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  • MySQLdb not INSERTING, _mysql does fine.

    - by Mad_Casual
    Okay, I log onto the MySQL command-line client as root. I then open or otherwise run a python app using the MySQLdb module as root. When I check the results using python (IDLE), everything looks fine. When I use the MySQL command-line client, no INSERT has occurred. If I change things around to _mysql instead of MySQLdb, everything works fine. I'd appreciate any clarification(s). "Works" until IDLE/Virtual machine is reset: <pre><code>import MySQLdb db = MySQLdb.connect(user='root', passwd='*******',db='test') cursor = db.cursor() cursor.execute("""INSERT INTO test VALUES ('somevalue');""",)</code></end> Works: <pre><code>import _mysql db = _mysql.connect(user='root', passwd='*******',db='test') db.query("INSERT INTO test VALUES ('somevalue');")</code></end> System info: Intel x86 WinXP Python 2.5 MySQL 5.1.41 MySQL-Python 1.2.2

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  • serving files using django - is this a security vulnerability

    - by Tom Tom
    I'm using the following code to serve uploaded files from a login secured view in a django app. Do you think that there is a security vulnerability in this code? I'm a bit concerned about that the user could place arbitrary strings in the url after the upload/ and this is directly mapped to the local filesystem. Actually I don't think that it is a vulnerability issue, since the access to the filesystem is restricted to the files in the folder defined with the UPLOAD_LOCATION setting. UPLOAD_LOCATION = is set to a not publicly available folder on the webserver url(r'^upload/(?P<file_url>[/,.,\s,_,\-,\w]+)', 'aeon_infrastructure.views.serve_upload_files', name='project_detail'), @login_required def serve_upload_files(request, file_url): import os.path import mimetypes mimetypes.init() try: file_path = settings.UPLOAD_LOCATION + '/' + file_url fsock = open(file_path,"r") file_name = os.path.basename(file_path) file_size = os.path.getsize(file_path) print "file size is: " + str(file_size) mime_type_guess = mimetypes.guess_type(file_name) if mime_type_guess is not None: response = HttpResponse(fsock, mimetype=mime_type_guess[0]) response['Content-Disposition'] = 'attachment; filename=' + file_name #response.write(file) except IOError: response = HttpResponseNotFound() return response

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  • Java "compare cannot be resolved to a type" error

    - by King Triumph
    I'm getting a strange error when attempting to use a comparator with a binary search on an array. The error states that "compareArtist cannot be resolved to a type" and is thrown by Eclipse on this code: Comparator<Song> compare = new Song.compareArtist(); I've done some searching and found references to a possible bug with Eclipse, although I have tried the code on a different computer and the error persists. I've also found similar issues regarding the capitalization of the compare method, in this case compareArtist. I've seen examples where the first word in the method name is capitalized, although it was my understanding that method names are traditionally started with a lower case letter. I have experimented with changing the capitalization but nothing has changed. I have also found references to this error if the class doesn't import the correct package. I have imported java.util in both classes in question, which to my knowledge allows the use of the Comparator. I've experimented with writing the compareArtist method within the class that has the binary search call as well as in the "Song" class, which according to my homework assignment is where it should be. I've changed the constructor accordingly and the issue persists. Lastly, I've attempted to override the Comparator compare method by implementing Comparator in the Song class and creating my own method called "compare". This returns the same error. I've only moved to calling the comparator method something different than "compare" after finding several examples that do the same. Here is the relevant code for the class that calls the binary search that uses the comparator. This code also has a local version of the compareArtist method. While it is not being called currently, the code for this method is the same as the in the class Song, where I am trying to call it from. Thanks for any advice and insight. import java.io.*; import java.util.*; public class SearchByArtistPrefix { private Song[] songs; // keep a direct reference to the song array private Song[] searchResults; // holds the results of the search private ArrayList<Song> searchList = new ArrayList<Song>(); // hold results of search while being populated. Converted to searchResults array. public SearchByArtistPrefix(SongCollection sc) { songs = sc.getAllSongs(); } public int compareArtist (Song firstSong, Song secondSong) { return firstSong.getArtist().compareTo(secondSong.getArtist()); } public Song[] search(String artistPrefix) { String artistInput = artistPrefix; int searchLength = artistInput.length(); Song searchSong = new Song(artistInput, "", ""); Comparator<Song> compare = new Song.compareArtist(); int search = Arrays.binarySearch(songs, searchSong, compare);

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  • fastest in-memory cache for XslCompiledTransform

    - by rudnev
    I have a set of xslt stylesheet files. I need to produce the fastest performance of XslConpiledTransform, so i want to make in-memory representation of these stylesheets. I can load them to in-memory collection as IXpathNavigable on application start, and then load each IXPAthNavigable into singleton XslCompiledTransform on each request. But this works only for styleshhets without xsl:import or xsl:include. (Xsl:import is only for files). also i can load into cache many instances of XSLCompiledTransform for each template. Is it reasonable? Are there other ways? What is the best? what are another tips for improving performance MS Xslt processor?

