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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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  • 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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  • 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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  • How to determine who changed a file?

    - by Cocowalla
    In Windows, how can I programmatically determine which user account last changed or deleted a file? I know that setting up object access auditing may be an option, but if I use that I then have the problem of trying to match up event log entries to specific files... sounds messy! I can't think of any other way, so does anyone either have any tips for this approach or any alternatives?

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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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  • Linux IO monitoring per file?

    - by MattK
    I am interested in a utility or process for monitoring disk IO per file on CentOS. On Win2008, the resmon utility allows this type of drilldown, but none of the Linux utilities I have found do this (iostat, iotop, dstat, nmon). My interest in monitoring IO bottlenecks on database servers. With MSSQL, I have found it an informative diagnostic to know which files / filespaces are getting hit the hardest.

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  • What else is needed to get iptables to log into this file I created?

    - by anthony01
    I want to create the logging of iptables DROP's and intrusion attemps. First, I put --log-prefix "iptables: " at the end of every iptables rules in my iptables rules file. But this doesn't work, as it says there is a syntax error. So where should I put that command? (I would want to have it included in the saved rules file) Secondly, I created a file iptables.conf within /etc/rsyslog.d/, and I put the following inside of it: :msg, startswith, "iptables: " -/var/log/iptables.log & ~ I assume that at this stage, I'm supposed to restart the rsyslog daemon. What else is needed to do what I'm attempting? Thanks a lot

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  • How can I see which applications have accessed a certain file within a given time period on Linux?

    - by Nikolaidis Fotis
    Is it possible on Linux to find out which applications have accessed a certain file in the last 24 hours? I've come with a few possible solutions: Watch lsof. It works, but it's constrained to watch's granularity. inotify sounds good... but no information of the application accessing the file is provided. auditd may be useful, but I haven't checked that yet. What ways can I see which applications have accessed a certain file within a given time period?

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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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  • Monitoring slow nginx/unicorn requests

    - by injekt
    I'm currently using Nginx to proxy requests to a Unicorn server running a Sinatra application. The application only has a couple of routes defined, those of which make fairly simple (non costly) queries to a PostgreSQL database, and finally return data in JSON format, these services are being monitored by God. I'm currently experiencing extremely slow response times from this application server. I have another two Unicorn servers being proxied via Nginx, and these are responding perfectly fine, so I think I can rule out any wrong doing from Nginx. Here is my God configuration: # God configuration APP_ROOT = File.expand_path '../', File.dirname(__FILE__) God.watch do |w| w.name = "app_name" w.interval = 30.seconds # default w.start = "cd #{APP_ROOT} && unicorn -c #{APP_ROOT}/config/unicorn.rb -D" # -QUIT = graceful shutdown, waits for workers to finish their current request before finishing w.stop = "kill -QUIT `cat #{APP_ROOT}/tmp/unicorn.pid`" w.restart = "kill -USR2 `cat #{APP_ROOT}/tmp/unicorn.pid`" w.start_grace = 10.seconds w.restart_grace = 10.seconds w.pid_file = "#{APP_ROOT}/tmp/unicorn.pid" # User under which to run the process w.uid = 'web' w.gid = 'web' # Cleanup the pid file (this is needed for processes running as a daemon) w.behavior(:clean_pid_file) # Conditions under which to start the process w.start_if do |start| start.condition(:process_running) do |c| c.interval = 5.seconds c.running = false end end # Conditions under which to restart the process w.restart_if do |restart| restart.condition(:memory_usage) do |c| c.above = 150.megabytes c.times = [3, 5] # 3 out of 5 intervals end restart.condition(:cpu_usage) do |c| c.above = 50.percent c.times = 5 end end w.lifecycle do |on| on.condition(:flapping) do |c| c.to_state = [:start, :restart] c.times = 5 c.within = 5.minute c.transition = :unmonitored c.retry_in = 10.minutes c.retry_times = 5 c.retry_within = 2.hours end end end Here is my Unicorn configuration: # Unicorn configuration file APP_ROOT = File.expand_path '../', File.dirname(__FILE__) worker_processes 8 preload_app true pid "#{APP_ROOT}/tmp/unicorn.pid" listen 8001 stderr_path "#{APP_ROOT}/log/unicorn.stderr.log" stdout_path "#{APP_ROOT}/log/unicorn.stdout.log" before_fork do |server, worker| old_pid = "#{APP_ROOT}/tmp/unicorn.pid.oldbin" if File.exists?(old_pid) && server.pid != old_pid begin Process.kill("QUIT", File.read(old_pid).to_i) rescue Errno::ENOENT, Errno::ESRCH # someone else did our job for us end end end I have checked God status logs but it appears CPU and Memory Usage are never out of bounds. I also have something to kill high memory workers, which can be found on the GitHub blog page here. When running a tail -f on the Unicorn logs I see some requests, but they're far and few between, when I was at around 60-100 a second before this trouble seemed to have arrived. This log also shows workers being reaped and started as expected. So my question is, how would I go about debugging this? What are the next steps I should be taking? I'm extremely baffled that the server will sometimes respond quickly, but at others time it's very slow, for long periods of time (which may or may not be peak traffic times). Any advice is much appreciated.

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