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• plotting results of hierarchical clustering ontop of a matrix of data in python

  - by user248237

  How can I plot a dendrogram right on top of a matrix of values, reordered appropriately to reflect the clustering, in Python? An example is in the bottom of the following figure: http://www.coriell.org/images/microarray.gif I use scipy.cluster.dendrogram to make my dendrogram and perform hierarchical clustering on a matrix of data. How can I then plot the data as a matrix where the rows have been reordered to reflect a clustering induced by the cutting the dendrogram at a particular threshold, and have the dendrogram plotted alongside the matrix? I know how to plot the dendrogram in scipy, but not how to plot the intensity matrix of data with the right scale bar next to it. Any help on this would be greatly appreciated.

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• XmlSerializer throws exception when serializing dynamically loaded type

  - by Dr. Sbaitso

  Hi I'm trying to use the System.Xml.Serialization.XmlSerializer to serialize a dynamically loaded (and compiled class). If I build the class in question into the main assembly, everything works as expected. But if I compile and load the class from an dynamically loaded assembly, the XmlSerializer throws an exception. What am I doing wrong? I've created the following .NET 3.5 C# application to reproduce the issue: using System; using System.Collections.Generic; using System.Xml.Serialization; using System.Text; using System.Reflection; using System.CodeDom.Compiler; using Microsoft.CSharp; public class StaticallyBuiltClass { public class Item { public string Name { get; set; } public int Value { get; set; } } private List<Item> values = new List<Item>(); public List<Item> Values { get { return values; } set { values = value; } } } static class Program { static void Main() { RunStaticTest(); RunDynamicTest(); } static void RunStaticTest() { Console.WriteLine("-------------------------------------"); Console.WriteLine(" Serializing StaticallyBuiltClass..."); Console.WriteLine("-------------------------------------"); var stat = new StaticallyBuiltClass(); Serialize(stat.GetType(), stat); Console.WriteLine(); } static void RunDynamicTest() { Console.WriteLine("-------------------------------------"); Console.WriteLine(" Serializing DynamicallyBuiltClass..."); Console.WriteLine("-------------------------------------"); CSharpCodeProvider csProvider = new CSharpCodeProvider(new Dictionary<string, string> { { "CompilerVersion", "v3.5" } }); CompilerParameters csParams = new System.CodeDom.Compiler.CompilerParameters(); csParams.GenerateInMemory = true; csParams.GenerateExecutable = false; csParams.ReferencedAssemblies.Add("System.dll"); csParams.CompilerOptions = "/target:library"; StringBuilder classDef = new StringBuilder(); classDef.AppendLine("using System;"); classDef.AppendLine("using System.Collections.Generic;"); classDef.AppendLine(""); classDef.AppendLine("public class DynamicallyBuiltClass"); classDef.AppendLine("{"); classDef.AppendLine(" public class Item"); classDef.AppendLine(" {"); classDef.AppendLine(" public string Name { get; set; }"); classDef.AppendLine(" public int Value { get; set; }"); classDef.AppendLine(" }"); classDef.AppendLine(" private List<Item> values = new List<Item>();"); classDef.AppendLine(" public List<Item> Values { get { return values; } set { values = value; } }"); classDef.AppendLine("}"); CompilerResults res = csProvider.CompileAssemblyFromSource(csParams, new string[] { classDef.ToString() }); foreach (var line in res.Output) { Console.WriteLine(line); } Assembly asm = res.CompiledAssembly; if (asm != null) { Type t = asm.GetType("DynamicallyBuiltClass"); object o = t.InvokeMember("", BindingFlags.CreateInstance, null, null, null); Serialize(t, o); } Console.WriteLine(); } static void Serialize(Type type, object o) { var serializer = new XmlSerializer(type); try { serializer.Serialize(Console.Out, o); } catch(Exception ex) { Console.WriteLine("Exception caught while serializing " + type.ToString()); Exception e = ex; while (e != null) { Console.WriteLine(e.Message); e = e.InnerException; Console.Write("Inner: "); } Console.WriteLine("null"); Console.WriteLine(); Console.WriteLine("Stack trace:"); Console.WriteLine(ex.StackTrace); } } } which generates the following output: ------------------------------------- Serializing StaticallyBuiltClass... ------------------------------------- <?xml version="1.0" encoding="IBM437"?> <StaticallyBuiltClass xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> <Values /> </StaticallyBuiltClass> ------------------------------------- Serializing DynamicallyBuiltClass... ------------------------------------- Exception caught while serializing DynamicallyBuiltClass There was an error generating the XML document. Inner: The type initializer for 'Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationWriterDynamicallyBuiltClass' threw an exception. Inner: Object reference not set to an instance of an object. Inner: null Stack trace: at System.Xml.Serialization.XmlSerializer.Serialize(XmlWriter xmlWriter, Object o, XmlSerializerNamespaces namespaces, String encodingStyle, String id) at System.Xml.Serialization.XmlSerializer.Serialize(TextWriter textWriter, Object o, XmlSerializerNamespaces namespaces) at System.Xml.Serialization.XmlSerializer.Serialize(TextWriter textWriter, Object o) at Program.Serialize(Type type, Object o) in c:\dev\SerTest\SerTest\Program.cs:line 100 Edit: Removed some extraneous referenced assemblies