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  • multiline gtk.Label ignores xalign=0.5

    - by thomas
    A gtk.Label can't be aligned in center when line-wrap is turned on. Example code: import pygtk pygtk.require('2.0') import gtk class testwin(gtk.Window): def __init__(self): gtk.Window.__init__(self) width,height = 300,300 self.set_size_request(width,height) self.set_position(gtk.WIN_POS_CENTER) self.set_title("test window") label = gtk.Label("test text") label.set_line_wrap(True) label.set_justify(gtk.JUSTIFY_CENTER) label.set_alignment(0.5,0.5) label.connect("size-allocate",lambda l,s: l.set_size_request(s.width-1, -1)) self.add(label) self.connect("destroy", gtk.main_quit) self.show_all() testwin() gtk.main() It looks like this, that means, it's aligned left: http://m45.img-up.net/?up=pic122x97.png If you comment out line 14 (set_line_wrap) everything is perfectly fine: http://o54.img-up.net/?up=pic2y00p9.png Please note that yalign works fine. So it seems like the first argument in the gtk.Misc.set_alignment-function has no effect when line wrap is turned on. Using Fedora 16, 64bit, gtk 3.2.4, pygtk 2.24.0, python 2.7.2 Question: Is this intended or a bug? How is it supposed to be made or is a workaround available?

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  • Whats wrong with this code.Runtime error

    - by javacode
    Hi I am writing this application in eclipse I added all the jar files.I am pasting the code and error.Please let me know what changes I should make to run the application properly. import javax.mail.*; import javax.mail.internet.*; import java.util.*; public class SendMail { public static void main(String [] args) { SendMail sm=new SendMail(); try{ sm.postMail(new String[]{"[email protected]"},"hi","hello","[email protected]"); } catch(MessagingException e) { e.printStackTrace(); } } public void postMail( String recipients[ ], String subject, String message , String from) throws MessagingException { boolean debug = false; //Set the host smtp address Properties props = new Properties(); props.put("mail.smtp.starttls.enable","true"); props.put("mail.smtp.host", "smtp.gmail.com"); props.setProperty("mail.smtp.port", "25"); // create some properties and get the default Session Session session = Session.getDefaultInstance(props, null); session.setDebug(debug); // create a message Message msg = new MimeMessage(session); // set the from and to address InternetAddress addressFrom = new InternetAddress(from); msg.setFrom(addressFrom); InternetAddress[] addressTo = new InternetAddress[recipients.length]; for (int i = 0; i < recipients.length; i++) { addressTo[i] = new InternetAddress(recipients[i]); } msg.setRecipients(Message.RecipientType.TO, addressTo); // Optional : You can also set your custom headers in the Email if you Want msg.addHeader("MyHeaderName", "myHeaderValue"); // Setting the Subject and Content Type msg.setSubject(subject); msg.setContent(message, "text/plain"); Transport.send(msg); } } Error: com.sun.mail.smtp.SMTPSendFailedException: 530 5.7.0 Must issue a STARTTLS command first. 13sm646598ewy.13 at com.sun.mail.smtp.SMTPTransport.issueSendCommand(SMTPTransport.java:1829) at com.sun.mail.smtp.SMTPTransport.mailFrom(SMTPTransport.java:1368) at com.sun.mail.smtp.SMTPTransport.sendMessage(SMTPTransport.java:886) at javax.mail.Transport.send0(Transport.java:191) at javax.mail.Transport.send(Transport.java:120) at SendMail.postMail(SendMail.java:54) at SendMail.main(SendMail.java:10)

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  • Why does my program crash when given negative values?

