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  • Subprocess fails to catch the standard output

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "<string>", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in <module> align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO\__init__.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • "Use of undefined constant CURLOPT_PROTOCOLS and CURLPROTO_HTTP" but it works?

    - by Dave
    Hi on our dev environment we have show all errors, warnings and notices. I'm getting this: Notice: Use of undefined constant CURLOPT_PROTOCOLS - assumed 'CURLOPT_PROTOCOLS' in C:\notion\implementation\development\asterix\library\ExternalLibs\panda.php on line 69 Notice: Use of undefined constant CURLPROTO_HTTP - assumed 'CURLPROTO_HTTP' in C:\notion\implementation\development\asterix\library\ExternalLibs\panda.php on line 69 The code on line 69: curl_setopt($curl, CURLOPT_PROTOCOLS, CURLPROTO_HTTP); But the CURL code works, it goes off to the other server and retrieves whats necessary. What do these notices mean? Thanks very much.

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  • MQ EOL Data conversion

    - by lemotdit
    we are sending data trough MQ from a z/OS/CICS system to an AS400. Original encoding of the message is CCSID 500 with a MQSTR Format. The client application is getting the message with the CONVERT option and CCSID 819. Data is almost converted correctly except for the end of line caracter. Any idea? The z/OS is sending 0D (CR) as end of line caracter. If they had 0D+0A (CR+LF), CCSID automatically change from 500 to 437, and the end of line still ain't right on the client side.

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  • How to make linq master detail query for 0..n relationship?

    - by JK
    Given a classic DB structure of Orders has zero or more OrderLines and OrderLine has exactly one Product, how do I write a linq query to express this? The output would be OrderNumber - OrderLine - Product Name Order-1 null null // (this order has no lines) Order-2 1 Red widget I tried this query but is not getting the orders with no lines var model = (from po in Orders from line in po.OrderLines select new { OrderNumber = po.Id, OrderLine = line.LineNumber, ProductName = line.Product.ProductDescription, } ) I think that the 2nd from is limiting the query to only those that have OrderLines, but I dont know another way to express it. LINQ is very non-obvious if you ask me!

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  • Problem getting puppet to sync custom fact

    - by byron-appelt
    I am having trouble getting puppet to sync a custom fact. I am using puppet version 0.25.4. The fact is inside a module as described in http://docs.reductivelabs.com/guides/plugins_in_modules.html If I specify --pluginsync on the command line it does sync correctly, but does not otherwise even though I have pluginsync=true in my puppet.conf. Is it correct that this command line option and the option in the puppet.conf should have the same behavior?

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  • Menu Control in Master Page fails to use CSS styles

    - by Shaun
    I'm working on a web application that uses ASP.NET 3.5 and C#. Structurally, I have a master page with a menu control on it. The control serves as my navigation, and it gets its items from a SiteMapDataSource control and a corresponding Web.sitemap file. The problem is that some styles do not render properly when you specify the CssClass property. More specifically, the selected and hover styles don't respond to css styles. Consider the code below: <%@ Master Language="C#" AutoEventWireup="true" CodeFile="Site.master.cs" Inherits="Site" %> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.or/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head runat="server"> <title>A webpage</title> </head> <body> <form id="form1" runat="server"> <div id="page"> <asp:Menu ID="navMenu" Orientation="Horizontal" StaticMenuStyle-CssClass="staticMenu" StaticMenuItemStyle-CssClass="staticMenuItem" StaticSelectedStyle-CssClass="staticSelectedItem" StaticHoverStyle-CssClass="staticHoverItem" runat="server"> </asp:Menu> <asp:SiteMapDataSource ID="srcSiteMap" runat="server" ShowStartingNode="false" /> <br /> <asp:ContentPlaceHolder id="ContentPlaceHolder1" runat="server"> </asp:ContentPlaceHolder> </div> </form> </body> </html> Suppose I had a corresponding .css file with the following: .staticMenuItem { background-color:Red; } .staticSelectedItem { background-color:Green; } .staticHoverItem { background-color:Blue; } What will happen is that my item backgrounds will properly be red, but my selected item will not be green and the item I'm hovering my mouse over will not be blue. This seems true regardless of whether or not I include the style in the head of the master page or in an external file in default theme as specified in the web.config file. If I specify the styles in the asp.net xml like so: <asp:Menu ID="navMenu" Orientation="Horizontal" runat="server"> <StaticSelectedStyle BackColor="Green" Font-Underline="True" Font-Bold="True" /> <StaticHoverStyle BackColor="Gray" /> </asp:Menu> It appears to work properly in Firefox, but the style is never embedded in the html in Internet Explorer. Odd. Does anybody have any insight into what is causing this problem and how to neatly work around it? I'm aware I might be able to programmically determine the current page and select the corresponding menu item manually so it receives the proper style class, but before I resort to hacking C# and Javascript together to fix this functionality, I'm open to ideas.