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• Svn - get the list of all repos on a server so I can svnsync

  - by egarcia

  I'm attempting to create a backup of my client's existing svn repositories, which is publicly available over http. If possible, I'd like to be able to make new repositories automatically, from any computer, without having to give console access to the server to external parties (i.e. the users could do a ls on my svn repo dir) My problem is that I need to know the list of svn repositories on the server - it isn't a fixed list, since the user will add new repositories over time. I'm able to list the repositories on an html page via Apache's mod_dav_svn module, using the SVNListParentPath On directive. I got this page: http://svn.ohwr.org/ My question is: what is the easiest way to obtain a usable list of such repositories? I'll need to parse that list in order to make syncs, probably using shell commands. Must I parse the HTML with shell commands, or is there a better way to get that list?

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• Freemarker template not found

  - by brock

  Hi, I'm currently trying to get Freemarker to work with my application using Spring. No matter what I try I keep getting template not found. I am not sure if I have the configuration set up properly, but it never finds my template. Here is my spring bean config: <bean id="freemarkerConfig" class="org.springframework.web.servlet.view.freemarker.FreeMarkerConfigurer"> <property name="templateLoaderPath" value="/WEB-INF/freemarker/"/> </bean> Whenever I try to call getTemplate on the freemaker configuration it always sends back a template not found error. So if I do configuration.getTemplate("testTemplate.ftl") it always throws an IOException. I'm not sure if anyone has an idea of what I'm doing wrong. Thanks for all your help!

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• pubsub link with Project Rome

  - by itsadok

  I want to use Project Rome to create an RSS feed, using the code from the tutorial as base. I would like to add a pubsubhubbub discovery link, but there doesn't seem to be a general way to do so. I can use a Link object if I create an atom feed (which I don't want to limit myself to), or I can just add foreign markup, like this: // import org.jdom.Element Element element = new Element("link"); element.setAttribute("rel", "hub"); element.setAttribute("href", "https://myhub.example.com/endpoint"); feed.setForeignMarkup(Arrays.asList(element)); But it feels ugly. Is this really the best way to do this?

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• Doctrine Mssql uniqueidentifier isn't cast as char or nvarchar when retrieved from the database.

  - by Tres

  When I retrieve a record from the database which has a column of type "uniqueidentifier", Doctrine fills it with "null" rather than the unique id from the database. Some research and testing has brought this down to a PDO/dblib driver issue. When directly querying via PDO, null is returned in place of the unique id. For reference, http://trac.doctrine-project.org/ticket/1096, has a bit on this, however, it was updated 11 months ago with no comment for resolution. A way around this, as mentioned at http://bugs.php.net/bug.php?id=24752&edit=1, is to cast the column as a char. However, it doesn't seem Doctrine exposes the native field type outside of generating models which makes it a bit hard to detect uniqueidentifier types and cast them internally when building the sql query. Has anyone found a workaround for this?