    - by Wayfarer
    Alright, I am very confused, so I hope you friends can help me out. I'm working on a project using Cocos2D, the most recent version (.99 RC 1). I make some player objects and some buttons to change the object's life. But the weird thing is, the code crashes when I try to change their life by -5. Or any negative value for that matter, besides -1. NSMutableArray *lifeButtons = [[NSMutableArray alloc] init]; CCTexture2D *buttonTexture = [[CCTextureCache sharedTextureCache] addImage:@"Button.png"]; LifeChangeButtons *button = nil; //top left button = [LifeChangeButtons lifeButton:buttonTexture ]; button.position = CGPointMake(50 , size.height - 30); [button buttonText:-5]; [lifeButtons addObject:button]; //top right button = [LifeChangeButtons lifeButton:buttonTexture ]; button.position = CGPointMake(size.width - 50 , size.height - 30); [button buttonText:1]; [lifeButtons addObject:button]; //bottom left button = [LifeChangeButtons lifeButton:buttonTexture ]; button.position = CGPointMake(50 , 30); [button buttonText:5]; [lifeButtons addObject:button]; //bottom right button = [LifeChangeButtons lifeButton:buttonTexture ]; button.position = CGPointMake(size.width - 50 , 30); [button buttonText:-1]; [lifeButtons addObject:button]; for (LifeChangeButtons *theButton in lifeButtons) { [self addChild:theButton]; } This is the code that makes the buttons. It simply makes 4 buttons, puts them in each corner of the screen (size is the screen) and adds their life change ability, 1,-1,5, or -5. It adds them to the array and then goes through the array at the end and adds all of them to the screen. This works fine. Here is my code for the button class: (header file) // // LifeChangeButtons.h // Coco2dTest2 // // Created by Ethan Mick on 3/14/10. // Copyright 2010 Wayfarer. All rights reserved. // #import "cocos2d.h" @interface LifeChangeButtons : CCSprite <CCTargetedTouchDelegate> { NSNumber *lifeChange; } @property (nonatomic, readonly) CGRect rect; @property (nonatomic, retain) NSNumber *lifeChange; + (id)lifeButton:(CCTexture2D *)texture; - (void)buttonText:(int)number; @end Implementation file: // // LifeChangeButtons.m // Coco2dTest2 // // Created by Ethan Mick on 3/14/10. // Copyright 2010 Wayfarer. All rights reserved. // #import "LifeChangeButtons.h" #import "cocos2d.h" #import "CustomCCNode.h" @implementation LifeChangeButtons @synthesize lifeChange; //Create the button +(id)lifeButton:(CCTexture2D *)texture { return [[[self alloc] initWithTexture:texture] autorelease]; } - (id)initWithTexture:(CCTexture2D *)atexture { if ((self = [super initWithTexture:atexture])) { //NSLog(@"wtf"); } return self; } //Set the text on the button - (void)buttonText:(int)number { lifeChange = [NSNumber numberWithInt:number]; NSString *text = [[NSString alloc] initWithFormat:@"%d", number]; CCLabel *label = [CCLabel labelWithString:text fontName:@"Times New Roman" fontSize:20]; label.position = CGPointMake(35, 20); [self addChild:label]; } - (CGRect)rect { CGSize s = [self.texture contentSize]; return CGRectMake(-s.width / 2, -s.height / 2, s.width, s.height); } - (BOOL)containsTouchLocation:(UITouch *)touch { return CGRectContainsPoint(self.rect, [self convertTouchToNodeSpaceAR:touch]); } - (void)onEnter { [[CCTouchDispatcher sharedDispatcher] addTargetedDelegate:self priority:0 swallowsTouches:YES]; [super onEnter]; } - (void)onExit { [[CCTouchDispatcher sharedDispatcher] removeDelegate:self]; [super onExit]; } - (BOOL)ccTouchBegan:(UITouch *)touch withEvent:(UIEvent *)event { CGPoint touchPoint = [touch locationInView:[touch view]]; touchPoint = [[CCDirector sharedDirector] convertToGL:touchPoint]; if ( ![self containsTouchLocation:touch] ) return NO; NSLog(@"Button touch event was called returning yes. "); //this is where we change the life to each selected player NSLog(@"Test1"); NSMutableArray *tempArray = [[[UIApplication sharedApplication] delegate] selectedPlayerObjects]; NSLog(@"Test2"); for (CustomCCNode *aPlayer in tempArray) { NSLog(@"we change the life by %d.", [lifeChange intValue]); [aPlayer changeLife:[lifeChange intValue]]; } NSLog(@"Test3"); return YES; } - (void)ccTouchMoved:(UITouch *)touch withEvent:(UIEvent *)event { CGPoint touchPoint = [touch locationInView:[touch view]]; touchPoint = [[CCDirector sharedDirector] convertToGL:touchPoint]; NSLog(@"You moved in a button!"); } - (void)ccTouchEnded:(UITouch *)touch withEvent:(UIEvent *)event { NSLog(@"You touched up in a button"); } @end Now, This function: - (BOOL)ccTouchBegan:(UITouch *)touch withEvent:(UIEvent *)event Is where all the shit goes down. It works for all of the buttons except the -5 one. And then, it gets to: NSLog(@"we change the life by %d.", [lifeChange integerValue]); And it crashes at that statement. It only crashes when given anything less than -1. -1 works, but nothing smaller does. Here is the code in the CustomCCNode Class, "changeLife" that is being called. - (void)changeLife:(int)lifeChange { NSLog(@"change life in Custom Class was called"); NSLog(@"wtf is lifechange: %d", lifeChange); life += lifeChange; lifeString = [[NSString alloc] initWithFormat:@"%d",life]; [text setString:lifeString]; } Straight forward, but when the NSnumber is -5, it doesn't even get called, it crashes at the NSlog statement. So... what's up with that?

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  • Video with QML Video plays choppy on Mac OS X

    - by avida
    I’m trying to create simple video player with QML. I have QtSdk installed and QtMobility compiled and installed from source. Then I put this simple video playing code to main qml file: import QtQuick 1.0 import QtMultimediaKit 1.1 Item{ width: 400; height: 300 Video { id: video source: "d:/Projects/Serenity - HD DVD Trailer.mp4" anchors.fill: parent MouseArea { anchors.fill: parent onClicked: { video.play() } } } } After compiling and running application, video plays choppy and on exiting application it puts this in log: 2011-06-07 11:13:44.055 video-player[323:903] *** __NSAutoreleaseNoPool(): Object 0x10225ea60 of class NSCFNumber autoreleased with no pool in place - just leaking 2011-06-07 11:13:45.007 video-player[323:903] *** __NSAutoreleaseNoPool(): Object 0x10264f030 of class __NSCFDate autoreleased with no pool in place - just leaking 2011-06-07 11:13:45.007 video-player[323:903] *** __NSAutoreleaseNoPool(): Object 0x11a409000 of class NSCFTimer autoreleased with no pool in place - just leaking 2011-06-07 11:13:45.008 video-player[323:903] *** __NSAutoreleaseNoPool(): Object 0x11a43e550 of class NSCFArray autoreleased with no pool in place - just leaking 2011-06-07 11:13:45.008 video-player[323:903] *** __NSAutoreleaseNoPool(): Object 0x11a462560 of class __NSFastEnumerationEnumerator autoreleased with no pool in place - just leaking If any way to make it playing smoothly and to prevent memory?