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  • SQL Get Top 10 records by date

    - by Pselus
    I have a table full of bugs. The BugTitle is the page erroring and I also capture the error line. I would like to build an SQL Query that selects the top 10 bugs based on bugtitle and error line. I have this query: SELECT COUNT(BugTitle) AS BugCount, BugTitle, ErrLine FROM Bugs WHERE BugDate >= DateAdd(Day, -30, DateDiff(Day, 0, GetDate())) GROUP BY BugTitle, ErrLine ORDER BY BugCount, ErrLine DESC But I'm not sure if it's correct. I'm pretty sure that my test data only has 1 bug that happens on the same line but that's not showing up with this query. Can anyone help?

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  • What does this JavaScript error mean?

    - by Tommy
    Using the “Venkman” JavaScript debugger for Mozilla and getting the following error: XML Parsing Error: not well-formed Location: x-jsd:source?location=http%3A%2F%2F192.168.1.150%2Fscript.js&instance=337 Line Number 557, Column 50:<line><margin x='t'> - </margin><num> 554</num> ?? valid = false;</line> Functions works but I don't understand the error. Any help is appreciated. Thanks. function ValidateCheckBoxes() { var valid; $(document).ready(function(){ if($('input[@name=boxesA]:checked').size() == 0) {     valid = false; } else { valid = true; } }); return valid; }

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  • JavaScript check field value based on variable value

    - by Nikita Sumeiko
    I have an anchor like this: <a href="#" rel="1 4 7 18 ">Anchor</a> Where 'rel' attribute values are ids of some items. Than I have a form with an input, where user should type an id and click submit button. On submit button click I need to check the value of input like this: var value = $('a').attr('rel'); if ( value == '1' || value == '4' || value == '7' || value == '18') { // however I need the line above are created dynamically based on 'value' var alert('The id exists'); return false; } else { return true; } So, the question is how to create a line below dynamically based on anchor 'rel' attribute values?! This is the line: if ( value == '1' || value == '4' || value == '7' || value == '18') {

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  • CSS code formatting from Autohotkey..........

    - by metal gear solid
    i need functionality of this tool in Autohotkey keyboard shortcut. If i would select all code and press AHK key combination then code should be set like this tool does. single line/ multiline. Need to AHK script for both multiline and single line http://www.newmediacampaigns.com/files/posts/css-formatting/clean.php

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  • How to create a Excel like spread sheet in WPF - C#

    - by Khue
    Hi I want to create a table like in Excel sheet. The table has rows' headers and columns' headers. How to make the rows header move when the vertical scrollbar is dragged and statistic when the horizontal scrollbar is dragged and vice versa for the Columns header like in Excel sheet. Does anyone have any ideas how to do it? Thank you very much for your help

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  • In Django : How to serialize dict object to json ?

    - by Rohit
    I have this very basic problem, >>> serializers.serialize("json", {'a':1}) Traceback (most recent call last): File "<console>", line 1, in <module> File "/usr/lib/pymodules/python2.6/django/core/serializers/__init__.py", line 87, in serialize s.serialize(queryset, **options) File "/usr/lib/pymodules/python2.6/django/core/serializers/base.py", line 40, in serialize for field in obj._meta.local_fields: AttributeError: 'str' object has no attribute '_meta' >>> How can this be done ? Thanks in advance !

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  • Trying to draw 2 objects on screen and store the selected item names in an array