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• Clustering [assessment] algorithm with distance matrix as an input

  - by Max

  Can anyone suggest some clustering algorithm which can work with distance matrix as an input? Or the algorithm which can assess the "goodness" of the clustering also based on the distance matrix? At this moment I'm using a modification of Kruskal's algorithm (http://en.wikipedia.org/wiki/Kruskal%27s_algorithm) to split data into two clusters. It has a problem though. When the data has no distinct clusters the algorithm will still create two clusters with one cluster containing one element and the other containing all the rest. In this case I would rather have one cluster containing all the elements and another one which is empty. Are there any algorithms which are capable of doing this type of clustering? Are there any algorithms which can estimate how well the clustering was done or even better how many clusters are there in the data? The algorithms should work only with distance(similarity) matrices as an input.

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• maximum execution time for javascript

  - by Andrew Chang

  I know both ie and firefox have limits for javascript execution here: hxxp://support.microsoft.com/?kbid=175500 Based on number of statements executed, I heard it was 5 million somewhere in ie hxxp://webcache.googleusercontent.com/search?q=cache:_iKHhdfpN-MJ:kb.mozillazine.org/Dom.max_script_run_time+dom.max_script_run_time&hl=en&gl=ca&strip=1 (google cache since site takes forever to load for me) based on number of seconds in firefox, it's 10 seconds by default for my version The thing I don't get is what cases will go over these limits: I'm sure a giant loop will go over the limit for execution time But will an event hander go over the limit, if itself it's execution time is under the limit but if it occurs multiple times? Example: Lets say I have a timer on my page, that executes some javascript every 20 seconds. The execution time for the timer handler is 1 second. Does firefox and ie treat each call of the timer function seperatly, so it never goes over the limit, or is it that firefox/ie adds up the time of each call so after the handler finishes, so after 200 seconds on my site (with the timer called 10 times) an error occurs even though the timer handler itself is only 1 second long?

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• Keycodes of function keys with F-lock off?

  - by ak

  Many recent keyboard from Microsoft and Logitech have a so-called F-Lock key, which toggles the function keys F1 to F12 between their traditional keycodes and new meanings that are printed onto the keys: F1=Help F2=Undo F3=Redo F4=Open ... . (See also http://en.wikipedia.org/wiki/F-Lock.) This means that long-established shortcuts such as Alt+F4 no longer work if the F-lock is off, and googling shows that quite a few people are unhappy about this. So I'm wondering, what virtual key (VK) codes do the function keys send when F-lock is off? VK_F13 to VK_F24 perhaps? Or do they not trigger standard keyboard events at all? (I haven't got such a keyboard to try and find out myself, and didn't manage to dig up anything on MSDN about this.)

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• Embed Javascript Module within Flex application

  - by Crimson

  I have a large module written in JS which uses Canvas to draw and animate trees. This module was written for a product which is now being migrated to flex. Is there a way in flex to embed this JS module as is? Or would I have to rewrite the whole module in AS3 (shudder)? Further, if embedding is possible, would user interactions (mouse clicks) etc. work seamlessly? An example of the tree structure I am talking about can be found here - http://thejit.org

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• WebKit and npapi and mingw-w64

  - by rubenvb

  Hi, The problem is the following: On Windows x64, pointers are 64-bit, but type long is 32-bit. MSVC doesn't seem to care, and even omits warnings about pointer truncation on the default warning level. Since recently, there is a GCC that target x86_64-w64-mingw32, or better Windows x64 native. GCC produces errors when pointers are truncated (which is the logical thing to do...), and this is causing trouble in WebKit and more specifically, the Netscape Plugin API: First, there's the files (I can only post one hyperlink...): http://trac.webkit.org/browser/trunk/WebCore/ bridge/npapi.h -- defines uint32 as 32-bit int type (~line 145) plugins/win/PluginViewWin.cpp -- casts Windows window handles to 32-bit int, truncating them (~line 450) My proposed fix was to change the uint32 casts to uintptr_t, which makes GCC happy, but still puts a 64-bit value in a uint32 (=unsigned long). I have no clue how to solve this, because clearly WebKit is happy truncating pointers on Win64... How can I solve this the right way? Thanks!