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  • pyplot: really slow creating heatmaps

    - by cvondrick
    I have a loop that executes the body about 200 times. In each loop iteration, it does a sophisticated calculation, and then as debugging, I wish to produce a heatmap of a NxM matrix. But, generating this heatmap is unbearably slow and significantly slow downs an already slow algorithm. My code is along the lines: import numpy import matplotlib.pyplot as plt for i in range(200): matrix = complex_calculation() plt.set_cmap("gray") plt.imshow(matrix) plt.savefig("frame{0}.png".format(i)) The matrix, from numpy, is not huge --- 300 x 600 of doubles. Even if I do not save the figure and instead update an on-screen plot, it's even slower. Surely I must be abusing pyplot. (Matlab can do this, no problem.) How do I speed this up?

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  • iphone - UIViewController header view errors

    - by Fiona
    Hi there, So to give a little background: I've an app that has a UITableViewController- (ContactDetailViewController) In this view at the top, I require a few labels and buttons, followed by a group style tableview. So I've created a nib file containing these elements. (ContactHeaderView.xib) Then in the viewDidLoad of ContactDetailViewController I've loaded this nib as the headerView. See implementation file below: #import "ContactDetailViewController.h" #import "DisplayInfoViewController.h" #import "ActionViewController.h" @implementation ContactDetailViewController @synthesize name; @synthesize date; @synthesize nextAction; @synthesize nameLabel; @synthesize usernameLabel; @synthesize nextActionTextField; @synthesize dateLabel; @synthesize contactInfoButton; @synthesize backgroundInfoButton; @synthesize actionDoneButton; - (void)viewDidLoad { [super viewDidLoad]; } - (void)didReceiveMemoryWarning { // Releases the view if it doesn't have a superview. [super didReceiveMemoryWarning]; // Release any cached data, images, etc that aren't in use. } - (void)viewDidUnload { // Release any retained subviews of the main view. // e.g. self.myOutlet = nil; } #pragma mark Table view methods - (NSInteger)numberOfSectionsInTableView:(UITableView *)tableView { return 1; } // Customize the number of rows in the table view. - (NSInteger)tableView:(UITableView *)tableView numberOfRowsInSection:(NSInteger)section { return 3; } - (UIView *) tableView:(UITableView *)tableView viewForHeaderInSection:(NSInteger)section { if (section == 0){ UIViewController *chv = [[[UIViewController alloc] initWithNibName:@"ContactHeaderView" bundle:nil] autorelease]; // self.nameLabel.text = self.name; return chv.view; }else{ return nil; } } - (CGFloat)tableView:(UITableView *)tableView heightForHeaderInSection:(NSInteger)section{ return 300.0; } // Customize the appearance of table view cells. - (UITableViewCell *)tableView:(UITableView *)tableView cellForRowAtIndexPath:(NSIndexPath *)indexPath { static NSString *CellIdentifier = @"Cell"; UITableViewCell *cell = [tableView dequeueReusableCellWithIdentifier:CellIdentifier]; if (cell == nil) { cell = [[[UITableViewCell alloc] initWithStyle:UITableViewCellStyleDefault reuseIdentifier:CellIdentifier] autorelease]; } // Set up the cell... return cell; } - (void)tableView:(UITableView *)tableView didSelectRowAtIndexPath:(NSIndexPath *)indexPath { // Navigation logic may go here. Create and push another view controller. // AnotherViewController *anotherViewController = [[AnotherViewController alloc] initWithNibName:@"AnotherView" bundle:nil]; // [self.navigationController pushViewController:anotherViewController]; // [anotherViewController release]; } /* // Override to support conditional editing of the table view. - (BOOL)tableView:(UITableView *)tableView canEditRowAtIndexPath:(NSIndexPath *)indexPath { // Return NO if you do not want the specified item to be editable. return YES; } */ - (void)dealloc { [name release]; [date release]; [nextAction release]; [nameLabel release]; [usernameLabel release]; [nextActionTextField release]; [dateLabel release]; [contactInfoButton release]; [backgroundInfoButton release]; [actionDoneButton release]; [super dealloc]; } -(IBAction)displayContactInfo:(id)sender{ DisplayInfoViewController *divc = [[DisplayInfoViewController alloc] init]; divc.textView = self.nextAction; divc.title = @"Contact Info"; [self.navigationController pushViewController:divc animated:YES]; [divc release]; } -(IBAction)displayBackgroundInfo:(id)sender{ DisplayInfoViewController *divc = [[DisplayInfoViewController alloc] init]; divc.textView = self.nextAction; divc.title = @"Background Info"; [self.navigationController pushViewController:divc animated:YES]; [divc release]; } -(IBAction)actionDone:(id)sender{ ActionViewController *avc = [[ActionViewController alloc] init]; avc.title = @"Action"; avc.nextAction = self.nextAction; [self.navigationController pushViewController:avc animated:YES]; [avc release]; } @end Here's the Header File: #import <UIKit/UIKit.h> @interface ContactDetailViewController : UITableViewController { NSString *name; NSString *date; NSString *nextAction; IBOutlet UILabel *nameLabel; IBOutlet UILabel *usernameLabel; IBOutlet UITextField *nextActionTextField; IBOutlet UILabel *dateLabel; IBOutlet UIButton *contactInfoButton; IBOutlet UIButton *backgroundInfoButton; IBOutlet UIButton *actionDoneButton; } @property (nonatomic, retain) NSString *name; @property (nonatomic, retain) NSString *date; @property (nonatomic, retain) NSString *nextAction; @property (nonatomic, retain) IBOutlet UILabel *nameLabel; @property (nonatomic, retain) IBOutlet UILabel *usernameLabel; @property (nonatomic, retain) IBOutlet UITextField *nextActionTextField; @property (nonatomic, retain) IBOutlet UILabel *dateLabel; @property (nonatomic, retain) IBOutlet UIButton *contactInfoButton; @property (nonatomic, retain) IBOutlet UIButton *backgroundInfoButton; @property (nonatomic, retain) IBOutlet UIButton *actionDoneButton; -(IBAction)displayContactInfo: (id)sender; -(IBAction)displayBackgroundInfo: (id)sender; -(IBAction)actionDone: (id)sender; @end However when I run it, I get the following error message: * Terminating app due to uncaught exception 'NSUnknownKeyException', reason: '[ setValue:forUndefinedKey:]: this class is not key value coding-compliant for the key nameLabel.' In IB I've hooked up the labels/buttons/textbox to the File's Owner (set the File's Owner Class to: ContactDetailViewController) Anyone any idea what I'm doing wrong? Regards, Fiona

