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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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  • How to log out from the Facebook in windows phone 7 using facebook api?

    - by Vijay
    I am trying to add Facebook into my application. I have try with a sample. public class FacebookLoginPageViewModel { private static WebBrowser _webBrowser; private Page _page; private const string ExtendedPermissions = "user_about_me,read_stream,publish_stream,user_birthday,offline_access,email"; private readonly FacebookClient _fb = new FacebookClient(); private const string AppId = "1XXX58XXXXXXXX9"; Uri url; public FacebookLoginPageViewModel(Panel container, Page page) { _page = page; _webBrowser = new WebBrowser(); var loginUrl = GetFacebookLoginUrl(AppId, ExtendedPermissions); url = loginUrl; container.Children.Add(_webBrowser); _webBrowser.Navigated += webBrowser_Navigated; _webBrowser.Navigate(loginUrl); } private Uri GetFacebookLoginUrl(string appId, string extendedPermissions) { var parameters = new Dictionary<string, object>(); parameters["client_id"] = appId; parameters["redirect_uri"] = "https://www.facebook.com/connect/login_success.html"; parameters["response_type"] = "token"; parameters["display"] = "touch"; // add the 'scope' only if we have extendedPermissions. if (!string.IsNullOrEmpty(extendedPermissions)) { // A comma-delimited list of permissions parameters["scope"] = extendedPermissions; } return _fb.GetLoginUrl(parameters); } void webBrowser_Navigated(object sender, System.Windows.Navigation.NavigationEventArgs e) { FacebookOAuthResult oauthResult; if (!_fb.TryParseOAuthCallbackUrl(e.Uri, out oauthResult)) { return; } if (oauthResult.IsSuccess) { var accessToken = oauthResult.AccessToken; LoginSucceded(accessToken); } else { // user cancelled MessageBox.Show(oauthResult.ErrorDescription); } } private void LoginSucceded(string accessToken) { var fb = new FacebookClient(accessToken); fb.GetCompleted += (o, e) => { if (e.Error != null) { Deployment.Current.Dispatcher.BeginInvoke(() => { MessageBox.Show(e.Error.Message); return; }); } var result = (IDictionary<string, object>)e.GetResultData(); var id = (string)result["id"]; var url = string.Format("/Views/FacebookInfoPage.xaml?access_token={0}&id={1}", accessToken, id); var rootFrame = (App.Current as App).RootFrame; Deployment.Current.Dispatcher.BeginInvoke(() => { rootFrame.Navigate(new Uri(url, UriKind.Relative)); }); }; fb.GetAsync("me?fields=id"); } This is working fine. But i want to Log out from the facebook when i click log out. How to achieve this? I have try with some examples. But it is not working for me. private void logout(object sender, RoutedEventArgs e) { webBrowser1.Navigated += new EventHandler<System.Windows.Navigation.NavigationEventArgs>(CheckForout); webBrowser1.Navigate(new Uri("http://m.facebook.com/logout.php?confirm=1")); webBrowser1.Visibility = Visibility.Visible; } private void CheckForout(object sender, System.Windows.Navigation.NavigationEventArgs e) { string fbLogoutDoc = webBrowser1.SaveToString(); Regex regex = new Regex ("\\<a href=\\\"/logout(.*)\\\".*data-sigil=\\\"logout\\\""); MatchCollection matches = regex.Matches(fbLogoutDoc); if (matches.Count > 0) { string finalLogout = string.Format("http://m.facebook.com/logout{0}", matches[0].Groups[1].ToString().Replace("amp;", "")); webBrowser1.Navigate(new Uri(finalLogout)); } } Please let me any idea to resolve this problem.

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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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  • 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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  • orbean forms bulder + custom persistance api: Why does it call /crud/.../data/data.xml?

    - by yankee
    I am currently implementing my own persistence layer for orbeon forms. As far as I have understood the virtual hierachy of data, creating a form with form builder in the application "myapp" with the name "myform" should cause the form builder to call /crud/myapp/myform/form/form.xhtml, passing the newly created form as HTTP-PUT data. Thus I created a spring method annotated with: @RequestMapping(method = RequestMethod.PUT, value = "/crud/{applicationName}/{formName}/form/form.xhtml") public void saveForm(@PathVariable String formName, @RequestBody String putData) I expected this method to be called with my form. But this method does not get called. Instead the method @RequestMapping(method = RequestMethod.PUT, value = "/crud/{applicationName}/{formName}/data/{uuid}/data.xml") public void saveInstance(@PathVariable String uuid, @RequestBody String putData) gets called. Put data contains the full xhtml form. Why is this happening? I thought that the second URL would only be called for saving an instance, more specifically the <xforms:instance id="fr-form-instance"> part of a form, once I fill in values for a form.

