software walk and software talk

Dropbox (Error code -36)

2011-02-07T11:49:00.000-08:00

Today, I was faced with Dropbox 'Error 36' on MacOS.
So, let's start from beginning... Dropbox has file name limitations, and those limitations are a bit different than operating system limitations (MacOSX).
I am convinced that there are good reasons for these, as they have special meaning on the command line level or would look really weird in the browser.

Let's start with the issues:
- Issue 1: File names can not start or end with blank character
- Issue 2: File names should not contain slashes

Where issue 2 is easy to spot, finder does not make it easy to spot issue 1. Thus I have created a short script that fixes blank characters in file names.

You can download dropbox_fix_script.pl. You need to navigate to the folder you are trying to copy, unzip and run this script from terminal.

Before you run this script, make sure to backup your data.

If there are enough interested readers, I may wrap this into application that you can drop a folder on.

--- script content is:
#!/usr/bin/env perl
#
sub fix()
{
    my @list = `find .` ;
    chomp(@list);
    for my $file (@list)
    {
    print "." ;
    my $base = `basename "$file"` ;
    my $dir = `dirname "$file"` ;
    chomp($base);
    chomp($dir);
        if( ($base =~ /\s+$/) || ($base =~ /^\s+/) || ($base =~ /\// )
        {
      print "match $file\n" ;
          $base =~ s/\s+$//mig ;
          $base =~ s/^\s+//mig ;
          $base =~ s/\//_/mig ;
    print "\n" ;
          return ( $file, "$dir/$base");
        }
    }
    return undef;
}

while( 1 )
{
    my ($file, $new_file) = &fix();
    if( defined( $file ) )
    {
        print "rename '$file' '$new_file'\n" ;
        if( -f $new_file )
        {
            print "file already exists $new_file -- fix $file \n" ;
            exit ;
        }
        if( -d $new_file )
        {
            print "dir already exists $new_file -- fix $file \n" ;
            exit ;
        }
        rename $file , $new_file ;
    }
    else
    {
        last;
    }

}

DNA reverse complement

2011-01-26T20:06:00.000-08:00

Just published simple DNA reverse complement tool. It features reverse sequence generation, complementary RNA and DNA generation and of course reverse complement for both DNA and RNA. Check it out.

Click-o-mania and cyclick-o-mania in pure HTML

2011-01-19T19:43:00.000-08:00

Last time I wrote click-o-mania clone was in summer of 1999. I wrote it in an MIT Athena cluster one summer day with the idea that it would help me with, than fresh Java skills.

Now the time has come, and I wanted to work on my GWT skills - thus - new HTML only, Flash-free, Java-free version of Click-o-mania and cyclick-o-mania are available. This simple games are written in using GWT/Java and compiled and tested on Mac and Windows, in variety of browsers and also adapted to work on iPhone. If they work well on Android, I would be interested to hear.

I hope you will enjoy these games as much as I enjoyed writing them.

Punnett Square at Bugaco.com

2010-09-08T08:23:00.001-07:00

I just started writing Punnett Square calculator. It seems to be a nice tool for understanding inheritance relationships. Check it out at: http://www.bugaco.com/calculators/punnett_square.php

Eclipse - Linux - Unable to connect to repository

2010-03-31T19:26:00.000-07:00

I just moved to new Ubuntu 10.4, and downloading Eclipse or Aptana Studio suddenly stopped working with repositories. This is very very annoying as I'm unable to install pydev and continue working on my improvements of Analytics@bugaco. So, what I had to do something to fix it. It seems that I am not the only one with this problem.

The problem seems to be related to Java's preference to use IPv6 stack over IPv4 stack that causes some systems to be unable to connect to web sites.

Fix for it is documented at debian's bug report's list. The reading is quite verbose, so I'll document cookbook solution that just works for me.