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  • Java: conditional initialization?

    - by HH
    Ruby has conditional initialization. Apparently, Java does not or does it? I try to write more succintly, to limit the range as small as possible. import java.io.*; import java.util.*; public class InitFor{ public static void main(String[] args){ for(int i=7,k=999;i+((String h="hello").size())<10;i++){} System.out.println("It should be: hello = "+h); } } Errors Press ENTER or type command to continue InitFor.java:8: ')' expected for(int i=7,k=999;i+((String h="hello").size())<10;i++){} ^

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  • Hadoop in a RESTful Java Web Application - Conflicting URI templates

    - by user1231583
    I have a small Java Web Application in which I am using Jersey 1.12 and the Hadoop 1.0.0 JAR file (hadoop-core-1.0.0.jar). When I deploy my application to my JBoss 5.0 server, the log file records the following error: SEVERE: Conflicting URI templates. The URI template / for root resource class org.apache.hadoop.hdfs.server.namenode.web.resources.NamenodeWebHdfsMethods and the URI template / transform to the same regular expression (/.*)? To make sure my code is not the problem, I have created a fresh web application that contains nothing but the Jersey and Hadoop JAR files along with a small stub. My web.xml is as follows: <?xml version="1.0" encoding="UTF-8"?> <web-app version="2.5" xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"> <servlet> <servlet-name>ServletAdaptor</servlet-name> <servlet-class>com.sun.jersey.spi.container.servlet.ServletContainer</servlet- class> <load-on-startup>1</load-on-startup> </servlet> <servlet-mapping> <servlet-name>ServletAdaptor</servlet-name> <url-pattern>/mytest/*</url-pattern> </servlet-mapping> <session-config> <session-timeout> 30 </session-timeout> </session-config> <welcome-file-list> <welcome-file>index.jsp</welcome-file> </welcome-file-list> </web-app> My simple RESTful stub is as follows: import javax.ws.rs.core.Context; import javax.ws.rs.core.UriInfo; import javax.ws.rs.Path; @Path("/mytest") public class MyRest { @Context private UriInfo context; public MyRest() { } } In my regular application, when I remove the Hadoop JAR files (and the code that is using Hadoop), everything works as I would expect. The deployment is successful and the remaining RESTful services work. I have also tried the Hadoop 1.0.1 JAR files and have had the same problems with the conflicting URL template in the NamenodeWebHdfsMethods class. Any suggestions or tips in solving this problem would be greatly appreciated.

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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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  • How to draw the "trail" in a maze solving application

    - by snow-spur
    Hello i have designed a maze and i want to draw a path between the cells as the 'person' moves from one cell to the next. So each time i move the cell a line is drawn Also i am using the graphics module The graphics module is an object oriented library Im importing from graphics import* from maze import* my circle which is my cell center = Point(15, 15) c = Circle(center, 12) c.setFill('blue') c.setOutline('yellow') c.draw(win) p1 = Point(c.getCenter().getX(), c.getCenter().getY()) this is my loop if mazez.blockedCount(cloc)> 2: mazez.addDecoration(cloc, "grey") mazez[cloc].deadend = True c.move(-25, 0) p2 = Point(getX(), getY()) line = graphics.Line(p1, p2) cloc.col = cloc.col - 1 Now it says getX not defined every time i press a key is this because of p2???

