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  • Parse large XML file w/ script or use BioPython API ?

    - by jeremy04
    Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the parser, but my initial reaction: how would I map the XML schema to the SAX parser? 2) BioPython - I already have BioSQL/Biopython installed, which literally created my SQL schema for me, and I was able to successfully insert one SwissProt/Uniprot txt file into the database. I'm running it right now (crosses fingers) on the entire 2.1gb. Here is the code I'm running: from Bio import SeqIO from BioSQL import BioSeqDatabase from Bio import SwissProt server = BioSeqDatabase.open_database(driver = "MySQLdb", user = "root", passwd = "", host="localhost", db = "bioseqdb") db = server["uniprot"] iterator = SeqIO.parse(open("/path/to/uniprot_sprot.dat", "r"), "swiss") db.load(iterator) server.commit() Edit: it's now crashing because the transactions are getting locked (since the tables are Innodb) Error Number: 1205 Lock wait timeout exceeded; try restarting transaction. I'm using MySQL version: 5.1.43 Should I switch my database to Postgrelsql ?

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  • Extend Linux Desktop to another X Windows Display

    - by unknown (google)
    Hello, I am a long time Linux user of the Xinerama and other technologies for extending a desktop to multiple monitors. However when I travel with my laptop I miss the multi-monitor support I enjoy at home. Recently I acquired a second laptop for a low price. Both laptops are running Fedora (versions 10 and 11 respectively). I use Gnome as my primary desktop environment. I know about synergy. I use synergy all the time to control the screen of other Windows / Linux systems I use. I would like to know, can I sit both my primary and secondary laptops together and achieve a Xinerama-like extended desktop environment? Ideally I would like to start a GNOME session on my primary laptop. And then start a X-Windows Desktop on my secondary laptop and extend my primary laptop's desktop onto it. I would like to be able to move Windows from the primary desktop to the secondary laptop desktop. Would I need to use synergy to do this with some other bit of X-Windows technology? Or is there X-Windows technology that will do all this for me? I am familiar with X Windows ability to display applications remotely. I am also familiar with Nomachine's NoX.

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  • It's possible to use google smtp for sending email from my server?

    - by Magnetic_dud
    Well, I am becoming crazy to let my email deliver to gmail/hotmail from my new ip. Last year, i had no problems with my past ip, but now my emails go straight to the spam folder of gmail and hotmail. I checked with mxtoolbox.com and i am not blacklisted, not an open proxy, rdns is configured the right way, SPF policy is present on the DNS. My spf is v=spf1 a mx ~all But, still, I am filtered. So, I am wondering: since gmail does not accept my emails, it's possible to use gmail smtp server to deliver all mails from my server? AFAIK, it will change all the "from" address, but maybe there is a way to not let it happen?

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  • How to call window developed in C# through FindWindow api.

    - by Sagar Mane
    Hello All, I am new to C# and xaml code. I have one sample code which implemented in C#. when I have reviewed xaml file I got <Window x:Class="test.MainWindow">. So does test.MainWindow indicate the class name for this window. I am trying to invoke this window from other application which is developed in win 32. I am trying to pass this class name to FindWindow("test.MainWindow",NULL) ,but it fails. does anything missing over there. how I can change the class name of window developed in C#? Thanks, Sagar

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  • USB hardwares driver installation

    - by unknown (google)
    I am using few USB hardwares like camera and scanners with my software application. I plugged my hardware in USB A installed the drivers and the device was working properly. Now I tried to connect the same hardware in USB B (ie, some other USB port), and again it is asking for the driver installation. I need to know the reason behind this. Is it something to do with the particular device or system? Anywork around for this during the first time driver installation? Please anyone explain me how the USB works physical address, how it is assigned and how the driver for a device getting installed. Thanks in advance.

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  • Using the windows api and C++, how could I load an exe from the hard drive and run it in its own thread?