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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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • How to avoid GUI freeze when calling Beginthread API?

    - by isa
    Below just a simple race between 2 button in 2 threads, and this will freeze other components on the form. procedure moveButton1(); var I: Integer; begin for I := 0 to 6000 do Form1.Button1.Left := Form1.Button1.Left - 1; Form1.Caption := 'Button1 won!'; EndThread(0); end; procedure moveButton2(); var I: Integer; begin for I := 0 to 6000 do Form1.Button2.Left := Form1.Button2.Left - 1; Form1.Caption := 'Button2 won!'; EndThread(0); end; procedure TForm1.Button3Click(Sender: TObject); var thread1, thread2,tick : Integer; id1, id2 : LongWord; begin thread1 := BeginThread(nil, 0, Addr(moveButton1), nil, 0, id1); thread2 := BeginThread(nil, 0, Addr(moveButton2), nil, 0, id2); CloseHandle(thread1); CloseHandle(thread2); end;

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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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  • File name containing more than 16 characters inside parentheses failing

    - by Tom anMoney
    I am generating file names that contain a timestamp in the following format: "base_name (yyyy-mm-dd hhmmss).ext" This seems to cause a problem on Android. Here's my log: /storage/sdcard0/anMoney/transfer/Net worth over time _ Forecast (2012-11-19 110550).pdf E/Gmail (11802): java.io.FileNotFoundException: /storage/sdcard0/myapp/transfer/Net worth over time _ Forecast (2012-11-19 110550).pdf: open failed: ENOENT (No such file or directory) E/Gmail (11802): at libcore.io.IoBridge.open(IoBridge.java:416) E/Gmail (11802): at java.io.FileInputStream.<init>(FileInputStream.java:78) E/Gmail (11802): at java.io.FileInputStream.<init>(FileInputStream.java:105) E/Gmail (11802): at android.content.ContentResolver.openInputStream(ContentResolver.java:445) E/Gmail (11802): at com.google.android.gm.provider.MailEngine.cacheAttachment(MailEngine.java:3054) E/Gmail (11802): at com.google.android.gm.provider.MailEngine.sendOrSaveDraft(MailEngine.java:2746) E/Gmail (11802): at com.google.android.gm.provider.MailProvider.sendOrSaveDraft(MailProvider.java:477) E/Gmail (11802): at com.google.android.gm.provider.MailProvider.insert(MailProvider.java:534) E/Gmail (11802): at android.content.ContentProvider$Transport.insert(ContentProvider.java:201) E/Gmail (11802): at android.content.ContentResolver.insert(ContentResolver.java:864) E/Gmail (11802): at com.google.android.gm.provider.Gmail$MessageModification.sendOrSaveNewMessage(Gmail.java:3576) E/Gmail (11802): at com.google.android.gm.ComposeActivity$SendOrSaveTask$1.onInitializationComplete(ComposeActivity.java:1765) E/Gmail (11802): at com.google.android.gm.provider.MailEngine$5.run(MailEngine.java:1006) E/Gmail (11802): at android.os.Handler.handleCallback(Handler.java:615) E/Gmail (11802): at android.os.Handler.dispatchMessage(Handler.java:92) E/Gmail (11802): at android.os.Looper.loop(Looper.java:137) E/Gmail (11802): at android.os.HandlerThread.run(HandlerThread.java:60) E/Gmail (11802): Caused by: libcore.io.ErrnoException: open failed: ENOENT (No such file or directory) Now, if I trim the file name to have only 16 characters within the parentheses, everything is working as expected. I am able to send the file as a GMail attachment. The following file name is working fine: /storage/sdcard0/myapp/transfer/Net worth over time _ Forecast (2012-11-19 11070).pdf I tried the following troubleshooting: It's not the overall length of the file name, as if I shorten the base name, the same behavior remains It's not GMail, uploading the file to Google Drive fails similarly 16 characters inside the parentheses work, but not 17 It's not the space character inside the parentheses that causes the issue, as I replaced it with a dash and it's the same problem. Anybody has any ideas on what's going on here?

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