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  • How to load a springframework ApplicationContext from Jython

    - by staticman
    I have a class that loads a springframework application context like so: package com.offlinesupport; import org.springframework.context.ApplicationContext; import org.springframework.context.support.ClassPathXmlApplicationContext; public class OfflineScriptSupport { private static ApplicationContext appCtx; public static final void initialize() { appCtx = new ClassPathXmlApplicationContext( new String[] { "mycontext.spring.xml" } ); } public static final ApplicationContext getApplicationContext() { return appCtx; } public static final void main( String[] args ) { System.out.println( "Starting..." ); initialize(); System.out.println( "loaded" ); } } The class OfflineScriptSupport, and the file mycontext.spring.xml are each deployed into separate jars (along with other classes and resources in their respective modules). Lets say the jar files are OfflineScriptSupport.jar and *MyContext.jar". mycontext.spring.xml is put at the root of the jar. In a Jython script (*myscript.jy"), I try to call the initialize method to create the application context: from com.offlinesupport import OfflineScriptSupport OfflineScriptSupport.initialize(); I execute the Jython script with the following command (from Linux): jython -Dpython.path=spring.jar:OfflineScriptSupport.jar:MyContext.jar myscript.jy The Springframework application context cannot find the mycontext.spring.xml file. It displays the following error: java.io.FileNotFoundException: class path resource [mycontext.spring.xml] cannot be opened because it does not exist at org.springframework.core.io.ClassPathResource.getInputStream(ClassPathResource.java:137) at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:167) at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:148) at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:126) at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:142) at org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:113) at org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:81) at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:89) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:269) at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:87) at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:72) at com.offlinesupport.OfflineScriptSupport.initialize(OfflineScriptSupport.java:27) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) If I run the jar directly from Java (using the main entry point in OfflineScriptSupport) it works and there is no error thrown. Is there something special about the way Jython handles classpaths making the Springframework's ClassPathXmlApplicationContext not work (i.e. not be able to find resource files in the classpath)?

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  • Enable PyGTK Eventbox motion-notify-event while is a Layout child

    - by mkotechno
    I noticed when a Eventbox is added into a Layout some events are missed, this does not happend for example adding it to a Fixed (very similar widget), I tried to restore the event mask in this way with no sucess: import pygtk import gtk def foo(widget, event): print event pygtk.require('2.0') window = gtk.Window(gtk.WINDOW_TOPLEVEL) window.connect('destroy', lambda x: gtk.main_quit()) eventbox = gtk.EventBox() eventbox.connect('button-press-event', foo) # works eventbox.connect('motion-notify-event', foo) # fail eventbox.set_events( gtk.gdk.BUTTON_MOTION_MASK| # restoring missed masks gtk.gdk.BUTTON1_MOTION_MASK| gtk.gdk.BUTTON2_MOTION_MASK| gtk.gdk.BUTTON3_MOTION_MASK) layout = gtk.Layout() image = gtk.image_new_from_file('/home/me/picture.jpg') layout.add(image) eventbox.add(layout) window.add(eventbox) window.show_all() gtk.main() How should I restore the missed event/mask?

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  • How to properly close a process with NppExec?

    - by Sam the Great
    I'm not sure what's going on here, but the following code continues running even after I end the process in the NppExec console with Ctrl-C (during the execution of the while loop). I restarted my computer to stop the Ctrl key sends. However, if I run the script in Window's cmd prompt, Ctrl-C ends the script just fine. import time import win32com.client shell = win32com.client.Dispatch("WScript.Shell") time.sleep(2) while True: shell.SendKeys('^') # Ctrl key time.sleep(0.5) The NppExec run command I used was: cmd /C python -u "$(FULL_CURRENT_PATH)" Let me know if there is any more information I can provide. Thanks.

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  • Multi-part template issue with Jinja2

    - by Alan Harris-Reid
    Hi, When creating templates I typically have 3 separate parts (header, body, footer) which I combine to pass a singe string to the web-server (CherryPy in this case). My first approach is as follows... from jinja2 import Environment, FileSystemLoader env = Environment(loader=FileSystemLoader('')) tmpl = env.get_template('Body.html') page_body = tmpl.render() tmpl = env.get_template('Header.html') page_header = tmpl.render() tmpl = env.get_template('Footer.html') page_footer = tmpl.render() page_code = page_header + page_body + page_footer but this contains repetitious code, so my next approach is... def render_template(html_file): from jinja2 import Environment, FileSystemLoader env = Environment(loader=FileSystemLoader('')) tmpl = env.get_template(html_file) return tmpl.render() page_header = render_template('Header.html') page_body = render_template('Body.html') page_footer = render_template('Footer.html) However, this means that each part is created in its own environment - can that be a problem? Are there any other downsides to this approach? I have chosen the 3-part approach over the child-template approach because I think it may be more flexible (and easier to follow), but I might be wrong. Anyone like to convince me that using header, body and footer blocks might be better? Any advice would be appreciated. Alan