    - by returneax
    For the sake of learning I'm trying to do what the OS does when launching a program ie. parsing a PE file and giving it a thread of execution. If I have two exe's one called foo.exe and the other bar.exe, how could I have foo.exe load the contents of bar.exe into memory then have it execute from there in its own thread? I know how to get it into memory using MapViewOfFile or by simple loading the contents on the hard drive into a buffer. I'm assuming simply copying the contents of bar.exe on disk into its own suspended thread and running it wouldn't work. I am semi-familiar with PE file internals. All help is very much appreciated, of course :)

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  • Twitter Search API is returning weird characters - is it more or is it them?

    - by DanSingerman
    We are building an app that accesses the Twitter search over JSONP. It mostly works fine, but occasionally the request returns a JSONP callback that exists of weird unparseable characters. Here is an example: http://search.twitter.com/search.json?result_type=recent&rpp=100&geocode=51.4375857,-0.1658648,1km&page=5&callback=jsonp1272532482854 (If you change page=5 to a value less than 5 in the URL it works fine) So Am I doing something wrong? Can anyone suggest a workaround?

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  • ATI driver in Fedora linux 11

    - by unknown (google)
    I recently built a pc with an ATI Radeon HD 5750. I have installed Fedora 11 and installed the device driver for the Radeon 5700 series proprietary drivers. I wanted to see if there is graphics hardware acceleration. I typed in glxinfo at the terminal and I got: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 135 (GLX) Minor opcode of failed request: 19 (X_GLXQueryServerString) Serial number of failed request: 14 Current serial number in output stream: 14 I don't know how to fix this. I tried to go to the ATI Catalyst Control Center; that worked, but the ATI Catalyst Control Center (Administrator) doesn't work. If anyone knows how to fix this problem then please let me know. Thanks

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  • WCF service is not getting called