Open your eclipse.ini file, at some stage it has -vmargs line, after that line add following define:
-Djava.net.preferIPv4Stack=true

Original file

-startup
plugins/org.eclipse.equinox.launcher_1.0.201.R35x_v20090715.jar
--launcher.library
plugins/org.eclipse.equinox.launcher.gtk.linux.x86_1.0.200.v20090520
-product
org.eclipse.epp.package.cpp.product
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
-vmargs
-Dosgi.requiredJavaVersion=1.5
-XX:MaxPermSize=256m
-Xms40m
-Xmx256m

New file

-startup
plugins/org.eclipse.equinox.launcher_1.0.201.R35x_v20090715.jar
--launcher.library
plugins/org.eclipse.equinox.launcher.gtk.linux.x86_1.0.200.v20090520
-product
org.eclipse.epp.package.cpp.product
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
-vmargs
-Djava.net.preferIPv4Stack=true 
-Dosgi.requiredJavaVersion=1.5
-XX:MaxPermSize=256m
-Xms40m
-Xmx256m

Good luck! Let me know if this fixes your problem...

Windows 7 on Acer TravelMate C110

2009-11-15T19:07:00.000-08:00

introduction

I got Acer travel mate Tablet PC. This is a great little workhorse - it has 900MHz CPU that is on par with most of the Atom's out there, so I find little reason to even consider getting a netbook.

My Acer was running Windows XP Table PC edition. I wasn't even thinking of upgrading it to Windows Vista (as it did not have enough resources), but with all the hype that Windows 7 is optimized operating systems - I was thinking - let's give it a try!

First, let's go with the setup of Acer - it has 1.25GB of memory, thereby passing a requirement for more than 1GB of RAM. It has 900MHz CPU, barely below 1GHz minimum, and I upgraded it with 80GB/5400 PATA drive that works just fine.

As you can see from "Windows Experience Index" the slowest part of the setup is graphics, but given that I don't plan to play first person shooters on it - it's just fine!

install

Acer does not have DVD drive, so I used USB key to boot Windows installation.

Check this blog post to create Windows 7 bootable USB Key.

I installed clean install of Windows 7 on the machine (I upgraded HDD before installing Windows 7, so there was no point of transfering XP over first).

Machine booted in safe graphics mode, and it was missing some of the drivers.

network

First I installed network drivers - it turns out one can install Intel 2100b drivers for XP on Windows 7. It turns out you can 'force' windows to use XP's driver. So I downloaded latest driver from Intel's site and forced Windows 7 to accept Intel drivers although it complained a lot!

This was not enough to get Windows 7 to start using networking adapter, and after some agony I remembered that friend of mine mentioned that Acer has stupidest software button that turns of wireless adapter. Linux has a app that can be used to flip the software switch, as button in itself is dead and wireless if off (remember that wireless is on only when red LED is turned on).

After trying to install most of the original Acer utilities I figured that I may need to return back to XP as Notebook Manager throws exceptions almost on any click. After a bit of frustration I noticed that 'Launch manager' althrough it does not help with the button has an option 'Wireless Device Boot Status' and it can be turned on.

This saved the day! Now networking works.

sleep & graphics

Acer is not functional, so let's see what is next issue on the list. Mysteriously Acer does not want to sleep. It just wants to hibernate or shut down. This is a bit of annoying as using XP I could just close the lid and it would sleep fine.

Another set of frustrating explorations led to the command that will list sleep states, and what prevents system from falling a sleep. Results of this command suggested that the issue is in graphics adapter that was generic VESA and as such it didn't know anything about sleeping.

It turns out that Intel didn't provide support for 855 chipset - can you blaim them? Chipset is about quite old and they would like us to buy new ones. Installing 915 drivers didn't work, but using XDDM mode of 855 drivers (produced for Vista) worked just well enough to get my machine to accept driver, and to be able to happily fall asleep.

Now finally sleep worked fine! Awesome!

not much sleep for the wary

While sleep would be really cool and I would enjoy it - it had one drawback. Remember network? And that stupid button? Well, if you sleep machine, on wake up network does not wake up.

So I just hibernate my Acer when I'm done using it.

conclusion

Windows 7 works well on Acer C110. It is an awesome little machine. Sleep does not work well, but most of the other functions are just fine. I also like how Windows 7 improved tablet functionality - hand writing recognition is way better than before.