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  • Exposing headers on iPhone static library

    - by leolobato
    Hello guys, I've followed this tutorial for setting up a static library with common classes from 3 projects we are working on. It's pretty simple, create a new static library project on xcode, add the code there, a change some headers role from project to public. The tutorial says I should add my library folder to the header search paths recursively. Is this the right way to go? I mean, on my library project, I have files separated in folders like Global/, InfoScreen/, Additions/. I was trying to setup one LOKit.h file on the root folder, and inside that file #import everything I need to expose. So on my host project I don't need to add the folder recursively to the header search path, and would just #import "LOKit.h". But I couldn't get this to work, the host project won't build complaining about all the classes I didn't add to LOKit.h, even though the library project builds. So, my question is, what is the right way of exposing header files when I setup a Cocoa Touch Static Library project on xCode?

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  • Identifying that a variable is a new-style class in Python?

    - by Dave Johansen
    I'm using Python 2.x and I'm wondering if there's a way to tell if a variable is a new-style class? I know that if it's an old-style class that I can do the following to find out. import types class oldclass: pass def test(): o = oldclass() if type(o) is types.InstanceType: print 'Is old-style' else: print 'Is NOT old-style' But I haven't been able to find anything that works for new-style classes. I found this question, but the proposed solutions don't seem to work as expected, because simple values as are identified as classes. import inspect def newclass(object): pass def test(): n = newclass() if inspect.isclass(n): print 'Is class' else: print 'Is NOT class' if inspect.isclass(type(n)): print 'Is class' else: print 'Is NOT class' if inspect.isclass(type(1)): print 'Is class' else: print 'Is NOT class' if isinstance(n, object): print 'Is class' else: print 'Is NOT class' if isinstance(1, object): print 'Is class' else: print 'Is NOT class' So is there anyway to do something like this? Or is everything in Python just a class and there's no way to get around that?

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  • Can't run jUnit with Eclipse

    - by KimKha
    I use new Eclipse. Create demo test with jUnit (I added default jUnit library built-in Eclipse). Then I write this code: import junit.framework.*; import org.junit.Test; public class SimpleTest extends TestCase { public SimpleTest(String name) { super(name); } public final void main(String method){ } @Test public final void testSimpleTest() { int answer = 2; assertEquals((1+1), answer); } } But it doesn't run. In the Debug tab: org.eclipse.jdt.internal.junit.runner.RemoteTestRunner at localhost:52754 Thread [main] (Suspended (exception ClassNotFoundException)) URLClassLoader$1.run() line: not available [local variables unavailable] AccessController.doPrivileged(PrivilegedExceptionAction<T>, AccessControlContext) line: not available [native method] Launcher$AppClassLoader(URLClassLoader).findClass(String) line: not available Launcher$AppClassLoader(ClassLoader).loadClass(String, boolean) line: not available Launcher$AppClassLoader.loadClass(String, boolean) line: not available Launcher$AppClassLoader(ClassLoader).loadClass(String) line: not available How can I solve this?

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  • read subprocess stdout line by line

    - by Caspin
    My python script uses subprocess to call a linux utility that is very noisy. I want to store all of the output to a log file, but only show some of it to the user. I thought the following would work, but the output does show up in my application until the utility has produced a significant amount of output. #fake_utility.py, just generates lots of output over time import time i = 0 while True: print hex(i)*512 i += 1 time.sleep(0.5) #filters output import subprocess proc = subprocess.Popen(['python','fake_utility.py'],stdout.subprocess.PIPE) for line in proc.stdout: #the real code does filtering here print "test:", line.rstrip() The behavior I really want is for the filter script to print each line as it is received from the subprocess. Sorta like what tee does but with python code. What am I missing? Is this even possible?

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  • AIR:- Desktop Application related to Window Component (Need some work around)