    - by thefonso
    Ok...this is a homework question, here is what i'm asked to do.... "Allow the user to draw two Shapes, which when instantiated, get put into the array myShapes...(store the shapes in the createShape() method." I want to know if I'm going in the right direction. Do I need to modify only Model.java or GUIDemo.java as well? Am I sufficient in thinking of only storing the values for the array via a loop inside my createShape() method? How do I go a bout checking to see if things work so far. There are many steps for this homework project after this one but i'm stuck here. Please point me in the right direction. The array myShapes lives inside my model class inside Model.java: package model; import java.awt.Color; import java.awt.Container; import shapes.Line; import shapes.Oval; import shapes.Rectangle; import shapes.Shape; import shapes.Triangle; import interfaces.Resettable; public class Model implements Resettable { private Container container; private String message; public final static String DRAW = "Draw"; public final static String MOVE = "Move"; public final static String REMOVE = "Remove"; public final static String RESIZE = "Resize"; public final static String FILL = "Fill"; public final static String CHANGE = "Change"; public final static String RECTANGLE = "Rectangle"; public final static String OVAL = "Oval"; public final static String LINE = "Line"; public final static String TRIANGLE = "Triangle"; private String action = DRAW; private boolean fill = false; public static String[] selections = {"Rectangle", "Oval", "Line", "Triangle"}; //project 9 begin public Shape[] myShapes = new Shape[2]; //project 9 stop private String currentShapeType; private Shape currentShape; public Color lineColor; private Color fillColor = Color.gray; public Shape createShape() { if(currentShapeType == RECTANGLE){ currentShape = new Rectangle(0, 0, 0, 0, lineColor, fillColor, fill); } if(currentShapeType == OVAL) { currentShape = new Oval(0,0,0,0, lineColor, fillColor, fill); } if(currentShapeType == LINE) { currentShape = new Line(0,0,0,0, lineColor, fillColor, fill); } if(currentShapeType == TRIANGLE) { currentShape = new Triangle(0,0,0,0, lineColor, fillColor, fill); } //project 9 start if(myShapes[0] == null) { myShapes[0]=currentShape; } else { myShapes[1]=currentShape; } //project 9 stop return currentShape; } public Shape getCurrentShape() { return currentShape; } public String getCurrentShapeType(){ return currentShapeType; } public void setCurrentShapeType(String shapeType){ currentShapeType = shapeType; } public Model(Container container) { this.container = container; } public void repaint() { container.repaint(); } public void resetComponents() { action = DRAW; currentShape = null; if (container instanceof Resettable) { ((Resettable) container).resetComponents(); } } public String getAction() { return action; } public void setAction(String action) { this.action = action; } public boolean isFill() { return fill; } public void setFill(boolean fill) { this.fill = fill; } public void setMessage(String msg) { this.message = msg; } public String getMessage() { return this.message; } public Color getLineColor() { return this.lineColor; } public void setLineColor(Color c) { this.lineColor = c; } public String toString() { return "Model:\n\tAction: " + action + "\n\tFill: " + fill; } } The application is run from GUIDemo.java: package ui.applet; import interfaces.Resettable; import java.applet.Applet; import java.awt.Graphics; import event.ShapeMouseHandler; import shapes.Shape; //import ui.panels.ButtonPanel; import ui.panels.ChoicePanel; import ui.panels.MainPanel; import model.Model; @SuppressWarnings("serial") public class GUIDemo extends Applet implements Resettable { MainPanel mainPanel; Model model; ChoicePanel choicePanel; public void init() { resize(600,400); model = new Model(this); choicePanel = new ChoicePanel(model); mainPanel = new MainPanel(model); this.add(choicePanel);//this is the drop down list this.add(mainPanel);//these are the radio buttons and reset button ShapeMouseHandler mouseHandler = new ShapeMouseHandler(model); addMouseListener(mouseHandler); addMouseMotionListener(mouseHandler); } public void paint(Graphics g) { Shape shape; shape = model.getCurrentShape(); if(shape != null) { shape.draw(g); } System.out.println(model); System.out.println(shape); } public void resetComponents() { mainPanel.resetComponents(); choicePanel.resetComponents(); } }

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  • What are useful functions for drawing text (MFC)?

    - by kobac
    I'm creating a line chart control, and I need to write (or better say draw) the axis names and axis values. I found DrawText and TextOut functions, but the text they show is flickering and don't know how to set the font and text orientation (I will need vertical text orientation as well as horizontal). Are there any other functions you could recoommend or how to use these stated above and get the results I need? Thanks in advance. Cheers.

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

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

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  • Finding text's bounding rect in Core Text

    - by Mo
    I'm trying to find the boundaries of a line of text in Core Text. For simplicity, assume it has a single character. At the moment I'm using the following method: line = CTLineCreateWithAttributedString(attrString); rect = CTLineGetImageBounds(line, context); It works most of the times, but for some characters, like math italic d (Unicode: 0x1D451) or math italic q (Unicode: 0x1D45E), the width is a bit short. I tried using CTLineGetTypographicBounds() or CTFramesetterSuggestFrameSizeWithConstraints, but they didn't help either (I think they use glyph's advance to find the width, not its graphical width.) As the font itself isn't italic, I also can't use slant angle to correct this. I tried accessing the glyphs directly and using CTFontCreatePathForGlyph(), but failed as CGGlyph and UniChar are both 16-bits and I need 32-bit characters. Does anyone know if I'm doing anything wrong? If so, what's the right way?

