across a perfectly fitting empty block. Find the first empty block which is equal or larger than the item you're inserting. Pro: you probably won't end up scanning the whole file, as you will find an empty block somewhere mid-way; this will keep the file size relatively low. Con: there will still be lots of leftover 0x00 bytes at the end of items which were inserted into bigger empty blocks than they are. Rigth now, I think the first deletion method and the last insertion method are probably the "best" mix, but they would still have their own small issues. Alternatively, the first insertion method and scheduled full database recreation. (Probably not a good idea when working with really large databases. Also, each small update in that method will clone the whole item to the end of the file, thus accelerating file growth at a potentially insane rate.) Unless there is a way of deleting/inserting blocks from/to the middle of the file in a file-system approved way, what's the best way to do this? More importantly, how do databases currently used in production usually handle this?

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  • Reading data from text file in C

    - by themake
    I have a text file which contains words separated by space. I want to take each word from the file and store it. So i have opened the file but am unsure how to assign the word to a char. FILE *fp; fp = fopen("file.txt", "r"); //then i want char one = the first word in the file char two = the second word in the file

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  • opening and viewing a file in php

    - by Christian Burgos
    how do i open/view for editing an uploaded file in php? i have tried this but it doesn't open the file. $my_file = 'file.txt'; $handle = fopen($my_file, 'r'); $data = fread($handle,filesize($my_file)); i've also tried this but it wont work. $my_file = 'file.txt'; $handle = fopen($my_file, 'w') or die('Cannot open file: '.$my_file); $data = 'This is the data'; fwrite($handle, $data); what i have in mind is like when you want to view an uploaded resume,documents or any other ms office files like .docx,.xls,.pptx and be able to edit them, save and close the said file. edit: latest tried code... <?php // Connects to your Database include "configdb.php"; //Retrieves data from MySQL $data = mysql_query("SELECT * FROM employees") or die(mysql_error()); //Puts it into an array while($info = mysql_fetch_array( $data )) { //Outputs the image and other data //Echo "<img src=localhost/uploadfile/images".$info['photo'] ."> <br>"; Echo "<b>Name:</b> ".$info['name'] . "<br> "; Echo "<b>Email:</b> ".$info['email'] . " <br>"; Echo "<b>Phone:</b> ".$info['phone'] . " <hr>"; //$file=fopen("uploadfile/images/".$info['photo'],"r+"); $file=fopen("Applications/XAMPP/xamppfiles/htdocs/uploadfile/images/file.odt","r") or exit("unable to open file");; } ?> i am getting the error: Warning: fopen(Applications/XAMPP/xamppfiles/htdocs/uploadfile/images/file.odt): failed to open stream: No such file or directory in /Applications/XAMPP/xamppfiles/htdocs/uploadfile/view.php on line 17 unable to open file the file is in that folder, i don't know it wont find it.

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  • Copied a file with winscp; only winscp can see it

    - by nilbus
    I recently copied a 25.5GB file from another machine using WinSCP. I copied it to C:\beth.tar.gz, and WinSCP can still see the file. However no other app (including Explorer) can see the file. What might cause this, and how can I fix it? The details that might or might not matter WinSCP shows the size of the file (C:\beth.tar.gz) correctly as 27,460,124,080 bytes, which matches the filesize on the remote host Neither explorer, cmd (command line prompt w/ dir C:\), the 7Zip archive program, nor any other File Open dialog can see the beth.tar.gz file under C:\ I have configured Explorer to show hidden files I can move the file to other directories using WinSCP If I try to move the file to Users/, UAC prompts me for administrative rights, which I grant, and I get this error: Could not find this item The item is no longer located in C:\ When I try to transfer the file back to the remote host in a new directory, the transfer starts successfully and transfers data The transfer had about 30 minutes remaining when I left it for the night The morning after the file transfer, I was greeted with a message saying that the connection to the server had been lost. I don't think this is relevant, since I did not tell it to disconnect after the file was done transferring, and it likely disconnected after the file transfer finished. I'm using an old version of WinSCP - v4.1.8 from 2008 I can view the file properties in WinSCP: Type of file: 7zip (.gz) Location: C:\ Attributes: none (Ready-only, Hidden, Archive, or Ready for indexing) Security: SYSTEM, my user, and Administrators group have full permissions - everything other than "special permissions" is checked under Allow for all 3 users/groups (my user, Administrators, SYSTEM) What's going on?!