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• Polling duplex does not scale... what's the alternative?

  - by user80855

  Our tests showed that the polling duplex binding simply does not scale and can not be used on a service within a web-farm or even a web garden. We have looked at TCP/IP sockets for a client push method, but the firewall issue is does allow us to use sockets. I was wondering what is the alternative "free" solution to this problem? allowing us to scale and allowing us to push data to client... I have also tried the solution in this article http://tomasz.janczuk.org/2009/09/scale-out-of-silverlight-http-polling.html but at the end, there was too much polling on a database, and performance was affected. Our Silverlight application need a pub/sub design, but it needs to be reliable and scalable... any ideas?

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• WCF Web Service chnage wsdl name and targetNamespace

  - by Graham

  All, I'm a little new to WCF over IIS but have done some ASMX web services before. My WCF service is up and running but the helper page generated by the web service for me has the default names, i.e. the page that says: You have created a service. To test this service, you will need to create a client and use it to call the service. You can do this using the svcutil.exe tool from the command line with the following syntax: svcutil.exe http://localhost:53456/ServicesHost.svc?wsdl In a standard ASMX site I would use method/class attributes to give the web service a name and a namespace. When I click on the link the WSDL has: <wsdl:definitions name="SearchServices" targetNamespace="http://tempuri.org/" i.e. not the WCF Service Contract Name and Namespace from my Interface. I assume the MEX is using some kind of default settings but I'd like to change them to be the correct names. How can I do this?

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• Migrate existing ROR app to GAE

  - by zengr

  I have managed to run a basic rails app1 on App Engine using: http://gist.github.com/268192 So, on my basic app2, I install CE, which works fine on local machine. (communityengine.org) But, when I follow the same steps on my actual app2, where community_engine plugin is installed and all the gems are frozen, the app engine installer script asks for to over write various files like boot.rb, routes.rb, which I don't allow. So, as expected, when I publish the rails + ce app to GAE, it's not published and it also screws the local installation of CE on app2. So, the problem is obvious, CE uses ActiveRecord, and GAE uses DataMapper. So, my question can also be rephrased as: Can we migrate an existing ROR App using Active Record to GAE which uses DataMapper? PS: This is my first project on ROR and GAE.

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• .NET equivalent to Perl regular expressions

  - by r_honey

  I need to convert a Perl script to VB.NET. I have managed almost the entire conversion, but some Perl (seemingly simple) regex are causing an headache. Can someone suggest me .NET equivalent of the following perl regex: 1) $letter =~ s/Users //,; $letter =~ s/Mailboxes //,; if($letter =~ m/$first_char/i){ 2) unless($storegroup =~ /Recovery/ || $storegroup =~ /Users U V W X Y Z/ || $storegroup =~ /Users S T/ || $storegroup =~ /Users Q R/){ The regex look simple to me. I tried to wade through perl.org but understanding a langugae regex takes sometime and I need to complete the conversion quickly.

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• Box2d Documentation - Outdated, any better api refs?

  - by GONeale

  Hi guys, I am working with cocos2d + box2d and as I look through the 'Hello World' tutorial and attempt others I am finding many constructs which do not seem to be documented in the latest api ref. Would anybody be able to shed some light on what's going on? or point me in the right direction to someone who has covered the new constructs such as b2PolygonDef changing to b2PolygonShape and likewise for circle + who knows what else, seems there has not been any doc updates since August '09. This is the only information I could find on the issue, of another user stating they have found many mismatches also. http://www.cocos2d-iphone.org/forum/topic/1683

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• IE6 + IE7 CSS problem with overflow: hidden; - position: relative; combo.