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  • mod_security: another rule with same ID

    - by Ashish
    I have installed httpd 2.2.15 on CentOS 6.5 (minimal installation with no cPanel) with modsecurity 2.8. When I am starting httpd I am getting this error: Starting httpd: Syntax error on line 23 of /etc/httpd/conf.d/modsecurity.conf: ModSecurity: Found another rule with the same id The line 23 is: "id:'200000',phase:1,t:none,t:lowercase,pass,nolog,ctl:requestBodyProcessor=XML" Please advise. Thx in advanced

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  • How can I use tinyscrolling plugin with fancybox?

    - by Noor
    I'm using the tinyscrolling plugin (the horizontal one), and I'm also using fancybox (the inline method) which is causing the fancybox to appear and the site to scroll to the box that is displayed. The fancybox appears as usual in the center and immediately the page scrolls to the right making the fancybox be on the left side of the page: |¯¯¯¯¯¯¯¯¯¯| |....................| |?..................| |....................| |__________|

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  • Handling newline character in input between Windows and Linux

    - by Fazal
    I think this is a standard problem which may have been asked before but I could not get the exact answer so posting the issue. The issue is that our server is running on a linux box. We access the server over the browser on a window box to enter data into field which is supposed to contain multiple lines which user can enter by pressing the enter key after each line Abc Def GHI When this input field (this is a text area),is read on the linux machine, we want to split the data based on new line character. I had three question on this. Does the incoming data contain "\r\n" or "\n" If incoming data does contain "\r\n", the linux line.separator property (vm property) would not work for me as it would say "\n" and therefore may leave "\r" in the data. If "\r" is left in the data, if I open the file on a windows machine, will this mean a newline character? Finally can anyone tell me the standard way to deal with this issue?

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  • php error: unexpected T_OBJECT_OPERATOR.... trying to install magento using ssh commands to dreamhos

    - by Jane
    I am trying to install magento (e-commerce platform) I am following a tutorial that tells me to run this command using ssh: ./pear mage-setup but i'm getting this error: Parse error: syntax error, unexpected T_OBJECT_OPERATOR in /home/domainname.com/downloader/pearlib/php/System.php on line 400 Line 400 is commented in the code snippit from the system.php file: /* Magento fix for set tmp dir in config.ini */ if (class_exists('Maged_Controller',false)) { /*line 400 */ $magedConfig = Maged_Controller::model('Config',true)->load();** if ($magedConfig->get('use_custom_permissions_mode') == '1' && $mode = $magedConfig->get('mkdir_mode')) { $result = System::mkDir(array('-m' . $mode, $tmpdir)); } else { $result = System::mkDir(array('-p', $tmpdir)); } if (!$result) { return false; } } Can anyone help my demystify this error?

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  • Enabled Apache mod_status but server-status was not found on SUSE enterprise 11 SP1

    - by Charles Yeung
    In /etc/apache2/httpd.conf, I have remove the line of Include mod_status and add the following to the last line, LoadModule status_module /usr/lib/apache2/mod_status.so ExtendedStatus On <Location /server-status> SetHandler server-status AllowOverride None Order Deny,Allow Deny from all Allow from all </Location> Then I restart Apache, and go to http://HOSTNAME/server-status, but I get the page not found, Did someone know why I get page not found? Is there any more step needed to do to see the Apache status? Thanks

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  • Stack trace in website project, when debug = false

    - by chandmk
    We have a website project. We are logging unhanded exceptions via a appdomain level exception handler. When we set debug= true in web.config, the exception log is showing the offending line numbers in the stack trace. But when we set debug = false, in web.config, log is not displaying the line numbers. We are not in a position to convert the website project in to webapplication project type at this time. Its legacy application and almost all the code is in aspx pages. We also need to leave the project in 'updatable' mode. i.e. We can't user pre-compile option. We are generating pdb files. Is there anyway to tell this kind of website projects to generate the pdb files, and show the line numbers in the stack trace?

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  • Handle mysql restart in SQLAlchemy

    - by wRAR
    My Pylons app uses local MySQL server via SQLAlchemy and python-MySQLdb. When the server is restarted, open pooled connections are apparently closed, but the application doesn't know about this and apparently when it tries to use such connection it receives "MySQL server has gone away": File '/usr/lib/pymodules/python2.6/sqlalchemy/engine/default.py', line 277 in do_execute cursor.execute(statement, parameters) File '/usr/lib/pymodules/python2.6/MySQLdb/cursors.py', line 166 in execute self.errorhandler(self, exc, value) File '/usr/lib/pymodules/python2.6/MySQLdb/connections.py', line 35 in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (2006, 'MySQL server has gone away') This exception is not caught anywhere so it bubbles up to the user. If I should handle this exception somewhere in my code, please show the place for such code in a Pylons WSGI app. Or maybe there is a solution in SA itself?

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