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  • C++, Ifstream opens local file but not file on HTTP Server

    - by fammi
    Hi, I am using ifstream to open a file and then read from it. My program works fine when i give location of the local file on my system. for eg /root/Desktop/abc.xxx works fine But once the location is on the http server the file fails to open. for eg http://192.168.0.10/abc.xxx fails to open. Is there any alternate for ifstream when using a URL address? thanks. part of the code where having problem: bool readTillEof = (endIndex == -1) ? true : false; // Open the file in binary mode and seek to the end to determine file size ifstream file ( fileName.c_str ( ), ios::in|ios::ate|ios::binary ); if ( file.is_open ( ) ) { long size = (long) file.tellg ( ); long numBytesRead; if ( readTillEof ) { numBytesRead = size - startIndex; } else { numBytesRead = endIndex - startIndex + 1; } // Allocate a new buffer ptr to read in the file data BufferSptr buf (new Buffer ( numBytesRead ) ); mpStreamingClientEngine->SetResponseBuffer ( nextRequest, buf ); // Seek to the start index of the byte range // and read the data file.seekg ( startIndex, ios::beg ); file.read ( (char *)buf->GetData(), numBytesRead ); // Pass on the data to the SCE // and signal completion of request mpStreamingClientEngine->HandleDataReceived( nextRequest, numBytesRead); mpStreamingClientEngine->MarkRequestCompleted( nextRequest ); // Close the file file.close ( ); } else { // Report error to the Streaming Client Engine // as unable to open file AHS_ERROR ( ConnectionManager, " Error while opening file \"%s\"\n", fileName.c_str ( ) ); mpStreamingClientEngine->HandleRequestFailed( nextRequest, CONNECTION_FAILED ); } }

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  • How do I open a file in such a way that if the file doesn't exist it will be created and opened automatically?

    - by snakile
    Here's how I open a file for writing+ : if( fopen_s( &f, fileName, "w+" ) !=0 ) { printf("Open file failed\n"); return; } fprintf_s(f, "content"); If the file doesn't exist the open operation fails. What's the right way to fopen if I want to create the file automatically if the file doesn't already exist? EDIT: If the file does exist, I would like fprintf to overwrite the file, not to append to it.

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  • Problem with File uplolad in javascript.

    - by Nikhil
    I have used javascript to upload more than one file. when user clicks on 'add more' javascript appends new object to older div using innerHTML. Now the problem is if I select a file and then click on "add more" then new file button exist but older selected file removes and two blank file buttons display. I want this old file must be selected when user add new file button. If anybody can, Help Plz!!! tnX.

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  • excel cannot open the file xxx.xlsx' because the file format is not valid error

    - by Yavuz
    I have difficulty open opening word and excel files suddenly. Only particular office file give me the problem. These files were previously scanned by combo fix and I believe they were damaged. The error response that I from office is Excel cannot open the file xxx.xlsx because the file format is not valid. Verify that the file has not been corrupted and that the file extension matches the format of the file. This is for excel and a similar kind of error response comes for word. The file looks fine. I mean the size vise... Please help me with this problem. I really appreciate your help and time....

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  • Upon clicking on a file, excel opens but not the file itself

    - by william
    Platform: Windows XP SP2, Excel 2007 Problem description: Upon clicking on a file in Windows Explorer (file is either .xls or .xlsx) Excel 2007 opens, but does not open the file itself. I need either to click on a file again in Windows Explorer or open it manually with File/Open ... from Excel. Does anyone know what could cause this rather strange behaviour ? The old versions of Excel worked "normally" ... i.e. upon clicking on a file, an Excel would open along with the file. Please, help !

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  • How to write files in specific order?

    - by Bernie
    Okay, here's a weird problem -- My wife just bought a 2014 Nissan Altima. So, I took her iTunes library and converted the .m4a files to .mp3, since the car audio system only supports .mp3 and .wma. So far so good. Then I copied the files to a DOS FAT-32 formatted USB thumb drive, and connected the drive to the car's USB port, only to find all of the tracks were out of sequence. All tracks begin with a two digit numeric prefix, i.e., 01, 02, 03, etc. So you would think they would be in order. So I called Nissan Connect support and the rep told me that there is a known problem with reading files in the correct order. He said the files are read in the same order they are written. So, I manually copied a few albums with the tracks in a predetermined order, and sure enough he was correct. So I copied about 6 albums for testing, then changed to the top level directory and did a "find . music.txt". Then I passed this file to rsync like this: rsync -av --files-from=music.txt . ../Marys\ Music\ Sequenced/ The files looked like they were copied in order, but when I listed the files in order of modified time, they were in the same sequence as the original files: ../Marys Music Sequenced/Air Supply/Air Supply Greatest Hits ls -1rt 01 Lost In Love.mp3 04 Every Woman In The World.mp3 03 Chances.mp3 02 All Out Of Love.mp3 06 Here I Am (Just When I Thought I Was Over You).mp3 05 The One That You Love.mp3 08 I Want To Give It All.mp3 07 Sweet Dreams.mp3 11 Young Love.mp3 So the question is, how can I copy files listed in a file named music.txt, and copy them to a destination, and ensure the modification times are in the same sequence as the files are listed?