  - by googletorp

  So I have created a slider for a homepage, that slides some images with a title and teaser text using jQuery. Everything works fine, and I went to check IE and found that IE 6 and 7 kills my slider css completely. I can't figure out why, but for some reason I can't hide the non active slides with overflow: hidden; I've tried tweaking the css back and forth, but haven't been able to figure out what's causing the problem. I've recreated the problem in a more isolated html page. <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="da" lang="da" dir="ltr"> <head> <style> body { width: 900px; } .column-1 { width: 500px; float: left; } .column-2 { width: 200px; float: left; } .column-3 { width: 200px; float: left; } ul { width: 2000px; left: -499px; position: relative; } li { list-style: none; display: block; float: left; } .item-list { overflow: hidden; width: 499px; } </style> </head> <body> <div class="column-1"> <div class="item-list clearfix"> <ul> <li class="first"> <div class="node-slide"> <img src="http://www.hanselman.com/blog/content/binary/lolcats-funny-pictures-leroy-jenkins.jpg" /> <div class="infobox"> <h4>Title 1</h4> <p>Teaser 1</p> </div> </div> </li> <li> <div class="slide"> <img src="http://www.hanselman.com/blog/content/binary/lolcats-funny-pictures-leroy-jenkins.jpg" /> <div class="infobox"> <h4>Title 2</h4> <p>Teaser 2</p> </div> </div> </li> <li class="last"> <div class="slide"> <img src="http://www.hanselman.com/blog/content/binary/lolcats-funny-pictures-leroy-jenkins.jpg" /> <div class="infobox"> <h4>Title 3</h4> <p>Teaser 3</p> </div> </div> </li> </ul> </div> </div> <div class="column-2"> ... </div> <div class="column-3"> ... </div> </body> </html> I've tracked down that it is the ul { position: relative; } on the ul element that is causing the overflow: hidden not to work, but why that is, I don't know. Also this is needed to make the slider javascript work using the left attribute on the ul to slide it. Any ideas as to how you can fix this is most welcome.

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• Java applet - access denied to file on same web server

  - by me_here

  I've written a simple Java applet to generate a technical image based upon some data in a CSV file. I'm passing in the CSV file as a parameter to the applet: <applet code = "assaymap.AssayMapApplet" archive = "http://localhost/applet_test/AssayMap.jar" height="600px" width="800px"> <param name="csvFile" value="http://localhost/applet_test/test.csv"> </applet> As far as I understood applet security restrictions, an applet should be able to read data from the host they're on. These applets here http://www.jalview.org/examples/applets.html are using the same approach of passing in a text data file as a parameter. So I'm not sure why my own applet isn't working. The error message I get thrown is: Error with processing the CSV data. java.security.AccessControlException: access denied (java.io.FilePermission http:\localhost\applet_test\test.csv read)

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• Java replace slow?

  - by cpf

  Hi StackOverflow, I have a Java application that makes heavy use of a large file, to read, process and give through to SolrEmbeddedServer (http://lucene.apache.org/solr/). One of the functions does basic HTML escaping: private String htmlEscape(String input) { return input.replace("&", "&amp;").replace(">", "&gt;").replace("<", "&lt;") .replace("'", "&apos;").replaceAll("\"", "&quot;"); } While profiling the application, the program spends roughly 58% of the time in this function, a total of 47% in replace, and 11% in replaceAll. Now, is the Java replace that slow, or am I on the right path and should I consider the program efficient enough to have its bottleneck in Java and not in my code? (Or am I replacing wrong?) Thanks in advance!

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• Producer/consumer in Grails?

  - by Mulone

  Hi all, I'm trying to implement a Consumer/Producer app in Grails, after several unsuccessful attempts at implementing concurrent threads. Basically I want to store all the events coming from a clients (through separate AJAX calls) in a single queue and then process such a queue in a linear way as soon as new events are added. This looks like a Producer/Consumer problem: http://en.wikipedia.org/wiki/Producer-consumer_problem How can I implement this in Grails (maybe with a timer or even better by generating an event 'process queue')? Basically I'd like to a have a singleton service waiting for new events in the queue and processing them linearly (even if the queue is loaded by several concurrent processes). Any hints? Cheers!