Setting Putty with Kerberos on Windows (including Windows 7)

2009-11-13T20:29:00.000-08:00

note
If you don't know what is Kerberos and SSH - you probably don't need it. So read some of the other posts that may be more relevant for you.

introduction

If you do know that you want Kerberos and SSH on your machine - welcome to the post that will explain how to set it up on Windows. Unlike MacOSX that comes with Kerberos and kerberos aware SSH and Ubuntu, Red Hat and other major Linux distributions that have Kerberos and Kerberos aware SSH easily accessible, finding good Kerberized SSH client for Windows was a challenge.

Although I like challenges, I like to solve them once, and reuse them often - so this post is on how to setup yourself with Kerberized SSH and SCP for Windows.

installation

Best SSH client I have found for Windows is Putty, but default installation does not came with Kerberos enabled, so if you need Kerberized Putty, you can download it from Mattew Loar's web page.

In addition to Kerberized Putty you will need to install MIT's Kerberos for Windows.

As kerberos needs to be in the path, Putty may not work until you add it to the path (by for example restarting CMD or slickrun)

Install these two packages and you should have whole install.

why kerberos?

Cool thing about Kerberos is that separates your credentials (authentication) from your privilegies (authorization). By default you should be able to login to your account SSH enabled Unix server, but Kerberos makes it easy to allow someone else to login as you without giving them password - for example I can login as both root and myself on our server with same Kerberos ticket, and so guy next to me; but unlike non-Kerberized SSH revoking and adding people is matter of editing .k5login file.

how to do it with Putty?

1. Get a ticket.

2. Open Putty and select 'connection -> data' and setup user account you are authorized to access - for example root.

3. login to server by setting server name in session tab.

resources

Putty with Kerberos authentication:

http://matthew.loar.name/software/putty/

MIT Kerberos Package:

http://web.mit.edu/kerberos/dist/index.html#kfw-3.2

Dual Boot USB stick with Windows 7 and Ubuntu 9.10 (Karmic Koala)

2009-11-13T06:41:00.000-08:00

introduction

I setup on doing a dual boot (or hopefully dual boot + dual install) of Windows and Ubuntu on USB stick. This proved to be more challenging than I would expect, so I'll try to outline what my conclusions are and how to make dual boot stick.

Let's start with the basics, unlike Vista, Windows 7 optimizes driver installation when it boots, preventing it from booting from USB stick on different machine (or different type of the machine) than it was installed on. This yields a simple result that one probably does not want to install Windows 7 on USB drive, but only to have bootable install partition.

Ubuntu's option to make bootalbe USB drive asks for amount of persistent space that you can use to keep your data on USB drive, thereby really making USB drive a full install without a need to additional partition with "full install".

This leads us to needing only bootable Ubuntu and bootable Windows 7 install. While it may be possible to boot Ubuntu from windows bcd bootloader, I opted for opposite direction thus booting into Ubuntu boot screen that has an option to start Windows 7 installer.

My first few attempts to get syslinux (Ubuntu installer to boot Windows from same partitino were unsuccessful). My next few attempts to get windows to boot from second USB partition were as well unsuccessful and at the end I found this prescription that works.

the prescription
1. Boot into Ubuntu Live CD
2. Start GParted and create two primary partitions (first at least 2.5Gb, and second at least 1.1Gb)
3. Format both partitions as FAT32
4. Boot into Windows
5. Note drive letter of your USB drive's first partiton (example Q:)
6. Go to Windows 7 installer DVD (or folder where you extracted ISO using 7-zip)
7. Go to boot folder and from command line (with Administrative privilegies) run:
bootsect /nt60 Q: /mbr
8. Extract Windows 7 DVD files to your USB drive (example Q: drive)
9. Boot back into Ubuntu
10. Make bootable usb drive (option from Administration menu)
11. Get chain.c32 from syslinux and copy to /isolinux folder
12. Get ldlinux.sys from syslinux and copy to / folder [this may be optional step]
13. Edit text.cfg and add at the end:
MENU LABEL Windows 7
COM32 /syslinux/chain.c32
APPEND hd0 1 ntldr=/BOOTMGR
14. Dual boot your Windows 7 Installation

Happy dual booting...

Analyics @ Bugaco allows embedding analytics data in web pages

2009-10-23T11:26:00.001-07:00

Analytics @ Bugaco is updated with a new feature - stored reports.
Currently only google maps report can be stored. When report is stored, user is given URL that can be embedded or shared with friends.