    - by Cheranga
    I have a web solution and I have a WCF service project inside it. We need to support "cookieless". so in the web.config, it's set as <sessionState mode="SQLServer" sqlConnectionString="Data Source=ds;Initial Catalog=db;User Id=uid;Password=pwd" allowCustomSqlDatabase="true" cookieless="true" timeout="720" regenerateExpiredSessionId="false"/> The WCF service will be supporting sessions, so we have also set "aspNetCompatibilityEnabled" to true in web.config. <serviceHostingEnvironment aspNetCompatibilityEnabled="true" multipleSiteBindingsEnabled="true"/> The service and interfaces are as follows, [ServiceContract(SessionMode=SessionMode.Allowed)] public interface ICDOCService { } [AspNetCompatibilityRequirements(RequirementsMode = AspNetCompatibilityRequirementsMode.Allowed)] public class CDOCService : ICDOCService { } The problem we are facing is we cannot access the service from any client application. (web app, WCF test client) The following error is showing, when we access it via WCF Test client, Failed to invoke the service. Possible causes: The service is offline or inaccessible; the client-side configuration does not match the proxy; the existing proxy is invalid. Refer to the stack trace for more detail. You can try to recover by starting a new proxy, restoring to default configuration, or refreshing the service. The content type text/html; charset=UTF-8 of the response message does not match the content type of the binding (multipart/related; type="application/xop+xml"). If using a custom encoder, be sure that the IsContentTypeSupported method is implemented properly. The first 1024 bytes of the response were: <HTML> <HEAD> <link rel="alternate" type="text/xml" href="http://localhost:53721/Services/CDOCService.svc?disco"/> <STYLE type="text/css">#content{ FONT-SIZE: 0.7em; PADDING-BOTTOM: 2em; MARGIN-LEFT: 30px}BODY{MARGIN-TOP: 0px; MARGIN-LEFT: 0px; COLOR: #000000; FONT-FAMILY: Verdana; BACKGROUND-COLOR: white}P{MARGIN-TOP: 0px; MARGIN-BOTTOM: 12px; COLOR: #000000; FONT-FAMILY: Verdana}PRE{BORDER-RIGHT: #f0f0e0 1px solid; PADDING-RIGHT: 5px; BORDER-TOP: #f0f0e0 1px solid; MARGIN-TOP: -5px; PADDING-LEFT: 5px; FONT-SIZE: 1.2em; PADDING-BOTTOM: 5px; BORDER-LEFT: #f0f0e0 1px solid; PADDING-TOP: 5px; BORDER-BOTTOM: #f0f0e0 1px solid; FONT-FAMILY: Courier New; BACKGROUND-COLOR: #e5e5cc}.heading1{MARGIN-TOP: 0px; PADDING-LEFT: 15px; FONT-WEIGHT: normal; FONT-SIZE: 26px; MARGIN-BOTTOM: 0px; PADDING-BOTTOM: 3px; MARGIN-LEFT: -30px; WIDTH: 100%; COLOR: #ffffff; PADDING-TOP: 10px; FONT-FAMILY: Tahoma; BACKGROUND-COLOR: #003366}.intro{MARGIN-LEFT: -15px} </STYLE> <TITLE>CDOCService Service</TITLE></HEAD><BODY><DIV id="content"><P '. Server stack trace: at System.ServiceModel.Channels.HttpChannelUtilities.ValidateRequestReplyResponse(HttpWebRequest request, HttpWebResponse response, HttpChannelFactory factory, WebException responseException, ChannelBinding channelBinding) at System.ServiceModel.Channels.HttpChannelFactory.HttpRequestChannel.HttpChannelRequest.WaitForReply(TimeSpan timeout) at System.ServiceModel.Channels.RequestChannel.Request(Message message, TimeSpan timeout) at System.ServiceModel.Dispatcher.RequestChannelBinder.Request(Message message, TimeSpan timeout) at System.ServiceModel.Channels.ServiceChannel.Call(String action, Boolean oneway, ProxyOperationRuntime operation, Object[] ins, Object[] outs, TimeSpan timeout) at System.ServiceModel.Channels.ServiceChannel.Call(String action, Boolean oneway, ProxyOperationRuntime operation, Object[] ins, Object[] outs) at System.ServiceModel.Channels.ServiceChannelProxy.InvokeService(IMethodCallMessage methodCall, ProxyOperationRuntime operation) at System.ServiceModel.Channels.ServiceChannelProxy.Invoke(IMessage message) Exception rethrown at [0]: at System.Runtime.Remoting.Proxies.RealProxy.HandleReturnMessage(IMessage reqMsg, IMessage retMsg) at System.Runtime.Remoting.Proxies.RealProxy.PrivateInvoke(MessageData& msgData, Int32 type) at ICDOCService.GetCDOCCount(String institutionID, String mrnID, String userID, String callingSystemID, String securityToken) at CDOCServiceClient.GetCDOCCount(String institutionID, String mrnID, String userID, String callingSystemID, String securityToken)

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  • Mail Server using Postfix

    - by unknown (google)
    I have currently set up my web application on Amazon EC2 server. As a well known fact sending email from EC2 has a problem. As a cheap and long lasting solution instead of using "authsmtp" is it possible to rent a server and use it as a Mail Server? I am currently looking for cheap hosting which will give me root access so that it can be configured and used as a relayhost. I am curently using Postfix as MTA. Has any one implemented this before? I am curious about its feasibility of this solution. I guess common requirements are: 1: Dedicated IP which is not black listed. 2: Open relay( open to my Server only) Any Tips for Header configurations to keep the mails out of spam folder. This is like exactly cloning authsmtp for personal use. Any suggestions for other Mail Server software instead of Postfix? Another problem is Reverse DNS for this server. Should PTR entry be present if a server is used as a relayhost?

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  • Ripping a CD to mp3 in C# - third party component or api out there?

    - by Jonathan Williamson
    We're working on a project that requires the ripping of audio tracks from CDs to MP3s (ideally also retrieving the track information from CDDB or similar). More background information: Various music labels send us CDs of music which we then deliver to people via an online delivery system. We're looking at automating the process of converting those CDs into MP3s with full track information where possible. We want to produce a simple desktop application that allows a member of editorial staff to setup the information about the new music we receive. To streamline the process we'd like to include the ripping of the audio and retrieval of the track information.

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  • which service response is good for iphone development?