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• Parsing atom/rss feed containing multiple <link> tags with Haml on RoR

  - by fenderplayer

  So, firstly, heres an atom feed snippet which i am trying to parse: // http://somelink.com/atom <feed xmlns="http://www.w3.org/2005/Atom"> <entry> <title>Title Here</title> <link href="http://somelink.com/link1&amp;amp;ref=rss" rel="alternate" /> <link href="http://somelink.com/link2&amp;amp;ref=rss" rel="tag:somelink.com/apply_url"/> ... </entry> i pull the atom feed like so, // In controller index method @rss = SimpleRSS.parse open('http://somelink.com/atom') Then i output the response in the view, which i am writing using haml, as follows: - @rss.entries.each do |item| .title-div = item.title .title-link = item.link //outputs the first link I could run a second loop for the links but is there a way to get the second link without it? Like reading the "rel" attribute and outputting the correct link? How do i do this in haml/rails?

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• Add jar to EAR in Eclipse

  - by Gerard

  I have several projects in an EAR in Eclipse. These projects themselves have dependency jar's on the build path marked as "do not export, do not contribute to others". Now in Eclipse I add jar's to the EAR via the EAR properties "Java EE Module Dependencies". I browse to the jar (add jar) and click ok. The jar is added to the list. When I click apply, the added jar is gone from the list, it cannot be found in other properties, it is contained in the hidden folder .settings in the file org.eclipse.wst.common.component. This behaviour does not make much sense to me, what am I missing?

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• AES Encryption. From Python (pyCrypto) to .NET

  - by Why

  I am currently trying to port a legacy Python app over to .NET which contains AES encrpytion using from what I can tell pyCrpyto. I have very limited Python and Crypto experience. The code uses the snippet from the following page. http://www.djangosnippets.org/snippets/1095/ So far I believe I have managed to work out that it that it calls Crypto.Cipher with AES and the first 32 character of our secret key as the password, but no mode or IV. It also puts a prefix on the encrpyed text when it is added to database. What I can't work out is how I can decrypt the existing ecrypted database records in .NET. I have been looking at RijndaelManaged but it requires an IV and can't see any reference to one in python. Can anyone point me in the dirrection to what method could be used in .NET to get the desired result.

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• Deadlock error in INSERT statement

  - by Gnanam

  We've got a web-based application. There is a time-bound database operation (INSERTs and UPDATEs) in the application which takes more time to complete, hence this particular flow has been changed into Java Thread so it will not wait (block) for the complete database operation to be completed. My problem is, if more than 1 user come across this particular flow, I'm facing the following error thrown by PostgreSQL: org.postgresql.util.PSQLException: ERROR: deadlock detected Detail: Process 13560 waits for ShareLock on transaction 3147316424; blocked by process 13566. Process 13566 waits for ShareLock on transaction 3147316408; blocked by process 13560. Above error is consistently thrown in INSERT statements. Additional Information: 1) I have PRIMARY KEY defined in this table. 2) There are FOREIGN KEY references in this table. 3) Separate database connection is passed to each Java Thread. Technologies Web Server: Tomcat v6.0.10 Java v1.6.0 Servlet Database: PostgreSQL v8.2.3 Connection Management: pgpool II

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• Selenium and HTTPS/SSL

  - by NerdyNick

  I'm running selenium-rc 1.0.3 on a Mac OS X & Windows 7 and both seem to be giving my the annoying accept cert error in firefox. In reading the docs they say I should be able to just use the *firefox run mode and rc should take care of it for me via a proxy or something, but this appears to not work. The only solution that I was able to find on the internet was to create a skeleton profile and pass the path into the rc startup, but thats not a real option. As that doesn't solve problems of testing in IE/Chrome/Safari. Does any know of any other solution that will work. Selenium-RC docs on HTTPS - http://seleniumhq.org/docs/05_selenium_rc.html#handling-https-and-security-popups

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