Analytis @ Bugaco is collection of freely available reports that utilize Google Analytics data to produce additional report. The tool was originally announced in this blog post.

Here is an example of stored report.

Seagate Date Calculator for iPhone

2009-10-07T08:42:00.000-07:00

In previous blog post I talked about seagate date code calculator. It seems to be useful tool for the people out there, and I decided to revamp it. It has better user interface, and I now created off-spin that works well on touch devices like iPhone.

Reports that were missing from Google Analytics are being developed at analytics.bugaco.com

2009-09-23T19:16:00.000-07:00

Did you ever feel like Google Analytics is somewhat constrained in reports it has?

If the answer to this question is NO - that stop here and go do something else.

If on the other hand you wanted to do more with google analytics, but it was almost impossible to get a report you wanted, you may be interested in a new effort at Analytics @ Bugaco.
It starts as a modest effort that created two custom reports that use Google Analyics API to provide different reports than ones provided by Google Analytics itself.
It is in early stages of development, and any comments that would make it better are welcomed by development team. All comments you do send will be seriously evaluated and prioritized.

So, what is Analytics@Bugaco at this early stage of development?

At this time Analytics@Bugaco has two reports - one is oriented toward developers - it allows you to determine what kind of screens your users have, and thus it will help you design better software/website layouts that will fit your real users.

Another report available is mapping visitors on google map. This is cool for a few reasons, and where we intend to go with it is to allow you to include generated map into your website. For an example of how this would work visit Software Tools for Academics and Researchers site. They have a map that displays visitors from last 30 days - it's an cool and impresive map, and what's really cool, you can zoom in and see your city!
At this stage, through map is not embeddable, but with sufficient interest (read comments) it will be put ahead of other priorities.

Thanks, and enjoy Analytics@Bugaco site

Sequence conversion tool

2009-09-14T20:47:00.000-07:00

There is new sequence conversion tool at Bioinf @ Bugaco.com. It allows conversion between 16 most popular sequence formats.
Here is direct link to sequence conversion utility

What is really cool is that it supports:

ace
embl
fasta
fastq
fastq-solexa
fastq-illumina
genbank
ig
nexus
phd
phylip
pir
stockholm
swiss
tab
qual

StarCluster - Open source StarCluster shines on Amazon cloud Dynamic computing allocation possible

2009-09-01T12:44:00.000-07:00

A new open source project dubbed StarCluster has been released aiming to simplify the management of virtual clusters hosted on Amazon's Elastic Compute Cloud (EC2) service. According to developer Justin Riley, StarCluster minimises the administrative overhead associated with obtaining, configuring, and managing a traditional computing cluster used in research labs or for general distributed computing applications. The StarCluster project started at MIT's Software Tools for Academics and Researchers (STAR) Program.

Source ComputerWorld AU

See your linux box on your wireless network

2009-08-31T16:36:00.001-07:00

I got new wireless router, and I wanted to make sure I can use machine names to ping other computers on the network. In my setup, I have windows, linux and macosx machines, and I was never able to really ping them by name on local wireless network. That is really an annoying thing, so... I decided to resolve it.

My new setup:
1. DD-WRT enabled router.

2. I setup DNS server to serve local network, and to expand local names by specifying additonal options:
local=/local/
expand-hosts

This almost worked... i.e. I was able to ping Windows machine from all three, I was able to ping MacOSX from all three machines, but Windows was unable to ping Linux.
After trying to figure out what is wrong I learned that you have to install samba, as nmbd is actually responsible with registering Linux with Windows.

I hope you will find this helpful.

Java Native Font Viewer

2009-07-21T11:44:00.001-07:00

Hi,

I just published a Java Applet that allows you to see how text looks when displayed using native fonts in various sizes.

The reason behind developing this applet is to experiment with ability to customize Swing application with better looking fonts that fonts used by default L&F.

How to create incremental project builder in Eclipse?

2009-04-01T11:46:00.000-07:00

I wanted to build incremental project builder in Eclipse today.
There is nothing on the top level of the "New Project" wizard to indicate how to build it. Quick search on the web didn't yield any usable result so, I guess posting a short post about it may be useful.