    - by Mahesh Parate
    Create custom component which contains Combobox and Datagrid. Application conations two button 1) Same Window and 2) New Window. (Label of two button) When you click on “Same Window” button your custom component should get added dynamically in your application. And when you click on “New Window” button your custom component should get open in different window (it should get shifted from application and should appear in Window component). Issue faced:- Clicking on Combobox, list is not getting open as change event doesn’t get fired in Native Window as it looses reference from main application. Issue with DataGrid in Native window (AIR). • DataGridEvent.COLUMN_STRETCH event get affected if try to open datagrid in Native Window. • DataGridEvent get fired but takes long time or even stuck while column stretch Note: Application is an Desktop Application. Only one instance is created in Application for your custom component to preserve current state on your custom component it can be Style, data, or other subcomponent state of your custom component (as above mentioned 2 component are just sample). Please find sample code below:- DataGridStretchIssue.mxml:- < ?xml version="1.0" encoding="utf-8"? < mx:WindowedApplication xmlns:mx="http://www.adobe.com/2006/mxml" layout="absolute" xmlns:local="*" width="800" height="500" < mx:Script < ![CDATA[ import mx.events.FlexEvent; import mx.core.Window; private var dgComp:DataGridComp = new DataGridComp(); private var win:Window; private function clickHandler(event:Event):void{ dgComp.percentWidth = 100; dgComp.percentHeight = 100; dgComp.x = 50; dgComp.y = 100; if(win){ win.close(); } this.addChild(dgComp); } private function openClickHandler(event:MouseEvent):void{ dgComp.x = 50; dgComp.y = 100; win = new Window();; win.width = 800; win.height = 500; win.addChild(dgComp); dgComp.percentWidth = 100; dgComp.percentHeight = 100; dgComp.x = 50; dgComp.y = 100; win.open(true) } ]]> < /mx:Script < mx:HBox <mx:Button id="btnID" click="clickHandler(event)" label="Same Window"/> <mx:Button id="btnIDOpen" click="openClickHandler(event)" label="New Window"/> < /mx:HBox < /mx:WindowedApplication DataGridComp.mxml < ?xml version="1.0" encoding="utf-8"? < mx:Canvas xmlns:mx="http://www.adobe.com/2006/mxml" width="100%" height="100%" <mx:Script> <![CDATA[ import mx.events.DataGridEvent; import mx.collections.ArrayCollection; [Bindable] public var cards:ArrayCollection = new ArrayCollection( [ {label:"Visa", data:1}, {label:"MasterCard", data:2}, {label:"American Express", data:3} ]); private function stretchFn(event:DataGridEvent):void{ trace("--- Stretched---") } ]]> </mx:Script> <mx:HBox> <mx:ComboBox dataProvider="{cards}" width="150"/> <mx:DataGrid columnStretch="stretchFn(event)" > <mx:ArrayCollection> <mx:Object> <mx:Artist>Pavement</mx:Artist> <mx:Price>11.99</mx:Price> <mx:Album>Slanted and Enchanted</mx:Album> </mx:Object> <mx:Object> <mx:Artist>Pavement</mx:Artist> <mx:Album>Brighten the Corners</mx:Album> <mx:Price>11.99</mx:Price> </mx:Object> </mx:ArrayCollection> </mx:DataGrid> </mx:HBox> < /mx:Canvas Can any one suggest me some work around to make my code workable... :)

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  • iPhone: error: request for member 'table' in something not a structure or union

    - by Jack Griffiths
    Hi there, When it comes to compiling my application, I get the error mentioned in the title. How would I go about remedying this error? Basically, I want to get from one table to the other. Hierarchy, navigation. NextViewController.m #import "RootViewController.h" #import "NextViewController.h" @implementation NextViewController - (void)didReceiveMemoryWarning { [super didReceiveMemoryWarning]; // Releases the view if it doesn't have a superview // Release anything that's not essential, such as cached data } - (void)dealloc { [super dealloc]; } - (IBAction) changeTable:(NSString *)str{ tblCSS.table = str; } The last line contains the error. If you need any more code, just ask. I'll amend this post with it. Cheers, Jack

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  • Flip clock showing time issue (animations invovled)

    - by Hwang
    I'm creating a flip clock (clock where you always see in airport), but I can't seems to get the time to show at the correct timing. After the flip, then will see the number changing. But I want it to change before it flips. Currently I'm not sure whether is the animation problem, or isit I have to do something else on the script. I've uploaded the FLA so that you could have a look on how I set up the flipping animation. http://www.mediafire.com/?nzmymjgtntz Below is the AS3 code: package { import flash.display.MovieClip; import flash.events.TimerEvent; import flash.utils.Timer; public class flipClock extends MovieClip { private var clock:clockMC=new clockMC(); //seconds private var secTop1=clock.second.top1.digit; private var secTop2=clock.second.top2.digit; private var secBot1=clock.second.bot1.digit; private var secBot2=clock.second.bot2.digit; private var seconds:Number; private var minutes:Number; private var hours:Number; private var days:Number; public function flipClock():void { decrease(); addChild(clock); } private function decrease():void { var countdownTimer:Timer=new Timer(1000); //Adding an event listener to the timer object countdownTimer.addEventListener(TimerEvent.TIMER,updateTime); //Initializing timer object countdownTimer.start(); } private function updateTime(event:TimerEvent):void { decreasTimerFunction(); updateSecond(); //updateMinute(); } private function updateSecond():void { clock.second.play(); secTop1.text=num2; secTop2.text=num1; if (num1<10) { num1="0"+num1; } if (num2<10) { num2="0"+num2; } if (num1==60) { num1=0; } if (num2==60) { num2=0; } secTop1.text=num1; secTop2.text=num2; //secBot1.text=num1; //secBot2.text=num2; } private function decreasTimerFunction():void { //Create a date object for Christmas Morning var endTime:Date=new Date(2010,4,26,0,0,0,0); //Current date object var now:Date=new Date(); // Set the difference between the two date and times in milliseconds var timeDiff:Number=endTime.getTime()-now.getTime(); seconds=Math.floor(timeDiff/1000); minutes=Math.floor(seconds/60); hours=Math.floor(minutes/60); days=Math.floor(hours/24); // Set the remainder of the division vars above hours%=24; minutes%=60; seconds%=60; } } }

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