    - by suchita
    So I'm brand new to rest's API and have never used an API ever before. I'm ok with Objective-C and Cocoa Touch but just have no clue where to start when accessing the API and how to in general. Can someone help me get started with some code that will access titles in rest or just how to access a REST API in general with authentication. Thanks.

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  • How to filter and intercept Linux packets by using net_dev_add() API?

    - by Khajavi
    I'm writing ethernet network driver for linux. I want to receive packets, edit and resend them. I know how to edit the packet in packet_interceptor function, but how can I drop incoming packets in this function?? #include <linux/netdevice.h> #include <linux/skbuff.h> #include <linux/ip.h> #include <net/sock.h> struct packet_type my_proto; int packet_interceptor(struct sk_buff *skb, struct net_device *dev, struct packet_type *pt, struct net_device *orig_dev) { // I dont want certain packets go to upper in net_devices for further processing. // How can I drop sk_buff here?! return 0; } static int hello_init( void ) { printk(KERN_INFO "Hello, world!\n"); my_proto.type = htons(ETH_P_ALL); my_proto.dev = NULL; my_proto.func = packet_interceptor; dev_add_pack(&my_proto); return 0; } static void hello_exit(void) { dev_remove_pack(&my_proto); printk(KERN_INFO "Bye, world\n"); } module_init(hello_init); module_exit(hello_exit);

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  • Is there a Java 1.5 varargs API for slf4j yet?

    - by Josh
    I want to get rid of this lot... public void info(String msg); public void info(String format, Object arg); public void info(String format, Object arg1, Object arg2); public void info(String format, Object[] argArray); ...and replace it with this one... public void info(String format, Object ... args); ...so that my logging syntax doesn't have to change depending on the number of arguments I want to log. There seems to be lots of discussion and work around it, but where is it? Or should I wrap the wrapper that is slf4j?

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  • Windows Home Server restore causes computer to be removed from the domain?

    - by unknown (google)
    I restored my Dell M4400 that is a company laptop, and now I get an error when I try to log on and am connected to our corporate network, which says that the domain controller could not be found or that the computer is not part of the domain. Everyone else can log on, so it seems my computer is no longer part of the domain, even though it thinks it is per the settings. One thing of note: my computer crashed on 1/14/10, but I restored from a backup that was made on 12/20/09. So I am not sure if that made a difference? Also, I tried running "gpupdate" to update my group policy, but that did not seem to help. Any ideas? Seems like a bit of a flaw in the backup system for computers that are part of a domain. I guess I wanted to hear from someone with more knowledge about how a computer is recognized as part of a domain to know if this should be expected when doing a restore or if I should file a trouble ticket.

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  • Simple graphics API with transparency, polygons, reading image pixels?

    - by M. Elkstein
    I need a simple graphics library that supports the following functionality: Ability to draw polygons (not just rectangles!) with RGBA colors (i.e., partially transparent), Ability to load bitmap images, Ability to read current color of pixel in a given coordinate. Ideally using JavaScript or Python. Seems like HTML 5 Canvas can handle #2 and #3 but not #1, whereas SVG can handle #1 and #2 but not #3. Am I missing something (about either of these two)? Or are there other alternatives?

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  • shell pipe behavior with MySQLDump

    - by unknown (google)
    I am using mysqldump for a large database (several GB) and import the result from a pipe, please see commands below, does it do incremental pipe, or wait until the first one finishes then import? is this a good way of importing large db across servers? I know you can export gz it, then pscp it then import. Quick alternative are welcome mysqldump -u root -ppass -q mydatabase | mysql -u root -ppass --host=xxx.xx.xxx.xx --port=3306 -C mydatabase

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  • iPhone keeps going into dim/sleep mode even with the proper API calls.

    - by Kyle
    I call: [[ UIApplication sharedApplication ] setIdleTimerDisabled: YES ] on the applicationDidFinishLaunching event.. I set a breakpoint on it, which fires so I know it's getting called.. I've also called this function in other places as well.. Basically, a 3G iPhone will still go into sleep mode, but my 3GS won't. Has anyone seen this behavior before? Both are running the latest OS versions. Thanks for reading!

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