One builds incremental project builder by selecting "Plug-in development" and after 2-3 steps one is able to select among:
- Hello World
- Hello World Command
- Plug-in with a multi-page editor
- Plug-in with a popup menu
- Plug-in with a property page
- Plug-in with a view
- Plug-in with an editor
- Plug-in with an incremental project builder
- Plug-in with sample help content.

Selecting incremental project builder adds sample project builder, project nature, problem marker and popup menu action - so all the things I need.

Cool!

Toner refill kit recommended

2008-12-14T08:57:00.000-08:00

My home laster printer (Samsung ML-1710) really needed a new toner. After a bit of comparison, I figured, I'll give a try to toner refill kits.

I got a Universal refill kit #6. It is a breeze to replace, but look at the instructions first. On Samsung's toner you need to drill the hole on the right, pour some toner in and put a cap on.

Happy printing.

Seagate date code

2008-12-14T08:47:00.000-08:00

Last week my Seagate hard drive broke. It had weird date code on it. I figured that on the internet there has to be a place where someone posted how to decrypt this 5 digit number.

After a bit of search I have found PDF explaining it, but I noticed I could not find a on-line calculator. Given that calculation is not hard to do, but still not intuitive for human to calculate I wrote a little calc that solves that problem for myself and anyone who is wandering what the date is (this may be important to figure out if your drive is under warranty).

So, here is Seagate date code calculator.

Enjoy.

jflvlib-0.1 released

2008-10-17T12:26:00.000-07:00

JFlvLib is a library that allows writing of Flash Videos (FLV format).

To use library user instantiates Capture instance using CaptureFactory class.
Capture c = CaptureFactory.getCapturer( os , new Dimension(xx , yy) ) ;

Capture interface provides 2 methods:
// generates new frame in compatible format for writing frame
BufferedImage newFrame();

// writes a frame to FLV stream
void writeFrame( BufferedImage image , int timestamp ) throws IOException;

At this stage library implements video only, SCREENVIDEO_CODEC and it generates only key frames. This is good for producting videos but they are larger than they need to be.

That's it.

TODO:
Optimize FLV creation writing not only keyframes but also interframes.
Implement other codecs (JPEG, H263, ...)
Add audio support

Example:

 package edu.mit.star.flvexample;
 
 import java.awt.Dimension;
 import java.awt.image.BufferedImage;
 import java.io.IOException;
 import java.io.OutputStream;
 
 import edu.mit.star.flv.Capture;
 import edu.mit.star.flv.CaptureFactory;
 
 
 public class Main
 {
 
     public static void main(String[] args)
     {
  try
  {
   OutputStream os = new java.io.FileOutputStream( "z:\\temp\\test.flv" );
   int xx = 256 ;
   int yy = 512 ;
   Capture c = CaptureFactory.getCapturer( os , new Dimension(xx , yy) ) ;
   int time = 0 ;
   while( time < 5000 )
   {
    BufferedImage image = c.newFrame() ;
    
    image.getGraphics().drawOval(0, 0, xx*time/5000, yy*time/5000);
    image.flush();
     
    c.writeFrame(image, time);
    time += 250;
    System.out.println( "Generating " + time + " ms frame.");
   }
   os.close();
  }
  catch( IOException ex )
  {
   ex.printStackTrace();
  }
     }
 }

Getting UNIX process ID in Java

2008-03-20T13:20:00.000-07:00

We encountered a need to kill process spawned by Runtime.getRuntime().exec() in java in a bit friendlier way than Process.destroy() provides for. To do this, easiest way is to execute "kill -number PID".
Process ID is not available as part of the interface, and below is outlined hack to get that information:

public class test
{
public static void main( String[] str )
{
try
{
Runtime r = Runtime.getRuntime() ;
Process p = r.exec( "sleep 200" ) ;
java.lang.reflect.Method m = p.getClass().getDeclaredMethod( "ac cess$100" , new Class[] { p.getClass() } ) ;
m.setAccessible(true);
Object ret = m.invoke( p , new Object[] { p } ) ;
System.out.println( "process ID " + ret ) ;
System.out.println( "Press Ctrl-Z and ps to confirm" ) ;
Thread.sleep( 100000 ) ;
}
catch( Exception e )
{
e.printStackTrace() ;
}
System.exit(1);
}

}

Java, HashSet, Equals and hashCode

2007-12-06T11:37:00.001-08:00

Today, I was working on the code that attempts to add 2D points to java.util.HashSet and test if HashSet contains them.
Point implemented equals method correctly, and accoding to java.util.Set documentation contains should: "Returns true if this set contains the specified element. More formally, returns true if and only if this set contains an element e such that (o==null ? e==null : o.equals(e))."