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  • rename files with the same name

    - by snorpey
    Hi. I use the following function to rename thumbnails. For example, if I upload a file called "image.png" to an upload folder, and this folder already has a file named "image.png" in it, the new file automatically gets renamed to "image-copy-1.png". If there also is a file called "image-copy-1.png" it gets renamed to "image-copy-2.png" and so on. The following function returns the new filename. At least that's what it is supposed to do... The renaming doesn't seeem to work correctly, though. Sometimes it produces strange results, like: 1.png 1-copy-1.png 1-copy-2.png 1-copy-2-copy-1.png 1-copy-2-copy-3.png I hope you understand my problem, despite my description being somewhat complex... Can you tell me what went wrong here? (bonus question: Is regular expressions the right tool for doing this kind of stuff?) <?php function renameDuplicates($path, $file) { $fileName = pathinfo($path . $file, PATHINFO_FILENAME); $fileExtension = "." . pathinfo($path . $file, PATHINFO_EXTENSION); if(file_exists($path . $file)) { $fileCopy = $fileName . "-copy-1"; if(file_exists($path . $fileCopy . $fileExtension)) { if ($contains = preg_match_all ("/.*?(copy)(-)(\\d+)/is", $fileCopy, $matches)) { $copyIndex = $matches[3][0]; $fileName = substr($fileCopy, 0, -(strlen("-copy-" . $copyIndex))) . "-copy-" . ($copyIndex + 1); } } else { $fileName .= "-copy-1"; } } $returnValue = $fileName . $fileExtension; return $returnValue; }?>

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  • Best Solution for Load Balancing NFS File Access?

    - by DairyKnight
    I'm trying to find an optimum solution for accessing the NFS file share in my company. We have a central file server in North America and has 30GB~50GB of updated data everyday. And it's very slow for our Europe and Asia branches to access directly. Therefore, I'm trying to setup two replicate servers in those continents. I'm currently using rsync, but wonder if there exists a better solution acts more like a distributed RAID, which allows the user to transparently access the file whether synced or not. And user request will be dispatched to remote server if the file is not yet synced. I'm now looking into DRBD, but it seems not to have the functionality of auto-dispatching requests. Does anyone know if there's a better solution?

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  • Puppet file transfer slow

    - by Noodles
    I have a puppet master and slaves in different datacenters. The latency between them is ~40ms. When I run "puppet agent --test" on a slave to apply the latest manifest it takes ~360 seconds to finish. After doing some digging I can see the main cause of the slow down is file transfers. It seems it's taking ~10 seconds to transfer each file. The files are only small (configuration files) so I can't understand why they would take so long. This is an example of a file in my manifest: file { "/etc/rsyncd.conf" : owner => "root", group => "root", mode => 644, source => "puppet:///files/rsyncd/rsyncd.conf" } Running puppet-profiler I see this: 10.21s - File[/etc/rsyncd.conf] It also seems I cannot update more than one server at once using puppet. If I run two servers at the same time then puppet takes twice as long. I have changed the puppet master from using webrick to mongrel, but this doesn't seem to help. This is making deploying changes painful. A simple config change can take an hour to roll out to all servers.

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  • Corrupt file indicative of corrupt hard drive?

    - by Elipsicon
    I have noticed that two files on my (almost full) 2 TB hard drive have been corrupted. One file has 20 kB (!) corrupted, i.e. consecutive 20 kB have changed, even though the modification date of the file hasn't changed and I haven't worked with this file for over a year. This tells me that something "below" the file system level has messed with the data and the only thing I can think of is hardware failure, most likely hard disk failure. I've tested my RAM already and it works flawlessly. I'm using ext4 on Linux, if that is of any help. Is this normal? Is it time to change my hard drive disk before something worse happens? What can I do to prevent that from happening in the future? Is there some built-in feature of, or extension to ext4 that includes additional error correcting code and/or watches files for changes that haven't been caused by the OS?

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