Well, documentation is wrong - and for a good reason - to implement specification as documented one would need to iterate all objects (in the set) for check for equality. What java.util.Set does is to use hashCode() value to index objects and compare them.

Therefore, if your class does not implement hashCode correctly, following test will fail:


  ArrayList points = new ArrayList() ;
  points.add( new IntPoint2D( 2, 2 ) ) ;
  assertTrue(points.contains(new IntPoint2D(2,2)));

A dilemma is what to return as hashCode? I opted, knowing that my data will be local to implement hashCode as:


 public int hashCode()
 { 
     return (x & 0xffff) | ((y & 0xffff)<<16) ; 
 }

That will be good enough solution for the problem I'm facing.

There is corollary of this implementation:
1. if one assumes that hashCode() is natively implemented to return a pointer to underlying objects, and one tests for identity of the objects contained in the set (often the case) than Set works great.
2. if one needs to overload hashCode() and stuff more complex object in it, it needs to be aware of remote or not-so-remote chance that hashCode will return same value for two different objects, thereby yielding incorrect code.

Man isn't this useless, but cute...

2007-08-07T19:58:00.000-07:00

Browsing for fast USB drives I found a useless feed. And this useless gadget is kind'a fun - check YouTube video.

Link: http://www.getusb.info/category/usb-novelty-gadget/

Java and backward/forward compatibility

2007-08-01T08:07:00.000-07:00

I just faced an issue with OrbitBehavior. Older Java3D don't have a field MOUSE_WHEEL_LISTENER, but it is a feature that I find very useful for my project (blog).

Here is a code on how I solved dynamical determination if runtime version of Java3D supports this new field without throwing an exception.


void addMouseWheelListener( int flags )
{
 int listenerFlags = MOUSE_LISTENER | MOUSE_MOTION_LISTENER | flags ;
 try
        {
  String field = "MOUSE_WHEEL_LISTENER";
  Class parent = getClass().getSuperclass(); 
         if( parent.getDeclaredField(field) != null )
         {
          int flag = parent.getDeclaredField(field).getInt(this);
          listenerFlags |= flag ;
         }
        }
        catch (SecurityException e)
        {
        }
        catch (NoSuchFieldException e)
        {
        }
        catch (IllegalArgumentException e)
        {
        }
        catch (IllegalAccessException e)
        {
        }
 setListenerFlags(listenerFlags);  
}

As you can see I use reflection to check first if the field exist, and if and if it does I modify my listenerFlags with field's value.

Even if the field is visible in this class it does not need to be declared there. In my case field is declared in superclass.

How to resize Vmware disk with Windows OS VM

2007-07-31T18:09:00.001-07:00

I was running a VMWare image. Given that I made image some time ago (like 2years or so), I made it with 2Gb disk partitions. 2Gb was too small to install .NET framework - and there was an issue.

To solve it I had few solutions, but easiest and most obvious one is to resize Windows partition to more space. Quick google search returned link to Carl Tyler's blog explaining how to use it.

Given that I had Ubuntu image handy on my laptop, resizing using QTParted was a breeze. I booted the image, and started doing install to HD process until I got to partition manager, selected size to grow from 2 to 8Gb and voile - I'm done.

Windows did notice something wasn't right on next reboot, it checked disk (chkdsk) and proceeded without a glitch.

Two thumbs up for Ubuntu. Thanks Carl :)

Add digg it to your site!

2007-07-31T12:31:00.000-07:00

Given that this are my early blogging days - here's a useful page that explains how to add "digg it" button to your site.
I'll need to explore more features like this - like adding technorati link.